From 4c96ed55664e48d2288e6981bad710a7ebffcd3b Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Wed, 2 Oct 2024 22:35:50 -0600
Subject: [PATCH 01/53] return all indices and check for duplicates

---
 .../cam/outfrq24h_port/user_nl_cam            |  2 +-
 src/control/cam_history.F90                   | 74 +++++++++++--------
 2 files changed, 45 insertions(+), 31 deletions(-)

diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam b/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
index e385809756..2d18788e39 100644
--- a/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
+++ b/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
@@ -2,7 +2,7 @@
  rad_data_fdh = .true.
  empty_htapes = .true.
  avgflag_pertape = 'A','I'
- fincl1 = 'SOLIN', 'QRS', 'FSNS', 'FSNT','FSNSC', 'FSDSC','FSNR','FLNR',
+ fincl1 = 'SOLIN', 'QRS', 'FSNS', 'FSNT','FSNSC', 'FSNR','FLNR',
           'FSNTOA', 'FSUTOA', 'FSNTOAC', 'FSNTC', 'FSDSC', 'FSDS', 'SWCF',
           'QRL', 'FLNS', 'FLDS', 'FLNT', 'LWCF', 'FLUT' ,'FLUTC', 'FLNTC', 
           'FLNSC', 'FLDSC'
diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 39222fc536..602280baf3 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -486,10 +486,6 @@ subroutine intht (model_doi_url_in)
     !
     do t=1,ptapes
       do fld=1,nflds(t)
-        if (nhtfrq(t) == 1) then
-           ! Override any non-I flags if nhtfrq equals 1
-           tape(t)%hlist(fld)%avgflag = 'I'
-        end if
         if (tape(t)%hlist(fld)%avgflag .ne. 'I') then
            hfile_accum(t) = .true.
         end if
@@ -2570,7 +2566,10 @@ subroutine fldlst ()
     !
     integer t, fld                 ! tape, field indices
     integer ffld                   ! index into include, exclude and fprec list
+    integer :: ffld_array(pflds, ptapes)
     integer :: i
+    integer :: duplicate_index           ! iterator for multiple occurrences of the same field
+    integer :: num_fields                ! Number of times field appears in field list
     character(len=fieldname_len) :: name ! field name portion of fincl (i.e. no avgflag separator)
     character(len=max_fieldname_len) :: mastername ! name from masterlist field
     character(len=max_chars) :: errormsg ! error output field
@@ -2645,8 +2644,8 @@ subroutine fldlst ()
       add_fincl_idx = fld
       if (fld > 1 .and. interpolate_output(t)) then
          do i = 1, n_vec_comp
-            call list_index(fincl(:,t), vec_comp_names(i), ffld)
-            if (ffld == 0) then
+            call list_index(fincl(:,t), vec_comp_names(i), ffld_array(:,t))
+            if (.not. any(ffld_array(:,t) > 0)) then
 
                ! Add vector component to fincl.  Don't need to check whether its in the master
                ! list since this was done at the time of registering the vector components.
@@ -2744,21 +2743,23 @@ subroutine fldlst ()
       listentry => masterlinkedlist
       do while(associated(listentry))
         mastername = listentry%field%name
-        call list_index (fincl(1,t), mastername, ffld)
+        call list_index (fincl(1,t), mastername, ffld_array(:,t))
 
         fieldontape = .false.
-        if (ffld > 0) then
+        if (any(ffld_array(:,t) > 0)) then
           fieldontape = .true.
+          num_fields = count(ffld_array(:,t) > 0)
         else if ((.not. empty_htapes) .or. (is_initfile(file_index=t))) then
-          call list_index (fexcl(1,t), mastername, ffld)
-          if (ffld == 0 .and. listentry%actflag(t)) then
+          call list_index (fexcl(1,t), mastername, ffld_array(:,t))
+          if ((.not. any(ffld_array(:,t) > 0)) .and. listentry%actflag(t)) then
             fieldontape = .true.
+            num_fields = 1
           end if
         end if
         if (fieldontape) then
-          ! The field is active so increment the number fo fields and add
+          ! The field is active so increment the number of fields and add
           ! its decomp type to the list of decomp types on this tape
-          nflds(t) = nflds(t) + 1
+          nflds(t) = nflds(t) + num_fields
           do ffld = 1, size(gridsontape, 1)
             if (listentry%field%decomp_type == gridsontape(ffld, t)) then
               exit
@@ -2821,21 +2822,23 @@ subroutine fldlst ()
       do while(associated(listentry))
         mastername = listentry%field%name
 
-        call list_index (fwrtpr(1,t), mastername, ffld)
-        if (ffld > 0) then
-          prec_wrt = getflag(fwrtpr(ffld,t))
+        call list_index (fwrtpr(1,t), mastername, ffld_array(:,t))
+        if (ffld_array(1,t) > 0) then
+           prec_wrt = getflag(fwrtpr(ffld_array(1,t), t))
         else
-          prec_wrt = ' '
+           prec_wrt = ' '
         end if
 
-        call list_index (fincl(1,t), mastername, ffld)
+        call list_index (fincl(1,t), mastername, ffld_array(:,t))
 
-        if (ffld > 0) then
-          avgflag = getflag (fincl(ffld,t))
-          call inifld (t, listentry, avgflag,  prec_wrt)
+        if (any(ffld_array(:,t) > 0)) then
+          do duplicate_index = 1, count(ffld_array(:,t) > 0)
+            avgflag = getflag (fincl(ffld_array(duplicate_index,t),t))
+            call inifld (t, listentry, avgflag,  prec_wrt)
+          end do
         else if ((.not. empty_htapes) .or. (is_initfile(file_index=t))) then
-          call list_index (fexcl(1,t), mastername, ffld)
-          if (ffld == 0 .and. listentry%actflag(t)) then
+          call list_index (fexcl(1,t), mastername, ffld_array(:,t))
+          if (.not. any(ffld_array(:,t) > 0) .and. listentry%actflag(t)) then
             call inifld (t, listentry, ' ', prec_wrt)
           else
             listentry%actflag(t) = .false.
@@ -2882,9 +2885,18 @@ subroutine fldlst ()
             tape(t)%hlist(ffld+1) = tmp
 
           else if (tape(t)%hlist(ffld)%field%name == tape(t)%hlist(ffld+1)%field%name) then
-
-            write(errormsg,'(2a,2(a,i3))') 'FLDLST: Duplicate field: ', &
-                 trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld
+            if (tape(t)%hlist(ffld)%avgflag == tape(t)%hlist(ffld+1)%avgflag) then
+              write(errormsg,'(2a,2(a,i3),2a)') &
+                   'FLDLST: Duplicate field with the same averaging flag. Check your fincl list: ', &
+                   trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld, &
+                   ', flag = ', trim(tape(t)%hlist(ffld)%avgflag)
+            else
+              write(errormsg,'(2a,2(a,i3),4a)') &
+                   'FLDLST: Duplicate field with different averaging flags. Place on separate tapes: ', &
+                   trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld, &
+                   ', flag1 = ', trim(tape(t)%hlist(ffld)%avgflag), ', flag2 = ', &
+                   trim(tape(t)%hlist(ffld+1)%avgflag)
+            end if
             call endrun(errormsg)
 
           end if
@@ -3507,18 +3519,20 @@ subroutine list_index (list, name, index)
     ! Input arguments
     !
     character(len=*), intent(in) :: list(pflds) ! input list of names, possibly ":" delimited
-    character(len=max_fieldname_len), intent(in) :: name ! name to be searched for
+    character(len=*), intent(in) :: name ! name to be searched for
     !
     ! Output arguments
     !
-    integer, intent(out) :: index               ! index of "name" in "list"
+    integer, intent(out) :: index(:)            ! indices of "name" in "list"
     !
     ! Local workspace
     !
     character(len=fieldname_len) :: listname    ! input name with ":" stripped off.
-    integer f                       ! field index
+    integer :: f                                ! field index
+    integer :: num_found                        ! number of time field appears in list
 
     index = 0
+    num_found = 1
     do f=1,pflds
       !
       ! Only list items
@@ -3526,8 +3540,8 @@ subroutine list_index (list, name, index)
       listname = getname (list(f))
       if (listname == ' ') exit
       if (listname == name) then
-        index = f
-        exit
+        index(num_found) = f
+        num_found = num_found + 1
       end if
     end do
 

From 3acb4b239775a7afa736fc1c74f4146eaaf9283e Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Wed, 2 Oct 2024 23:40:24 -0600
Subject: [PATCH 02/53] update to git-fleximod 0.9.2

---
 .lib/git-fleximod/git_fleximod/cli.py         |   2 +-
 .../git-fleximod/git_fleximod/git_fleximod.py |   6 +-
 .../git-fleximod/git_fleximod/gitinterface.py |   7 +-
 .lib/git-fleximod/git_fleximod/submodule.py   | 101 ++++++++++--------
 .lib/git-fleximod/git_fleximod/utils.py       |  10 +-
 .lib/git-fleximod/pyproject.toml              |   2 +-
 .lib/git-fleximod/tbump.toml                  |   2 +-
 7 files changed, 72 insertions(+), 58 deletions(-)

diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
index b6f728f881..208bc04684 100644
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ b/.lib/git-fleximod/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.8.4"
+__version__ = "0.9.2"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
index 50e0ef83df..0851e9d095 100755
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ b/.lib/git-fleximod/git_fleximod/git_fleximod.py
@@ -124,8 +124,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     # set the repository remote
 
     logger.info("Setting remote origin in {}/{}".format(root_dir, path))
-    status = sprepo_git.git_operation("remote", "-v")
-    if url not in status:
+    _, remotelist = sprepo_git.git_operation("remote", "-v")
+    if url not in remotelist:
         sprepo_git.git_operation("remote", "add", "origin", url)
 
     topgit = os.path.join(gitroot, ".git")
@@ -213,7 +213,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False, depth=0):
 
 def git_toplevelroot(root_dir, logger):
     rgit = GitInterface(root_dir, logger)
-    superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+    _, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
     return superroot
 
 def submodules_update(gitmodules, root_dir, requiredlist, force):
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
index 5831201446..fb20883cd0 100644
--- a/.lib/git-fleximod/git_fleximod/gitinterface.py
+++ b/.lib/git-fleximod/git_fleximod/gitinterface.py
@@ -59,11 +59,12 @@ def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *newargs)
         if isinstance(command, list):
             try:
-                return utils.execute_subprocess(command, output_to_caller=True)
+                status, output = utils.execute_subprocess(command, status_to_caller=True, output_to_caller=True)
+                return status, output.rstrip()
             except Exception as e:
                 sys.exit(e)
         else:
-            return command
+            return 0, command
 
     def config_get_value(self, section, name):
         if self._use_module:
@@ -81,6 +82,8 @@ def config_get_value(self, section, name):
     def config_set_value(self, section, name, value):
         if self._use_module:
             with self.repo.config_writer() as writer:
+                if "." in section:  
+                    section = section.replace("."," \"")+'"'           
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:
diff --git a/.lib/git-fleximod/git_fleximod/submodule.py b/.lib/git-fleximod/git_fleximod/submodule.py
index 70a3018a42..c939d54bc9 100644
--- a/.lib/git-fleximod/git_fleximod/submodule.py
+++ b/.lib/git-fleximod/git_fleximod/submodule.py
@@ -60,8 +60,9 @@ def status(self):
         if not os.path.exists(os.path.join(smpath, ".git")):
             rootgit = GitInterface(self.root_dir, self.logger)
             # submodule commands use path, not name
-            tags = rootgit.git_operation("ls-remote", "--tags", self.url)
-            result = rootgit.git_operation("submodule","status",smpath).split()
+            status, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
+            status, result = rootgit.git_operation("submodule","status",smpath)
+            result = result.split()
             
             if result:
                 ahash = result[0][1:]
@@ -80,9 +81,9 @@ def status(self):
                 result = f"e {self.name:>20} not checked out, aligned at tag {self.fxtag}{optional}"
                 needsupdate = True
             elif self.fxtag:
-                ahash = rootgit.git_operation(
+                status, ahash = rootgit.git_operation(
                     "submodule", "status", "{}".format(self.path)
-                ).rstrip()
+                )
                 ahash = ahash[1 : len(self.fxtag) + 1]
                 if self.fxtag == ahash:
                     result = f"e {self.name:>20} not checked out, aligned at hash {ahash}{optional}"
@@ -96,14 +97,15 @@ def status(self):
         else:
             with utils.pushd(smpath):
                 git = GitInterface(smpath, self.logger)
-                remote = git.git_operation("remote").rstrip()
+                status, remote = git.git_operation("remote")
                 if remote == '':
                     result = f"e {self.name:>20} has no associated remote"
                     testfails = True
                     needsupdate = True
                     return result, needsupdate, localmods, testfails                    
-                rurl = git.git_operation("ls-remote","--get-url").rstrip()
-                line = git.git_operation("log", "--pretty=format:\"%h %d\"").partition('\n')[0]
+                status, rurl = git.git_operation("ls-remote","--get-url")
+                status, lines = git.git_operation("log", "--pretty=format:\"%h %d\"")
+                line = lines.partition('\n')[0]
                 parts = line.split()
                 ahash = parts[0][1:]
                 atag = None
@@ -120,7 +122,7 @@ def status(self):
 
                 
                 #print(f"line is {line} ahash is {ahash} atag is {atag} {parts}")
-                #                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                #                atag = git.git_operation("describe", "--tags", "--always")
                 # ahash =  git.git_operation("rev-list", "HEAD").partition("\n")[0]
                     
                 recurse = False
@@ -149,10 +151,10 @@ def status(self):
                         result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {ahash}"
                     testfails = False
                     
-                status = git.git_operation("status", "--ignore-submodules", "-uno")
-                if "nothing to commit" not in status:
+                status, output = git.git_operation("status", "--ignore-submodules", "-uno")
+                if "nothing to commit" not in output:
                     localmods = True
-                    result = "M" + textwrap.indent(status, "                      ")
+                    result = "M" + textwrap.indent(output, "                      ")
 #        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
         return result, needsupdate, localmods, testfails
 
@@ -171,10 +173,11 @@ def _add_remote(self, git):
         Returns:
             str: The name of the new remote if added, or the name of the existing remote that matches the submodule's URL.
         """ 
-        remotes = git.git_operation("remote", "-v").splitlines()
+        status, remotes = git.git_operation("remote", "-v")
+        remotes = remotes.splitlines()
         upstream = None
         if remotes:
-            upstream = git.git_operation("ls-remote", "--get-url").rstrip()
+            status, upstream = git.git_operation("ls-remote", "--get-url")
             newremote = "newremote.00"
             tmpurl = self.url.replace("git@github.com:", "https://github.com/")
             line = next((s for s in remotes if self.url in s or tmpurl in s), None)
@@ -183,7 +186,7 @@ def _add_remote(self, git):
                 return newremote
             else:
                 i = 0
-                while "newremote" in remotes:
+                while newremote in remotes:
                     i = i + 1
                     newremote = f"newremote.{i:02d}"
         else:
@@ -214,12 +217,19 @@ def sparse_checkout(self):
         """ 
         self.logger.info("Called sparse_checkout for {}".format(self.name))
         rgit = GitInterface(self.root_dir, self.logger)
-        superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+        status, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
         if superroot:
             gitroot = superroot.strip()
         else:
             gitroot = self.root_dir.strip()
-        assert os.path.isdir(os.path.join(gitroot, ".git"))
+        # Now need to move the .git dir to the submodule location
+        rootdotgit = os.path.join(self.root_dir, ".git")
+        while os.path.isfile(rootdotgit):
+            with open(rootdotgit) as f:
+                line = f.readline().rstrip()
+                if line.startswith("gitdir: "):
+                    rootdotgit = os.path.abspath(os.path.join(self.root_dir,line[8:]))
+        assert os.path.isdir(rootdotgit)
         # first create the module directory
         if not os.path.isdir(os.path.join(self.root_dir, self.path)):
             os.makedirs(os.path.join(self.root_dir, self.path))
@@ -244,8 +254,8 @@ def sparse_checkout(self):
         # set the repository remote
         
         self.logger.info("Setting remote origin in {}/{}".format(self.root_dir, self.path))
-        status = sprepo_git.git_operation("remote", "-v")
-        if self.url not in status:
+        status, remotes = sprepo_git.git_operation("remote", "-v")
+        if self.url not in remotes:
             sprepo_git.git_operation("remote", "add", "origin", self.url)
 
         topgit = os.path.join(gitroot, ".git")
@@ -256,46 +266,46 @@ def sparse_checkout(self):
                     os.path.join(self.root_dir, f.read().split()[1]),
                     start=os.path.join(self.root_dir, self.path),
                 )
-                topgit = os.path.join(gitpath, "modules")
+                rootdotgit = os.path.join(gitpath, "modules", self.name)
         else:
-            topgit = os.path.relpath(
-                os.path.join(self.root_dir, ".git", "modules"),
+            rootdotgit = os.path.relpath(
+                os.path.join(self.root_dir, ".git", "modules", self.name),
                 start=os.path.join(self.root_dir, self.path),
             )
 
-        with utils.pushd(sprep_repo):
-            if not os.path.isdir(topgit):
-                os.makedirs(topgit)
-        topgit += os.sep + self.name
-
         if os.path.isdir(os.path.join(self.root_dir, self.path, ".git")):
             with utils.pushd(sprep_repo):
-                if os.path.isdir(os.path.join(topgit,".git")):
-                    shutil.rmtree(os.path.join(topgit,".git"))
-                shutil.move(".git", topgit)
+                if os.path.isdir(os.path.join(rootdotgit,".git")):
+                    shutil.rmtree(os.path.join(rootdotgit,".git"))
+                shutil.move(".git", rootdotgit)
                 with open(".git", "w") as f:
-                    f.write("gitdir: " + os.path.relpath(topgit))
-                #    assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo)))
-                gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout"))
+                    f.write("gitdir: " + os.path.relpath(rootdotgit))
+                infodir = os.path.join(rootdotgit, "info")
+                if not os.path.isdir(infodir):
+                    os.makedirs(infodir)
+                gitsparse = os.path.abspath(os.path.join(infodir, "sparse-checkout"))
             if os.path.isfile(gitsparse):
                 self.logger.warning(
-                    "submodule {} is already initialized {}".format(self.name, topgit)
+                    "submodule {} is already initialized {}".format(self.name, rootdotgit)
                 )
                 return
 
             with utils.pushd(sprep_repo):
                 if os.path.isfile(self.fxsparse):
+                    
                     shutil.copy(self.fxsparse, gitsparse)
                 
 
         # Finally checkout the repo
         sprepo_git.git_operation("fetch", "origin", "--tags")
-        sprepo_git.git_operation("checkout", self.fxtag)
-
-        print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
-        rgit.config_set_value(f'submodule "{self.name}"', "active", "true")
-        rgit.config_set_value(f'submodule "{self.name}"', "url", self.url)
-        rgit.config_set_value(f'submodule "{self.name}"', "path", self.path)
+        status,_ = sprepo_git.git_operation("checkout", self.fxtag)
+        if status:
+            print(f"Error checking out {self.name:>20} at {self.fxtag}")
+        else:
+            print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
+        rgit.config_set_value('submodule.' + self.name, "active", "true")
+        rgit.config_set_value('submodule.' + self.name, "url", self.url)
+        rgit.config_set_value('submodule.' + self.name, "path", self.path)
 
     def update(self):
         """
@@ -342,7 +352,7 @@ def update(self):
                     git.git_operation("clone", self.url, self.path)
                     smgit = GitInterface(repodir, self.logger)
                     if not tag:
-                        tag = smgit.git_operation("describe", "--tags", "--always").rstrip()
+                        status, tag = smgit.git_operation("describe", "--tags", "--always")
                     smgit.git_operation("checkout", tag)
                     # Now need to move the .git dir to the submodule location
                     rootdotgit = os.path.join(self.root_dir, ".git")
@@ -350,7 +360,7 @@ def update(self):
                         with open(rootdotgit) as f:
                             line = f.readline()
                             if line.startswith("gitdir: "):
-                                rootdotgit = line[8:].rstrip()
+                                rootdotgit = line[8:]
 
                     newpath = os.path.abspath(os.path.join(self.root_dir, rootdotgit, "modules", self.name))
                     if os.path.exists(newpath):
@@ -393,15 +403,16 @@ def update(self):
                 git = GitInterface(submoddir, self.logger)
                 # first make sure the url is correct
                 newremote = self._add_remote(git)
-                tags = git.git_operation("tag", "-l")
+                status, tags = git.git_operation("tag", "-l")
                 fxtag = self.fxtag
                 if fxtag and fxtag not in tags:
                     git.git_operation("fetch", newremote, "--tags")
-                atag = git.git_operation("describe", "--tags", "--always").rstrip()
+                status, atag = git.git_operation("describe", "--tags", "--always")
                 if fxtag and fxtag != atag:
                     try:
-                        git.git_operation("checkout", fxtag)
-                        print(f"{self.name:>20} updated to {fxtag}")
+                        status, _ = git.git_operation("checkout", fxtag)
+                        if not status:
+                            print(f"{self.name:>20} updated to {fxtag}")
                     except Exception as error:
                         print(error)
                     
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
index 1a2d5ccf2f..c4f43d5238 100644
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ b/.lib/git-fleximod/git_fleximod/utils.py
@@ -307,12 +307,12 @@ def execute_subprocess(commands, status_to_caller=False, output_to_caller=False)
         # simple status check. If returning, it is the callers
         # responsibility determine if an error occurred and handle it
         # appropriately.
+        msg_context = (
+            "Process did not run successfully; "
+            "returned status {0}".format(error.returncode)
+        )
+        msg = failed_command_msg(msg_context, commands, output=error.output)
         if not return_to_caller:
-            msg_context = (
-                "Process did not run successfully; "
-                "returned status {0}".format(error.returncode)
-            )
-            msg = failed_command_msg(msg_context, commands, output=error.output)
             logging.error(error)
             logging.error(msg)
             log_process_output(error.output)
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
index 850e57d59d..619cdabe3b 100644
--- a/.lib/git-fleximod/pyproject.toml
+++ b/.lib/git-fleximod/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.8.4"
+version = "0.9.2"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
index bd82c557ad..920ff0591c 100644
--- a/.lib/git-fleximod/tbump.toml
+++ b/.lib/git-fleximod/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.8.4"
+current = "0.9.2"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

From 5c343d9b35e86bf162360f576a1f4cf23f51cc3f Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Wed, 2 Oct 2024 23:55:57 -0600
Subject: [PATCH 03/53] remove duplicate fields from use cases

---
 .../use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml              | 2 +-
 bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml             | 2 +-
 bld/namelist_files/use_cases/sd_waccm_sulfur.xml              | 2 +-
 bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml            | 2 +-
 bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml            | 2 +-
 bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml     | 2 +-
 bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml          | 4 ++--
 bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml          | 2 +-
 bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml          | 2 +-
 bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml        | 2 +-
 14 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml b/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
index 15306d5711..4141549d60 100644
--- a/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
+++ b/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
@@ -80,7 +80,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
 	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+	 'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
 	 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml b/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
index 753c2e0035..5888b56ff9 100644
--- a/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
+++ b/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
@@ -76,7 +76,7 @@
   'FSDS', 'FSNS', 'FSNSC', 'FSNT', 'FSNTC', 'HORZ', 'LANDFRAC', 'LHFLX', 'OCNFRAC',
   'OH', 'OMEGA', 'PHIS', 'PRECC', 'PRECL', 'PS', 'QFLX', 'QRL', 'QRLNLTE',
   'QRS', 'RELHUM', 'SHFLX', 'SOLIN', 'SWCF', 'QCP', 'QTHERMAL', 'QRL_TOT', 'QRS_TOT',
-  'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
+  'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
   'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
diff --git a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
index 7a02c11544..6d1055cd1f 100644
--- a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
+++ b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
@@ -76,7 +76,7 @@
   'N', 'N2O', 'N2O5', 'NO', 'NO2', 'NO3', 'O', 'O1D', 'O2', 'O3',
   'OCLO', 'OCNFRAC', 'OH', 'OMEGA', 'PHIS', 'PRECC', 'PRECL', 'PS', 'Q', 'QFLX',
   'QPERT', 'QRL', 'QRLNLTE', 'QRS', 'RELHUM', 'SHFLX', 'SOLIN', 'SWCF', 'QCP',
-  'QTHERMAL', 'QRL_TOT', 'QRS_TOT', 'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT',
+  'QTHERMAL', 'QRL_TOT', 'QRS_TOT', 'PSL', 'HNO3_STS', 'HNO3_NAT',
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
diff --git a/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml b/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
index 6ec178700a..f50160948e 100644
--- a/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
+++ b/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
@@ -80,7 +80,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
 	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+	 'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
 	 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml b/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
index 6493ed584b..984ab0b002 100644
--- a/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
+++ b/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
@@ -67,7 +67,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
          'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-         'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+         'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
          'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
          'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml b/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
index 1429770e8e..c04967bace 100644
--- a/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
+++ b/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
@@ -90,7 +90,7 @@
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
-  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI',
+  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI',
   'VI', 'UIONTEND', 'VIONTEND', 'DTCORE', 'T_24_COS',  'T_24_SIN', 'T_12_COS', 'T_12_SIN',
   'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS', 'OMEGA_12_SIN',
   'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
index 24b55facc2..d978796e4a 100644
--- a/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
@@ -63,7 +63,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
index 9ccac8892f..5443a10f83 100644
--- a/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
@@ -158,7 +158,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml b/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
index e2376e4a70..6526502ba5 100644
--- a/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
@@ -86,7 +86,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
index 042a153fe4..30deb2b74d 100644
--- a/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
@@ -57,7 +57,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml b/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
index 017cc3362e..c5bc7e2f57 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
@@ -87,7 +87,7 @@
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
-  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE','UI','VI','WI',
+  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI','VI','WI',
   'UIONTEND', 'VIONTEND', 'DTCORE', 'T_24_COS',  'T_24_SIN', 'T_12_COS', 'T_12_SIN',
   'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS', 'OMEGA_12_SIN',
   'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS',
@@ -134,7 +134,7 @@
   'Qbkgndtot','Qbkgnd_o1','Qbkgnd_o2','Qbkgnd_n2','Qbkgnd_n1','Qbkgnd_no',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT', 'TTGW', 'U',
   'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S', 'O2_1D', 'NOX', 'NOY',
-  'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UIONTEND', 'VIONTEND',
+  'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'CLDLIQ', 'CLDICE', 'CONCLD', 'FRONTGF:I', 'BUTGWSPEC', 'BTAUE', 'BTAUW', 'BTAUN', 'BTAUS', 'TAUE',
   'TAUW', 'TAUN', 'TAUS', 'TAUGWX', 'TAUGWY', 'TAUX', 'TAUY', 'SNOWHLND', 'SNOWHICE', 'ICEFRAC', 'FSDSC',
   'SFNO', 'SFCO', 'SFCH2O', 'CFC11STAR', 'TROPP_FD', 'Op', 'O2p', 'Np', 'NOp',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml b/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
index 06520cc3fb..713ad27c86 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
@@ -48,7 +48,7 @@
          'WI', 'ElecColDens', 'PHIM2D', 'PS', 'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2', 'O', 'O2',
          'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op', 'Np', 'N2p',
          'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2', 'QNO',
-         'QO3P', 'QHC2S', 'QJOULE', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
+         'QO3P', 'QHC2S', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
          'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS',
          'U_08_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
          'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml b/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
index 37ca427cd2..02d3b04009 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
@@ -46,7 +46,7 @@
          'WI', 'ElecColDens', 'PHIM2D', 'PS', 'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2', 'O', 'O2',
          'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op', 'Np', 'N2p',
          'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2', 'QNO',
-         'QO3P', 'QHC2S', 'QJOULE', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
+         'QO3P', 'QHC2S', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
          'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS',
          'U_08_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
          'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml b/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
index 5fe9c654dd..ae18c1113c 100644
--- a/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
+++ b/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
@@ -98,7 +98,7 @@
 <fincl1>
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
-	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
+	 'Np', 'N2p', 'O2p', 'NOp', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
 	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',

From 8abd7cf89cc365f4320465a6dfa66440cc57a3da Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 14:23:20 -0600
Subject: [PATCH 04/53] change methodology to allow for duplicate fields with
 the same flag

---
 src/control/cam_history.F90 | 80 ++++++++++++++++++++++---------------
 1 file changed, 48 insertions(+), 32 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 602280baf3..c91287899b 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -2566,10 +2566,8 @@ subroutine fldlst ()
     !
     integer t, fld                 ! tape, field indices
     integer ffld                   ! index into include, exclude and fprec list
-    integer :: ffld_array(pflds, ptapes)
     integer :: i
-    integer :: duplicate_index           ! iterator for multiple occurrences of the same field
-    integer :: num_fields                ! Number of times field appears in field list
+    logical :: duplicate_error           ! flag for whether there is an incompatible duplicate found
     character(len=fieldname_len) :: name ! field name portion of fincl (i.e. no avgflag separator)
     character(len=max_fieldname_len) :: mastername ! name from masterlist field
     character(len=max_chars) :: errormsg ! error output field
@@ -2644,8 +2642,8 @@ subroutine fldlst ()
       add_fincl_idx = fld
       if (fld > 1 .and. interpolate_output(t)) then
          do i = 1, n_vec_comp
-            call list_index(fincl(:,t), vec_comp_names(i), ffld_array(:,t))
-            if (.not. any(ffld_array(:,t) > 0)) then
+            call list_index(fincl(:,t), vec_comp_names(i), ffld)
+            if (ffld == 0) then
 
                ! Add vector component to fincl.  Don't need to check whether its in the master
                ! list since this was done at the time of registering the vector components.
@@ -2743,23 +2741,27 @@ subroutine fldlst ()
       listentry => masterlinkedlist
       do while(associated(listentry))
         mastername = listentry%field%name
-        call list_index (fincl(1,t), mastername, ffld_array(:,t))
+        call list_index (fincl(1,t), mastername, ffld, duplicate_error=duplicate_error)
+        if (duplicate_error) then
+          write(errormsg,'(2a,2(a,i3))') &
+               'FLDLST: Duplicate field with different averaging flags. Place on separate tapes: ', &
+                trim(mastername),', tape = ', t, ', ffld = ', ffld
+          call endrun(trim(errormsg))
+        end if
 
         fieldontape = .false.
-        if (any(ffld_array(:,t) > 0)) then
+        if (ffld > 0) then
           fieldontape = .true.
-          num_fields = count(ffld_array(:,t) > 0)
         else if ((.not. empty_htapes) .or. (is_initfile(file_index=t))) then
-          call list_index (fexcl(1,t), mastername, ffld_array(:,t))
-          if ((.not. any(ffld_array(:,t) > 0)) .and. listentry%actflag(t)) then
+          call list_index (fexcl(1,t), mastername, ffld)
+          if (ffld == 0 .and. listentry%actflag(t)) then
             fieldontape = .true.
-            num_fields = 1
           end if
         end if
         if (fieldontape) then
           ! The field is active so increment the number of fields and add
           ! its decomp type to the list of decomp types on this tape
-          nflds(t) = nflds(t) + num_fields
+          nflds(t) = nflds(t) + 1
           do ffld = 1, size(gridsontape, 1)
             if (listentry%field%decomp_type == gridsontape(ffld, t)) then
               exit
@@ -2822,23 +2824,21 @@ subroutine fldlst ()
       do while(associated(listentry))
         mastername = listentry%field%name
 
-        call list_index (fwrtpr(1,t), mastername, ffld_array(:,t))
-        if (ffld_array(1,t) > 0) then
-           prec_wrt = getflag(fwrtpr(ffld_array(1,t), t))
+        call list_index (fwrtpr(1,t), mastername, ffld)
+        if (ffld > 0) then
+          prec_wrt = getflag(fwrtpr(ffld,t))
         else
-           prec_wrt = ' '
+          prec_wrt = ' '
         end if
 
-        call list_index (fincl(1,t), mastername, ffld_array(:,t))
+        call list_index (fincl(1,t), mastername, ffld)
 
-        if (any(ffld_array(:,t) > 0)) then
-          do duplicate_index = 1, count(ffld_array(:,t) > 0)
-            avgflag = getflag (fincl(ffld_array(duplicate_index,t),t))
-            call inifld (t, listentry, avgflag,  prec_wrt)
-          end do
+        if (ffld > 0) then
+          avgflag = getflag (fincl(ffld,t))
+          call inifld (t, listentry, avgflag,  prec_wrt)
         else if ((.not. empty_htapes) .or. (is_initfile(file_index=t))) then
-          call list_index (fexcl(1,t), mastername, ffld_array(:,t))
-          if (.not. any(ffld_array(:,t) > 0) .and. listentry%actflag(t)) then
+          call list_index (fexcl(1,t), mastername, ffld)
+          if (ffld == 0 .and. listentry%actflag(t)) then
             call inifld (t, listentry, ' ', prec_wrt)
           else
             listentry%actflag(t) = .false.
@@ -3514,25 +3514,30 @@ end function getflag
 
   !#######################################################################
 
-  subroutine list_index (list, name, index)
+  subroutine list_index (list, name, index, duplicate_error)
     !
     ! Input arguments
     !
-    character(len=*), intent(in) :: list(pflds) ! input list of names, possibly ":" delimited
-    character(len=*), intent(in) :: name ! name to be searched for
+    character(len=*),   intent(in) :: list(pflds) ! input list of names, possibly ":" delimited
+    character(len=*),   intent(in) :: name        ! name to be searched for
+    logical, optional, intent(out) :: duplicate_error ! .true. if a duplicate field was found with different flags
     !
     ! Output arguments
     !
-    integer, intent(out) :: index(:)            ! indices of "name" in "list"
+    integer, intent(out) :: index               ! index of "name" in "list"
     !
     ! Local workspace
     !
     character(len=fieldname_len) :: listname    ! input name with ":" stripped off.
+    character(len=fieldname_len) :: flag        ! accumulate flag for field
+    character(len=fieldname_len) :: flag_comp   ! accumulate flag to compare with previous entry
     integer :: f                                ! field index
-    integer :: num_found                        ! number of time field appears in list
 
     index = 0
-    num_found = 1
+    if (present(duplicate_error)) then
+       duplicate_error = .false.
+    end if
+
     do f=1,pflds
       !
       ! Only list items
@@ -3540,8 +3545,19 @@ subroutine list_index (list, name, index)
       listname = getname (list(f))
       if (listname == ' ') exit
       if (listname == name) then
-        index(num_found) = f
-        num_found = num_found + 1
+        if (index /= 0 .and. present(duplicate_error)) then
+          ! This already exists in the field list - check the flag
+          flag_comp = getflag(list(f))
+          if (trim(flag_comp) /= trim(flag)) then
+            duplicate_error = .true.
+            return
+          ! No else - if the flags are identical, we're ok to return the first
+          !  instance
+          end if
+        else
+          index = f
+          flag = getflag(list(f))
+        end if
       end if
     end do
 

From 33b6ffbd92da49a720ee409cc197c89204fcd466 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 14:29:18 -0600
Subject: [PATCH 05/53] code cleanup; fix bad comment

---
 bld/namelist_files/use_cases/sd_waccm_sulfur.xml |  2 +-
 src/control/cam_history.F90                      | 14 ++------------
 2 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
index 6d1055cd1f..4c2d827633 100644
--- a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
+++ b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
@@ -133,7 +133,7 @@
 <met_data_path>atm/cam/met/GEOS5</met_data_path>
 <met_filenames_list>atm/cam/met/GEOS5_filenames_list_c120516.txt</met_filenames_list>
 
-<!-- bnd_topo --->
+<!-- bnd_topo -->
 <bnd_topo>atm/cam/met/USGS-gtopo30_1.9x2.5_phys_geos5_c100929.nc</bnd_topo>
 
 <!-- sim_year used for CLM datasets and SSTs forcings -->
diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index c91287899b..0d3a4dc823 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -2885,18 +2885,8 @@ subroutine fldlst ()
             tape(t)%hlist(ffld+1) = tmp
 
           else if (tape(t)%hlist(ffld)%field%name == tape(t)%hlist(ffld+1)%field%name) then
-            if (tape(t)%hlist(ffld)%avgflag == tape(t)%hlist(ffld+1)%avgflag) then
-              write(errormsg,'(2a,2(a,i3),2a)') &
-                   'FLDLST: Duplicate field with the same averaging flag. Check your fincl list: ', &
-                   trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld, &
-                   ', flag = ', trim(tape(t)%hlist(ffld)%avgflag)
-            else
-              write(errormsg,'(2a,2(a,i3),4a)') &
-                   'FLDLST: Duplicate field with different averaging flags. Place on separate tapes: ', &
-                   trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld, &
-                   ', flag1 = ', trim(tape(t)%hlist(ffld)%avgflag), ', flag2 = ', &
-                   trim(tape(t)%hlist(ffld+1)%avgflag)
-            end if
+            write(errormsg,'(2a,2(a,i3))') 'FLDLST: Duplicate field: ', &
+                 trim(tape(t)%hlist(ffld)%field%name),', tape = ', t, ', ffld = ', ffld
             call endrun(errormsg)
 
           end if

From b29a8dea9954ee1584bcc63a6b8c15cc5e7c8ed3 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 14:37:13 -0600
Subject: [PATCH 06/53] revert duplicate removal

---
 .../use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml              | 2 +-
 bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml             | 2 +-
 bld/namelist_files/use_cases/sd_waccm_sulfur.xml              | 2 +-
 bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml            | 2 +-
 bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml            | 2 +-
 bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml     | 2 +-
 bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml           | 2 +-
 bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml           | 2 +-
 bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml          | 4 ++--
 bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml          | 2 +-
 bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml          | 2 +-
 bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml        | 2 +-
 .../testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam     | 2 +-
 15 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml b/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
index 4141549d60..15306d5711 100644
--- a/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
+++ b/bld/namelist_files/use_cases/1950-2010_ccmi_refc1_waccmx_ma.xml
@@ -80,7 +80,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
 	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-	 'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
 	 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml b/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
index 5888b56ff9..753c2e0035 100644
--- a/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
+++ b/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml
@@ -76,7 +76,7 @@
   'FSDS', 'FSNS', 'FSNSC', 'FSNT', 'FSNTC', 'HORZ', 'LANDFRAC', 'LHFLX', 'OCNFRAC',
   'OH', 'OMEGA', 'PHIS', 'PRECC', 'PRECL', 'PS', 'QFLX', 'QRL', 'QRLNLTE',
   'QRS', 'RELHUM', 'SHFLX', 'SOLIN', 'SWCF', 'QCP', 'QTHERMAL', 'QRL_TOT', 'QRS_TOT',
-  'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
+  'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
   'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
diff --git a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
index 4c2d827633..d035ea8b79 100644
--- a/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
+++ b/bld/namelist_files/use_cases/sd_waccm_sulfur.xml
@@ -76,7 +76,7 @@
   'N', 'N2O', 'N2O5', 'NO', 'NO2', 'NO3', 'O', 'O1D', 'O2', 'O3',
   'OCLO', 'OCNFRAC', 'OH', 'OMEGA', 'PHIS', 'PRECC', 'PRECL', 'PS', 'Q', 'QFLX',
   'QPERT', 'QRL', 'QRLNLTE', 'QRS', 'RELHUM', 'SHFLX', 'SOLIN', 'SWCF', 'QCP',
-  'QTHERMAL', 'QRL_TOT', 'QRS_TOT', 'PSL', 'HNO3_STS', 'HNO3_NAT',
+  'QTHERMAL', 'QRL_TOT', 'QRS_TOT', 'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT',
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
diff --git a/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml b/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
index f50160948e..6ec178700a 100644
--- a/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
+++ b/bld/namelist_files/use_cases/sd_waccmx_ma_cam4.xml
@@ -80,7 +80,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
 	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-	 'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
 	 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml b/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
index 984ab0b002..6493ed584b 100644
--- a/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
+++ b/bld/namelist_files/use_cases/sd_waccmx_ma_cam6.xml
@@ -67,7 +67,7 @@
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
          'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
-         'QNO', 'QO3P', 'QHC2S', 'EKGW', 'TTGW', 'UTGW_TOTAL',
+         'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
          'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
          'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
diff --git a/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml b/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
index c04967bace..1429770e8e 100644
--- a/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
+++ b/bld/namelist_files/use_cases/waccm_carma_bc_2013_cam4.xml
@@ -90,7 +90,7 @@
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
-  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI',
+  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI',
   'VI', 'UIONTEND', 'VIONTEND', 'DTCORE', 'T_24_COS',  'T_24_SIN', 'T_12_COS', 'T_12_SIN',
   'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS', 'OMEGA_12_SIN',
   'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
index d978796e4a..24b55facc2 100644
--- a/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml
@@ -63,7 +63,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
index 5443a10f83..9ccac8892f 100644
--- a/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml
@@ -158,7 +158,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml b/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
index 6526502ba5..e2376e4a70 100644
--- a/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml
@@ -86,7 +86,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml b/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
index 30deb2b74d..042a153fe4 100644
--- a/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
+++ b/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml
@@ -57,7 +57,7 @@
   'QJOULE', 'PSL', 'HNO3_STS', 'HNO3_NAT', 'HNO3_GAS', 'NO_Lightning', 'QNO', 'QRS_AUR',
   'QRS_CO2NIR', 'QRS_EUV', 'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'TREFHT', 'TTGW',
   'UTGWORO', 'UTGWSPEC', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'HOX', 'NOX', 'NOY', 'CLOX',
-  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
+  'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UI', 'VI', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'OMEGA_24_COS', 'OMEGA_24_SIN',
   'OMEGA_12_COS', 'OMEGA_12_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN',
   'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'PS_24_COS', 'PS_24_SIN', 'PS_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml b/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
index c5bc7e2f57..017cc3362e 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_2000_cam4.xml
@@ -87,7 +87,7 @@
   'HNO3_GAS', 'NO_Aircraft', 'NO_Lightning', 'QNO', 'QRS_AUR', 'QRS_CO2NIR', 'QRS_EUV',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT',
   'TTGW', 'U', 'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S',
-  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UI','VI','WI',
+  'O2_1D', 'NOX', 'NOY', 'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE','UI','VI','WI',
   'UIONTEND', 'VIONTEND', 'DTCORE', 'T_24_COS',  'T_24_SIN', 'T_12_COS', 'T_12_SIN',
   'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS', 'OMEGA_12_SIN',
   'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS',
@@ -134,7 +134,7 @@
   'Qbkgndtot','Qbkgnd_o1','Qbkgnd_o2','Qbkgnd_n2','Qbkgnd_n1','Qbkgnd_no',
   'SAD_ICE', 'SAD_LNAT', 'SAD_SULFC', 'T', 'TREFHT', 'TTGW', 'U',
   'UTGWORO', 'UTGWSPEC', 'V', 'VERT', 'VTGWORO', 'VTGWSPEC', 'Z3', 'O2_1S', 'O2_1D', 'NOX', 'NOY',
-  'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'UIONTEND', 'VIONTEND',
+  'CLOX', 'CLOY', 'BROX', 'BROY', 'TCLY', 'TOTH', 'QJOULE', 'UIONTEND', 'VIONTEND',
   'DTCORE', 'CLDLIQ', 'CLDICE', 'CONCLD', 'FRONTGF:I', 'BUTGWSPEC', 'BTAUE', 'BTAUW', 'BTAUN', 'BTAUS', 'TAUE',
   'TAUW', 'TAUN', 'TAUS', 'TAUGWX', 'TAUGWY', 'TAUX', 'TAUY', 'SNOWHLND', 'SNOWHICE', 'ICEFRAC', 'FSDSC',
   'SFNO', 'SFCO', 'SFCH2O', 'CFC11STAR', 'TROPP_FD', 'Op', 'O2p', 'Np', 'NOp',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml b/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
index 713ad27c86..06520cc3fb 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
@@ -48,7 +48,7 @@
          'WI', 'ElecColDens', 'PHIM2D', 'PS', 'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2', 'O', 'O2',
          'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op', 'Np', 'N2p',
          'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2', 'QNO',
-         'QO3P', 'QHC2S', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
+         'QO3P', 'QHC2S', 'QJOULE', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
          'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS',
          'U_08_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
          'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml b/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
index 02d3b04009..37ca427cd2 100644
--- a/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
+++ b/bld/namelist_files/use_cases/waccmx_ma_hist_cam6.xml
@@ -46,7 +46,7 @@
          'WI', 'ElecColDens', 'PHIM2D', 'PS', 'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2', 'O', 'O2',
          'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op', 'Np', 'N2p',
          'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2', 'QNO',
-         'QO3P', 'QHC2S', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
+         'QO3P', 'QHC2S', 'QJOULE', 'QEN', 'QIN', 'QEI', 'EKGW', 'TTGW', 'UTGW_TOTAL', 'T_24_COS',
          'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN', 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS',
          'U_08_SIN', 'V_24_COS', 'V_24_SIN', 'V_12_COS', 'V_12_SIN', 'V_08_COS', 'V_08_SIN',
          'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS',
diff --git a/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml b/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
index ae18c1113c..5fe9c654dd 100644
--- a/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
+++ b/bld/namelist_files/use_cases/waccmxie_ma_2000_cam4.xml
@@ -98,7 +98,7 @@
 <fincl1>
          'Z3', 'T', 'TIon', 'TElec', 'e', 'U', 'V', 'OMEGA', 'UI', 'VI', 'WI', 'ElecColDens', 'PHIM2D', 'PS',
          'PED_CONDUCTANCE', 'HALL_CONDUCTANCE', 'ED1', 'ED2' 'O', 'O2', 'H', 'NO', 'CO2', 'N', 'O1D', 'Op2P', 'Op2D', 'Op',
-	 'Np', 'N2p', 'O2p', 'NOp', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
+	 'Np', 'N2p', 'O2p', 'NOp', 'QJOULE', 'SIGMAHAL', 'SIGMAPED', 'SolIonRate_Tot', 'QRS_TOT', 'QO3', 'QCO2',
 	 'QNO', 'QO3P', 'QHC2S', 'QJOULE', 'EKGW', 'TTGW', 'UTGW_TOTAL',
          'T_24_COS', 'T_24_SIN', 'T_12_COS', 'T_12_SIN', 'T_08_COS', 'T_08_SIN',
 	 'U_24_COS', 'U_24_SIN', 'U_12_COS', 'U_12_SIN', 'U_08_COS', 'U_08_SIN',
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam b/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
index 2d18788e39..e385809756 100644
--- a/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
+++ b/cime_config/testdefs/testmods_dirs/cam/outfrq24h_port/user_nl_cam
@@ -2,7 +2,7 @@
  rad_data_fdh = .true.
  empty_htapes = .true.
  avgflag_pertape = 'A','I'
- fincl1 = 'SOLIN', 'QRS', 'FSNS', 'FSNT','FSNSC', 'FSNR','FLNR',
+ fincl1 = 'SOLIN', 'QRS', 'FSNS', 'FSNT','FSNSC', 'FSDSC','FSNR','FLNR',
           'FSNTOA', 'FSUTOA', 'FSNTOAC', 'FSNTC', 'FSDSC', 'FSDS', 'SWCF',
           'QRL', 'FLNS', 'FLDS', 'FLNT', 'LWCF', 'FLUT' ,'FLUTC', 'FLNTC', 
           'FLNSC', 'FLDSC'

From 31e7e6b73a07454b3e56684d3d266bba087e5008 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 16:17:53 -0600
Subject: [PATCH 07/53] improve error handling

---
 src/control/cam_history.F90 | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 0d3a4dc823..acbcbd266d 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -2552,6 +2552,7 @@ subroutine fldlst ()
     use cam_grid_support, only: cam_grid_num_grids
     use spmd_utils,       only: mpicom
     use dycore,           only: dycore_is
+    use shr_kind_mod,     only: cm => shr_kind_cm
 
     !-----------------------------------------------------------------------
     !
@@ -2567,7 +2568,8 @@ subroutine fldlst ()
     integer t, fld                 ! tape, field indices
     integer ffld                   ! index into include, exclude and fprec list
     integer :: i
-    logical :: duplicate_error           ! flag for whether there is an incompatible duplicate found
+    character(len=cm) :: duplicate_error ! string to be populated if an incompatible duplicate is found
+    character(len=cm) :: tempmsg         ! string to be populated if an incompatible duplicate is found
     character(len=fieldname_len) :: name ! field name portion of fincl (i.e. no avgflag separator)
     character(len=max_fieldname_len) :: mastername ! name from masterlist field
     character(len=max_chars) :: errormsg ! error output field
@@ -2730,6 +2732,7 @@ subroutine fldlst ()
 
     allocate(gridsontape(cam_grid_num_grids() + 1, ptapes))
     gridsontape = -1
+    errormsg = ''
     do t=1,ptapes
       !
       ! Add the field to the tape if specified via namelist (FINCL[1-ptapes]), or if
@@ -2742,11 +2745,13 @@ subroutine fldlst ()
       do while(associated(listentry))
         mastername = listentry%field%name
         call list_index (fincl(1,t), mastername, ffld, duplicate_error=duplicate_error)
-        if (duplicate_error) then
-          write(errormsg,'(2a,2(a,i3))') &
-               'FLDLST: Duplicate field with different averaging flags. Place on separate tapes: ', &
-                trim(mastername),', tape = ', t, ', ffld = ', ffld
-          call endrun(trim(errormsg))
+        if (len(trim(duplicate_error)) > 0) then
+          if (len_trim(errormsg) == 0) then
+            write(errormsg,*) &
+              'FLDLST: Found duplicate field(s) with different averaging flags. Place on separate tapes: '
+          end if
+          write(tempmsg, '(2a, i0, a)') trim(duplicate_error), ' (tape ', t, '). '
+          errormsg = trim(errormsg) // trim(tempmsg)
         end if
 
         fieldontape = .false.
@@ -2774,6 +2779,9 @@ subroutine fldlst ()
         listentry=>listentry%next_entry
       end do
     end do
+    if (len(errormsg) > 0) then
+       call endrun(trim(errormsg))
+    end if
     !
     ! Determine total number of active history tapes
     !
@@ -3510,7 +3518,7 @@ subroutine list_index (list, name, index, duplicate_error)
     !
     character(len=*),   intent(in) :: list(pflds) ! input list of names, possibly ":" delimited
     character(len=*),   intent(in) :: name        ! name to be searched for
-    logical, optional, intent(out) :: duplicate_error ! .true. if a duplicate field was found with different flags
+    character(len=*), optional, intent(out) :: duplicate_error ! if present, check the flags and return an error if incompatible
     !
     ! Output arguments
     !
@@ -3525,7 +3533,7 @@ subroutine list_index (list, name, index, duplicate_error)
 
     index = 0
     if (present(duplicate_error)) then
-       duplicate_error = .false.
+       duplicate_error = ''
     end if
 
     do f=1,pflds
@@ -3539,7 +3547,9 @@ subroutine list_index (list, name, index, duplicate_error)
           ! This already exists in the field list - check the flag
           flag_comp = getflag(list(f))
           if (trim(flag_comp) /= trim(flag)) then
-            duplicate_error = .true.
+            write(duplicate_error,*) &
+              '"', trim(list(f)), '", "', trim(name), &
+              ':', trim(flag), '"'
             return
           ! No else - if the flags are identical, we're ok to return the first
           !  instance

From ca138950be0819fe86f870c618201afd1f346681 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 16:32:09 -0600
Subject: [PATCH 08/53] remove reference to tapes

---
 src/control/cam_history.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index acbcbd266d..156d70f573 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -2748,9 +2748,9 @@ subroutine fldlst ()
         if (len(trim(duplicate_error)) > 0) then
           if (len_trim(errormsg) == 0) then
             write(errormsg,*) &
-              'FLDLST: Found duplicate field(s) with different averaging flags. Place on separate tapes: '
+              'FLDLST: Found duplicate field(s) with different averaging flags. Place in separate fincl lists: '
           end if
-          write(tempmsg, '(2a, i0, a)') trim(duplicate_error), ' (tape ', t, '). '
+          write(tempmsg, '(2a, i0, a)') trim(duplicate_error), ' (fincl', t, '). '
           errormsg = trim(errormsg) // trim(tempmsg)
         end if
 

From b960ffb79a952f7cab6ce1e2671a566d80e92fc5 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Thu, 3 Oct 2024 17:05:44 -0600
Subject: [PATCH 09/53] don't error all the time perhaps

---
 src/control/cam_history.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 156d70f573..0b7ce50944 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -2779,7 +2779,7 @@ subroutine fldlst ()
         listentry=>listentry%next_entry
       end do
     end do
-    if (len(errormsg) > 0) then
+    if (len_trim(errormsg) > 0) then
        call endrun(trim(errormsg))
     end if
     !

From 225f7e3a5e836688ec1168f5b0369051fd34cd2c Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Fri, 11 Oct 2024 14:47:49 -0600
Subject: [PATCH 10/53] add sampled_on_subcycle flag and remove time_bounds
 field from instantaneous files

---
 src/control/cam_history.F90                  |  53 ++-
 src/control/cam_history_support.F90          |   3 +
 src/physics/cam/cam_diagnostics.F90          |   6 +-
 src/physics/cam/check_energy.F90             |  12 +-
 src/physics/cam/clubb_intr.F90               | 170 ++++----
 src/physics/cam/macrop_driver.F90            |  70 ++--
 src/physics/cam/micro_pumas_cam.F90          | 336 +++++++--------
 src/physics/cam/microp_aero.F90              |   6 +-
 src/physics/cam7/micro_pumas_cam.F90         | 410 +++++++++----------
 src/physics/cam7/stochastic_emulated_cam.F90 |  72 ++--
 src/physics/cam7/stochastic_tau_cam.F90      |  72 ++--
 11 files changed, 618 insertions(+), 592 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 0b7ce50944..e86f885f0e 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -486,6 +486,12 @@ subroutine intht (model_doi_url_in)
     !
     do t=1,ptapes
       do fld=1,nflds(t)
+        if ((.not. tape(t)%hlist(fld)%field%sampled_on_subcycle) .and. nhtfrq(t) == 1) then
+           ! Override accumulate flag to "I" if nhtfrq equals 1 and subcycle
+           ! averaging is not enabled
+           tape(t)%hlist(fld)%avgflag = 'I'
+        end if
+
         if (tape(t)%hlist(fld)%avgflag .ne. 'I') then
            hfile_accum(t) = .true.
         end if
@@ -4022,7 +4028,9 @@ subroutine h_inquire (t)
             ierr=pio_inq_varid (tape(t)%Files(f),'nscur   ',    tape(t)%nscurid)
             ierr=pio_inq_varid (tape(t)%Files(f),'nsteph  ',    tape(t)%nstephid)
          end if
-         ierr=pio_inq_varid (tape(t)%Files(f),'time_bounds',   tape(t)%tbndid)
+         if (f == accumulated_file_index) then
+            ierr=pio_inq_varid (tape(t)%Files(f),'time_bounds',   tape(t)%tbndid)
+         end if
          ierr=pio_inq_varid (tape(t)%Files(f),'date_written',  tape(t)%date_writtenid)
          ierr=pio_inq_varid (tape(t)%Files(f),'time_written',  tape(t)%time_writtenid)
 #if ( defined BFB_CAM_SCAM_IOP )
@@ -4321,6 +4329,7 @@ subroutine h_define (t, restart)
                       cam_snapshot_before_num_out = cam_snapshot_before_num,  &
                       cam_snapshot_after_num_out  = cam_snapshot_after_num)
 
+
     if(restart) then
       tape => restarthistory_tape
       if(masterproc) write(iulog,*)'Opening netcdf history restart file ', trim(hrestpath(t))
@@ -4500,13 +4509,14 @@ subroutine h_define (t, restart)
 
        if(.not. is_satfile(t)) then
 
-         ierr=pio_put_att (tape(t)%Files(f), tape(t)%timeid, 'bounds', 'time_bounds')
-
-         ierr=pio_def_var (tape(t)%Files(f),'time_bounds',pio_double,(/bnddim,timdim/),tape(t)%tbndid)
-         ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'long_name', 'time interval endpoints')
-         str = 'days since ' // date2yyyymmdd(nbdate) // ' ' // sec2hms(nbsec)
-         ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'units', trim(str))
-         ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'calendar', trim(calendar))
+         if (f == accumulated_file_index) then
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%timeid, 'bounds', 'time_bounds')
+            ierr=pio_def_var (tape(t)%Files(f),'time_bounds',pio_double,(/bnddim,timdim/),tape(t)%tbndid)
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'long_name', 'time interval endpoints')
+            str = 'days since ' // date2yyyymmdd(nbdate) // ' ' // sec2hms(nbsec)
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'units', trim(str))
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'calendar', trim(calendar))
+         end if
          !
          ! Character
          !
@@ -5843,14 +5853,16 @@ subroutine wshist (rgnht_in)
                 cycle
              end if
              ! We have two files - one for accumulated and one for instantaneous fields
-             if (f == accumulated_file_index .and. .not. restart .and. .not. is_initfile(t)) then
-                ! accumulated tape - time is midpoint of time_bounds
-                ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/(tdata(1) + tdata(2)) / 2._r8/))
+             if (f == accumulated_file_index) then
+                ierr=pio_put_var (tape(t)%Files(f), tape(t)%tbndid, startc, countc, tdata)
+                if (.not. restart .and. .not. is_initfile(t)) then
+                   ! accumulated tape - time is midpoint of time_bounds
+                   ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/(tdata(1) + tdata(2)) / 2._r8/))
+                end if
              else
                 ! not an accumulated history tape - time is current time
                 ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/time/))
              end if
-             ierr=pio_put_var (tape(t)%Files(f), tape(t)%tbndid, startc, countc, tdata)
           end do
           if(.not.restart) beg_time(t) = time  ! update beginning time of next interval
           startc(1) = 1
@@ -5938,7 +5950,7 @@ end subroutine wshist
 
   subroutine addfld_1d(fname, vdim_name, avgflag, units, long_name,           &
        gridname, flag_xyfill, sampling_seq, standard_name, fill_value,        &
-       optype, op_f1name, op_f2name)
+       optype, op_f1name, op_f2name, sampled_on_subcycle)
 
     !
     !-----------------------------------------------------------------------
@@ -5970,6 +5982,7 @@ subroutine addfld_1d(fname, vdim_name, avgflag, units, long_name,           &
     character(len=*), intent(in), optional :: optype       ! currently 'dif' or 'sum' is supported
     character(len=*), intent(in), optional :: op_f1name    ! first field to be operated on
     character(len=*), intent(in), optional :: op_f2name    ! second field which is subtracted from or added to first field
+    logical,          intent(in), optional :: sampled_on_subcycle   ! If .true., subcycle averaging is enabled
     !
     ! Local workspace
     !
@@ -5988,13 +6001,13 @@ subroutine addfld_1d(fname, vdim_name, avgflag, units, long_name,           &
     end if
     call addfld(fname, dimnames, avgflag, units, long_name, gridname,         &
          flag_xyfill, sampling_seq, standard_name, fill_value, optype, op_f1name, &
-         op_f2name)
+         op_f2name, sampled_on_subcycle)
 
   end subroutine addfld_1d
 
   subroutine addfld_nd(fname, dimnames, avgflag, units, long_name,            &
        gridname, flag_xyfill, sampling_seq, standard_name, fill_value, optype,    &
-       op_f1name, op_f2name)
+       op_f1name, op_f2name, sampled_on_subcycle)
 
     !
     !-----------------------------------------------------------------------
@@ -6030,6 +6043,7 @@ subroutine addfld_nd(fname, dimnames, avgflag, units, long_name,            &
     character(len=*), intent(in), optional :: optype       ! currently 'dif' or 'sum' supported
     character(len=*), intent(in), optional :: op_f1name    ! first field to be operated on
     character(len=*), intent(in), optional :: op_f2name    ! second field which is subtracted from or added to first field
+    logical,          intent(in), optional :: sampled_on_subcycle   ! If .true., subcycle averaging is enabled
 
     !
     ! Local workspace
@@ -6154,6 +6168,15 @@ subroutine addfld_nd(fname, dimnames, avgflag, units, long_name,            &
       listentry%field%fillvalue = fillvalue
     endif
 
+    !
+    ! Whether to allow subcycle averages; default is false
+    !
+    if (present(sampled_on_subcycle)) then
+       listentry%field%sampled_on_subcycle = sampled_on_subcycle
+    else
+       listentry%field%sampled_on_subcycle = .false.
+    end if
+
     !
     ! Process shape
     !
diff --git a/src/control/cam_history_support.F90 b/src/control/cam_history_support.F90
index 940dc8c177..5e5983e784 100644
--- a/src/control/cam_history_support.F90
+++ b/src/control/cam_history_support.F90
@@ -118,6 +118,9 @@ module cam_history_support
     integer :: meridional_complement         ! meridional field id or -1
     integer :: zonal_complement              ! zonal field id or -1
 
+    ! Logical to determine if subcycle averages are allowed
+    logical :: sampled_on_subcycle = .false.
+
     character(len=field_op_len) :: field_op = ''        ! 'sum' or 'dif'
     integer                     :: op_field1_id         ! first field id or -1
     integer                     :: op_field2_id         ! second field id or -1
diff --git a/src/physics/cam/cam_diagnostics.F90 b/src/physics/cam/cam_diagnostics.F90
index 97dad2ba01..082a2df9d8 100644
--- a/src/physics/cam/cam_diagnostics.F90
+++ b/src/physics/cam/cam_diagnostics.F90
@@ -232,9 +232,9 @@ subroutine diag_init_dry(pbuf2d)
     call register_vector_field('UTEND_TOT','VTEND_TOT')
 
     ! Debugging negative water output fields
-    call addfld ('INEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud ice tendency due to clipping neg values after microp')
-    call addfld ('LNEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud liq tendency due to clipping neg values after microp')
-    call addfld ('VNEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Vapor tendency due to clipping neg values after microp')
+    call addfld ('INEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud ice tendency due to clipping neg values after microp', sampled_on_subcycle=.true.)
+    call addfld ('LNEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud liq tendency due to clipping neg values after microp', sampled_on_subcycle=.true.)
+    call addfld ('VNEGCLPTEND ', (/ 'lev' /), 'A', 'kg/kg/s', 'Vapor tendency due to clipping neg values after microp', sampled_on_subcycle=.true.)
 
     call addfld ('Z3',         (/ 'lev' /), 'A', 'm',         'Geopotential Height (above sea level)')
     call addfld ('Z1000',      horiz_only,  'A', 'm',         'Geopotential Z at 1000 mbar pressure surface')
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 9c569387e0..94ef9a05e1 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -201,12 +201,12 @@ subroutine check_energy_init()
                        history_waccm_out = history_waccm )
 
 ! register history variables
-    call addfld('TEINP',  horiz_only,  'A', 'J/m2', 'Total energy of physics input')
-    call addfld('TEOUT',  horiz_only,  'A', 'J/m2', 'Total energy of physics output')
-    call addfld('TEFIX',  horiz_only,  'A', 'J/m2', 'Total energy after fixer')
-    call addfld('EFIX',   horiz_only,  'A', 'W/m2', 'Effective sensible heat flux due to energy fixer')
-    call addfld('DTCORE', (/ 'lev' /), 'A', 'K/s' , 'T tendency due to dynamical core')
-    call addfld('DQCORE', (/ 'lev' /), 'A', 'kg/kg/s' , 'Water vapor tendency due to dynamical core')
+    call addfld('TEINP',  horiz_only,  'A', 'J/m2', 'Total energy of physics input', sampled_on_subcycle=.true.)
+    call addfld('TEOUT',  horiz_only,  'A', 'J/m2', 'Total energy of physics output', sampled_on_subcycle=.true.)
+    call addfld('TEFIX',  horiz_only,  'A', 'J/m2', 'Total energy after fixer', sampled_on_subcycle=.true.)
+    call addfld('EFIX',   horiz_only,  'A', 'W/m2', 'Effective sensible heat flux due to energy fixer', sampled_on_subcycle=.true.)
+    call addfld('DTCORE', (/ 'lev' /), 'A', 'K/s' , 'T tendency due to dynamical core', sampled_on_subcycle=.true.)
+    call addfld('DQCORE', (/ 'lev' /), 'A', 'kg/kg/s' , 'Water vapor tendency due to dynamical core', sampled_on_subcycle=.true.)
 
     if ( history_budget ) then
        call add_default ('DTCORE', history_budget_histfile_num, ' ')
diff --git a/src/physics/cam/clubb_intr.F90 b/src/physics/cam/clubb_intr.F90
index 9bbf211fba..872bbc4963 100644
--- a/src/physics/cam/clubb_intr.F90
+++ b/src/physics/cam/clubb_intr.F90
@@ -1777,96 +1777,96 @@ subroutine clubb_ini_cam(pbuf2d)
     ! ----------------------------------------------------------------- !
 
     !  These are default CLUBB output.  Not the higher order history budgets
-    call addfld ('RHO_CLUBB',        (/ 'lev' /),  'A', 'kg/m3',    'Air Density')
-    call addfld ('UP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Zonal Velocity Variance')
-    call addfld ('VP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Meridional Velocity Variance')
-    call addfld ('WP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Vertical Velocity Variance')
-    call addfld ('WP2_ZT_CLUBB',     (/ 'lev' /),  'A', 'm2/s2',    'Vert Vel Variance on zt grid')
-    call addfld ('UPWP_CLUBB',       (/ 'ilev' /), 'A', 'm2/s2',    'Zonal Momentum Flux')
-    call addfld ('VPWP_CLUBB',       (/ 'ilev' /), 'A', 'm2/s2',    'Meridional Momentum Flux')
-    call addfld ('WP3_CLUBB',        (/ 'lev' /),  'A', 'm3/s3',    'Third Moment Vertical Velocity')
-    call addfld ('WPTHLP_CLUBB',     (/ 'ilev' /), 'A', 'W/m2',     'Heat Flux')
-    call addfld ('WPRTP_CLUBB',      (/ 'ilev' /), 'A', 'W/m2',     'Moisture Flux')
-    call addfld ('RTP2_CLUBB',       (/ 'ilev' /), 'A', 'kg^2/kg^2', 'Moisture Variance')
-    call addfld ('RTP2_ZT_CLUBB',    (/ 'lev' /),  'A', 'kg^2/kg^2','Moisture Variance on zt grid')
-    call addfld ('PDFP_RTP2_CLUBB',  (/ 'ilev' /), 'A', 'kg^2/kg^2','PDF Rtot Variance')
-    call addfld ('THLP2_CLUBB',      (/ 'ilev' /), 'A', 'K^2',      'Temperature Variance')
-    call addfld ('THLP2_ZT_CLUBB',   (/ 'lev' /),  'A', 'K^2',      'Temperature Variance on zt grid')
-    call addfld ('RTPTHLP_CLUBB',    (/ 'ilev' /), 'A', 'K kg/kg',   'Temp. Moist. Covariance')
-    call addfld ('RCM_CLUBB',        (/ 'lev' /),  'A', 'kg/kg',     'Cloud Water Mixing Ratio')
-    call addfld ('RTM_CLUBB',        (/ 'lev' /),  'A', 'kg/kg',     'Total Water Mixing Ratio')
-    call addfld ('THLM_CLUBB',       (/ 'lev' /),  'A', 'K',         'Liquid Water Potential Temperature')
-    call addfld ('WPRCP_CLUBB',      (/ 'ilev' /), 'A', 'W/m2',     'Liquid Water Flux')
-    call addfld ('CLOUDFRAC_CLUBB',  (/ 'lev' /),  'A', 'fraction', 'Cloud Fraction')
-    call addfld ('RCMINLAYER_CLUBB', (/ 'lev' /),  'A', 'kg/kg',     'Cloud Water in Layer')
-    call addfld ('CLOUDCOVER_CLUBB', (/ 'lev' /),  'A', 'fraction', 'Cloud Cover')
-    call addfld ('WPTHVP_CLUBB',     (/ 'ilev' /), 'A', 'W/m2',     'Buoyancy Flux')
-    call addfld ('RVMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Water vapor tendency')
-    call addfld ('STEND_CLUBB',      (/ 'lev' /),  'A', 'J/(kg s)', 'Static energy tendency')
-    call addfld ('RCMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Cloud Liquid Water Tendency')
-    call addfld ('RIMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Cloud Ice Tendency')
-    call addfld ('UTEND_CLUBB',      (/ 'lev' /),  'A', 'm/s /s',   'U-wind Tendency')
-    call addfld ('VTEND_CLUBB',      (/ 'lev' /),  'A', 'm/s /s',   'V-wind Tendency')
-    call addfld ('ZT_CLUBB',         (/ 'lev' /),  'A', 'm',        'Thermodynamic Heights')
-    call addfld ('ZM_CLUBB',         (/ 'ilev' /), 'A', 'm',        'Momentum Heights')
-    call addfld ('UM_CLUBB',         (/ 'lev' /),  'A', 'm/s',      'Zonal Wind')
-    call addfld ('VM_CLUBB',         (/ 'lev' /),  'A', 'm/s',      'Meridional Wind')
-    call addfld ('WM_ZT_CLUBB',      (/ 'lev' /),  'A', 'm/s',      'Vertical Velocity')
-    call addfld ('PBLH',             horiz_only,   'A', 'm',        'PBL height')
-    call addfld ('CLDST',            (/ 'lev' /),  'A', 'fraction', 'Stratus cloud fraction')
-    call addfld ('ZMDLF',            (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained liquid water from ZM convection')
-    call addfld ('TTENDICE',         (/ 'lev' /),  'A', 'K/s',      'T tendency from Ice Saturation Adjustment')
-    call addfld ('QVTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'Q tendency from Ice Saturation Adjustment')
-    call addfld ('QITENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment')
-    call addfld ('NITENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment')
-
-
-    call addfld ('QCTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment')
-    call addfld ('NCTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment')
-    call addfld ('FQTENDICE',        (/ 'lev' /),  'A', 'fraction', 'Frequency of Ice Saturation Adjustment')
-
-    call addfld ('DPDLFLIQ',         (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained liquid water from deep convection')
-    call addfld ('DPDLFICE',         (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained ice from deep convection')
-    call addfld ('DPDLFT',           (/ 'lev' /),  'A', 'K/s',      'T-tendency due to deep convective detrainment')
-    call addfld ('RELVAR',           (/ 'lev' /),  'A', '-',        'Relative cloud water variance')
-    call addfld ('CLUBB_GRID_SIZE',  horiz_only,   'A', 'm',        'Horizontal grid box size seen by CLUBB')
-
-
-    call addfld ('ZMDLFI',           (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained ice water from ZM convection')
-    call addfld ('CONCLD',           (/ 'lev' /),  'A', 'fraction', 'Convective cloud cover')
-    call addfld ('CMELIQ',           (/ 'lev' /),  'A', 'kg/kg/s',  'Rate of cond-evap of liq within the cloud')
-    call addfld ('DETNLIQTND',       (/ 'lev' /),  'A', '1/kg/s',   'CLDNUM tendency in detrained water')
-
-    call addfld ('QSATFAC',          (/ 'lev' /),  'A', '-', 'Subgrid cloud water saturation scaling factor')
-    call addfld ('KVH_CLUBB',        (/ 'ilev' /), 'A', 'm2/s', 'CLUBB vertical diffusivity of heat/moisture on interface levels')
-    call addfld ('ELEAK_CLUBB',      horiz_only,   'A', 'W/m2', 'CLUBB energy leak')
-    call addfld ('TFIX_CLUBB',       horiz_only,   'A', 'K', 'Temperature increment to conserve energy')
+    call addfld ('RHO_CLUBB',        (/ 'lev' /),  'A', 'kg/m3',    'Air Density', sampled_on_subcycle=.true.)
+    call addfld ('UP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Zonal Velocity Variance', sampled_on_subcycle=.true.)
+    call addfld ('VP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Meridional Velocity Variance', sampled_on_subcycle=.true.)
+    call addfld ('WP2_CLUBB',        (/ 'ilev' /), 'A', 'm2/s2',    'Vertical Velocity Variance', sampled_on_subcycle=.true.)
+    call addfld ('WP2_ZT_CLUBB',     (/ 'lev' /),  'A', 'm2/s2',    'Vert Vel Variance on zt grid', sampled_on_subcycle=.true.)
+    call addfld ('UPWP_CLUBB',       (/ 'ilev' /), 'A', 'm2/s2',    'Zonal Momentum Flux', sampled_on_subcycle=.true.)
+    call addfld ('VPWP_CLUBB',       (/ 'ilev' /), 'A', 'm2/s2',    'Meridional Momentum Flux', sampled_on_subcycle=.true.)
+    call addfld ('WP3_CLUBB',        (/ 'lev' /),  'A', 'm3/s3',    'Third Moment Vertical Velocity', sampled_on_subcycle=.true.)
+    call addfld ('WPTHLP_CLUBB',     (/ 'ilev' /), 'A', 'W/m2',     'Heat Flux', sampled_on_subcycle=.true.)
+    call addfld ('WPRTP_CLUBB',      (/ 'ilev' /), 'A', 'W/m2',     'Moisture Flux', sampled_on_subcycle=.true.)
+    call addfld ('RTP2_CLUBB',       (/ 'ilev' /), 'A', 'kg^2/kg^2', 'Moisture Variance', sampled_on_subcycle=.true.)
+    call addfld ('RTP2_ZT_CLUBB',    (/ 'lev' /),  'A', 'kg^2/kg^2','Moisture Variance on zt grid', sampled_on_subcycle=.true.)
+    call addfld ('PDFP_RTP2_CLUBB',  (/ 'ilev' /), 'A', 'kg^2/kg^2','PDF Rtot Variance', sampled_on_subcycle=.true.)
+    call addfld ('THLP2_CLUBB',      (/ 'ilev' /), 'A', 'K^2',      'Temperature Variance', sampled_on_subcycle=.true.)
+    call addfld ('THLP2_ZT_CLUBB',   (/ 'lev' /),  'A', 'K^2',      'Temperature Variance on zt grid', sampled_on_subcycle=.true.)
+    call addfld ('RTPTHLP_CLUBB',    (/ 'ilev' /), 'A', 'K kg/kg',   'Temp. Moist. Covariance', sampled_on_subcycle=.true.)
+    call addfld ('RCM_CLUBB',        (/ 'lev' /),  'A', 'kg/kg',     'Cloud Water Mixing Ratio', sampled_on_subcycle=.true.)
+    call addfld ('RTM_CLUBB',        (/ 'lev' /),  'A', 'kg/kg',     'Total Water Mixing Ratio', sampled_on_subcycle=.true.)
+    call addfld ('THLM_CLUBB',       (/ 'lev' /),  'A', 'K',         'Liquid Water Potential Temperature', sampled_on_subcycle=.true.)
+    call addfld ('WPRCP_CLUBB',      (/ 'ilev' /), 'A', 'W/m2',     'Liquid Water Flux', sampled_on_subcycle=.true.)
+    call addfld ('CLOUDFRAC_CLUBB',  (/ 'lev' /),  'A', 'fraction', 'Cloud Fraction', sampled_on_subcycle=.true.)
+    call addfld ('RCMINLAYER_CLUBB', (/ 'lev' /),  'A', 'kg/kg',     'Cloud Water in Layer', sampled_on_subcycle=.true.)
+    call addfld ('CLOUDCOVER_CLUBB', (/ 'lev' /),  'A', 'fraction', 'Cloud Cover', sampled_on_subcycle=.true.)
+    call addfld ('WPTHVP_CLUBB',     (/ 'ilev' /), 'A', 'W/m2',     'Buoyancy Flux', sampled_on_subcycle=.true.)
+    call addfld ('RVMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Water vapor tendency', sampled_on_subcycle=.true.)
+    call addfld ('STEND_CLUBB',      (/ 'lev' /),  'A', 'J/(kg s)', 'Static energy tendency', sampled_on_subcycle=.true.)
+    call addfld ('RCMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Cloud Liquid Water Tendency', sampled_on_subcycle=.true.)
+    call addfld ('RIMTEND_CLUBB',    (/ 'lev' /),  'A', 'kg/kg /s',  'Cloud Ice Tendency', sampled_on_subcycle=.true.)
+    call addfld ('UTEND_CLUBB',      (/ 'lev' /),  'A', 'm/s /s',   'U-wind Tendency', sampled_on_subcycle=.true.)
+    call addfld ('VTEND_CLUBB',      (/ 'lev' /),  'A', 'm/s /s',   'V-wind Tendency', sampled_on_subcycle=.true.)
+    call addfld ('ZT_CLUBB',         (/ 'lev' /),  'A', 'm',        'Thermodynamic Heights', sampled_on_subcycle=.true.)
+    call addfld ('ZM_CLUBB',         (/ 'ilev' /), 'A', 'm',        'Momentum Heights', sampled_on_subcycle=.true.)
+    call addfld ('UM_CLUBB',         (/ 'lev' /),  'A', 'm/s',      'Zonal Wind', sampled_on_subcycle=.true.)
+    call addfld ('VM_CLUBB',         (/ 'lev' /),  'A', 'm/s',      'Meridional Wind', sampled_on_subcycle=.true.)
+    call addfld ('WM_ZT_CLUBB',      (/ 'lev' /),  'A', 'm/s',      'Vertical Velocity', sampled_on_subcycle=.true.)
+    call addfld ('PBLH',             horiz_only,   'A', 'm',        'PBL height', sampled_on_subcycle=.true.)
+    call addfld ('CLDST',            (/ 'lev' /),  'A', 'fraction', 'Stratus cloud fraction', sampled_on_subcycle=.true.)
+    call addfld ('ZMDLF',            (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained liquid water from ZM convection', sampled_on_subcycle=.true.)
+    call addfld ('TTENDICE',         (/ 'lev' /),  'A', 'K/s',      'T tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+    call addfld ('QVTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'Q tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+    call addfld ('QITENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+    call addfld ('NITENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+
+
+    call addfld ('QCTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+    call addfld ('NCTENDICE',        (/ 'lev' /),  'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+    call addfld ('FQTENDICE',        (/ 'lev' /),  'A', 'fraction', 'Frequency of Ice Saturation Adjustment', sampled_on_subcycle=.true.)
+
+    call addfld ('DPDLFLIQ',         (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained liquid water from deep convection', sampled_on_subcycle=.true.)
+    call addfld ('DPDLFICE',         (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained ice from deep convection', sampled_on_subcycle=.true.)
+    call addfld ('DPDLFT',           (/ 'lev' /),  'A', 'K/s',      'T-tendency due to deep convective detrainment', sampled_on_subcycle=.true.)
+    call addfld ('RELVAR',           (/ 'lev' /),  'A', '-',        'Relative cloud water variance', sampled_on_subcycle=.true.)
+    call addfld ('CLUBB_GRID_SIZE',  horiz_only,   'A', 'm',        'Horizontal grid box size seen by CLUBB', sampled_on_subcycle=.true.)
+
+
+    call addfld ('ZMDLFI',           (/ 'lev' /),  'A', 'kg/kg/s',  'Detrained ice water from ZM convection', sampled_on_subcycle=.true.)
+    call addfld ('CONCLD',           (/ 'lev' /),  'A', 'fraction', 'Convective cloud cover', sampled_on_subcycle=.true.)
+    call addfld ('CMELIQ',           (/ 'lev' /),  'A', 'kg/kg/s',  'Rate of cond-evap of liq within the cloud', sampled_on_subcycle=.true.)
+    call addfld ('DETNLIQTND',       (/ 'lev' /),  'A', '1/kg/s',   'CLDNUM tendency in detrained water', sampled_on_subcycle=.true.)
+
+    call addfld ('QSATFAC',          (/ 'lev' /),  'A', '-', 'Subgrid cloud water saturation scaling factor', sampled_on_subcycle=.true.)
+    call addfld ('KVH_CLUBB',        (/ 'ilev' /), 'A', 'm2/s', 'CLUBB vertical diffusivity of heat/moisture on interface levels', sampled_on_subcycle=.true.)
+    call addfld ('ELEAK_CLUBB',      horiz_only,   'A', 'W/m2', 'CLUBB energy leak', sampled_on_subcycle=.true.)
+    call addfld ('TFIX_CLUBB',       horiz_only,   'A', 'K', 'Temperature increment to conserve energy', sampled_on_subcycle=.true.)
 
     ! ---------------------------------------------------------------------------- !
     ! Below are for detailed analysis of EDMF Scheme                               !
     ! ---------------------------------------------------------------------------- !
     if (do_clubb_mf) then
-      call addfld ( 'edmf_DRY_A'    , (/ 'ilev' /), 'A', 'fraction', 'Dry updraft area fraction (EDMF)' )
-      call addfld ( 'edmf_MOIST_A'  , (/ 'ilev' /), 'A', 'fraction', 'Moist updraft area fraction (EDMF)' )
-      call addfld ( 'edmf_DRY_W'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft vertical velocity (EDMF)' )
-      call addfld ( 'edmf_MOIST_W'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft vertical velocity (EDMF)' )
-      call addfld ( 'edmf_DRY_QT'   , (/ 'ilev' /), 'A', 'kg/kg'   , 'Dry updraft total water mixing ratio (EDMF)' )
-      call addfld ( 'edmf_MOIST_QT' , (/ 'ilev' /), 'A', 'kg/kg'   , 'Moist updraft total water mixing ratio (EDMF)' )
-      call addfld ( 'edmf_DRY_THL'  , (/ 'ilev' /), 'A', 'K'       , 'Dry updraft liquid-ice potential temperature (EDMF)' )
-      call addfld ( 'edmf_MOIST_THL', (/ 'ilev' /), 'A', 'K'       , 'Moist updraft liquid-ice potential temperature (EDMF)' )
-      call addfld ( 'edmf_DRY_U'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft zonal velocity (EDMF)' )
-      call addfld ( 'edmf_MOIST_U'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft zonal velocity (EDMF)' )
-      call addfld ( 'edmf_DRY_V'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft meridional velocity (EDMF)' )
-      call addfld ( 'edmf_MOIST_V'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft meridional velocity (EDMF)' )
-      call addfld ( 'edmf_MOIST_QC' , (/ 'ilev' /), 'A', 'kg/kg'   , 'Moist updraft condensate mixing ratio (EDMF)' )
-      call addfld ( 'edmf_S_AE'     , (/ 'ilev' /), 'A', 'fraction', '1 minus sum of a_i*w_i (EDMF)' )
-      call addfld ( 'edmf_S_AW'     , (/ 'ilev' /), 'A', 'm/s'     , 'Sum of a_i*w_i (EDMF)' )
-      call addfld ( 'edmf_S_AWTHL'  , (/ 'ilev' /), 'A', 'K m/s'   , 'Sum of a_i*w_i*thl_i (EDMF)' )
-      call addfld ( 'edmf_S_AWQT'   , (/ 'ilev' /), 'A', 'kgm/kgs' , 'Sum of a_i*w_i*q_ti (EDMF)' )
-      call addfld ( 'edmf_S_AWU'    , (/ 'ilev' /), 'A', 'm2/s2'   , 'Sum of a_i*w_i*u_i (EDMF)' )
-      call addfld ( 'edmf_S_AWV'    , (/ 'ilev' /), 'A', 'm2/s2'   , 'Sum of a_i*w_i*v_i (EDMF)' )
-      call addfld ( 'edmf_thlflx'   , (/ 'ilev' /), 'A', 'W/m2'    , 'thl flux (EDMF)' )
-      call addfld ( 'edmf_qtflx'    , (/ 'ilev' /), 'A', 'W/m2'    , 'qt flux (EDMF)' )
+      call addfld ( 'edmf_DRY_A'    , (/ 'ilev' /), 'A', 'fraction', 'Dry updraft area fraction (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_A'  , (/ 'ilev' /), 'A', 'fraction', 'Moist updraft area fraction (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_DRY_W'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft vertical velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_W'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft vertical velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_DRY_QT'   , (/ 'ilev' /), 'A', 'kg/kg'   , 'Dry updraft total water mixing ratio (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_QT' , (/ 'ilev' /), 'A', 'kg/kg'   , 'Moist updraft total water mixing ratio (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_DRY_THL'  , (/ 'ilev' /), 'A', 'K'       , 'Dry updraft liquid-ice potential temperature (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_THL', (/ 'ilev' /), 'A', 'K'       , 'Moist updraft liquid-ice potential temperature (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_DRY_U'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft zonal velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_U'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft zonal velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_DRY_V'    , (/ 'ilev' /), 'A', 'm/s'     , 'Dry updraft meridional velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_V'  , (/ 'ilev' /), 'A', 'm/s'     , 'Moist updraft meridional velocity (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_MOIST_QC' , (/ 'ilev' /), 'A', 'kg/kg'   , 'Moist updraft condensate mixing ratio (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AE'     , (/ 'ilev' /), 'A', 'fraction', '1 minus sum of a_i*w_i (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AW'     , (/ 'ilev' /), 'A', 'm/s'     , 'Sum of a_i*w_i (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AWTHL'  , (/ 'ilev' /), 'A', 'K m/s'   , 'Sum of a_i*w_i*thl_i (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AWQT'   , (/ 'ilev' /), 'A', 'kgm/kgs' , 'Sum of a_i*w_i*q_ti (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AWU'    , (/ 'ilev' /), 'A', 'm2/s2'   , 'Sum of a_i*w_i*u_i (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_S_AWV'    , (/ 'ilev' /), 'A', 'm2/s2'   , 'Sum of a_i*w_i*v_i (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_thlflx'   , (/ 'ilev' /), 'A', 'W/m2'    , 'thl flux (EDMF)', sampled_on_subcycle=.true.)
+      call addfld ( 'edmf_qtflx'    , (/ 'ilev' /), 'A', 'W/m2'    , 'qt flux (EDMF)', sampled_on_subcycle=.true.)
     end if
 
     if ( trim(subcol_scheme) /= 'SILHS' ) then
diff --git a/src/physics/cam/macrop_driver.F90 b/src/physics/cam/macrop_driver.F90
index 92d52fff8c..d381387bfc 100644
--- a/src/physics/cam/macrop_driver.F90
+++ b/src/physics/cam/macrop_driver.F90
@@ -237,53 +237,53 @@ subroutine macrop_driver_init(pbuf2d)
         use_shfrc = .false.
     endif
 
-    call addfld ('DPDLFLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from deep convection'       )
-    call addfld ('DPDLFICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained ice from deep convection'                )
-    call addfld ('SHDLFLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from shallow convection'    )
-    call addfld ('SHDLFICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained ice from shallow convection'             )
-    call addfld ('DPDLFT',    (/ 'lev' /), 'A', 'K/s',      'T-tendency due to deep convective detrainment'     )
-    call addfld ('SHDLFT',    (/ 'lev' /), 'A', 'K/s',      'T-tendency due to shallow convective detrainment'  )
+    call addfld ('DPDLFLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from deep convection',       sampled_on_subcycle=.true.)
+    call addfld ('DPDLFICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained ice from deep convection',                sampled_on_subcycle=.true.)
+    call addfld ('SHDLFLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from shallow convection',    sampled_on_subcycle=.true.)
+    call addfld ('SHDLFICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained ice from shallow convection',             sampled_on_subcycle=.true.)
+    call addfld ('DPDLFT',    (/ 'lev' /), 'A', 'K/s',      'T-tendency due to deep convective detrainment',     sampled_on_subcycle=.true.)
+    call addfld ('SHDLFT',    (/ 'lev' /), 'A', 'K/s',      'T-tendency due to shallow convective detrainment',  sampled_on_subcycle=.true.)
 
-    call addfld ('ZMDLF',     (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from ZM convection'         )
+    call addfld ('ZMDLF',     (/ 'lev' /), 'A', 'kg/kg/s',  'Detrained liquid water from ZM convection',         sampled_on_subcycle=.true.)
 
-    call addfld ('MACPDT',    (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Revised  macrophysics'          )
-    call addfld ('MACPDQ',    (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Revised macrophysics'                 )
-    call addfld ('MACPDLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Revised macrophysics'            )
-    call addfld ('MACPDICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Revised macrophysics'            )
+    call addfld ('MACPDT',    (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Revised  macrophysics',          sampled_on_subcycle=.true.)
+    call addfld ('MACPDQ',    (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Revised macrophysics',                 sampled_on_subcycle=.true.)
+    call addfld ('MACPDLIQ',  (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Revised macrophysics',            sampled_on_subcycle=.true.)
+    call addfld ('MACPDICE',  (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Revised macrophysics',            sampled_on_subcycle=.true.)
 
     call addfld ('CLDVAPADJ', (/ 'lev' /), 'A', 'kg/kg/s',  &
-         'Q tendency associated with liq/ice adjustment - Revised macrophysics'                                 )
-    call addfld ('CLDLIQADJ', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ adjustment tendency - Revised macrophysics' )
-    call addfld ('CLDICEADJ', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE adjustment tendency - Revised macrophysics' )
+         'Q tendency associated with liq/ice adjustment - Revised macrophysics',                                 sampled_on_subcycle=.true.)
+    call addfld ('CLDLIQADJ', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ adjustment tendency - Revised macrophysics', sampled_on_subcycle=.true.)
+    call addfld ('CLDICEADJ', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE adjustment tendency - Revised macrophysics', sampled_on_subcycle=.true.)
     call addfld ('CLDLIQDET', (/ 'lev' /), 'A', 'kg/kg/s',  &
-         'Detrainment of conv cld liq into envrionment  - Revised macrophysics'                                 )
+         'Detrainment of conv cld liq into envrionment  - Revised macrophysics',                                 sampled_on_subcycle=.true.)
     call addfld ('CLDICEDET', (/ 'lev' /), 'A', 'kg/kg/s',  &
-         'Detrainment of conv cld ice into envrionment  - Revised macrophysics'                                 )
-    call addfld ('CLDLIQLIM', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ limiting tendency - Revised macrophysics'   )
-    call addfld ('CLDICELIM', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE limiting tendency - Revised macrophysics'   )
+         'Detrainment of conv cld ice into envrionment  - Revised macrophysics',                                 sampled_on_subcycle=.true.)
+    call addfld ('CLDLIQLIM', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ limiting tendency - Revised macrophysics',   sampled_on_subcycle=.true.)
+    call addfld ('CLDICELIM', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE limiting tendency - Revised macrophysics',   sampled_on_subcycle=.true.)
 
-    call addfld ('AST',       (/ 'lev' /), 'A', '1',        'Stratus cloud fraction'                            )
-    call addfld ('LIQCLDF',   (/ 'lev' /), 'A', '1',        'Stratus Liquid cloud fraction'                     )
-    call addfld ('ICECLDF',   (/ 'lev' /), 'A', '1',        'Stratus ICE cloud fraction'                        )
+    call addfld ('AST',       (/ 'lev' /), 'A', '1',        'Stratus cloud fraction',                            sampled_on_subcycle=.true.)
+    call addfld ('LIQCLDF',   (/ 'lev' /), 'A', '1',        'Stratus Liquid cloud fraction',                     sampled_on_subcycle=.true.)
+    call addfld ('ICECLDF',   (/ 'lev' /), 'A', '1',        'Stratus ICE cloud fraction',                        sampled_on_subcycle=.true.)
 
-    call addfld ('CLDST',     (/ 'lev' /), 'A', 'fraction', 'Stratus cloud fraction'                            )
-    call addfld ('CONCLD',    (/ 'lev' /), 'A', 'fraction', 'Convective cloud cover'                            )
+    call addfld ('CLDST',     (/ 'lev' /), 'A', 'fraction', 'Stratus cloud fraction',                            sampled_on_subcycle=.true.)
+    call addfld ('CONCLD',    (/ 'lev' /), 'A', 'fraction', 'Convective cloud cover',                            sampled_on_subcycle=.true.)
 
-    call addfld ('CLR_LIQ',   (/ 'lev' /), 'A', 'fraction', 'Clear sky fraction for liquid stratus'             )
-    call addfld ('CLR_ICE',   (/ 'lev' /), 'A', 'fraction', 'Clear sky fraction for ice stratus'                )
+    call addfld ('CLR_LIQ',   (/ 'lev' /), 'A', 'fraction', 'Clear sky fraction for liquid stratus',             sampled_on_subcycle=.true.)
+    call addfld ('CLR_ICE',   (/ 'lev' /), 'A', 'fraction', 'Clear sky fraction for ice stratus',                sampled_on_subcycle=.true.)
 
-    call addfld ('CLDLIQSTR', (/ 'lev' /), 'A', 'kg/kg',    'Stratiform CLDLIQ'                                 )
-    call addfld ('CLDICESTR', (/ 'lev' /), 'A', 'kg/kg',    'Stratiform CLDICE'                                 )
-    call addfld ('CLDLIQCON', (/ 'lev' /), 'A', 'kg/kg',    'Convective CLDLIQ'                                 )
-    call addfld ('CLDICECON', (/ 'lev' /), 'A', 'kg/kg',    'Convective CLDICE'                                 )
+    call addfld ('CLDLIQSTR', (/ 'lev' /), 'A', 'kg/kg',    'Stratiform CLDLIQ',                                 sampled_on_subcycle=.true.)
+    call addfld ('CLDICESTR', (/ 'lev' /), 'A', 'kg/kg',    'Stratiform CLDICE',                                 sampled_on_subcycle=.true.)
+    call addfld ('CLDLIQCON', (/ 'lev' /), 'A', 'kg/kg',    'Convective CLDLIQ',                                 sampled_on_subcycle=.true.)
+    call addfld ('CLDICECON', (/ 'lev' /), 'A', 'kg/kg',    'Convective CLDICE',                                 sampled_on_subcycle=.true.)
 
-    call addfld ('CLDSICE',   (/ 'lev' /), 'A', 'kg/kg',    'CloudSat equivalent ice mass mixing ratio'         )
-    call addfld ('CMELIQ',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap of liq within the cloud'         )
+    call addfld ('CLDSICE',   (/ 'lev' /), 'A', 'kg/kg',    'CloudSat equivalent ice mass mixing ratio',         sampled_on_subcycle=.true.)
+    call addfld ('CMELIQ',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap of liq within the cloud',         sampled_on_subcycle=.true.)
 
-    call addfld ('TTENDICE',  (/ 'lev' /), 'A', 'K/s',      'T tendency from Ice Saturation Adjustment'         )
-    call addfld ('QVTENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency from Ice Saturation Adjustment'         )
-    call addfld ('QITENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment'    )
-    call addfld ('NITENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment'    )
+    call addfld ('TTENDICE',  (/ 'lev' /), 'A', 'K/s',      'T tendency from Ice Saturation Adjustment',         sampled_on_subcycle=.true.)
+    call addfld ('QVTENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency from Ice Saturation Adjustment',         sampled_on_subcycle=.true.)
+    call addfld ('QITENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency from Ice Saturation Adjustment',    sampled_on_subcycle=.true.)
+    call addfld ('NITENDICE', (/ 'lev' /), 'A', 'kg/kg/s',  'NUMICE tendency from Ice Saturation Adjustment',    sampled_on_subcycle=.true.)
     if ( history_budget ) then
 
           call add_default ('DPDLFLIQ ', history_budget_histfile_num, ' ')
diff --git a/src/physics/cam/micro_pumas_cam.F90 b/src/physics/cam/micro_pumas_cam.F90
index a0c66eb7f1..d5f98c9813 100644
--- a/src/physics/cam/micro_pumas_cam.F90
+++ b/src/physics/cam/micro_pumas_cam.F90
@@ -925,251 +925,251 @@ subroutine micro_pumas_cam_init(pbuf2d)
       call cnst_get_ind(cnst_names(m), mm)
       if ( any(mm == (/ ixcldliq, ixcldice, ixrain, ixsnow, ixgraupel /)) ) then
          ! mass mixing ratios
-         call addfld(cnst_name(mm), (/ 'lev' /), 'A', 'kg/kg', cnst_longname(mm)                   )
-         call addfld(sflxnam(mm),    horiz_only, 'A',   'kg/m2/s', trim(cnst_name(mm))//' surface flux')
+         call addfld(cnst_name(mm), (/ 'lev' /), 'A', 'kg/kg', cnst_longname(mm), sampled_on_subcycle=.true.)
+         call addfld(sflxnam(mm),    horiz_only, 'A',   'kg/m2/s', trim(cnst_name(mm))//' surface flux', sampled_on_subcycle=.true.)
       else if ( any(mm == (/ ixnumliq, ixnumice, ixnumrain, ixnumsnow, ixnumgraupel /)) ) then
          ! number concentrations
-         call addfld(cnst_name(mm), (/ 'lev' /), 'A', '1/kg', cnst_longname(mm)                   )
-         call addfld(sflxnam(mm),    horiz_only, 'A',   '1/m2/s', trim(cnst_name(mm))//' surface flux')
+         call addfld(cnst_name(mm), (/ 'lev' /), 'A', '1/kg', cnst_longname(mm), sampled_on_subcycle=.true.)
+         call addfld(sflxnam(mm),    horiz_only, 'A',   '1/m2/s', trim(cnst_name(mm))//' surface flux', sampled_on_subcycle=.true.)
       else
          call endrun( "micro_pumas_cam_init: &
               &Could not call addfld for constituent with unknown units.")
       endif
    end do
 
-   call addfld(apcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' after physics'  )
-   call addfld(apcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' after physics'  )
-   call addfld(bpcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' before physics' )
-   call addfld(bpcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' before physics' )
+   call addfld(apcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(apcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' before physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' before physics', sampled_on_subcycle=.true.)
 
    if (micro_mg_version > 1) then
-      call addfld(apcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' after physics'  )
-      call addfld(apcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' after physics'  )
-      call addfld(bpcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' before physics' )
-      call addfld(bpcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' before physics' )
+      call addfld(apcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' after physics', sampled_on_subcycle=.true.)
+      call addfld(apcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' after physics', sampled_on_subcycle=.true.)
+      call addfld(bpcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' before physics', sampled_on_subcycle=.true.)
+      call addfld(bpcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' before physics', sampled_on_subcycle=.true.)
    end if
 
    if (micro_mg_version > 2) then
-      call addfld(apcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' after physics'  )
-      call addfld(bpcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' before physics' )
+      call addfld(apcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' after physics', sampled_on_subcycle=.true.)
+      call addfld(bpcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' before physics', sampled_on_subcycle=.true.)
    end if
 
-   call addfld ('CME',        (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap within the cloud'                      )
-   call addfld ('PRODPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of conversion of condensate to precip'              )
-   call addfld ('EVAPPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling precip'                   )
-   call addfld ('EVAPSNOW',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling snow'                     )
-   call addfld ('HPROGCLD',   (/ 'lev' /), 'A', 'W/kg'    , 'Heating from prognostic clouds'                          )
-   call addfld ('FICE',       (/ 'lev' /), 'A', 'fraction', 'Fractional ice content within cloud'                     )
-   call addfld ('CLDFSNOW',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for snow'                        )
-   call addfld ('ICWMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus water mixing ratio'                )
-   call addfld ('ICIMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus ice mixing ratio'                  )
+   call addfld ('CME',        (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap within the cloud', sampled_on_subcycle=.true.)
+   call addfld ('PRODPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of conversion of condensate to precip', sampled_on_subcycle=.true.)
+   call addfld ('EVAPPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling precip', sampled_on_subcycle=.true.)
+   call addfld ('EVAPSNOW',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling snow', sampled_on_subcycle=.true.)
+   call addfld ('HPROGCLD',   (/ 'lev' /), 'A', 'W/kg'    , 'Heating from prognostic clouds', sampled_on_subcycle=.true.)
+   call addfld ('FICE',       (/ 'lev' /), 'A', 'fraction', 'Fractional ice content within cloud', sampled_on_subcycle=.true.)
+   call addfld ('CLDFSNOW',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for snow', sampled_on_subcycle=.true.)
+   call addfld ('ICWMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus water mixing ratio', sampled_on_subcycle=.true.)
+   call addfld ('ICIMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus ice mixing ratio', sampled_on_subcycle=.true.)
 
    ! MG microphysics diagnostics
-   call addfld ('QCSEVAP',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling cloud water'              )
-   call addfld ('QISEVAP',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of sublimation of falling cloud ice'                )
-   call addfld ('QVRES',      (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of residual condensation term'                      )
-   call addfld ('CMEIOUT',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of deposition/sublimation of cloud ice'             )
-   call addfld ('VTRMC',      (/ 'lev' /), 'A', 'm/s',      'Mass-weighted cloud water fallspeed'                     )
-   call addfld ('VTRMI',      (/ 'lev' /), 'A', 'm/s',      'Mass-weighted cloud ice fallspeed'                       )
-   call addfld ('QCSEDTEN',   (/ 'lev' /), 'A', 'kg/kg/s',  'Cloud water mixing ratio tendency from sedimentation'    )
-   call addfld ('QISEDTEN',   (/ 'lev' /), 'A', 'kg/kg/s',  'Cloud ice mixing ratio tendency from sedimentation'      )
-   call addfld ('PRAO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by rain'                        )
-   call addfld ('PRCO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud water'                           )
-   call addfld ('MNUCCCO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Immersion freezing of cloud water'                       )
-   call addfld ('MNUCCTO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Contact freezing of cloud water'                         )
-   call addfld ('MNUCCDO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous and heterogeneous nucleation from vapor'     )
-   call addfld ('MNUCCDOhet', (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous nucleation from vapor'                     )
-   call addfld ('MSACWIO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water from rime-splintering'         )
-   call addfld ('PSACWSO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by snow'                        )
-   call addfld ('BERGSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to snow from bergeron'         )
-   call addfld ('BERGO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to cloud ice from bergeron'    )
-   call addfld ('MELTO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of cloud ice'                                    )
-   call addfld ('MELTSTOT',   (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of snow'                                    )
-   call addfld ('MNUDEPO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition Nucleation'                                    )
-   call addfld ('HOMOO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous freezing of cloud water'                     )
-   call addfld ('QCRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual condensation term for cloud water'              )
-   call addfld ('PRCIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud ice to snow'                     )
-   call addfld ('PRAIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud ice to snow'                          )
-   call addfld ('QIRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual deposition term for cloud ice'                  )
-   call addfld ('MNUCCRO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to snow'                  )
-   call addfld ('MNUCCRIO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to ice'                  )
-   call addfld ('PRACSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of rain by snow'                               )
-   call addfld ('MELTSDT',    (/ 'lev' /), 'A', 'W/kg',     'Latent heating rate due to melting of snow'              )
-   call addfld ('FRZRDT',     (/ 'lev' /), 'A', 'W/kg',     'Latent heating rate due to homogeneous freezing of rain' )
+   call addfld ('QCSEVAP',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling cloud water', sampled_on_subcycle=.true.)
+   call addfld ('QISEVAP',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of sublimation of falling cloud ice',   sampled_on_subcycle=.true.)
+   call addfld ('QVRES',      (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of residual condensation term',         sampled_on_subcycle=.true.)
+   call addfld ('CMEIOUT',    (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of deposition/sublimation of cloud ice',sampled_on_subcycle=.true.)
+   call addfld ('VTRMC',      (/ 'lev' /), 'A', 'm/s',      'Mass-weighted cloud water fallspeed',        sampled_on_subcycle=.true.)
+   call addfld ('VTRMI',      (/ 'lev' /), 'A', 'm/s',      'Mass-weighted cloud ice fallspeed',          sampled_on_subcycle=.true.)
+   call addfld ('QCSEDTEN',   (/ 'lev' /), 'A', 'kg/kg/s',  'Cloud water mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+   call addfld ('QISEDTEN',   (/ 'lev' /), 'A', 'kg/kg/s',  'Cloud ice mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+   call addfld ('PRAO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by rain',           sampled_on_subcycle=.true.)
+   call addfld ('PRCO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud water',              sampled_on_subcycle=.true.)
+   call addfld ('MNUCCCO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Immersion freezing of cloud water',          sampled_on_subcycle=.true.)
+   call addfld ('MNUCCTO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Contact freezing of cloud water',            sampled_on_subcycle=.true.)
+   call addfld ('MNUCCDO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous and heterogeneous nucleation from vapor', sampled_on_subcycle=.true.)
+   call addfld ('MNUCCDOhet', (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous nucleation from vapor',        sampled_on_subcycle=.true.)
+   call addfld ('MSACWIO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water from rime-splintering', sampled_on_subcycle=.true.)
+   call addfld ('PSACWSO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by snow',           sampled_on_subcycle=.true.)
+   call addfld ('BERGSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to snow from bergeron', sampled_on_subcycle=.true.)
+   call addfld ('BERGO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to cloud ice from bergeron', sampled_on_subcycle=.true.)
+   call addfld ('MELTO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of cloud ice',                       sampled_on_subcycle=.true.)
+   call addfld ('MELTSTOT',   (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of snow',                            sampled_on_subcycle=.true.)
+   call addfld ('MNUDEPO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition Nucleation',                       sampled_on_subcycle=.true.)
+   call addfld ('HOMOO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous freezing of cloud water',        sampled_on_subcycle=.true.)
+   call addfld ('QCRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual condensation term for cloud water', sampled_on_subcycle=.true.)
+   call addfld ('PRCIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud ice to snow',        sampled_on_subcycle=.true.)
+   call addfld ('PRAIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud ice to snow',             sampled_on_subcycle=.true.)
+   call addfld ('QIRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual deposition term for cloud ice',     sampled_on_subcycle=.true.)
+   call addfld ('MNUCCRO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to snow',     sampled_on_subcycle=.true.)
+   call addfld ('MNUCCRIO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to ice',      sampled_on_subcycle=.true.)
+   call addfld ('PRACSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of rain by snow',                  sampled_on_subcycle=.true.)
+   call addfld ('MELTSDT',    (/ 'lev' /), 'A', 'W/kg',     'Latent heating rate due to melting of snow', sampled_on_subcycle=.true.)
+   call addfld ('FRZRDT',     (/ 'lev' /), 'A', 'W/kg',     'Latent heating rate due to homogeneous freezing of rain', sampled_on_subcycle=.true.)
    if (micro_mg_version > 1) then
-      call addfld ('QRSEDTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Rain mixing ratio tendency from sedimentation'           )
-      call addfld ('QSSEDTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from sedimentation'           )
+      call addfld ('QRSEDTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Rain mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+      call addfld ('QSSEDTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
    end if
 
 
    if (micro_mg_version > 2) then
 
-         call addfld ('PSACRO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Collisions between rain & snow (Graupel collecting snow)')
-         call addfld ('PRACGO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection rain by graupel'             )
-         call addfld ('PSACWGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection droplets by graupel'         )
-         call addfld ('PGSACWO',   (/ 'lev' /), 'A', 'kg/kg/s', 'Q conversion to graupel due to collection droplets by snow')
-         call addfld ('PGRACSO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection rain by snow')
-         call addfld ('PRDGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition of graupel')
-         call addfld ('QMULTGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult droplets/graupel')
-         call addfld ('QMULTRGO',  (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult rain/graupel')
-         call addfld ('QGSEDTEN',  (/ 'lev' /), 'A', 'kg/kg/s',  'Graupel/Hail mixing ratio tendency from sedimentation')
-         call addfld ('NPRACGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Change N collection rain by graupel')
-         call addfld ('NSCNGO', (/'lev'/),'A','kg/kg/s','Change N conversion to graupel due to collection droplets by snow')
-         call addfld ('NGRACSO',(/'lev'/),'A','kg/kg/s','Change N conversion to graupel due to collection rain by snow')
-         call addfld ('NMULTGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice mult due to acc droplets by graupel ')
-         call addfld ('NMULTRGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice mult due to acc rain by graupel')
-         call addfld ('NPSACWGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Change N collection droplets by graupel')
-         call addfld ('CLDFGRAU',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for graupel'                        )
-         call addfld ('MELTGTOT',   (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of graupel'                                    )
+         call addfld ('PSACRO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Collisions between rain & snow (Graupel collecting snow)', sampled_on_subcycle=.true.)
+         call addfld ('PRACGO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection rain by graupel', sampled_on_subcycle=.true.)
+         call addfld ('PSACWGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection droplets by graupel', sampled_on_subcycle=.true.)
+         call addfld ('PGSACWO',   (/ 'lev' /), 'A', 'kg/kg/s', 'Q conversion to graupel due to collection droplets by snow', sampled_on_subcycle=.true.)
+         call addfld ('PGRACSO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection rain by snow', sampled_on_subcycle=.true.)
+         call addfld ('PRDGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition of graupel', sampled_on_subcycle=.true.)
+         call addfld ('QMULTGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult droplets/graupel', sampled_on_subcycle=.true.)
+         call addfld ('QMULTRGO',  (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult rain/graupel', sampled_on_subcycle=.true.)
+         call addfld ('QGSEDTEN',  (/ 'lev' /), 'A', 'kg/kg/s',  'Graupel/Hail mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+         call addfld ('NPRACGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Change N collection rain by graupel', sampled_on_subcycle=.true.)
+         call addfld ('NSCNGO', (/'lev'/),'A','kg/kg/s','Change N conversion to graupel due to collection droplets by snow', sampled_on_subcycle=.true.)
+         call addfld ('NGRACSO',(/'lev'/),'A','kg/kg/s','Change N conversion to graupel due to collection rain by snow', sampled_on_subcycle=.true.)
+         call addfld ('NMULTGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice mult due to acc droplets by graupel', sampled_on_subcycle=.true.)
+         call addfld ('NMULTRGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice mult due to acc rain by graupel', sampled_on_subcycle=.true.)
+         call addfld ('NPSACWGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Change N collection droplets by graupel', sampled_on_subcycle=.true.)
+         call addfld ('CLDFGRAU',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for graupel', sampled_on_subcycle=.true.)
+         call addfld ('MELTGTOT',   (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of graupel',                  sampled_on_subcycle=.true.)
 
    end if
 
-   call addfld ('RBFRAC',  horiz_only, 'A', 'Fraction',  'Fraction of sky covered by a potential rainbow' )
-   call addfld ('RBFREQ',  horiz_only, 'A', 'Frequency',  'Potential rainbow frequency' )
-   call addfld( 'rbSZA', horiz_only, 'I', 'degrees', 'solar zenith angle' )
+   call addfld ('RBFRAC',  horiz_only, 'A', 'Fraction',  'Fraction of sky covered by a potential rainbow', sampled_on_subcycle=.true.)
+   call addfld ('RBFREQ',  horiz_only, 'A', 'Frequency',  'Potential rainbow frequency', sampled_on_subcycle=.true.)
+   call addfld( 'rbSZA', horiz_only, 'I', 'degrees', 'solar zenith angle', sampled_on_subcycle=.true.)
       
    ! History variables for CAM5 microphysics
-   call addfld ('MPDT',       (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Morrison microphysics'                )
-   call addfld ('MPDQ',       (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Morrison microphysics'                      )
-   call addfld ('MPDLIQ',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Morrison microphysics'                 )
-   call addfld ('MPDICE',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Morrison microphysics'                 )
-   call addfld ('MPDNLIQ',    (/ 'lev' /), 'A', '1/kg/s',   'NUMLIQ tendency - Morrison microphysics'                 )
-   call addfld ('MPDNICE',    (/ 'lev' /), 'A', '1/kg/s',   'NUMICE tendency - Morrison microphysics'                 )
-   call addfld ('MPDW2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Vapor tendency - Morrison microphysics'       )
-   call addfld ('MPDW2I',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Ice tendency - Morrison microphysics'         )
-   call addfld ('MPDW2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Precip tendency - Morrison microphysics'      )
-   call addfld ('MPDI2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Vapor tendency - Morrison microphysics'         )
-   call addfld ('MPDI2W',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Water tendency - Morrison microphysics'         )
-   call addfld ('MPDI2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Precip tendency - Morrison microphysics'        )
-   call addfld ('ICWNC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud water number conc'                   )
-   call addfld ('ICINC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud ice number conc'                     )
-   call addfld ('EFFLIQ_IND', (/ 'lev' /), 'A','Micron',    'Prognostic droplet effective radius (indirect effect)'   )
-   call addfld ('CDNUMC',     horiz_only,  'A', '1/m2',     'Vertically-integrated droplet concentration'             )
+   call addfld ('MPDT',       (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDQ',       (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Morrison microphysics',       sampled_on_subcycle=.true.)
+   call addfld ('MPDLIQ',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Morrison microphysics',  sampled_on_subcycle=.true.)
+   call addfld ('MPDICE',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Morrison microphysics',  sampled_on_subcycle=.true.)
+   call addfld ('MPDNLIQ',    (/ 'lev' /), 'A', '1/kg/s',   'NUMLIQ tendency - Morrison microphysics',  sampled_on_subcycle=.true.)
+   call addfld ('MPDNICE',    (/ 'lev' /), 'A', '1/kg/s',   'NUMICE tendency - Morrison microphysics',  sampled_on_subcycle=.true.)
+   call addfld ('MPDW2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Vapor tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDW2I',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Ice tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDW2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Precip tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDI2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Vapor tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDI2W',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Water tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDI2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Precip tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('ICWNC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud water number conc',    sampled_on_subcycle=.true.)
+   call addfld ('ICINC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud ice number conc',      sampled_on_subcycle=.true.)
+   call addfld ('EFFLIQ_IND', (/ 'lev' /), 'A','Micron',    'Prognostic droplet effective radius (indirect effect)', sampled_on_subcycle=.true.)
+   call addfld ('CDNUMC',     horiz_only,  'A', '1/m2',     'Vertically-integrated droplet concentration', sampled_on_subcycle=.true.)
    call addfld ('MPICLWPI',   horiz_only,  'A', 'kg/m2',    'Vertically-integrated &
-        &in-cloud Initial Liquid WP (Before Micro)' )
+        &in-cloud Initial Liquid WP (Before Micro)', sampled_on_subcycle=.true.)
    call addfld ('MPICIWPI',   horiz_only,  'A', 'kg/m2',    'Vertically-integrated &
-        &in-cloud Initial Ice WP (Before Micro)'    )
+        &in-cloud Initial Ice WP (Before Micro)', sampled_on_subcycle=.true.)
 
    ! This is provided as an example on how to write out subcolumn output
    ! NOTE -- only 'I' should be used for sub-column fields as subc-columns could shift from time-step to time-step
    if (use_subcol_microp) then
       call addfld('FICE_SCOL', (/'psubcols','lev     '/), 'I', 'fraction', &
-           'Sub-column fractional ice content within cloud', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column fractional ice content within cloud', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('MPDICE_SCOL', (/'psubcols','lev     '/), 'I', 'kg/kg/s', &
-           'Sub-column CLDICE tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column CLDICE tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('MPDLIQ_SCOL', (/'psubcols','lev     '/), 'I', 'kg/kg/s', &
-           'Sub-column CLDLIQ tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column CLDLIQ tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
    end if
 
 
    ! This is only if the coldpoint temperatures are being adjusted.
    ! NOTE: Some fields related to these and output later are added in tropopause.F90.
    if (micro_mg_adjust_cpt) then
-     call addfld ('TROPF_TADJ', (/ 'lev' /), 'A', 'K',  'Temperatures after cold point adjustment'                    )
-     call addfld ('TROPF_RHADJ', (/ 'lev' /), 'A', 'K', 'Relative Hunidity after cold point adjustment'               )
-     call addfld ('TROPF_CDT',   horiz_only,  'A', 'K',  'Cold point temperature adjustment'                           )
-     call addfld ('TROPF_CDZ',   horiz_only,  'A', 'm',  'Distance of coldpoint from coldest model level'              )
+     call addfld ('TROPF_TADJ', (/ 'lev' /), 'A', 'K',  'Temperatures after cold point adjustment',        sampled_on_subcycle=.true.)
+     call addfld ('TROPF_RHADJ', (/ 'lev' /), 'A', 'K', 'Relative Hunidity after cold point adjustment',   sampled_on_subcycle=.true.)
+     call addfld ('TROPF_CDT',   horiz_only,  'A', 'K',  'Cold point temperature adjustment',              sampled_on_subcycle=.true.)
+     call addfld ('TROPF_CDZ',   horiz_only,  'A', 'm',  'Distance of coldpoint from coldest model level', sampled_on_subcycle=.true.)
    end if
 
 
    ! Averaging for cloud particle number and size
-   call addfld ('AWNC',        (/ 'lev' /),  'A', 'm-3',      'Average cloud water number conc'                                   )
-   call addfld ('AWNI',        (/ 'lev' /),  'A', 'm-3',      'Average cloud ice number conc'                                     )
-   call addfld ('AREL',        (/ 'lev' /),  'A', 'Micron',   'Average droplet effective radius'                                  )
-   call addfld ('AREI',        (/ 'lev' /),  'A', 'Micron',   'Average ice effective radius'                                      )
+   call addfld ('AWNC',        (/ 'lev' /),  'A', 'm-3',      'Average cloud water number conc',  sampled_on_subcycle=.true.)
+   call addfld ('AWNI',        (/ 'lev' /),  'A', 'm-3',      'Average cloud ice number conc',    sampled_on_subcycle=.true.)
+   call addfld ('AREL',        (/ 'lev' /),  'A', 'Micron',   'Average droplet effective radius', sampled_on_subcycle=.true.)
+   call addfld ('AREI',        (/ 'lev' /),  'A', 'Micron',   'Average ice effective radius',     sampled_on_subcycle=.true.)
    ! Frequency arrays for above
-   call addfld ('FREQL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of liquid'                                   )
-   call addfld ('FREQI',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of ice'                                      )
+   call addfld ('FREQL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of liquid',  sampled_on_subcycle=.true.)
+   call addfld ('FREQI',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of ice',     sampled_on_subcycle=.true.)
 
    ! Average cloud top particle size and number (liq, ice) and frequency
-   call addfld ('ACTREL',      horiz_only,   'A', 'Micron',   'Average Cloud Top droplet effective radius'                        )
-   call addfld ('ACTREI',      horiz_only,   'A', 'Micron',   'Average Cloud Top ice effective radius'                            )
-   call addfld ('ACTNL',       horiz_only,   'A', 'm-3',   'Average Cloud Top droplet number'                                  )
-   call addfld ('ACTNI',       horiz_only,   'A', 'm-3',   'Average Cloud Top ice number'                                      )
+   call addfld ('ACTREL',      horiz_only,   'A', 'Micron',   'Average Cloud Top droplet effective radius', sampled_on_subcycle=.true.)
+   call addfld ('ACTREI',      horiz_only,   'A', 'Micron',   'Average Cloud Top ice effective radius',     sampled_on_subcycle=.true.)
+   call addfld ('ACTNL',       horiz_only,   'A', 'm-3',   'Average Cloud Top droplet number',              sampled_on_subcycle=.true.)
+   call addfld ('ACTNI',       horiz_only,   'A', 'm-3',   'Average Cloud Top ice number',                  sampled_on_subcycle=.true.)
 
-   call addfld ('FCTL',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top liquid'                         )
-   call addfld ('FCTI',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top ice'                            )
+   call addfld ('FCTL',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top liquid',  sampled_on_subcycle=.true.)
+   call addfld ('FCTI',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top ice',     sampled_on_subcycle=.true.)
 
    ! New frequency arrays for mixed phase and supercooled liquid (only and mixed) for (a) Cloud Top and (b) everywhere..
-   call addfld ('FREQM',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of mixed phase'                              )
-   call addfld ('FREQSL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of only supercooled liquid'                  )
-   call addfld ('FREQSLM',     (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of super cooled liquid with ice'             )
-   call addfld ('FCTM',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top mixed phase'                    )
-   call addfld ('FCTSL',       horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top only supercooled liquid'        )
-   call addfld ('FCTSLM',      horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top super cooled liquid with ice'   )
-
-   call addfld ('LS_FLXPRC',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface rain+snow flux'                         )
-   call addfld ('LS_FLXSNW',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface snow flux'                              )
-
-   call addfld ('REL',         (/ 'lev' /),  'A', 'micron',   'MG REL stratiform cloud effective radius liquid'                   )
-   call addfld ('REI',         (/ 'lev' /),  'A', 'micron',   'MG REI stratiform cloud effective radius ice'                      )
-   call addfld ('LS_REFFRAIN', (/ 'lev' /),  'A', 'micron',   'ls stratiform rain effective radius'                               )
-   call addfld ('LS_REFFSNOW', (/ 'lev' /),  'A', 'micron',   'ls stratiform snow effective radius'                               )
-   call addfld ('CV_REFFLIQ',  (/ 'lev' /),  'A', 'micron',   'convective cloud liq effective radius'                             )
-   call addfld ('CV_REFFICE',  (/ 'lev' /),  'A', 'micron',   'convective cloud ice effective radius'                             )
-   call addfld ('MG_SADICE',   (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density ice'                                       )
-   call addfld ('MG_SADSNOW',  (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density snow'                                       )
+   call addfld ('FREQM',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of mixed phase',                  sampled_on_subcycle=.true.)
+   call addfld ('FREQSL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of only supercooled liquid',      sampled_on_subcycle=.true.)
+   call addfld ('FREQSLM',     (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of super cooled liquid with ice', sampled_on_subcycle=.true.)
+   call addfld ('FCTM',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top mixed phase',        sampled_on_subcycle=.true.)
+   call addfld ('FCTSL',       horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top only supercooled liquid', sampled_on_subcycle=.true.)
+   call addfld ('FCTSLM',      horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top super cooled liquid with ice', sampled_on_subcycle=.true.)
+
+   call addfld ('LS_FLXPRC',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface rain+snow flux',             sampled_on_subcycle=.true.)
+   call addfld ('LS_FLXSNW',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface snow flux',                  sampled_on_subcycle=.true.)
+
+   call addfld ('REL',         (/ 'lev' /),  'A', 'micron',   'MG REL stratiform cloud effective radius liquid',       sampled_on_subcycle=.true.)
+   call addfld ('REI',         (/ 'lev' /),  'A', 'micron',   'MG REI stratiform cloud effective radius ice',          sampled_on_subcycle=.true.)
+   call addfld ('LS_REFFRAIN', (/ 'lev' /),  'A', 'micron',   'ls stratiform rain effective radius',                   sampled_on_subcycle=.true.)
+   call addfld ('LS_REFFSNOW', (/ 'lev' /),  'A', 'micron',   'ls stratiform snow effective radius',                   sampled_on_subcycle=.true.)
+   call addfld ('CV_REFFLIQ',  (/ 'lev' /),  'A', 'micron',   'convective cloud liq effective radius',                 sampled_on_subcycle=.true.)
+   call addfld ('CV_REFFICE',  (/ 'lev' /),  'A', 'micron',   'convective cloud ice effective radius',                 sampled_on_subcycle=.true.)
+   call addfld ('MG_SADICE',   (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density ice',                           sampled_on_subcycle=.true.)
+   call addfld ('MG_SADSNOW',  (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density snow',                          sampled_on_subcycle=.true.)
 
    ! diagnostic precip
-   call addfld ('QRAIN',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean rain mixing ratio'                            )
-   call addfld ('QSNOW',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean snow mixing ratio'                            )
-   call addfld ('NRAIN',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean rain number conc'                             )
-   call addfld ('NSNOW',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean snow number conc'                             )
+   call addfld ('QRAIN',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean rain mixing ratio',    sampled_on_subcycle=.true.)
+   call addfld ('QSNOW',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean snow mixing ratio',    sampled_on_subcycle=.true.)
+   call addfld ('NRAIN',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean rain number conc',     sampled_on_subcycle=.true.)
+   call addfld ('NSNOW',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean snow number conc',     sampled_on_subcycle=.true.)
 
    ! size of precip
-   call addfld ('RERCLD',      (/ 'lev' /),  'A', 'm',         'Diagnostic effective radius of Liquid Cloud and Rain'             )
-   call addfld ('DSNOW',       (/ 'lev' /),  'A', 'm',         'Diagnostic grid-mean snow diameter'                               )
+   call addfld ('RERCLD',      (/ 'lev' /),  'A', 'm',         'Diagnostic effective radius of Liquid Cloud and Rain', sampled_on_subcycle=.true.)
+   call addfld ('DSNOW',       (/ 'lev' /),  'A', 'm',         'Diagnostic grid-mean snow diameter',                   sampled_on_subcycle=.true.)
 
    ! diagnostic radar reflectivity, cloud-averaged
-   call addfld ('REFL',        (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity'                                         )
-   call addfld ('AREFL',       (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity'                                 )
-   call addfld ('FREFL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity'                       )
+   call addfld ('REFL',        (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity',                   sampled_on_subcycle=.true.)
+   call addfld ('AREFL',       (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity',           sampled_on_subcycle=.true.)
+   call addfld ('FREFL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity', sampled_on_subcycle=.true.)
 
-   call addfld ('CSRFL',       (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity (CloudSat thresholds)'                   )
-   call addfld ('ACSRFL',      (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity (CloudSat thresholds)'           )
-   call addfld ('FCSRFL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity (CloudSat thresholds)' )
+   call addfld ('CSRFL',       (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity (CloudSat thresholds)', sampled_on_subcycle=.true.)
+   call addfld ('ACSRFL',      (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity (CloudSat thresholds)', sampled_on_subcycle=.true.)
+   call addfld ('FCSRFL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity (CloudSat thresholds)', sampled_on_subcycle=.true.)
 
-   call addfld ('AREFLZ',      (/ 'lev' /),  'A', 'mm^6/m^3', 'Average 94 GHz radar reflectivity'                                 )
+   call addfld ('AREFLZ',      (/ 'lev' /),  'A', 'mm^6/m^3', 'Average 94 GHz radar reflectivity',           sampled_on_subcycle=.true.)
 
    ! Aerosol information
-   call addfld ('NCAL',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Liquid'                          )
-   call addfld ('NCAI',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Ice'                             )
+   call addfld ('NCAL',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Liquid',    sampled_on_subcycle=.true.)
+   call addfld ('NCAI',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Ice',       sampled_on_subcycle=.true.)
 
    ! Average rain and snow mixing ratio (Q), number (N) and diameter (D), with frequency
-   call addfld ('AQRAIN',      (/ 'lev' /),  'A', 'kg/kg',    'Average rain mixing ratio'                                         )
-   call addfld ('AQSNOW',      (/ 'lev' /),  'A', 'kg/kg',    'Average snow mixing ratio'                                         )
-   call addfld ('ANRAIN',      (/ 'lev' /),  'A', 'm-3',      'Average rain number conc'                                          )
-   call addfld ('ANSNOW',      (/ 'lev' /),  'A', 'm-3',      'Average snow number conc'                                          )
-   call addfld ('ADRAIN',      (/ 'lev' /),  'A', 'm',        'Average rain effective Diameter'                                   )
-   call addfld ('ADSNOW',      (/ 'lev' /),  'A', 'm',        'Average snow effective Diameter'                                   )
-   call addfld ('FREQR',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of rain'                                     )
-   call addfld ('FREQS',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of snow'                                     )
+   call addfld ('AQRAIN',      (/ 'lev' /),  'A', 'kg/kg',    'Average rain mixing ratio',                   sampled_on_subcycle=.true.)
+   call addfld ('AQSNOW',      (/ 'lev' /),  'A', 'kg/kg',    'Average snow mixing ratio',                   sampled_on_subcycle=.true.)
+   call addfld ('ANRAIN',      (/ 'lev' /),  'A', 'm-3',      'Average rain number conc',                    sampled_on_subcycle=.true.)
+   call addfld ('ANSNOW',      (/ 'lev' /),  'A', 'm-3',      'Average snow number conc',                    sampled_on_subcycle=.true.)
+   call addfld ('ADRAIN',      (/ 'lev' /),  'A', 'm',        'Average rain effective Diameter',             sampled_on_subcycle=.true.)
+   call addfld ('ADSNOW',      (/ 'lev' /),  'A', 'm',        'Average snow effective Diameter',             sampled_on_subcycle=.true.)
+   call addfld ('FREQR',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of rain',               sampled_on_subcycle=.true.)
+   call addfld ('FREQS',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of snow',               sampled_on_subcycle=.true.)
 
    ! precipitation efficiency & other diagnostic fields
-   call addfld('PE'    ,       horiz_only,   'A', '1',        'Stratiform Precipitation Efficiency  (precip/cmeliq)'              )
-   call addfld('APRL'  ,       horiz_only,   'A', 'm/s',      'Average Stratiform Precip Rate over efficiency calculation'        )
-   call addfld('PEFRAC',       horiz_only,   'A', '1',        'Fraction of timesteps precip efficiency reported'                  )
-   call addfld('VPRCO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of autoconversion rate'                           )
-   call addfld('VPRAO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of accretion rate'                                )
-   call addfld('RACAU' ,       horiz_only,   'A', 'kg/kg/s',  'Accretion/autoconversion ratio from vertical average'              )
+   call addfld('PE'    ,       horiz_only,   'A', '1',        'Stratiform Precipitation Efficiency  (precip/cmeliq)',       sampled_on_subcycle=.true.)
+   call addfld('APRL'  ,       horiz_only,   'A', 'm/s',      'Average Stratiform Precip Rate over efficiency calculation', sampled_on_subcycle=.true.)
+   call addfld('PEFRAC',       horiz_only,   'A', '1',        'Fraction of timesteps precip efficiency reported',           sampled_on_subcycle=.true.)
+   call addfld('VPRCO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of autoconversion rate',                    sampled_on_subcycle=.true.)
+   call addfld('VPRAO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of accretion rate',                         sampled_on_subcycle=.true.)
+   call addfld('RACAU' ,       horiz_only,   'A', 'kg/kg/s',  'Accretion/autoconversion ratio from vertical average',       sampled_on_subcycle=.true.)
 
    if (micro_mg_version > 1) then
-      call addfld('UMR', (/ 'lev' /), 'A',   'm/s', 'Mass-weighted rain  fallspeed'              )
-      call addfld('UMS', (/ 'lev' /), 'A',   'm/s', 'Mass-weighted snow fallspeed'               )
+      call addfld('UMR', (/ 'lev' /), 'A',   'm/s', 'Mass-weighted rain  fallspeed', sampled_on_subcycle=.true.)
+      call addfld('UMS', (/ 'lev' /), 'A',   'm/s', 'Mass-weighted snow fallspeed',  sampled_on_subcycle=.true.)
    end if
 
    if (micro_mg_version > 2) then
-      call addfld('UMG',    (/ 'lev' /), 'A',   'm/s', 'Mass-weighted graupel/hail  fallspeed'                    )
-      call addfld ('FREQG', (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of Graupel'                     )
-      call addfld ('LS_REFFGRAU', (/ 'lev' /),  'A', 'micron',   'ls stratiform graupel/hail effective radius'    )
-      call addfld ('AQGRAU',      (/ 'lev' /),  'A', 'kg/kg',    'Average graupel/hail mixing ratio'              )
-      call addfld ('ANGRAU',      (/ 'lev' /),  'A', 'm-3',      'Average graupel/hail number conc'               )
+      call addfld('UMG',    (/ 'lev' /), 'A',   'm/s', 'Mass-weighted graupel/hail  fallspeed',                 sampled_on_subcycle=.true.)
+      call addfld ('FREQG', (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of Graupel',                  sampled_on_subcycle=.true.)
+      call addfld ('LS_REFFGRAU', (/ 'lev' /),  'A', 'micron',   'ls stratiform graupel/hail effective radius', sampled_on_subcycle=.true.)
+      call addfld ('AQGRAU',      (/ 'lev' /),  'A', 'kg/kg',    'Average graupel/hail mixing ratio',           sampled_on_subcycle=.true.)
+      call addfld ('ANGRAU',      (/ 'lev' /),  'A', 'm-3',      'Average graupel/hail number conc',            sampled_on_subcycle=.true.)
    end if
 
 
    ! qc limiter (only output in versions 1.5 and later)
    if (.not. (micro_mg_version == 1 .and. micro_mg_sub_version == 0)) then
-      call addfld('QCRAT', (/ 'lev' /), 'A', 'fraction', 'Qc Limiter: Fraction of qc tendency applied')
+      call addfld('QCRAT', (/ 'lev' /), 'A', 'fraction', 'Qc Limiter: Fraction of qc tendency applied', sampled_on_subcycle=.true.)
    end if
 
    ! determine the add_default fields
diff --git a/src/physics/cam/microp_aero.F90 b/src/physics/cam/microp_aero.F90
index 4961a139a8..51303e1830 100644
--- a/src/physics/cam/microp_aero.F90
+++ b/src/physics/cam/microp_aero.F90
@@ -334,10 +334,10 @@ subroutine microp_aero_init(phys_state,pbuf2d)
 
    end if
 
-   call addfld('LCLOUD', (/ 'lev' /), 'A', ' ',   'Liquid cloud fraction used in stratus activation')
+   call addfld('LCLOUD', (/ 'lev' /), 'A', ' ',   'Liquid cloud fraction used in stratus activation', sampled_on_subcycle=.true.)
 
-   call addfld('WSUB',   (/ 'lev' /), 'A', 'm/s', 'Diagnostic sub-grid vertical velocity'                   )
-   call addfld('WSUBI',  (/ 'lev' /), 'A', 'm/s', 'Diagnostic sub-grid vertical velocity for ice'           )
+   call addfld('WSUB',   (/ 'lev' /), 'A', 'm/s', 'Diagnostic sub-grid vertical velocity',            sampled_on_subcycle=.true.)
+   call addfld('WSUBI',  (/ 'lev' /), 'A', 'm/s', 'Diagnostic sub-grid vertical velocity for ice',    sampled_on_subcycle=.true.)
 
    if (history_amwg) then
       call add_default ('WSUB     ', 1, ' ')
diff --git a/src/physics/cam7/micro_pumas_cam.F90 b/src/physics/cam7/micro_pumas_cam.F90
index 0d9f448e2f..5d76f36be5 100644
--- a/src/physics/cam7/micro_pumas_cam.F90
+++ b/src/physics/cam7/micro_pumas_cam.F90
@@ -958,286 +958,286 @@ subroutine micro_pumas_cam_init(pbuf2d)
       call cnst_get_ind(cnst_names(m), mm)
       if ( any(mm == (/ ixcldliq, ixcldice, ixrain, ixsnow, ixgraupel /)) ) then
          ! mass mixing ratios
-         call addfld(cnst_name(mm), (/ 'lev' /), 'A', 'kg/kg', cnst_longname(mm)                   )
-         call addfld(sflxnam(mm),    horiz_only, 'A',   'kg/m2/s', trim(cnst_name(mm))//' surface flux')
+         call addfld(cnst_name(mm), (/ 'lev' /), 'A', 'kg/kg', cnst_longname(mm),  sampled_on_subcycle=.true.)
+         call addfld(sflxnam(mm),    horiz_only, 'A',   'kg/m2/s', trim(cnst_name(mm))//' surface flux', sampled_on_subcycle=.true.)
       else if ( any(mm == (/ ixnumliq, ixnumice, ixnumrain, ixnumsnow, ixnumgraupel /)) ) then
          ! number concentrations
-         call addfld(cnst_name(mm), (/ 'lev' /), 'A', '1/kg', cnst_longname(mm)                   )
-         call addfld(sflxnam(mm),    horiz_only, 'A',   '1/m2/s', trim(cnst_name(mm))//' surface flux')
+         call addfld(cnst_name(mm), (/ 'lev' /), 'A', '1/kg', cnst_longname(mm), sampled_on_subcycle=.true.)
+         call addfld(sflxnam(mm),    horiz_only, 'A',   '1/m2/s', trim(cnst_name(mm))//' surface flux', sampled_on_subcycle=.true.)
       else
          call endrun( "micro_pumas_cam_init: &
               &Could not call addfld for constituent with unknown units.")
       endif
    end do
 
-   call addfld(apcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' after physics'  )
-   call addfld(apcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' after physics'  )
-   call addfld(bpcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' before physics' )
-   call addfld(bpcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' before physics' )
+   call addfld(apcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(apcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixcldliq), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldliq))//' before physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixcldice), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixcldice))//' before physics', sampled_on_subcycle=.true.)
 
-   call addfld(apcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' after physics'  )
-   call addfld(apcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' after physics'  )
-   call addfld(bpcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' before physics' )
-   call addfld(bpcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' before physics' )
+   call addfld(apcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(apcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' after physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixrain), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixrain))//' before physics', sampled_on_subcycle=.true.)
+   call addfld(bpcnst(ixsnow), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixsnow))//' before physics', sampled_on_subcycle=.true.)
 
    if (micro_mg_version > 2) then
-      call addfld(apcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' after physics'  )
-      call addfld(bpcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' before physics' )
+      call addfld(apcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' after physics',  sampled_on_subcycle=.true.)
+      call addfld(bpcnst(ixgraupel), (/ 'lev' /), 'A', 'kg/kg', trim(cnst_name(ixgraupel))//' before physics', sampled_on_subcycle=.true.)
    end if
 
-   call addfld ('CME',        (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap within the cloud'                      )
-   call addfld ('PRODPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of conversion of condensate to precip'              )
-   call addfld ('EVAPPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling precip'                   )
-   call addfld ('EVAPSNOW',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling snow'                     )
-   call addfld ('HPROGCLD',   (/ 'lev' /), 'A', 'W/kg'    , 'Heating from prognostic clouds'                          )
-   call addfld ('FICE',       (/ 'lev' /), 'A', 'fraction', 'Fractional ice content within cloud'                     )
-   call addfld ('CLDFSNOW',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for snow'                        )
-   call addfld ('ICWMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus water mixing ratio'                )
-   call addfld ('ICIMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus ice mixing ratio'                  )
+   call addfld ('CME',        (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of cond-evap within the cloud',              sampled_on_subcycle=.true.)
+   call addfld ('PRODPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of conversion of condensate to precip',      sampled_on_subcycle=.true.)
+   call addfld ('EVAPPREC',   (/ 'lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling precip',           sampled_on_subcycle=.true.)
+   call addfld ('EVAPSNOW',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling snow',    sampled_on_subcycle=.true.)
+   call addfld ('HPROGCLD',   (/ 'lev' /), 'A', 'W/kg'    , 'Heating from prognostic clouds',                  sampled_on_subcycle=.true.)
+   call addfld ('FICE',       (/ 'lev' /), 'A', 'fraction', 'Fractional ice content within cloud',             sampled_on_subcycle=.true.)
+   call addfld ('CLDFSNOW',   (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for snow',                sampled_on_subcycle=.true.)
+   call addfld ('ICWMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus water mixing ratio',        sampled_on_subcycle=.true.)
+   call addfld ('ICIMRST',    (/ 'lev' /), 'A', 'kg/kg',    'Prognostic in-stratus ice mixing ratio',          sampled_on_subcycle=.true.)
 
    ! MG microphysics diagnostics
-   call addfld ('QCSEVAP',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling cloud water'              )
-   call addfld ('QISEVAP',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of sublimation of falling cloud ice'                )
-   call addfld ('QVRES',      (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of residual condensation term'                      )
-   call addfld ('CMEIOUT',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of deposition/sublimation of cloud ice'             )
-   call addfld ('VTRMC',      (/ 'trop_cld_lev' /), 'A', 'm/s',      'Mass-weighted cloud water fallspeed'                     )
-   call addfld ('VTRMI',      (/ 'trop_cld_lev' /), 'A', 'm/s',      'Mass-weighted cloud ice fallspeed'                       )
-   call addfld ('QCSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Cloud water mixing ratio tendency from sedimentation'    )
-   call addfld ('QISEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Cloud ice mixing ratio tendency from sedimentation'      )
-   call addfld ('PRAO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by rain'                        )
-   call addfld ('PRCO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud water'                           )
-   call addfld ('MNUCCCO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Immersion freezing of cloud water'                       )
-   call addfld ('MNUCCTO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Contact freezing of cloud water'                         )
-   call addfld ('MNUCCDO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Homogeneous and heterogeneous nucleation from vapor'     )
-   call addfld ('MNUCCDOhet', (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous nucleation from vapor'                     )
-   call addfld ('MSACWIO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water from rime-splintering'         )
-   call addfld ('PSACWSO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by snow'                        )
-   call addfld ('BERGSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to snow from bergeron'         )
-   call addfld ('BERGO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to cloud ice from bergeron'    )
-   call addfld ('MELTO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of cloud ice'                                    )
-   call addfld ('MELTSTOT',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Melting of snow'                                    )
-   call addfld ('MNUDEPO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Deposition Nucleation'                                    )
-   call addfld ('HOMOO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous freezing of cloud water'                     )
-   call addfld ('QCRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual condensation term for cloud water'              )
-   call addfld ('PRCIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud ice to snow'                     )
-   call addfld ('PRAIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud ice to snow'                          )
-   call addfld ('QIRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual deposition term for cloud ice'                  )
-   call addfld ('MNUCCRO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to snow'                  )
-   call addfld ('MNUCCRIO',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to ice'                  )
-   call addfld ('PRACSO',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Accretion of rain by snow'                               )
-   call addfld ('VAPDEPSO',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Vapor deposition onto snow'                            )
-   call addfld ('MELTSDT',    (/ 'trop_cld_lev' /), 'A', 'W/kg',     'Latent heating rate due to melting of snow'              )
-   call addfld ('FRZRDT',     (/ 'trop_cld_lev' /), 'A', 'W/kg',     'Latent heating rate due to homogeneous freezing of rain' )
-   call addfld ('QRSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s', 'Rain mixing ratio tendency from sedimentation'           )
-   call addfld ('QSSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from sedimentation'           )
-   call addfld ('NNUCCCO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Immersion freezing of cloud water')
-   call addfld ('NNUCCTO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Contact freezing of cloud water')
-   call addfld ('NNUCCDO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Ice nucleation')
-   call addfld ('NNUDEPO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Deposition Nucleation')
-   call addfld ('NHOMO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Homogeneous freezing of cloud water')
-   call addfld ('NNUCCRO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to heterogeneous freezing of rain to snow')
-   call addfld ('NNUCCRIO',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Heterogeneous freezing of rain to ice')
-   call addfld ('NSACWIO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Ice Multiplication- Rime-splintering')
-   call addfld ('NPRAO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud water by rain')
-   call addfld ('NPSACWSO',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud water by snow')
-   call addfld ('NPRAIO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud ice to snow')
-   call addfld ('NPRACSO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of rain by snow')
-   call addfld ('NPRCO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s', 'Number Tendency due to Autoconversion of cloud water [to rain]')
-   call addfld ('NPRCIO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Autoconversion of cloud ice to snow')
-   call addfld ('NCSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to cloud liquid sedimentation')
-   call addfld ('NISEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to cloud ice sedimentation')
-   call addfld ('NRSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to rain sedimentation')
-   call addfld ('NSSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to snow sedimentation')
-   call addfld ('NMELTO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of cloud ice ')
-   call addfld ('NMELTS',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of snow')
+   call addfld ('QCSEVAP',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of evaporation of falling cloud water', sampled_on_subcycle=.true.)
+   call addfld ('QISEVAP',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of sublimation of falling cloud ice',   sampled_on_subcycle=.true.)
+   call addfld ('QVRES',      (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of residual condensation term',         sampled_on_subcycle=.true.)
+   call addfld ('CMEIOUT',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Rate of deposition/sublimation of cloud ice',sampled_on_subcycle=.true.)
+   call addfld ('VTRMC',      (/ 'trop_cld_lev' /), 'A', 'm/s',      'Mass-weighted cloud water fallspeed',        sampled_on_subcycle=.true.)
+   call addfld ('VTRMI',      (/ 'trop_cld_lev' /), 'A', 'm/s',      'Mass-weighted cloud ice fallspeed',          sampled_on_subcycle=.true.)
+   call addfld ('QCSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Cloud water mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+   call addfld ('QISEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Cloud ice mixing ratio tendency from sedimentation',   sampled_on_subcycle=.true.)
+   call addfld ('PRAO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by rain',                    sampled_on_subcycle=.true.)
+   call addfld ('PRCO',       (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud water',                       sampled_on_subcycle=.true.)
+   call addfld ('MNUCCCO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Immersion freezing of cloud water',                   sampled_on_subcycle=.true.)
+   call addfld ('MNUCCTO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Contact freezing of cloud water',                     sampled_on_subcycle=.true.)
+   call addfld ('MNUCCDO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Homogeneous and heterogeneous nucleation from vapor', sampled_on_subcycle=.true.)
+   call addfld ('MNUCCDOhet', (/ 'lev' /), 'A', 'kg/kg/s',  'Heterogeneous nucleation from vapor',                 sampled_on_subcycle=.true.)
+   call addfld ('MSACWIO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water from rime-splintering',     sampled_on_subcycle=.true.)
+   call addfld ('PSACWSO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud water by snow',                    sampled_on_subcycle=.true.)
+   call addfld ('BERGSO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to snow from bergeron',     sampled_on_subcycle=.true.)
+   call addfld ('BERGO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Conversion of cloud water to cloud ice from bergeron',sampled_on_subcycle=.true.)
+   call addfld ('MELTO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Melting of cloud ice',                                sampled_on_subcycle=.true.)
+   call addfld ('MELTSTOT',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Melting of snow',                            sampled_on_subcycle=.true.)
+   call addfld ('MNUDEPO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Deposition Nucleation',                      sampled_on_subcycle=.true.)
+   call addfld ('HOMOO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Homogeneous freezing of cloud water',                 sampled_on_subcycle=.true.)
+   call addfld ('QCRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual condensation term for cloud water',          sampled_on_subcycle=.true.)
+   call addfld ('PRCIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Autoconversion of cloud ice to snow',                 sampled_on_subcycle=.true.)
+   call addfld ('PRAIO',      (/ 'lev' /), 'A', 'kg/kg/s',  'Accretion of cloud ice to snow',                      sampled_on_subcycle=.true.)
+   call addfld ('QIRESO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Residual deposition term for cloud ice',              sampled_on_subcycle=.true.)
+   call addfld ('MNUCCRO',    (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to snow',     sampled_on_subcycle=.true.)
+   call addfld ('MNUCCRIO',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Heterogeneous freezing of rain to ice',      sampled_on_subcycle=.true.)
+   call addfld ('PRACSO',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Accretion of rain by snow',                  sampled_on_subcycle=.true.)
+   call addfld ('VAPDEPSO',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Vapor deposition onto snow',                 sampled_on_subcycle=.true.)
+   call addfld ('MELTSDT',    (/ 'trop_cld_lev' /), 'A', 'W/kg',     'Latent heating rate due to melting of snow', sampled_on_subcycle=.true.)
+   call addfld ('FRZRDT',     (/ 'trop_cld_lev' /), 'A', 'W/kg',     'Latent heating rate due to homogeneous freezing of rain', sampled_on_subcycle=.true.)
+   call addfld ('QRSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s', 'Rain mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+   call addfld ('QSSEDTEN',   (/ 'trop_cld_lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+   call addfld ('NNUCCCO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Immersion freezing of cloud water', sampled_on_subcycle=.true.)
+   call addfld ('NNUCCTO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Contact freezing of cloud water',   sampled_on_subcycle=.true.)
+   call addfld ('NNUCCDO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Ice nucleation',                    sampled_on_subcycle=.true.)
+   call addfld ('NNUDEPO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Deposition Nucleation',             sampled_on_subcycle=.true.)
+   call addfld ('NHOMO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Homogeneous freezing of cloud water',    sampled_on_subcycle=.true.)
+   call addfld ('NNUCCRO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to heterogeneous freezing of rain to snow', sampled_on_subcycle=.true.)
+   call addfld ('NNUCCRIO',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Heterogeneous freezing of rain to ice',  sampled_on_subcycle=.true.)
+   call addfld ('NSACWIO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Ice Multiplication- Rime-splintering',   sampled_on_subcycle=.true.)
+   call addfld ('NPRAO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud water by rain',       sampled_on_subcycle=.true.)
+   call addfld ('NPSACWSO',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud water by snow',       sampled_on_subcycle=.true.)
+   call addfld ('NPRAIO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of cloud ice to snow',         sampled_on_subcycle=.true.)
+   call addfld ('NPRACSO',    (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Accretion of rain by snow',              sampled_on_subcycle=.true.)
+   call addfld ('NPRCO',      (/ 'trop_cld_lev' /), 'A', '#/kg/s', 'Number Tendency due to Autoconversion of cloud water [to rain]', sampled_on_subcycle=.true.)
+   call addfld ('NPRCIO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Autoconversion of cloud ice to snow',    sampled_on_subcycle=.true.)
+   call addfld ('NCSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to cloud liquid sedimentation',             sampled_on_subcycle=.true.)
+   call addfld ('NISEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to cloud ice sedimentation',                sampled_on_subcycle=.true.)
+   call addfld ('NRSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to rain sedimentation',                     sampled_on_subcycle=.true.)
+   call addfld ('NSSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to snow sedimentation',                     sampled_on_subcycle=.true.)
+   call addfld ('NMELTO',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of cloud ice',                   sampled_on_subcycle=.true.)
+   call addfld ('NMELTS',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of snow',                        sampled_on_subcycle=.true.)
 
    if (trim(micro_mg_warm_rain) == 'kk2000') then
-      call addfld ('qctend_KK2000',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'cloud liquid mass tendency due to autoconversion  & accretion from KK2000')
-      call addfld ('nctend_KK2000',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'cloud number mass tendency due to autoconversion  & accretion from KK2000')
-      call addfld ('qrtend_KK2000',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'rain mass tendency due to autoconversion  & accretion from KK2000')
-      call addfld ('nrtend_KK2000',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'rain number tendency due to autoconversion  & accretion from KK2000')
+      call addfld ('qctend_KK2000',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'cloud liquid mass tendency due to autoconversion  & accretion from KK2000', sampled_on_subcycle=.true.)
+      call addfld ('nctend_KK2000',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'cloud number mass tendency due to autoconversion  & accretion from KK2000',  sampled_on_subcycle=.true.)
+      call addfld ('qrtend_KK2000',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'rain mass tendency due to autoconversion  & accretion from KK2000',         sampled_on_subcycle=.true.)
+      call addfld ('nrtend_KK2000',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'rain number tendency due to autoconversion  & accretion from KK2000',        sampled_on_subcycle=.true.)
    end if
    if (trim(micro_mg_warm_rain) == 'sb2001') then
-      call addfld ('qctend_SB2001',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'cloud liquid mass tendency due to autoconversion  & accretion from SB2001')
-      call addfld ('nctend_SB2001',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'cloud liquid number tendency due to autoconversion  & accretion from SB2001')
-      call addfld ('qrtend_SB2001',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'rain mass tendency due to autoconversion  & accretion from SB2001')
-      call addfld ('nrtend_SB2001',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'rain number tendency due to autoconversion  & accretion from SB2001')
+      call addfld ('qctend_SB2001',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'cloud liquid mass tendency due to autoconversion  & accretion from SB2001', sampled_on_subcycle=.true.)
+      call addfld ('nctend_SB2001',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'cloud liquid number tendency due to autoconversion  & accretion from SB2001',sampled_on_subcycle=.true.)
+      call addfld ('qrtend_SB2001',     (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'rain mass tendency due to autoconversion  & accretion from SB2001',         sampled_on_subcycle=.true.)
+      call addfld ('nrtend_SB2001',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'rain number tendency due to autoconversion  & accretion from SB2001',        sampled_on_subcycle=.true.)
    end if
-   call addfld ('LAMC',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter lambda for liquid'     )
-   call addfld ('LAMR',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter lambda for rain'   )
-   call addfld ('PGAM',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter mu (pgam) for liquid' )
-   call addfld ('N0R',     (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter n0 for rain' )
+   call addfld ('LAMC',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter lambda for liquid',    sampled_on_subcycle=.true. )
+   call addfld ('LAMR',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter lambda for rain',      sampled_on_subcycle=.true.)
+   call addfld ('PGAM',    (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter mu (pgam) for liquid', sampled_on_subcycle=.true.)
+   call addfld ('N0R',     (/ 'trop_cld_lev' /), 'A', 'unitless',  'Size distribution parameter n0 for rain',          sampled_on_subcycle=.true.)
 
    if (micro_mg_version > 2) then
-         call addfld ('NMELTG',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of graupel')
-         call addfld ('NGSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to graupel sedimentation')
-         call addfld ('PSACRO',    (/ 'lev' /), 'A', 'kg/kg/s', 'Collisions between rain & snow (Graupel collecting snow)')
-         call addfld ('PRACGO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection rain by graupel'             )
-         call addfld ('PSACWGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection droplets by graupel'         )
-         call addfld ('PGSACWO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection droplets by snow')
-         call addfld ('PGRACSO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection rain by snow')
-         call addfld ('PRDGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition of graupel')
-         call addfld ('QMULTGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult droplets/graupel')
-         call addfld ('QMULTRGO',  (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult rain/graupel')
-         call addfld ('QGSEDTEN',  (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Graupel/Hail mixing ratio tendency from sedimentation')
-         call addfld ('NPRACGO',   (/ 'lev' /), 'A', '#/kg/s',   'Change N collection rain by graupel')
-         call addfld ('NSCNGO',    (/ 'lev' /), 'A', '#/kg/s',   'Change N conversion to graupel due to collection droplets by snow')
-         call addfld ('NGRACSO',   (/ 'lev' /), 'A', '#/kg/s',   'Change N conversion to graupel due to collection rain by snow')
-         call addfld ('NMULTGO',   (/ 'lev' /), 'A', '#/kg/s',  'Ice mult due to acc droplets by graupel ')
-         call addfld ('NMULTRGO',  (/ 'lev' /), 'A', '#/kg/s',  'Ice mult due to acc rain by graupel')
-         call addfld ('NPSACWGO',  (/ 'lev' /), 'A', '#/kg/s',   'Change N collection droplets by graupel')
-         call addfld ('CLDFGRAU',  (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for graupel'                        )
-         call addfld ('MELTGTOT',  (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Melting of graupel'                                    )
+         call addfld ('NMELTG',     (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to Melting of graupel',     sampled_on_subcycle=.true.)
+         call addfld ('NGSEDTEN',   (/ 'trop_cld_lev' /), 'A', '#/kg/s',  'Number Tendency due to graupel sedimentation',  sampled_on_subcycle=.true.)
+         call addfld ('PSACRO',    (/ 'lev' /), 'A', 'kg/kg/s', 'Collisions between rain & snow (Graupel collecting snow)',sampled_on_subcycle=.true.)
+         call addfld ('PRACGO',    (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection rain by graupel',                 sampled_on_subcycle=.true.)
+         call addfld ('PSACWGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Change in q collection droplets by graupel',             sampled_on_subcycle=.true.)
+         call addfld ('PGSACWO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection droplets by snow', sampled_on_subcycle=.true.)
+         call addfld ('PGRACSO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q conversion to graupel due to collection rain by snow',     sampled_on_subcycle=.true.)
+         call addfld ('PRDGO',     (/ 'lev' /), 'A', 'kg/kg/s',  'Deposition of graupel',                                  sampled_on_subcycle=.true.)
+         call addfld ('QMULTGO',   (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult droplets/graupel',              sampled_on_subcycle=.true.)
+         call addfld ('QMULTRGO',  (/ 'lev' /), 'A', 'kg/kg/s',  'Q change due to ice mult rain/graupel',                  sampled_on_subcycle=.true.)
+         call addfld ('QGSEDTEN',  (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Graupel/Hail mixing ratio tendency from sedimentation', sampled_on_subcycle=.true.)
+         call addfld ('NPRACGO',   (/ 'lev' /), 'A', '#/kg/s',   'Change N collection rain by graupel',                    sampled_on_subcycle=.true.)
+         call addfld ('NSCNGO',    (/ 'lev' /), 'A', '#/kg/s',   'Change N conversion to graupel due to collection droplets by snow', sampled_on_subcycle=.true.)
+         call addfld ('NGRACSO',   (/ 'lev' /), 'A', '#/kg/s',   'Change N conversion to graupel due to collection rain by snow',     sampled_on_subcycle=.true.)
+         call addfld ('NMULTGO',   (/ 'lev' /), 'A', '#/kg/s',  'Ice mult due to acc droplets by graupel',                            sampled_on_subcycle=.true.)
+         call addfld ('NMULTRGO',  (/ 'lev' /), 'A', '#/kg/s',  'Ice mult due to acc rain by graupel',                                sampled_on_subcycle=.true.)
+         call addfld ('NPSACWGO',  (/ 'lev' /), 'A', '#/kg/s',   'Change N collection droplets by graupel',                           sampled_on_subcycle=.true.)
+         call addfld ('CLDFGRAU',  (/ 'lev' /), 'A', '1',        'Cloud fraction adjusted for graupel',                               sampled_on_subcycle=.true.)
+         call addfld ('MELTGTOT',  (/ 'trop_cld_lev' /), 'A', 'kg/kg/s',  'Melting of graupel',                                       sampled_on_subcycle=.true.)
 
    end if
 
-   call addfld ('RBFRAC',  horiz_only, 'A', 'Fraction',  'Fraction of sky covered by a potential rainbow' )
-   call addfld ('RBFREQ',  horiz_only, 'A', 'Frequency',  'Potential rainbow frequency' )
-   call addfld( 'rbSZA', horiz_only, 'I', 'degrees', 'solar zenith angle' )
+   call addfld ('RBFRAC',  horiz_only, 'A', 'Fraction',  'Fraction of sky covered by a potential rainbow', sampled_on_subcycle=.true.)
+   call addfld ('RBFREQ',  horiz_only, 'A', 'Frequency',  'Potential rainbow frequency',                   sampled_on_subcycle=.true.)
+   call addfld( 'rbSZA', horiz_only, 'I', 'degrees', 'solar zenith angle',                                 sampled_on_subcycle=.true.)
 
    ! History variables for CAM5 microphysics
-   call addfld ('MPDT',       (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Morrison microphysics'                )
-   call addfld ('MPDQ',       (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Morrison microphysics'                      )
-   call addfld ('MPDLIQ',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Morrison microphysics'                 )
-   call addfld ('MPDICE',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Morrison microphysics'                 )
-   call addfld ('MPDNLIQ',    (/ 'lev' /), 'A', '1/kg/s',   'NUMLIQ tendency - Morrison microphysics'                 )
-   call addfld ('MPDNICE',    (/ 'lev' /), 'A', '1/kg/s',   'NUMICE tendency - Morrison microphysics'                 )
-   call addfld ('MPDW2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Vapor tendency - Morrison microphysics'       )
-   call addfld ('MPDW2I',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Ice tendency - Morrison microphysics'         )
-   call addfld ('MPDW2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Precip tendency - Morrison microphysics'      )
-   call addfld ('MPDI2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Vapor tendency - Morrison microphysics'         )
-   call addfld ('MPDI2W',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Water tendency - Morrison microphysics'         )
-   call addfld ('MPDI2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Precip tendency - Morrison microphysics'        )
-   call addfld ('ICWNC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud water number conc'                   )
-   call addfld ('ICINC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud ice number conc'                     )
-   call addfld ('EFFLIQ_IND', (/ 'lev' /), 'A','Micron',    'Prognostic droplet effective radius (indirect effect)'   )
-   call addfld ('CDNUMC',     horiz_only,  'A', '1/m2',     'Vertically-integrated droplet concentration'             )
+   call addfld ('MPDT',       (/ 'lev' /), 'A', 'W/kg',     'Heating tendency - Morrison microphysics',   sampled_on_subcycle=.true.)
+   call addfld ('MPDQ',       (/ 'lev' /), 'A', 'kg/kg/s',  'Q tendency - Morrison microphysics',         sampled_on_subcycle=.true.)
+   call addfld ('MPDLIQ',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDLIQ tendency - Morrison microphysics',    sampled_on_subcycle=.true.)
+   call addfld ('MPDICE',     (/ 'lev' /), 'A', 'kg/kg/s',  'CLDICE tendency - Morrison microphysics',    sampled_on_subcycle=.true.)
+   call addfld ('MPDNLIQ',    (/ 'lev' /), 'A', '1/kg/s',   'NUMLIQ tendency - Morrison microphysics',    sampled_on_subcycle=.true.)
+   call addfld ('MPDNICE',    (/ 'lev' /), 'A', '1/kg/s',   'NUMICE tendency - Morrison microphysics',    sampled_on_subcycle=.true.)
+   call addfld ('MPDW2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Vapor tendency - Morrison microphysics', sampled_on_subcycle=.true.)
+   call addfld ('MPDW2I',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Ice tendency - Morrison microphysics',   sampled_on_subcycle=.true.)
+   call addfld ('MPDW2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Water <--> Precip tendency - Morrison microphysics',sampled_on_subcycle=.true.)
+   call addfld ('MPDI2V',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Vapor tendency - Morrison microphysics',   sampled_on_subcycle=.true.)
+   call addfld ('MPDI2W',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Water tendency - Morrison microphysics',   sampled_on_subcycle=.true.)
+   call addfld ('MPDI2P',     (/ 'lev' /), 'A', 'kg/kg/s',  'Ice <--> Precip tendency - Morrison microphysics',  sampled_on_subcycle=.true.)
+   call addfld ('ICWNC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud water number conc',             sampled_on_subcycle=.true.)
+   call addfld ('ICINC',      (/ 'lev' /), 'A', 'm-3',      'Prognostic in-cloud ice number conc',               sampled_on_subcycle=.true.)
+   call addfld ('EFFLIQ_IND', (/ 'lev' /), 'A','Micron',    'Prognostic droplet effective radius (indirect effect)', sampled_on_subcycle=.true.)
+   call addfld ('CDNUMC',     horiz_only,  'A', '1/m2',     'Vertically-integrated droplet concentration',           sampled_on_subcycle=.true.)
    call addfld ('MPICLWPI',   horiz_only,  'A', 'kg/m2',    'Vertically-integrated &
-        &in-cloud Initial Liquid WP (Before Micro)' )
+        &in-cloud Initial Liquid WP (Before Micro)', sampled_on_subcycle=.true.)
    call addfld ('MPICIWPI',   horiz_only,  'A', 'kg/m2',    'Vertically-integrated &
-        &in-cloud Initial Ice WP (Before Micro)'    )
+        &in-cloud Initial Ice WP (Before Micro)',    sampled_on_subcycle=.true.)
 
    ! This is provided as an example on how to write out subcolumn output
    ! NOTE -- only 'I' should be used for sub-column fields as subc-columns could shift from time-step to time-step
    if (use_subcol_microp) then
       call addfld('FICE_SCOL', (/'psubcols','lev     '/), 'I', 'fraction', &
-           'Sub-column fractional ice content within cloud', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column fractional ice content within cloud', flag_xyfill=.true., fill_value=1.e30_r8,     sampled_on_subcycle=.true.)
       call addfld('MPDICE_SCOL', (/'psubcols','lev     '/), 'I', 'kg/kg/s', &
-           'Sub-column CLDICE tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column CLDICE tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('MPDLIQ_SCOL', (/'psubcols','lev     '/), 'I', 'kg/kg/s', &
-           'Sub-column CLDLIQ tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Sub-column CLDLIQ tendency - Morrison microphysics', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
    end if
 
 
    ! This is only if the coldpoint temperatures are being adjusted.
    ! NOTE: Some fields related to these and output later are added in tropopause.F90.
    if (micro_mg_adjust_cpt) then
-     call addfld ('TROPF_TADJ', (/ 'lev' /), 'A', 'K',  'Temperatures after cold point adjustment'                    )
-     call addfld ('TROPF_RHADJ', (/ 'lev' /), 'A', 'K', 'Relative Hunidity after cold point adjustment'               )
-     call addfld ('TROPF_CDT',   horiz_only,  'A', 'K',  'Cold point temperature adjustment'                           )
-     call addfld ('TROPF_CDZ',   horiz_only,  'A', 'm',  'Distance of coldpoint from coldest model level'              )
+     call addfld ('TROPF_TADJ', (/ 'lev' /), 'A', 'K',  'Temperatures after cold point adjustment',       sampled_on_subcycle=.true.)
+     call addfld ('TROPF_RHADJ', (/ 'lev' /), 'A', 'K', 'Relative Hunidity after cold point adjustment',  sampled_on_subcycle=.true.)
+     call addfld ('TROPF_CDT',   horiz_only,  'A', 'K',  'Cold point temperature adjustment',             sampled_on_subcycle=.true.)
+     call addfld ('TROPF_CDZ',   horiz_only,  'A', 'm',  'Distance of coldpoint from coldest model level',sampled_on_subcycle=.true.)
    end if
 
 
    ! Averaging for cloud particle number and size
-   call addfld ('AWNC',        (/ 'lev' /),  'A', 'm-3',      'Average cloud water number conc'                                   )
-   call addfld ('AWNI',        (/ 'lev' /),  'A', 'm-3',      'Average cloud ice number conc'                                     )
-   call addfld ('AREL',        (/ 'lev' /),  'A', 'Micron',   'Average droplet effective radius'                                  )
-   call addfld ('AREI',        (/ 'lev' /),  'A', 'Micron',   'Average ice effective radius'                                      )
+   call addfld ('AWNC',        (/ 'lev' /),  'A', 'm-3',      'Average cloud water number conc',          sampled_on_subcycle=.true.)
+   call addfld ('AWNI',        (/ 'lev' /),  'A', 'm-3',      'Average cloud ice number conc',            sampled_on_subcycle=.true.)
+   call addfld ('AREL',        (/ 'lev' /),  'A', 'Micron',   'Average droplet effective radius',         sampled_on_subcycle=.true.)
+   call addfld ('AREI',        (/ 'lev' /),  'A', 'Micron',   'Average ice effective radius',             sampled_on_subcycle=.true.)
    ! Frequency arrays for above
-   call addfld ('FREQL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of liquid'                                   )
-   call addfld ('FREQI',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of ice'                                      )
+   call addfld ('FREQL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of liquid',          sampled_on_subcycle=.true.)
+   call addfld ('FREQI',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of ice',             sampled_on_subcycle=.true.)
 
    ! Average cloud top particle size and number (liq, ice) and frequency
-   call addfld ('ACTREL',      horiz_only,   'A', 'Micron',   'Average Cloud Top droplet effective radius'                        )
-   call addfld ('ACTREI',      horiz_only,   'A', 'Micron',   'Average Cloud Top ice effective radius'                            )
-   call addfld ('ACTNL',       horiz_only,   'A', 'm-3',   'Average Cloud Top droplet number'                                  )
-   call addfld ('ACTNI',       horiz_only,   'A', 'm-3',   'Average Cloud Top ice number'                                      )
+   call addfld ('ACTREL',      horiz_only,   'A', 'Micron',   'Average Cloud Top droplet effective radius', sampled_on_subcycle=.true.)
+   call addfld ('ACTREI',      horiz_only,   'A', 'Micron',   'Average Cloud Top ice effective radius',     sampled_on_subcycle=.true.)
+   call addfld ('ACTNL',       horiz_only,   'A', 'm-3',   'Average Cloud Top droplet number',              sampled_on_subcycle=.true.)
+   call addfld ('ACTNI',       horiz_only,   'A', 'm-3',   'Average Cloud Top ice number',                  sampled_on_subcycle=.true.)
 
-   call addfld ('FCTL',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top liquid'                         )
-   call addfld ('FCTI',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top ice'                            )
+   call addfld ('FCTL',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top liquid',  sampled_on_subcycle=.true.)
+   call addfld ('FCTI',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top ice',     sampled_on_subcycle=.true.)
 
    ! New frequency arrays for mixed phase and supercooled liquid (only and mixed) for (a) Cloud Top and (b) everywhere..
-   call addfld ('FREQM',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of mixed phase'                              )
-   call addfld ('FREQSL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of only supercooled liquid'                  )
-   call addfld ('FREQSLM',     (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of super cooled liquid with ice'             )
-   call addfld ('FCTM',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top mixed phase'                    )
-   call addfld ('FCTSL',       horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top only supercooled liquid'        )
-   call addfld ('FCTSLM',      horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top super cooled liquid with ice'   )
-
-   call addfld ('LS_FLXPRC',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface rain+snow flux'                         )
-   call addfld ('LS_FLXSNW',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface snow flux'                              )
-
-   call addfld ('REL',         (/ 'lev' /),  'A', 'micron',   'MG REL stratiform cloud effective radius liquid'                   )
-   call addfld ('REI',         (/ 'lev' /),  'A', 'micron',   'MG REI stratiform cloud effective radius ice'                      )
-   call addfld ('LS_REFFRAIN', (/ 'lev' /),  'A', 'micron',   'ls stratiform rain effective radius'                               )
-   call addfld ('LS_REFFSNOW', (/ 'lev' /),  'A', 'micron',   'ls stratiform snow effective radius'                               )
-   call addfld ('CV_REFFLIQ',  (/ 'lev' /),  'A', 'micron',   'convective cloud liq effective radius'                             )
-   call addfld ('CV_REFFICE',  (/ 'lev' /),  'A', 'micron',   'convective cloud ice effective radius'                             )
-   call addfld ('MG_SADICE',   (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density ice'                                       )
-   call addfld ('MG_SADSNOW',  (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density snow'                                       )
+   call addfld ('FREQM',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of mixed phase',                  sampled_on_subcycle=.true.)
+   call addfld ('FREQSL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of only supercooled liquid',      sampled_on_subcycle=.true.)
+   call addfld ('FREQSLM',     (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of super cooled liquid with ice', sampled_on_subcycle=.true.)
+   call addfld ('FCTM',        horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top mixed phase',        sampled_on_subcycle=.true.)
+   call addfld ('FCTSL',       horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top only supercooled liquid',      sampled_on_subcycle=.true.)
+   call addfld ('FCTSLM',      horiz_only,   'A', 'fraction', 'Fractional occurrence of cloud top super cooled liquid with ice', sampled_on_subcycle=.true.)
+
+   call addfld ('LS_FLXPRC',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface rain+snow flux', sampled_on_subcycle=.true.)
+   call addfld ('LS_FLXSNW',   (/ 'ilev' /), 'A', 'kg/m2/s', 'ls stratiform gbm interface snow flux',      sampled_on_subcycle=.true.)
+
+   call addfld ('REL',         (/ 'lev' /),  'A', 'micron',   'MG REL stratiform cloud effective radius liquid', sampled_on_subcycle=.true.)
+   call addfld ('REI',         (/ 'lev' /),  'A', 'micron',   'MG REI stratiform cloud effective radius ice',    sampled_on_subcycle=.true.)
+   call addfld ('LS_REFFRAIN', (/ 'lev' /),  'A', 'micron',   'ls stratiform rain effective radius',             sampled_on_subcycle=.true.)
+   call addfld ('LS_REFFSNOW', (/ 'lev' /),  'A', 'micron',   'ls stratiform snow effective radius',             sampled_on_subcycle=.true.)
+   call addfld ('CV_REFFLIQ',  (/ 'lev' /),  'A', 'micron',   'convective cloud liq effective radius',           sampled_on_subcycle=.true.)
+   call addfld ('CV_REFFICE',  (/ 'lev' /),  'A', 'micron',   'convective cloud ice effective radius',           sampled_on_subcycle=.true.)
+   call addfld ('MG_SADICE',   (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density ice',                     sampled_on_subcycle=.true.)
+   call addfld ('MG_SADSNOW',  (/ 'lev' /),  'A', 'cm2/cm3',  'MG surface area density snow',                    sampled_on_subcycle=.true.)
 
    ! diagnostic precip
-   call addfld ('QRAIN',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean rain mixing ratio'                            )
-   call addfld ('QSNOW',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean snow mixing ratio'                            )
-   call addfld ('NRAIN',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean rain number conc'                             )
-   call addfld ('NSNOW',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean snow number conc'                             )
+   call addfld ('QRAIN',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean rain mixing ratio',          sampled_on_subcycle=.true.)
+   call addfld ('QSNOW',       (/ 'lev' /),  'A', 'kg/kg',    'Diagnostic grid-mean snow mixing ratio',          sampled_on_subcycle=.true.)
+   call addfld ('NRAIN',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean rain number conc',           sampled_on_subcycle=.true.)
+   call addfld ('NSNOW',       (/ 'lev' /),  'A', 'm-3',      'Diagnostic grid-mean snow number conc',           sampled_on_subcycle=.true.)
 
    ! size of precip
-   call addfld ('RERCLD',      (/ 'lev' /),  'A', 'm',         'Diagnostic effective radius of Liquid Cloud and Rain'             )
-   call addfld ('DSNOW',       (/ 'lev' /),  'A', 'm',         'Diagnostic grid-mean snow diameter'                               )
+   call addfld ('RERCLD',      (/ 'lev' /),  'A', 'm',         'Diagnostic effective radius of Liquid Cloud and Rain', sampled_on_subcycle=.true.)
+   call addfld ('DSNOW',       (/ 'lev' /),  'A', 'm',         'Diagnostic grid-mean snow diameter',                   sampled_on_subcycle=.true.)
 
    ! diagnostic radar reflectivity, cloud-averaged
-   call addfld ('REFL',        (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity'                                         )
-   call addfld ('AREFL',       (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity'                                 )
-   call addfld ('FREFL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity'                       )
+   call addfld ('REFL',        (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity',                   sampled_on_subcycle=.true.)
+   call addfld ('AREFL',       (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity',           sampled_on_subcycle=.true.)
+   call addfld ('FREFL',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity', sampled_on_subcycle=.true.)
 
-   call addfld ('CSRFL',       (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity (CloudSat thresholds)'                   )
-   call addfld ('ACSRFL',      (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity (CloudSat thresholds)'           )
-   call addfld ('FCSRFL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity (CloudSat thresholds)' )
+   call addfld ('CSRFL',       (/ 'lev' /),  'A', 'DBz',      '94 GHz radar reflectivity (CloudSat thresholds)',                   sampled_on_subcycle=.true.)
+   call addfld ('ACSRFL',      (/ 'lev' /),  'A', 'DBz',      'Average 94 GHz radar reflectivity (CloudSat thresholds)',           sampled_on_subcycle=.true.)
+   call addfld ('FCSRFL',      (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of radar reflectivity (CloudSat thresholds)', sampled_on_subcycle=.true.)
 
-   call addfld ('AREFLZ',      (/ 'lev' /),  'A', 'mm^6/m^3', 'Average 94 GHz radar reflectivity'                                 )
+   call addfld ('AREFLZ',      (/ 'lev' /),  'A', 'mm^6/m^3', 'Average 94 GHz radar reflectivity',                                 sampled_on_subcycle=.true.)
 
    ! 10cm (rain) radar reflectivity
-   call addfld ('REFL10CM',    (/ 'lev' /),  'A', 'DBz',      '10cm (Rain) radar reflectivity (Dbz)'                              )
-   call addfld ('REFLZ10CM',   (/ 'lev' /),  'A', 'mm^6/m^3', '10cm (Rain) radar reflectivity (Z units)'                          )
+   call addfld ('REFL10CM',    (/ 'lev' /),  'A', 'DBz',      '10cm (Rain) radar reflectivity (Dbz)',     sampled_on_subcycle=.true.)
+   call addfld ('REFLZ10CM',   (/ 'lev' /),  'A', 'mm^6/m^3', '10cm (Rain) radar reflectivity (Z units)', sampled_on_subcycle=.true.)
 
    ! Aerosol information
-   call addfld ('NCAL',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Liquid'                          )
-   call addfld ('NCAI',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Ice'                             )
+   call addfld ('NCAL',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Liquid', sampled_on_subcycle=.true.)
+   call addfld ('NCAI',        (/ 'lev' /),  'A', '1/m3',     'Number Concentation Activated for Ice',    sampled_on_subcycle=.true.)
 
    ! Average rain and snow mixing ratio (Q), number (N) and diameter (D), with frequency
-   call addfld ('AQRAIN',      (/ 'lev' /),  'A', 'kg/kg',    'Average rain mixing ratio'                                         )
-   call addfld ('AQSNOW',      (/ 'lev' /),  'A', 'kg/kg',    'Average snow mixing ratio'                                         )
-   call addfld ('ANRAIN',      (/ 'lev' /),  'A', 'm-3',      'Average rain number conc'                                          )
-   call addfld ('ANSNOW',      (/ 'lev' /),  'A', 'm-3',      'Average snow number conc'                                          )
-   call addfld ('ADRAIN',      (/ 'lev' /),  'A', 'm',        'Average rain effective Diameter'                                   )
-   call addfld ('ADSNOW',      (/ 'lev' /),  'A', 'm',        'Average snow effective Diameter'                                   )
-   call addfld ('FREQR',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of rain'                                     )
-   call addfld ('FREQS',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of snow'                                     )
+   call addfld ('AQRAIN',      (/ 'lev' /),  'A', 'kg/kg',    'Average rain mixing ratio',                sampled_on_subcycle=.true.)
+   call addfld ('AQSNOW',      (/ 'lev' /),  'A', 'kg/kg',    'Average snow mixing ratio',                sampled_on_subcycle=.true.)
+   call addfld ('ANRAIN',      (/ 'lev' /),  'A', 'm-3',      'Average rain number conc',                 sampled_on_subcycle=.true.)
+   call addfld ('ANSNOW',      (/ 'lev' /),  'A', 'm-3',      'Average snow number conc',                 sampled_on_subcycle=.true.)
+   call addfld ('ADRAIN',      (/ 'lev' /),  'A', 'm',        'Average rain effective Diameter',          sampled_on_subcycle=.true.)
+   call addfld ('ADSNOW',      (/ 'lev' /),  'A', 'm',        'Average snow effective Diameter',          sampled_on_subcycle=.true.)
+   call addfld ('FREQR',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of rain',            sampled_on_subcycle=.true.)
+   call addfld ('FREQS',       (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of snow',            sampled_on_subcycle=.true.)
 
    ! precipitation efficiency & other diagnostic fields
-   call addfld('PE'    ,       horiz_only,   'A', '1',        'Stratiform Precipitation Efficiency  (precip/cmeliq)'              )
-   call addfld('APRL'  ,       horiz_only,   'A', 'm/s',      'Average Stratiform Precip Rate over efficiency calculation'        )
-   call addfld('PEFRAC',       horiz_only,   'A', '1',        'Fraction of timesteps precip efficiency reported'                  )
-   call addfld('VPRCO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of autoconversion rate'                           )
-   call addfld('VPRAO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of accretion rate'                                )
-   call addfld('RACAU' ,       horiz_only,   'A', 'kg/kg/s',  'Accretion/autoconversion ratio from vertical average'              )
+   call addfld('PE'    ,       horiz_only,   'A', '1',        'Stratiform Precipitation Efficiency  (precip/cmeliq)',       sampled_on_subcycle=.true.)
+   call addfld('APRL'  ,       horiz_only,   'A', 'm/s',      'Average Stratiform Precip Rate over efficiency calculation', sampled_on_subcycle=.true.)
+   call addfld('PEFRAC',       horiz_only,   'A', '1',        'Fraction of timesteps precip efficiency reported',           sampled_on_subcycle=.true.)
+   call addfld('VPRCO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of autoconversion rate',                    sampled_on_subcycle=.true.)
+   call addfld('VPRAO' ,       horiz_only,   'A', 'kg/kg/s',  'Vertical average of accretion rate',                         sampled_on_subcycle=.true.)
+   call addfld('RACAU' ,       horiz_only,   'A', 'kg/kg/s',  'Accretion/autoconversion ratio from vertical average',       sampled_on_subcycle=.true.)
 
-   call addfld('UMR', (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted rain  fallspeed'              )
-   call addfld('UMS', (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted snow fallspeed'               )
+   call addfld('UMR', (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted rain  fallspeed', sampled_on_subcycle=.true.)
+   call addfld('UMS', (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted snow fallspeed',  sampled_on_subcycle=.true.)
 
    if (micro_mg_version > 2) then
-      call addfld('UMG',    (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted graupel/hail  fallspeed'                    )
-      call addfld ('FREQG', (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of Graupel'                     )
-      call addfld ('LS_REFFGRAU', (/ 'lev' /),  'A', 'micron',   'ls stratiform graupel/hail effective radius'    )
-      call addfld ('AQGRAU',      (/ 'lev' /),  'A', 'kg/kg',    'Average graupel/hail mixing ratio'              )
-      call addfld ('ANGRAU',      (/ 'lev' /),  'A', 'm-3',      'Average graupel/hail number conc'               )
+      call addfld('UMG',    (/ 'trop_cld_lev' /), 'A',   'm/s', 'Mass-weighted graupel/hail  fallspeed', sampled_on_subcycle=.true.)
+      call addfld ('FREQG', (/ 'lev' /),  'A', 'fraction', 'Fractional occurrence of Graupel',           sampled_on_subcycle=.true.)
+      call addfld ('LS_REFFGRAU', (/ 'lev' /),  'A', 'micron',   'ls stratiform graupel/hail effective radius', sampled_on_subcycle=.true.)
+      call addfld ('AQGRAU',      (/ 'lev' /),  'A', 'kg/kg',    'Average graupel/hail mixing ratio',           sampled_on_subcycle=.true.)
+      call addfld ('ANGRAU',      (/ 'lev' /),  'A', 'm-3',      'Average graupel/hail number conc',            sampled_on_subcycle=.true.)
    end if
 
 
    ! qc limiter (only output in versions 1.5 and later)
-   call addfld('QCRAT', (/ 'lev' /), 'A', 'fraction', 'Qc Limiter: Fraction of qc tendency applied')
+   call addfld('QCRAT', (/ 'lev' /), 'A', 'fraction', 'Qc Limiter: Fraction of qc tendency applied', sampled_on_subcycle=.true.)
 
    ! determine the add_default fields
    call phys_getopts(history_amwg_out           = history_amwg         , &
diff --git a/src/physics/cam7/stochastic_emulated_cam.F90 b/src/physics/cam7/stochastic_emulated_cam.F90
index 8fbc9e44a1..1433c940e3 100644
--- a/src/physics/cam7/stochastic_emulated_cam.F90
+++ b/src/physics/cam7/stochastic_emulated_cam.F90
@@ -85,44 +85,44 @@ subroutine stochastic_emulated_init_cam(stochastic_emulated_filename_quantile_ou
 
     call add_hist_coord('bins_ncd', ncd, 'bins for TAU microphysics')
 
-    call addfld('amk_c',(/'trop_cld_lev','bins_ncd    '/),'A','kg','cloud liquid mass from bins')
-    call addfld('ank_c',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','cloud liquid number concentration from bins')
-    call addfld('amk_r',(/'trop_cld_lev','bins_ncd    '/),'A','kg','rain mass from bins')
-    call addfld('ank_r',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','rain number concentration from bins')
-    call addfld('amk',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins')
-    call addfld('ank',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins')
-    call addfld('amk_out',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins')
-    call addfld('ank_out',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins')
-
-    call addfld('scale_nc',(/'trop_cld_lev'/),'A','1','scaling factor for nc') 
-    call addfld('scale_nr',(/'trop_cld_lev'/),'A','1','scaling factor for nr') 
-    call addfld('scale_qc',(/'trop_cld_lev'/),'A','1','scaling factor for qc') 
-    call addfld('scale_qr',(/'trop_cld_lev'/),'A','1','scaling factor for qr')
+    call addfld('amk_c',(/'trop_cld_lev','bins_ncd    '/),'A','kg','cloud liquid mass from bins',                  sampled_on_subcycle=.true.)
+    call addfld('ank_c',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','cloud liquid number concentration from bins',sampled_on_subcycle=.true.)
+    call addfld('amk_r',(/'trop_cld_lev','bins_ncd    '/),'A','kg','rain mass from bins',                          sampled_on_subcycle=.true.)
+    call addfld('ank_r',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','rain number concentration from bins',        sampled_on_subcycle=.true.)
+    call addfld('amk',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins',                      sampled_on_subcycle=.true.)
+    call addfld('ank',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins',    sampled_on_subcycle=.true.)
+    call addfld('amk_out',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins',                  sampled_on_subcycle=.true.)
+    call addfld('ank_out',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins',sampled_on_subcycle=.true.)
+
+    call addfld('scale_nc',(/'trop_cld_lev'/),'A','1','scaling factor for nc', sampled_on_subcycle=.true.)
+    call addfld('scale_nr',(/'trop_cld_lev'/),'A','1','scaling factor for nr', sampled_on_subcycle=.true.) 
+    call addfld('scale_qc',(/'trop_cld_lev'/),'A','1','scaling factor for qc', sampled_on_subcycle=.true.)
+    call addfld('scale_qr',(/'trop_cld_lev'/),'A','1','scaling factor for qr', sampled_on_subcycle=.true.)
  
-    call addfld('QC_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qc in TAU')
-    call addfld('NC_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nc in TAU')
-    call addfld('QR_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qr in TAU')
-    call addfld('NR_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nr in TAU')
-    call addfld('QC_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qc out TAU')
-    call addfld('NC_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nc out TAU')
-    call addfld('QR_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qr out TAU')
-    call addfld('NR_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nr out TAU')  
+    call addfld('QC_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qc in TAU',    sampled_on_subcycle=.true.)
+    call addfld('NC_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nc in TAU',     sampled_on_subcycle=.true.)
+    call addfld('QR_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qr in TAU',    sampled_on_subcycle=.true.)
+    call addfld('NR_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nr in TAU',     sampled_on_subcycle=.true.)
+    call addfld('QC_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qc out TAU',  sampled_on_subcycle=.true.)
+    call addfld('NC_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nc out TAU',   sampled_on_subcycle=.true.)
+    call addfld('QR_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qr out TAU',  sampled_on_subcycle=.true.)
+    call addfld('NR_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nr out TAU',   sampled_on_subcycle=.true.)  
  
-    call addfld('qctend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code') 
-    call addfld('nctend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code')
-    call addfld('qrtend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code') 
-    call addfld('nrtend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code')
-    call addfld('qctend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code')
-    call addfld('nctend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code')
-    call addfld('qrtend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code')
-    call addfld('nrtend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code')
-
-    call addfld('gmnnn_lmnnn_TAU',(/'trop_cld_lev'/),'A','1','sum of mass gain and loss from bin code')
-    call addfld('ML_fixer',(/'trop_cld_lev'/),'A','1','frequency that ML fixer is activated')
-    call addfld('qc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qc due to ML fixer')
-    call addfld('nc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nc due to ML fixer')
-    call addfld('qr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qr due to ML fixer')
-    call addfld('nr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nr due to ML fixer')
+    call addfld('qctend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nctend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qrtend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nrtend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qctend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nctend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qrtend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nrtend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+
+    call addfld('gmnnn_lmnnn_TAU',(/'trop_cld_lev'/),'A','1','sum of mass gain and loss from bin code', sampled_on_subcycle=.true.)
+    call addfld('ML_fixer',(/'trop_cld_lev'/),'A','1','frequency that ML fixer is activated',           sampled_on_subcycle=.true.)
+    call addfld('qc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qc due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('nc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nc due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('qr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qr due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('nr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nr due to ML fixer',                   sampled_on_subcycle=.true.)
 
     stochastic_emulated_filename_quantile_out     = stochastic_emulated_filename_quantile
     stochastic_emulated_filename_input_scale_out  = stochastic_emulated_filename_input_scale
diff --git a/src/physics/cam7/stochastic_tau_cam.F90 b/src/physics/cam7/stochastic_tau_cam.F90
index b305201e7c..0cea0201a0 100644
--- a/src/physics/cam7/stochastic_tau_cam.F90
+++ b/src/physics/cam7/stochastic_tau_cam.F90
@@ -72,44 +72,44 @@ subroutine stochastic_tau_init_cam
     call add_hist_coord('bins_ncd', ncd, 'bins for TAU microphysics')
 
     !Note: lev needs to be trop_cld_lev for proc_rates....
-    call addfld('amk_c',(/'trop_cld_lev','bins_ncd    '/),'A','kg','cloud liquid mass from bins')
-    call addfld('ank_c',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','cloud liquid number concentration from bins')
-    call addfld('amk_r',(/'trop_cld_lev','bins_ncd    '/),'A','kg','rain mass from bins')
-    call addfld('ank_r',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','rain number concentration from bins')
-    call addfld('amk',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins')
-    call addfld('ank',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins')
-    call addfld('amk_out',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins')
-    call addfld('ank_out',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins')
-
-    call addfld('scale_nc',(/'trop_cld_lev'/),'A','1','scaling factor for nc') 
-    call addfld('scale_nr',(/'trop_cld_lev'/),'A','1','scaling factor for nr') 
-    call addfld('scale_qc',(/'trop_cld_lev'/),'A','1','scaling factor for qc') 
-    call addfld('scale_qr',(/'trop_cld_lev'/),'A','1','scaling factor for qr')
+    call addfld('amk_c',(/'trop_cld_lev','bins_ncd    '/),'A','kg','cloud liquid mass from bins', sampled_on_subcycle=.true.)
+    call addfld('ank_c',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','cloud liquid number concentration from bins', sampled_on_subcycle=.true.)
+    call addfld('amk_r',(/'trop_cld_lev','bins_ncd    '/),'A','kg','rain mass from bins',         sampled_on_subcycle=.true.)
+    call addfld('ank_r',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','rain number concentration from bins', sampled_on_subcycle=.true.)
+    call addfld('amk',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins',     sampled_on_subcycle=.true.)
+    call addfld('ank',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins', sampled_on_subcycle=.true.)
+    call addfld('amk_out',(/'trop_cld_lev','bins_ncd    '/),'A','kg','all liquid mass from bins', sampled_on_subcycle=.true.)
+    call addfld('ank_out',(/'trop_cld_lev','bins_ncd    '/),'A','1/kg','all liquid number concentration from bins', sampled_on_subcycle=.true.)
+
+    call addfld('scale_nc',(/'trop_cld_lev'/),'A','1','scaling factor for nc', sampled_on_subcycle=.true.)
+    call addfld('scale_nr',(/'trop_cld_lev'/),'A','1','scaling factor for nr', sampled_on_subcycle=.true.) 
+    call addfld('scale_qc',(/'trop_cld_lev'/),'A','1','scaling factor for qc', sampled_on_subcycle=.true.) 
+    call addfld('scale_qr',(/'trop_cld_lev'/),'A','1','scaling factor for qr', sampled_on_subcycle=.true.)
  
-    call addfld('QC_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qc in TAU')
-    call addfld('NC_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nc in TAU')
-    call addfld('QR_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qr in TAU')
-    call addfld('NR_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nr in TAU')
-    call addfld('QC_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qc out TAU')
-    call addfld('NC_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nc out TAU')
-    call addfld('QR_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qr out TAU')
-    call addfld('NR_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nr out TAU')  
+    call addfld('QC_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qc in TAU',    sampled_on_subcycle=.true.)
+    call addfld('NC_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nc in TAU',     sampled_on_subcycle=.true.)
+    call addfld('QR_TAU_in',(/'trop_cld_lev'/),'A','kg/kg','qr in TAU',    sampled_on_subcycle=.true.)
+    call addfld('NR_TAU_in',(/'trop_cld_lev'/),'A','1/kg','nr in TAU',     sampled_on_subcycle=.true.)
+    call addfld('QC_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qc out TAU',  sampled_on_subcycle=.true.)
+    call addfld('NC_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nc out TAU',   sampled_on_subcycle=.true.)
+    call addfld('QR_TAU_out',(/'trop_cld_lev'/),'A','kg/kg','qr out TAU',  sampled_on_subcycle=.true.)
+    call addfld('NR_TAU_out',(/'trop_cld_lev'/),'A','1/kg','nr out TAU',   sampled_on_subcycle=.true.)  
    
-    call addfld('qctend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code') 
-    call addfld('nctend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code')
-    call addfld('qrtend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code') 
-    call addfld('nrtend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code')
-    call addfld('qctend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code')
-    call addfld('nctend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code')
-    call addfld('qrtend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code')
-    call addfld('nrtend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code')
-
-    call addfld('gmnnn_lmnnn_TAU',(/'trop_cld_lev'/),'A','1','sum of mass gain and loss from bin code')
-    call addfld('ML_fixer',(/'trop_cld_lev'/),'A','1','frequency that ML fixer is activated')
-    call addfld('qc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qc due to ML fixer')
-    call addfld('nc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nc due to ML fixer')
-    call addfld('qr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qr due to ML fixer')
-    call addfld('nr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nr due to ML fixer')
+    call addfld('qctend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nctend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qrtend_TAU',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code', sampled_on_subcycle=.true.) 
+    call addfld('nrtend_TAU',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qctend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qc tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nctend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nc tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+    call addfld('qrtend_TAU_diag',(/'trop_cld_lev'/),'A','kg/kg/s','qr tendency due to TAU bin code', sampled_on_subcycle=.true.)
+    call addfld('nrtend_TAU_diag',(/'trop_cld_lev'/),'A','1/kg/s','nr tendency due to TAU bin code',  sampled_on_subcycle=.true.)
+
+    call addfld('gmnnn_lmnnn_TAU',(/'trop_cld_lev'/),'A','1','sum of mass gain and loss from bin code', sampled_on_subcycle=.true.)
+    call addfld('ML_fixer',(/'trop_cld_lev'/),'A','1','frequency that ML fixer is activated',           sampled_on_subcycle=.true.)
+    call addfld('qc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qc due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('nc_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nc due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('qr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta qr due to ML fixer',                   sampled_on_subcycle=.true.)
+    call addfld('nr_fixer',(/'trop_cld_lev'/),'A','kg/kg','delta nr due to ML fixer',                   sampled_on_subcycle=.true.)
 
 end subroutine stochastic_tau_init_cam
 end module stochastic_tau_cam

From 34e981615a9fc8e1320555df38f14f12f1884336 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Tue, 22 Oct 2024 13:57:21 -0600
Subject: [PATCH 11/53] move file-dependent fields to end of if block

---
 src/control/cam_history.F90 | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index e86f885f0e..867c84eaea 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -4329,7 +4329,6 @@ subroutine h_define (t, restart)
                       cam_snapshot_before_num_out = cam_snapshot_before_num,  &
                       cam_snapshot_after_num_out  = cam_snapshot_after_num)
 
-
     if(restart) then
       tape => restarthistory_tape
       if(masterproc) write(iulog,*)'Opening netcdf history restart file ', trim(hrestpath(t))
@@ -4509,14 +4508,6 @@ subroutine h_define (t, restart)
 
        if(.not. is_satfile(t)) then
 
-         if (f == accumulated_file_index) then
-            ierr=pio_put_att (tape(t)%Files(f), tape(t)%timeid, 'bounds', 'time_bounds')
-            ierr=pio_def_var (tape(t)%Files(f),'time_bounds',pio_double,(/bnddim,timdim/),tape(t)%tbndid)
-            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'long_name', 'time interval endpoints')
-            str = 'days since ' // date2yyyymmdd(nbdate) // ' ' // sec2hms(nbsec)
-            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'units', trim(str))
-            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'calendar', trim(calendar))
-         end if
          !
          ! Character
          !
@@ -4565,7 +4556,6 @@ subroutine h_define (t, restart)
             ierr=pio_put_att (tape(t)%Files(f), tape(t)%nscurid, 'long_name', trim(str))
          end if
 
-
          if (.not. is_initfile(file_index=t) .and. f == instantaneous_file_index) then
            ! Don't write the GHG/Solar forcing data to the IC file.
            ! Only write the GHG/Solar forcing data to the instantaneous file
@@ -4668,6 +4658,13 @@ subroutine h_define (t, restart)
             ierr=pio_def_var (tape(t)%Files(f),'nsteph  ',pio_int,(/timdim/),tape(t)%nstephid)
             str = 'current timestep'
             ierr=pio_put_att (tape(t)%Files(f), tape(t)%nstephid, 'long_name', trim(str))
+         else if (f == accumulated_file_index) then
+            ierr=pio_def_var (tape(t)%Files(f),'time_bounds',pio_double,(/bnddim,timdim/),tape(t)%tbndid)
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%timeid, 'bounds', 'time_bounds')
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'long_name', 'time interval endpoints')
+            str = 'days since ' // date2yyyymmdd(nbdate) // ' ' // sec2hms(nbsec)
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'units', trim(str))
+            ierr=pio_put_att (tape(t)%Files(f), tape(t)%tbndid, 'calendar', trim(calendar))
          end if
        end if ! .not. is_satfile
 
@@ -5031,6 +5028,7 @@ subroutine h_define (t, restart)
       deallocate(header_info)
     end if
 
+
     ! Write the mdim variable data
     do f = 1, maxsplitfiles
        if (pio_file_is_open(tape(t)%Files(f))) then
@@ -5854,11 +5852,14 @@ subroutine wshist (rgnht_in)
              end if
              ! We have two files - one for accumulated and one for instantaneous fields
              if (f == accumulated_file_index) then
-                ierr=pio_put_var (tape(t)%Files(f), tape(t)%tbndid, startc, countc, tdata)
                 if (.not. restart .and. .not. is_initfile(t)) then
                    ! accumulated tape - time is midpoint of time_bounds
                    ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/(tdata(1) + tdata(2)) / 2._r8/))
+                else
+                   ! restart or initfile - time is current time
+                   ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/time/))
                 end if
+                ierr=pio_put_var (tape(t)%Files(f), tape(t)%tbndid, startc, countc, tdata)
              else
                 ! not an accumulated history tape - time is current time
                 ierr=pio_put_var (tape(t)%Files(f), tape(t)%timeid, (/start/),(/count1/),(/time/))

From 2772bb4aa280d4c4dc4d5253fa2fc672dde09b48 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 9 Sep 2024 20:04:06 -0400
Subject: [PATCH 12/53] Port check_energy_chng, check_energy_timestep_init to
 CCPP-ized subroutines

---
 bld/configure                        |   1 +
 src/dynamics/eul/dp_coupling.F90     |   4 +-
 src/dynamics/fv/dp_coupling.F90      |   4 +-
 src/dynamics/mpas/dp_coupling.F90    |   4 +-
 src/dynamics/se/dp_coupling.F90      |   4 +-
 src/physics/cam/check_energy.F90     | 302 +--------------------------
 src/physics/cam/check_energy_cam.F90 | 211 +++++++++++++++++++
 src/physics/cam/physpkg.F90          |   5 +-
 src/physics/cam/zm_conv_intr.F90     |   1 -
 src/physics/cam7/physpkg.F90         |   6 +-
 10 files changed, 232 insertions(+), 310 deletions(-)
 create mode 100644 src/physics/cam/check_energy_cam.F90

diff --git a/bld/configure b/bld/configure
index 86c6c4e65b..4b898b9d88 100755
--- a/bld/configure
+++ b/bld/configure
@@ -2340,6 +2340,7 @@ sub write_filepath
     print $fh "$camsrcdir/src/atmos_phys/schemes/tropopause_find\n";
     print $fh "$camsrcdir/src/atmos_phys/schemes/zhang_mcfarlane\n";
     print $fh "$camsrcdir/src/atmos_phys/schemes/dry_adiabatic_adjust\n";
+    print $fh "$camsrcdir/src/atmos_phys/schemes/check_energy\n";
     print $fh "$camsrcdir/src/atmos_phys/schemes/utilities\n";
 
     # Dynamics package and test utilities
diff --git a/src/dynamics/eul/dp_coupling.F90 b/src/dynamics/eul/dp_coupling.F90
index bc900e2d0e..8e3eb64a21 100644
--- a/src/dynamics/eul/dp_coupling.F90
+++ b/src/dynamics/eul/dp_coupling.F90
@@ -14,7 +14,7 @@ module dp_coupling
    use physconst,         only: cpair, gravit, rair, zvir
    use air_composition,   only: rairv
    use geopotential,      only: geopotential_t
-   use check_energy,      only: check_energy_timestep_init
+   use check_energy_cam,  only: check_energy_cam_timestep_init
 #if (defined SPMD)
    use spmd_dyn,          only: buf1, buf1win, buf2, buf2win, &
                                 spmdbuf_siz, local_dp_map, &
@@ -291,7 +291,7 @@ subroutine d_p_coupling(ps, t3, u3, v3, q3, &
 
 ! Compute energy and water integrals of input state
        pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-       call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk )
+       call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk )
 
     end do
 
diff --git a/src/dynamics/fv/dp_coupling.F90 b/src/dynamics/fv/dp_coupling.F90
index fc02821471..af2d13b12e 100644
--- a/src/dynamics/fv/dp_coupling.F90
+++ b/src/dynamics/fv/dp_coupling.F90
@@ -12,7 +12,7 @@ module dp_coupling
    use physconst,         only: gravit, zvir
    use air_composition,   only: cpairv, rairv
    use geopotential,      only: geopotential_t
-   use check_energy,      only: check_energy_timestep_init
+   use check_energy_cam,  only: check_energy_cam_timestep_init
    use dynamics_vars,     only: T_FVDYCORE_GRID, t_fvdycore_state
    use dyn_internal_state,only: get_dyn_state
    use dyn_comp,          only: dyn_import_t, dyn_export_t, fv_print_dpcoup_warn
@@ -621,7 +621,7 @@ subroutine d_p_coupling(grid, phys_state, phys_tend,  pbuf2d, dyn_out)
 ! Compute energy and water integrals of input state
 
        pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-       call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+       call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
     end do
     call t_stopf('derived_fields')
diff --git a/src/dynamics/mpas/dp_coupling.F90 b/src/dynamics/mpas/dp_coupling.F90
index 10d75b4b8c..c312f1e2f9 100644
--- a/src/dynamics/mpas/dp_coupling.F90
+++ b/src/dynamics/mpas/dp_coupling.F90
@@ -413,7 +413,7 @@ subroutine derived_phys(phys_state, phys_tend, pbuf2d)
    ! MPAS prognostic fields.
 
    use geopotential,    only: geopotential_t
-   use check_energy,    only: check_energy_timestep_init
+   use check_energy_cam,  only: check_energy_cam_timestep_init
    use shr_vmath_mod,   only: shr_vmath_log
    use phys_control,    only: waccmx_is
    use cam_thermo,      only: cam_thermo_dry_air_update, cam_thermo_water_update
@@ -564,7 +564,7 @@ subroutine derived_phys(phys_state, phys_tend, pbuf2d)
 
       ! Compute energy and water integrals of input state
       pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-      call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+      call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
    end do
 
diff --git a/src/dynamics/se/dp_coupling.F90 b/src/dynamics/se/dp_coupling.F90
index 919b7f3510..9de31132a2 100644
--- a/src/dynamics/se/dp_coupling.F90
+++ b/src/dynamics/se/dp_coupling.F90
@@ -546,7 +546,7 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
    use phys_control,    only: waccmx_is
    use geopotential,    only: geopotential_t
    use static_energy,   only: update_dry_static_energy_run
-   use check_energy,    only: check_energy_timestep_init
+   use check_energy_cam,only: check_energy_cam_timestep_init
    use hycoef,          only: hyai, ps0
    use shr_vmath_mod,   only: shr_vmath_log
    use qneg_module,     only: qneg3
@@ -707,7 +707,7 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
                                         cpairv(1:ncol,:,lchnk), errflg, errmsg)
       ! Compute energy and water integrals of input state
       pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-      call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+      call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
 
    end do  ! lchnk
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 9c569387e0..5e1df3a967 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -26,10 +26,9 @@ module check_energy
 
   use gmean_mod,       only: gmean
   use physconst,       only: gravit, rga, latvap, latice, cpair, rair
-  use air_composition, only: cpairv, rairv, cp_or_cv_dycore
+  use air_composition, only: cpairv, cp_or_cv_dycore
   use physics_types,   only: physics_state, physics_tend, physics_ptend, physics_ptend_init
   use constituents,    only: cnst_get_ind, pcnst, cnst_name, cnst_get_type_byind
-  use time_manager,    only: is_first_step
   use cam_logfile,     only: iulog
   use scamMod,         only: single_column, use_camiop, heat_glob_scm
   use cam_history,     only: outfld, write_camiop
@@ -45,8 +44,6 @@ module check_energy
   public :: check_energy_register  ! register fields in physics buffer
   public :: check_energy_get_integrals ! get energy integrals computed in check_energy_gmean
   public :: check_energy_init      ! initialization of module
-  public :: check_energy_timestep_init  ! timestep initialization of energy integrals and cumulative boundary fluxes
-  public :: check_energy_chng      ! check changes in integrals against cumulative boundary fluxes
   public :: check_energy_gmean     ! global means of physics input and output total energy
   public :: check_energy_fix       ! add global mean energy difference as a heating
   public :: check_tracers_init      ! initialize tracer integrals and cumulative boundary fluxes
@@ -67,11 +64,11 @@ module check_energy
 
 ! Physics buffer indices
 
-  integer  :: teout_idx  = 0       ! teout index in physics buffer
-  integer  :: dtcore_idx = 0       ! dtcore index in physics buffer
-  integer  :: dqcore_idx = 0       ! dqcore index in physics buffer
-  integer  :: ducore_idx = 0       ! ducore index in physics buffer
-  integer  :: dvcore_idx = 0       ! dvcore index in physics buffer
+  integer, public  :: teout_idx  = 0       ! teout index in physics buffer
+  integer, public  :: dtcore_idx = 0       ! dtcore index in physics buffer
+  integer, public  :: dqcore_idx = 0       ! dqcore index in physics buffer
+  integer, public  :: ducore_idx = 0       ! ducore index in physics buffer
+  integer, public  :: dvcore_idx = 0       ! dvcore index in physics buffer
 
   type check_tracers_data
      real(r8) :: tracer(pcols,pcnst)       ! initial vertically integrated total (kinetic + static) energy
@@ -219,293 +216,6 @@ end subroutine check_energy_init
 
 !===============================================================================
 
-  subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
-    use cam_thermo,      only: get_hydrostatic_energy
-    use physics_buffer,  only: physics_buffer_desc, pbuf_set_field
-    use cam_abortutils,  only: endrun
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
-    use physics_types,   only: phys_te_idx, dyn_te_idx
-!-----------------------------------------------------------------------
-! Compute initial values of energy and water integrals,
-! zero cumulative tendencies
-!-----------------------------------------------------------------------
-!------------------------------Arguments--------------------------------
-
-    type(physics_state),   intent(inout)    :: state
-    type(physics_tend ),   intent(inout)    :: tend
-    type(physics_buffer_desc), pointer      :: pbuf(:)
-    integer, optional                       :: col_type  ! Flag inidicating whether using grid or subcolumns
-!---------------------------Local storage-------------------------------
-    real(r8)              :: cp_or_cv(state%psetcols,pver)
-    integer lchnk                                  ! chunk identifier
-    integer ncol                                   ! number of atmospheric columns
-!-----------------------------------------------------------------------
-
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    ! cp_or_cv needs to be allocated to a size which matches state and ptend
-    ! If psetcols == pcols, cpairv is the correct size and just copy into cp_or_cv
-    ! If psetcols > pcols and all cpairv match cpair, then assign the constant cpair
-
-    if (state%psetcols == pcols) then
-       cp_or_cv(:,:) = cpairv(:,:,lchnk)
-    else if (state%psetcols > pcols .and. all(cpairv(:,:,lchnk) == cpair)) then
-       cp_or_cv(1:ncol,:) = cpair
-    else
-       call endrun('check_energy_timestep_init: cpairv is not allowed to vary when subcolumns are turned on')
-    end if
-    !
-    ! CAM physics total energy
-    !
-    call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-         state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-         state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), state%T(1:ncol,1:pver),     &
-         vc_physics, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),&
-         te = state%te_ini(1:ncol,phys_te_idx), H2O = state%tw_ini(1:ncol))
-    !
-    ! Dynamical core total energy
-    !
-    state%temp_ini(:ncol,:) = state%T(:ncol,:)
-    state%z_ini(:ncol,:)    = state%zm(:ncol,:)
-    if (vc_dycore == vc_height) then
-      !
-      ! MPAS specific hydrostatic energy computation (internal energy)
-      !
-      if (state%psetcols == pcols) then
-        cp_or_cv(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-      else
-        cp_or_cv(:ncol,:) = cpair-rair
-      endif
-
-      call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-           state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-           state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), state%T(1:ncol,1:pver),     &
-           vc_dycore, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),         &
-           z_mid = state%z_ini(1:ncol,:),                                              &
-           te = state%te_ini(1:ncol,dyn_te_idx), H2O = state%tw_ini(1:ncol))
-    else if (vc_dycore == vc_dry_pressure) then
-      !
-      ! SE specific hydrostatic energy (enthalpy)
-      !
-      if (state%psetcols == pcols) then
-        cp_or_cv(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-      else
-        cp_or_cv(:ncol,:) = cpair
-      endif
-      call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-           state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-           state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), state%T(1:ncol,1:pver),     &
-           vc_dry_pressure, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),   &
-           te = state%te_ini(1:ncol,dyn_te_idx), H2O = state%tw_ini(1:ncol))
-    else
-      !
-      ! dycore energy is the same as physics
-      !
-      state%te_ini(1:ncol,dyn_te_idx) = state%te_ini(1:ncol,phys_te_idx)
-    end if
-    state%te_cur(:ncol,:) = state%te_ini(:ncol,:)
-    state%tw_cur(:ncol)   = state%tw_ini(:ncol)
-
-! zero cummulative boundary fluxes
-    tend%te_tnd(:ncol) = 0._r8
-    tend%tw_tnd(:ncol) = 0._r8
-
-    state%count = 0
-
-! initialize physics buffer
-    if (is_first_step()) then
-       call pbuf_set_field(pbuf, teout_idx, state%te_ini(:,dyn_te_idx), col_type=col_type)
-    end if
-
-  end subroutine check_energy_timestep_init
-
-!===============================================================================
-
-  subroutine check_energy_chng(state, tend, name, nstep, ztodt,        &
-       flx_vap, flx_cnd, flx_ice, flx_sen)
-    use cam_thermo,      only: get_hydrostatic_energy
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
-    use cam_abortutils,  only: endrun
-    use physics_types,   only: phys_te_idx, dyn_te_idx
-!-----------------------------------------------------------------------
-! Check that the energy and water change matches the boundary fluxes
-!-----------------------------------------------------------------------
-!------------------------------Arguments--------------------------------
-
-    type(physics_state)    , intent(inout) :: state
-    type(physics_tend )    , intent(inout) :: tend
-    character*(*),intent(in) :: name               ! parameterization name for fluxes
-    integer , intent(in   ) :: nstep               ! current timestep number
-    real(r8), intent(in   ) :: ztodt               ! 2 delta t (model time increment)
-    real(r8), intent(in   ) :: flx_vap(:)          ! (pcols) - boundary flux of vapor         (kg/m2/s)
-    real(r8), intent(in   ) :: flx_cnd(:)          ! (pcols) -boundary flux of liquid+ice    (m/s) (precip?)
-    real(r8), intent(in   ) :: flx_ice(:)          ! (pcols) -boundary flux of ice           (m/s) (snow?)
-    real(r8), intent(in   ) :: flx_sen(:)          ! (pcols) -boundary flux of sensible heat (w/m2)
-
-!******************** BAB ******************************************************
-!******* Note that the precip and ice fluxes are in precip units (m/s). ********
-!******* I would prefer to have kg/m2/s.                                ********
-!******* I would also prefer liquid (not total) and ice fluxes          ********
-!*******************************************************************************
-
-!---------------------------Local storage-------------------------------
-
-    real(r8) :: te_xpd(state%ncol)                 ! expected value (f0 + dt*boundary_flux)
-    real(r8) :: te_dif(state%ncol)                 ! energy of input state - original energy
-    real(r8) :: te_tnd(state%ncol)                 ! tendency from last process
-    real(r8) :: te_rer(state%ncol)                 ! relative error in energy column
-
-    real(r8) :: tw_xpd(state%ncol)                 ! expected value (w0 + dt*boundary_flux)
-    real(r8) :: tw_dif(state%ncol)                 ! tw_inp - original water
-    real(r8) :: tw_tnd(state%ncol)                 ! tendency from last process
-    real(r8) :: tw_rer(state%ncol)                 ! relative error in water column
-
-    real(r8) :: te(state%ncol)                     ! vertical integral of total energy
-    real(r8) :: tw(state%ncol)                     ! vertical integral of total water
-    real(r8) :: cp_or_cv(state%psetcols,pver)      ! cp or cv depending on vcoord
-    real(r8) :: scaling(state%psetcols,pver)       ! scaling for conversion of temperature increment
-    real(r8) :: temp(state%ncol,pver)              ! temperature
-
-    real(r8) :: se(state%ncol)                     ! enthalpy or internal energy (J/m2)
-    real(r8) :: po(state%ncol)                     ! surface potential or potential energy (J/m2)
-    real(r8) :: ke(state%ncol)                     ! kinetic energy    (J/m2)
-    real(r8) :: wv(state%ncol)                     ! column integrated vapor       (kg/m2)
-    real(r8) :: liq(state%ncol)                    ! column integrated liquid      (kg/m2)
-    real(r8) :: ice(state%ncol)                    ! column integrated ice         (kg/m2)
-
-    integer lchnk                                  ! chunk identifier
-    integer ncol                                   ! number of atmospheric columns
-    integer  i                                     ! column index
-!-----------------------------------------------------------------------
-
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    ! If psetcols == pcols, cpairv is the correct size and just copy into cp_or_cv
-    ! If psetcols > pcols and all cpairv match cpair, then assign the constant cpair
-
-    if (state%psetcols == pcols) then
-       cp_or_cv(:,:) = cpairv(:,:,lchnk)
-    else if (state%psetcols > pcols .and. all(cpairv(:,:,:) == cpair)) then
-       cp_or_cv(:,:) = cpair
-    else
-       call endrun('check_energy_chng: cpairv is not allowed to vary when subcolumns are turned on')
-    end if
-
-    call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-         state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-         state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), state%T(1:ncol,1:pver),     &
-         vc_physics, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),        &
-         te = te(1:ncol), H2O = tw(1:ncol), se=se(1:ncol),po=po(1:ncol),             &
-         ke=ke(1:ncol),wv=wv(1:ncol),liq=liq(1:ncol),ice=ice(1:ncol))
-    ! compute expected values and tendencies
-    do i = 1, ncol
-       ! change in static energy and total water
-       te_dif(i) = te(i) - state%te_cur(i,phys_te_idx)
-       tw_dif(i) = tw(i) - state%tw_cur(i)
-
-       ! expected tendencies from boundary fluxes for last process
-       te_tnd(i) = flx_vap(i)*(latvap+latice) - (flx_cnd(i) - flx_ice(i))*1000._r8*latice + flx_sen(i)
-       tw_tnd(i) = flx_vap(i) - flx_cnd(i) *1000._r8
-
-       ! cummulative tendencies from boundary fluxes
-       tend%te_tnd(i) = tend%te_tnd(i) + te_tnd(i)
-       tend%tw_tnd(i) = tend%tw_tnd(i) + tw_tnd(i)
-
-       ! expected new values from previous state plus boundary fluxes
-       te_xpd(i) = state%te_cur(i,phys_te_idx) + te_tnd(i)*ztodt
-       tw_xpd(i) = state%tw_cur(i)             + tw_tnd(i)*ztodt
-
-       ! relative error, expected value - input state / previous state
-       te_rer(i) = (te_xpd(i) - te(i)) / state%te_cur(i,phys_te_idx)
-    end do
-
-    ! relative error for total water (allow for dry atmosphere)
-    tw_rer = 0._r8
-    where (state%tw_cur(:ncol) > 0._r8)
-       tw_rer(:ncol) = (tw_xpd(:ncol) - tw(:ncol)) / state%tw_cur(:ncol)
-    end where
-
-    ! error checking
-    if (print_energy_errors) then
-       if (any(abs(te_rer(1:ncol)) > 1.E-14_r8 .or. abs(tw_rer(1:ncol)) > 1.E-10_r8)) then
-          do i = 1, ncol
-             ! the relative error threshold for the water budget has been reduced to 1.e-10
-             ! to avoid messages generated by QNEG3 calls
-             ! PJR- change to identify if error in energy or water
-             if (abs(te_rer(i)) > 1.E-14_r8 ) then
-                state%count = state%count + 1
-                write(iulog,*) "significant energy conservation error after ", name,        &
-                      " count", state%count, " nstep", nstep, "chunk", lchnk, "col", i
-                write(iulog,*) te(i),te_xpd(i),te_dif(i),tend%te_tnd(i)*ztodt,  &
-                      te_tnd(i)*ztodt,te_rer(i)
-             endif
-             if ( abs(tw_rer(i)) > 1.E-10_r8) then
-                state%count = state%count + 1
-                write(iulog,*) "significant water conservation error after ", name,        &
-                      " count", state%count, " nstep", nstep, "chunk", lchnk, "col", i
-                write(iulog,*) tw(i),tw_xpd(i),tw_dif(i),tend%tw_tnd(i)*ztodt,  &
-                      tw_tnd(i)*ztodt,tw_rer(i)
-             end if
-          end do
-       end if
-    end if
-
-    ! copy new value to state
-
-    do i = 1, ncol
-      state%te_cur(i,phys_te_idx) = te(i)
-      state%tw_cur(i)             = tw(i)
-    end do
-
-    !
-    ! Dynamical core total energy
-    !
-    if (vc_dycore == vc_height) then
-      !
-      ! compute cv if vertical coordinate is height: cv = cp - R
-      !
-      ! Note: cp_or_cv set above for pressure coordinate
-      if (state%psetcols == pcols) then
-        cp_or_cv(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-      else
-        cp_or_cv(:ncol,:) = cpair-rair
-      endif
-      scaling(:,:)   = cpairv(:,:,lchnk)/cp_or_cv(:,:) !cp/cv scaling
-      temp(1:ncol,:) = state%temp_ini(1:ncol,:)+scaling(1:ncol,:)*(state%T(1:ncol,:)-state%temp_ini(1:ncol,:))
-      call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-           state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-           state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), temp(1:ncol,1:pver),        &
-           vc_dycore, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),         &
-           z_mid = state%z_ini(1:ncol,:),                                              &
-           te = state%te_cur(1:ncol,dyn_te_idx), H2O = state%tw_cur(1:ncol))
-    else if (vc_dycore == vc_dry_pressure) then
-      !
-      ! SE specific hydrostatic energy
-      !
-      if (state%psetcols == pcols) then
-        cp_or_cv(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-        scaling(:ncol,:)  = cpairv(:ncol,:,lchnk)/cp_or_cv_dycore(:ncol,:,lchnk)
-      else
-        cp_or_cv(:ncol,:) = cpair
-        scaling(:ncol,:)  = 1.0_r8
-      endif
-      !
-      ! enthalpy scaling for energy consistency
-      !
-      temp(1:ncol,:)   = state%temp_ini(1:ncol,:)+scaling(1:ncol,:)*(state%T(1:ncol,:)-state%temp_ini(1:ncol,:))
-      call get_hydrostatic_energy(state%q(1:ncol,1:pver,1:pcnst),.true.,               &
-           state%pdel(1:ncol,1:pver), cp_or_cv(1:ncol,1:pver),                         &
-           state%u(1:ncol,1:pver), state%v(1:ncol,1:pver), temp(1:ncol,1:pver),        &
-           vc_dry_pressure, ptop=state%pintdry(1:ncol,1), phis = state%phis(1:ncol),   &
-           te = state%te_cur(1:ncol,dyn_te_idx), H2O = state%tw_cur(1:ncol))
-    else
-      state%te_cur(1:ncol,dyn_te_idx) = te(1:ncol)
-    end if
-  end subroutine check_energy_chng
-
-
   subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
 
     use physics_buffer, only : physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
new file mode 100644
index 0000000000..2bc48d5327
--- /dev/null
+++ b/src/physics/cam/check_energy_cam.F90
@@ -0,0 +1,211 @@
+! Shim for CCPP-ized check_energy routines in CAM
+module check_energy_cam
+  use shr_kind_mod,    only: r8 => shr_kind_r8
+  use ppgrid,          only: pcols, pver
+  use constituents,    only: pcnst
+  use physics_types,   only: physics_state, physics_tend
+
+  implicit none
+  private
+
+  public :: check_energy_cam_chng      ! check changes in integrals against cumulative boundary fluxes
+  public :: check_energy_cam_timestep_init  ! timestep initialization of energy integrals and cumulative boundary fluxes
+
+contains
+  ! Compute initial values of energy and water integrals,
+  ! zero cumulative tendencies
+  subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
+    use physics_buffer,  only: physics_buffer_desc, pbuf_set_field
+    use cam_abortutils,  only: endrun
+    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
+    use physics_types,   only: phys_te_idx, dyn_te_idx
+    use time_manager,    only: is_first_step
+    use physconst,       only: cpair, rair
+    use air_composition, only: cpairv, cp_or_cv_dycore
+
+    ! To remove, pbuf indices in check_energy
+    use check_energy,    only: teout_idx
+
+    ! CCPP-ized subroutine
+    use check_energy_chng, only: check_energy_chng_timestep_init
+
+    type(physics_state),   intent(inout)    :: state
+    type(physics_tend ),   intent(inout)    :: tend
+    type(physics_buffer_desc), pointer      :: pbuf(:)
+    integer, optional                       :: col_type  ! Flag indicating whether using grid or subcolumns
+
+    real(r8)  :: local_cp_phys(state%psetcols,pver)
+    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
+    integer   :: lchnk     ! chunk identifier
+    integer   :: ncol      ! number of atmospheric columns
+    character(len=512) :: errmsg
+    integer            :: errflg
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    ! The code below is split into not-subcolumns and subcolumns code, as there is different handling of the
+    ! cp passed into the hydrostatic energy call. CAM-SIMA does not support subcolumns, so we keep this special
+    ! handling inside this shim module. (hplin, 9/9/24)
+    if(state%psetcols == pcols) then
+        ! No subcolumns
+        local_cp_phys(:,:) = cpairv(:,:,lchnk)
+        local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
+    else if (state%psetcols > pcols) then
+        ! Subcolumns code
+        ! Subcolumns specific error handling
+        if(.not. all(cpairv(:,:,lchnk) == cpair)) then
+            call endrun('check_energy_timestep_init: cpairv is not allowed to vary when subcolumns are turned on')
+        endif
+
+        local_cp_phys(1:ncol,:) = cpair
+
+        if (vc_dycore == vc_height) then
+            ! MPAS specific hydrostatic energy computation (internal energy)
+            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
+        else if(vc_dycore == vc_dry_pressure) then
+            ! SE specific hydrostatic energy (enthalpy)
+            local_cp_or_cv_dycore(:ncol,:) = cpair
+        else
+            ! cp_or_cv is not used in the underlying subroutine, zero it out to be sure
+            local_cp_or_cv_dycore(:ncol,:) = 0.0_r8
+        endif
+    end if
+
+    ! Call CCPP-ized underlying subroutine.
+    call check_energy_chng_timestep_init( &
+        ncol            = ncol, &
+        pver            = pver, &
+        pcnst           = pcnst, &
+        q               = state%q(1:ncol,1:pver,1:pcnst), &
+        pdel            = state%pdel(1:ncol,1:pver), &
+        u               = state%u(1:ncol,1:pver), &
+        v               = state%v(1:ncol,1:pver), &
+        T               = state%T(1:ncol,1:pver), &
+        pintdry         = state%pintdry(1:ncol,1:pver), &
+        phis            = state%phis(1:ncol), &
+        zm              = state%zm(1:ncol,:), &
+        temp_ini        = state%temp_ini(:ncol,:), &
+        z_ini           = state%z_ini(:ncol,:), &
+        cp_phys         = local_cp_phys(1:ncol,:), &
+        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:), &
+        te_ini_phys     = state%te_ini(1:ncol,phys_te_idx), &
+        te_ini_dyn      = state%te_ini(1:ncol,dyn_te_idx),  &
+        tw_ini          = state%tw_ini(1:ncol),             &
+        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
+        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
+        tw_cur          = state%tw_cur(1:ncol),             &
+        tend_te_tnd     = tend%te_tnd(1:ncol),              &
+        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
+        count           = state%count,                      &
+        vc_physics      = vc_physics, &
+        vc_dycore       = vc_dycore, &
+        errmsg          = errmsg, &
+        errflg          = errflg  &
+    )
+
+    ! initialize physics buffer
+    if (is_first_step()) then
+       call pbuf_set_field(pbuf, teout_idx, state%te_ini(:,dyn_te_idx), col_type=col_type)
+    end if
+
+  end subroutine check_energy_cam_timestep_init
+
+  ! Check that the energy and water change matches the boundary fluxes
+  subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
+       flx_vap, flx_cnd, flx_ice, flx_sen)
+    use cam_thermo,      only: get_hydrostatic_energy
+    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
+    use cam_abortutils,  only: endrun
+    use physics_types,   only: phys_te_idx, dyn_te_idx
+    use physconst,       only: cpair, rair
+    use air_composition, only: cpairv, cp_or_cv_dycore
+
+    ! CCPP-ized subroutine
+    use check_energy_chng, only: check_energy_chng_run
+
+    type(physics_state), intent(inout) :: state
+    type(physics_tend ), intent(inout) :: tend
+    character*(*),intent(in) :: name               ! parameterization name for fluxes
+    integer , intent(in) :: nstep                  ! current timestep number
+    real(r8), intent(in) :: ztodt                  ! 2 delta t (model time increment)
+    real(r8), intent(in) :: flx_vap(:)             ! (pcols) - boundary flux of vapor         (kg/m2/s)
+    real(r8), intent(in) :: flx_cnd(:)             ! (pcols) -boundary flux of liquid+ice    (m/s) (precip?)
+    real(r8), intent(in) :: flx_ice(:)             ! (pcols) -boundary flux of ice           (m/s) (snow?)
+    real(r8), intent(in) :: flx_sen(:)             ! (pcols) -boundary flux of sensible heat (w/m2)
+
+    integer :: lchnk                               ! chunk identifier
+    integer :: ncol                                ! number of atmospheric columns
+    integer :: i                                   ! column index
+    real(r8)  :: local_cp_phys(state%psetcols,pver)
+    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
+    real(r8)  :: scaling_dycore(state%ncol,pver)
+    character(len=512) :: errmsg
+    integer            :: errflg
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    if(state%psetcols == pcols) then
+        ! No subcolumns
+        local_cp_phys(:,:) = cpairv(:,:,lchnk)
+        local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
+
+        scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+    elseif(state%psetcols > pcols) then
+        ! Subcolumns
+        if(.not. all(cpairv(:,:,:) == cpair)) then
+            call endrun('check_energy_chng: cpairv is not allowed to vary when subcolumns are turned on')
+        endif
+
+        local_cp_phys(:,:) = cpair
+
+        ! Note: cp_or_cv set above for pressure coordinate
+        if (vc_dycore == vc_height) then
+            ! compute cv if vertical coordinate is height: cv = cp - R
+            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
+            scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        else if (vc_dycore == vc_dry_pressure) then
+            ! SE specific hydrostatic energy
+            local_cp_or_cv_dycore(:ncol,:) = cpair
+            scaling_dycore(:ncol,:) = 1.0_r8
+        else
+            ! Moist pressure... use phys formula
+            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:,lchnk)
+            scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        end if
+    endif
+
+    ! Call CCPP-ized underlying subroutine.
+    call check_energy_chng_run( &
+        ncol            = ncol, &
+        pver            = pver, &
+        pcnst           = pcnst, &
+        q               = state%q(1:ncol,1:pver,1:pcnst), &
+        pdel            = state%pdel(1:ncol,1:pver), &
+        u               = state%u(1:ncol,1:pver), &
+        v               = state%v(1:ncol,1:pver), &
+        T               = state%T(1:ncol,1:pver), &
+        pintdry         = state%pintdry(1:ncol,1:pver), &
+        phis            = state%phis(1:ncol), &
+        zm              = state%zm(1:ncol,:), &
+        cp_phys         = local_cp_phys(1:ncol,:), &
+        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:),  &
+        scaling_dycore  = scaling_dycore(1:ncol,:),         &
+        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
+        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
+        tw_cur          = state%tw_cur(1:ncol),             &
+        tend_te_tnd     = tend%te_tnd(1:ncol),              &
+        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
+        temp_ini        = state%temp_ini(:ncol,:),          &
+        z_ini           = state%z_ini(:ncol,:),             &
+        count           = state%count,                      &
+        ztodt           = ztodt,                            &
+        vc_physics      = vc_physics, &
+        vc_dycore       = vc_dycore,  &
+        errmsg          = errmsg, &
+        errflg          = errflg  &
+    )
+
+  end subroutine check_energy_cam_chng
+end module check_energy_cam
\ No newline at end of file
diff --git a/src/physics/cam/physpkg.F90 b/src/physics/cam/physpkg.F90
index ba36670ce8..227274355e 100644
--- a/src/physics/cam/physpkg.F90
+++ b/src/physics/cam/physpkg.F90
@@ -2044,7 +2044,8 @@ subroutine tphysbc (ztodt, state,  &
     use convect_deep,    only: convect_deep_tend, convect_deep_tend_2, deep_scheme_does_scav_trans
     use time_manager,    only: is_first_step, get_nstep
     use convect_shallow, only: convect_shallow_tend
-    use check_energy,    only: check_energy_chng, check_energy_fix, check_energy_timestep_init
+    use check_energy_cam,only: check_energy_cam_timestep_init, check_energy_cam_chng
+    use check_energy,    only: check_energy_fix
     use check_energy,    only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
@@ -2630,7 +2631,7 @@ subroutine tphysbc (ztodt, state,  &
              call subcol_gen(state, tend, state_sc, tend_sc, pbuf)
 
              !Initialize check energy for subcolumns
-             call check_energy_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
+             call check_energy_cam_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
           end if
 
           if (trim(cam_take_snapshot_before) == "microp_section") then
diff --git a/src/physics/cam/zm_conv_intr.F90 b/src/physics/cam/zm_conv_intr.F90
index 4113c33a4b..5db6d1bc03 100644
--- a/src/physics/cam/zm_conv_intr.F90
+++ b/src/physics/cam/zm_conv_intr.F90
@@ -393,7 +393,6 @@ subroutine zm_conv_tend(pblh    ,mcon    ,cme     , &
    use time_manager,  only: get_nstep, is_first_step
    use physics_buffer, only : pbuf_get_field, physics_buffer_desc, pbuf_old_tim_idx
    use constituents,  only: pcnst, cnst_get_ind, cnst_is_convtran1
-   use check_energy,  only: check_energy_chng
    use physconst,     only: gravit, latice, latvap, tmelt, cpwv, cpliq, rh2o
 
    use phys_control,  only: cam_physpkg_is
diff --git a/src/physics/cam7/physpkg.F90 b/src/physics/cam7/physpkg.F90
index 83d03c46d1..ad5bc9913e 100644
--- a/src/physics/cam7/physpkg.F90
+++ b/src/physics/cam7/physpkg.F90
@@ -1366,7 +1366,8 @@ subroutine tphysac (ztodt,   cam_in,  &
     use aoa_tracers,        only: aoa_tracers_timestep_tend
     use physconst,          only: rhoh2o
     use aero_model,         only: aero_model_drydep
-    use check_energy,       only: check_energy_chng, tot_energy_phys
+    use check_energy_cam,   only: check_energy_cam_timestep_init, check_energy_cam_chng
+    use check_energy,       only: tot_energy_phys
     use check_energy,       only: check_tracers_data, check_tracers_init, check_tracers_chng
     use time_manager,       only: get_nstep
     use cam_abortutils,     only: endrun
@@ -1405,7 +1406,6 @@ subroutine tphysac (ztodt,   cam_in,  &
     use aero_model,         only: aero_model_wetdep
     use aero_wetdep_cam,    only: wetdep_lq
     use physics_buffer,     only: col_type_subcol
-    use check_energy,       only: check_energy_timestep_init
     use carma_intr,         only: carma_wetdep_tend, carma_timestep_tend, carma_emission_tend
     use carma_flags_mod,    only: carma_do_aerosol, carma_do_emission, carma_do_detrain
     use carma_flags_mod,    only: carma_do_cldice, carma_do_cldliq, carma_do_wetdep
@@ -1775,7 +1775,7 @@ subroutine tphysac (ztodt,   cam_in,  &
              call subcol_gen(state, tend, state_sc, tend_sc, pbuf)
 
              !Initialize check energy for subcolumns
-             call check_energy_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
+             call check_energy_cam_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
           end if
 
           if (trim(cam_take_snapshot_before) == "microp_section") then

From 50afaa6917eb7a40f4f344a8943be30a71c0240f Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 9 Sep 2024 23:56:53 -0400
Subject: [PATCH 13/53] Update physical constants to pass into subroutine

---
 src/physics/cam/check_energy_cam.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
index 2bc48d5327..4f686b598d 100644
--- a/src/physics/cam/check_energy_cam.F90
+++ b/src/physics/cam/check_energy_cam.F90
@@ -118,7 +118,7 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
     use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
     use cam_abortutils,  only: endrun
     use physics_types,   only: phys_te_idx, dyn_te_idx
-    use physconst,       only: cpair, rair
+    use physconst,       only: cpair, rair, latice, latvap
     use air_composition, only: cpairv, cp_or_cv_dycore
 
     ! CCPP-ized subroutine
@@ -201,6 +201,8 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         z_ini           = state%z_ini(:ncol,:),             &
         count           = state%count,                      &
         ztodt           = ztodt,                            &
+        latice          = latice, &
+        latvap          = latvap, &
         vc_physics      = vc_physics, &
         vc_dycore       = vc_dycore,  &
         errmsg          = errmsg, &

From 80d5b86fb3d2018c978642c21902b31af6c56716 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 10 Sep 2024 00:11:10 -0400
Subject: [PATCH 14/53] Build updates; now use check_energy_cam_chng

---
 src/physics/cam/check_energy_cam.F90 |  7 ++++-
 src/physics/cam/physpkg.F90          | 42 ++++++++++++++--------------
 src/physics/cam7/physpkg.F90         | 39 +++++++++++++-------------
 src/physics/simple/physpkg.F90       | 11 ++++----
 src/physics/spcam/crm_physics.F90    |  4 +--
 src/physics/spcam/spcam_drivers.F90  |  7 +++--
 6 files changed, 59 insertions(+), 51 deletions(-)

diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
index 4f686b598d..d5ae76ca48 100644
--- a/src/physics/cam/check_energy_cam.F90
+++ b/src/physics/cam/check_energy_cam.F90
@@ -171,7 +171,7 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
             scaling_dycore(:ncol,:) = 1.0_r8
         else
             ! Moist pressure... use phys formula
-            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:,lchnk)
+            local_cp_or_cv_dycore(:,:) = local_cp_phys(:,:)
             scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
         end if
     endif
@@ -205,6 +205,11 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         latvap          = latvap, &
         vc_physics      = vc_physics, &
         vc_dycore       = vc_dycore,  &
+        name            = name,       &
+        flx_vap         = flx_vap,    &
+        flx_cnd         = flx_cnd,    &
+        flx_ice         = flx_ice,    &
+        flx_sen         = flx_sen,    &
         errmsg          = errmsg, &
         errflg          = errflg  &
     )
diff --git a/src/physics/cam/physpkg.F90 b/src/physics/cam/physpkg.F90
index 227274355e..21e693fa17 100644
--- a/src/physics/cam/physpkg.F90
+++ b/src/physics/cam/physpkg.F90
@@ -1390,7 +1390,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     use aero_model,         only: aero_model_drydep
     use carma_intr,         only: carma_emission_tend, carma_timestep_tend
     use carma_flags_mod,    only: carma_do_aerosol, carma_do_emission
-    use check_energy,       only: check_energy_chng, tot_energy_phys
+    use check_energy,       only: tot_energy_phys
     use check_energy,       only: check_tracers_data, check_tracers_init, check_tracers_chng
     use time_manager,       only: get_nstep
     use cam_abortutils,     only: endrun
@@ -1615,7 +1615,7 @@ subroutine tphysac (ztodt,   cam_in,  &
           call cam_snapshot_all_outfld_tphysac(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf,&
                     fh2o, surfric, obklen, flx_heat)
        end if
-       call check_energy_chng(state, tend, "chem", nstep, ztodt, fh2o, zero, zero, zero)
+       call check_energy_cam_chng(state, tend, "chem", nstep, ztodt, fh2o, zero, zero, zero)
        call check_tracers_chng(state, tracerint, "chem_timestep_tend", nstep, ztodt, &
             cam_in%cflx)
     end if
@@ -1677,9 +1677,9 @@ subroutine tphysac (ztodt,   cam_in,  &
     call t_stopf('rayleigh_friction')
 
     if (do_clubb_sgs) then
-      call check_energy_chng(state, tend, "vdiff", nstep, ztodt, zero, zero, zero, zero)
+      call check_energy_cam_chng(state, tend, "vdiff", nstep, ztodt, zero, zero, zero, zero)
     else
-      call check_energy_chng(state, tend, "vdiff", nstep, ztodt, cam_in%cflx(:,1), zero, &
+      call check_energy_cam_chng(state, tend, "vdiff", nstep, ztodt, cam_in%cflx(:,1), zero, &
            zero, cam_in%shf)
     endif
 
@@ -1719,7 +1719,7 @@ subroutine tphysac (ztodt,   cam_in,  &
      call carma_timestep_tend(state, cam_in, cam_out, ptend, ztodt, pbuf, obklen=obklen, ustar=surfric)
      call physics_update(state, ptend, ztodt, tend)
 
-     call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, zero, zero, zero)
+     call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, zero, zero, zero)
      call t_stopf('carma_timestep_tend')
    end if
 
@@ -1759,7 +1759,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "gwdrag", nstep, ztodt, zero, &
+    call check_energy_cam_chng(state, tend, "gwdrag", nstep, ztodt, zero, &
          zero, zero, flx_heat)
     call t_stopf('gw_tend')
 
@@ -1789,7 +1789,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "qborelax", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "qborelax", nstep, ztodt, zero, zero, zero, zero)
 
     ! Lunar tides
     call lunar_tides_tend( state, ptend )
@@ -1801,7 +1801,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
     call physics_update(state, ptend, ztodt, tend)
     ! Check energy integrals
-    call check_energy_chng(state, tend, "lunar_tides", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "lunar_tides", nstep, ztodt, zero, zero, zero, zero)
 
     ! Ion drag calculation
     call t_startf ( 'iondrag' )
@@ -1851,7 +1851,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     endif
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "iondrag", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "iondrag", nstep, ztodt, zero, zero, zero, zero)
 
     call t_stopf  ( 'iondrag' )
 
@@ -1866,7 +1866,7 @@ subroutine tphysac (ztodt,   cam_in,  &
         call outfld( 'VTEND_NDG', ptend%v, pcols, lchnk)
       end if
       call physics_update(state,ptend,ztodt,tend)
-      call check_energy_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
+      call check_energy_cam_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
     endif
 
     !-------------- Energy budget checks vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
@@ -2257,7 +2257,7 @@ subroutine tphysbc (ztodt, state,  &
     if (.not.dycore_is('EUL')) then
        call check_energy_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
-       call check_energy_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
+       call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
     end if
     call tot_energy_phys(state, 'phBP')
@@ -2385,7 +2385,7 @@ subroutine tphysbc (ztodt, state,  &
     ! Check energy integrals, including "reserved liquid"
     flx_cnd(:ncol) = prec_dp(:ncol) + rliq(:ncol)
     snow_dp(:ncol) = snow_dp(:ncol) + rice(:ncol)
-    call check_energy_chng(state, tend, "convect_deep", nstep, ztodt, zero, flx_cnd, snow_dp, zero)
+    call check_energy_cam_chng(state, tend, "convect_deep", nstep, ztodt, zero, flx_cnd, snow_dp, zero)
     snow_dp(:ncol) = snow_dp(:ncol) - rice(:ncol)
 
     !
@@ -2428,7 +2428,7 @@ subroutine tphysbc (ztodt, state,  &
     end if
 
     flx_cnd(:ncol) = prec_sh(:ncol) + rliq2(:ncol)
-    call check_energy_chng(state, tend, "convect_shallow", nstep, ztodt, zero, flx_cnd, snow_sh, zero)
+    call check_energy_cam_chng(state, tend, "convect_shallow", nstep, ztodt, zero, flx_cnd, snow_sh, zero)
 
     call check_tracers_chng(state, tracerint, "convect_shallow", nstep, ztodt, zero_tracers)
 
@@ -2460,9 +2460,9 @@ subroutine tphysbc (ztodt, state,  &
        ! Before the detrainment, the reserved condensate is all liquid, but if CARMA is doing
        ! detrainment, then the reserved condensate is snow.
        if (carma_do_detrain) then
-          call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str+rliq, snow_str+rliq, zero)
+          call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str+rliq, snow_str+rliq, zero)
        else
-          call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
+          call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
        end if
     end if
 
@@ -2484,7 +2484,7 @@ subroutine tphysbc (ztodt, state,  &
             cam_in%ts,      cam_in%sst,        zdu)
 
        call physics_update(state, ptend, ztodt, tend)
-       call check_energy_chng(state, tend, "cldwat_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
+       call check_energy_cam_chng(state, tend, "cldwat_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
 
        call t_stopf('rk_stratiform_tend')
 
@@ -2556,7 +2556,7 @@ subroutine tphysbc (ztodt, state,  &
                      flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
              end if
 
-             call check_energy_chng(state, tend, "macrop_tend", nstep, ztodt, &
+             call check_energy_cam_chng(state, tend, "macrop_tend", nstep, ztodt, &
                   zero, flx_cnd(:ncol)/cld_macmic_num_steps, &
                   det_ice(:ncol)/cld_macmic_num_steps, &
                   flx_heat(:ncol)/cld_macmic_num_steps)
@@ -2603,7 +2603,7 @@ subroutine tphysbc (ztodt, state,  &
              end if
 
              ! Use actual qflux (not lhf/latvap) for consistency with surface fluxes and revised code
-             call check_energy_chng(state, tend, "clubb_tend", nstep, ztodt, &
+             call check_energy_cam_chng(state, tend, "clubb_tend", nstep, ztodt, &
                 cam_in%cflx(:ncol,1)/cld_macmic_num_steps, &
                 flx_cnd(:ncol)/cld_macmic_num_steps, &
                 det_ice(:ncol)/cld_macmic_num_steps, &
@@ -2704,7 +2704,7 @@ subroutine tphysbc (ztodt, state,  &
                    flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
              end if
 
-             call check_energy_chng(state_sc, tend_sc, "microp_tend_subcol", &
+             call check_energy_cam_chng(state_sc, tend_sc, "microp_tend_subcol", &
                   nstep, ztodt, zero_sc, &
                   prec_str_sc(:state_sc%ncol)/cld_macmic_num_steps, &
                   snow_str_sc(:state_sc%ncol)/cld_macmic_num_steps, zero_sc)
@@ -2736,7 +2736,7 @@ subroutine tphysbc (ztodt, state,  &
                   flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
           end if
 
-          call check_energy_chng(state, tend, "microp_tend", nstep, ztodt, &
+          call check_energy_cam_chng(state, tend, "microp_tend", nstep, ztodt, &
                zero, prec_str(:ncol)/cld_macmic_num_steps, &
                snow_str(:ncol)/cld_macmic_num_steps, zero)
 
@@ -2889,7 +2889,7 @@ subroutine tphysbc (ztodt, state,  &
                   flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, net_flx)
     end if
 
-    call check_energy_chng(state, tend, "radheat", nstep, ztodt, zero, zero, zero, net_flx)
+    call check_energy_cam_chng(state, tend, "radheat", nstep, ztodt, zero, zero, zero, net_flx)
 
     call t_stopf('radiation')
 
diff --git a/src/physics/cam7/physpkg.F90 b/src/physics/cam7/physpkg.F90
index ad5bc9913e..b31a3fcd04 100644
--- a/src/physics/cam7/physpkg.F90
+++ b/src/physics/cam7/physpkg.F90
@@ -1644,7 +1644,7 @@ subroutine tphysac (ztodt,   cam_in,  &
 
     call physics_update(state, ptend, ztodt, tend)
 
-    call check_energy_chng(state, tend, "clubb_emissions_tend", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "clubb_emissions_tend", nstep, ztodt, zero, zero, zero, zero)
 
     call t_stopf('clubb_emissions_tend')
 
@@ -1672,9 +1672,9 @@ subroutine tphysac (ztodt,   cam_in,  &
        ! CARMA is doing
        ! detrainment, then the reserved condensate is snow.
        if (carma_do_detrain) then
-          call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str+rliq, snow_str+rliq, zero)
+          call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str+rliq, snow_str+rliq, zero)
        else
-          call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
+          call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, prec_str, snow_str, zero)
        end if
     end if
 
@@ -1749,7 +1749,7 @@ subroutine tphysac (ztodt,   cam_in,  &
              end if
 
              ! Use actual qflux (not lhf/latvap) for consistency with surface fluxes and revised code
-             call check_energy_chng(state, tend, "clubb_tend", nstep, ztodt, &
+             call check_energy_cam_chng(state, tend, "clubb_tend", nstep, ztodt, &
                 cam_in%cflx(:ncol,1)/cld_macmic_num_steps, &
                 flx_cnd(:ncol)/cld_macmic_num_steps, &
                 det_ice(:ncol)/cld_macmic_num_steps, &
@@ -1848,7 +1848,7 @@ subroutine tphysac (ztodt,   cam_in,  &
                    fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
              end if
 
-             call check_energy_chng(state_sc, tend_sc, "microp_tend_subcol", &
+             call check_energy_cam_chng(state_sc, tend_sc, "microp_tend_subcol", &
                   nstep, ztodt, zero_sc, &
                   prec_str_sc(:state_sc%ncol)/cld_macmic_num_steps, &
                   snow_str_sc(:state_sc%ncol)/cld_macmic_num_steps, zero_sc)
@@ -1880,7 +1880,7 @@ subroutine tphysac (ztodt,   cam_in,  &
                   fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
           end if
 
-          call check_energy_chng(state, tend, "microp_tend", nstep, ztodt, &
+          call check_energy_cam_chng(state, tend, "microp_tend", nstep, ztodt, &
                zero, prec_str(:ncol)/cld_macmic_num_steps, &
                snow_str(:ncol)/cld_macmic_num_steps, zero)
 
@@ -2036,7 +2036,7 @@ subroutine tphysac (ztodt,   cam_in,  &
                   fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
     end if
 
-    call check_energy_chng(state, tend, "radheat", nstep, ztodt, zero, zero, zero, net_flx)
+    call check_energy_cam_chng(state, tend, "radheat", nstep, ztodt, zero, zero, zero, net_flx)
 
     call t_stopf('radiation')
 
@@ -2113,7 +2113,7 @@ subroutine tphysac (ztodt,   cam_in,  &
           call cam_snapshot_all_outfld_tphysac(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf,&
                     fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
        end if
-       call check_energy_chng(state, tend, "chem", nstep, ztodt, fh2o, zero, zero, zero)
+       call check_energy_cam_chng(state, tend, "chem", nstep, ztodt, fh2o, zero, zero, zero)
        call check_tracers_chng(state, tracerint, "chem_timestep_tend", nstep, ztodt, &
             cam_in%cflx)
     end if
@@ -2175,9 +2175,9 @@ subroutine tphysac (ztodt,   cam_in,  &
     call t_stopf('rayleigh_friction')
 
     if (do_clubb_sgs) then
-      call check_energy_chng(state, tend, "vdiff", nstep, ztodt, zero, zero, zero, zero)
+      call check_energy_cam_chng(state, tend, "vdiff", nstep, ztodt, zero, zero, zero, zero)
     else
-      call check_energy_chng(state, tend, "vdiff", nstep, ztodt, cam_in%cflx(:,1), zero, &
+      call check_energy_cam_chng(state, tend, "vdiff", nstep, ztodt, cam_in%cflx(:,1), zero, &
            zero, cam_in%shf)
     endif
 
@@ -2221,7 +2221,7 @@ subroutine tphysac (ztodt,   cam_in,  &
      call carma_timestep_tend(state, cam_in, cam_out, ptend, ztodt, pbuf, obklen=obklen, ustar=surfric)
      call physics_update(state, ptend, ztodt, tend)
 
-     call check_energy_chng(state, tend, "carma_tend", nstep, ztodt, zero, zero, zero, zero)
+     call check_energy_cam_chng(state, tend, "carma_tend", nstep, ztodt, zero, zero, zero, zero)
      call t_stopf('carma_timestep_tend')
    end if
 
@@ -2260,7 +2260,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "gwdrag", nstep, ztodt, zero, &
+    call check_energy_cam_chng(state, tend, "gwdrag", nstep, ztodt, zero, &
          zero, zero, flx_heat)
     call t_stopf('gw_tend')
 
@@ -2290,7 +2290,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "qborelax", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "qborelax", nstep, ztodt, zero, zero, zero, zero)
 
     ! Lunar tides
     call lunar_tides_tend( state, ptend )
@@ -2302,7 +2302,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     end if
     call physics_update(state, ptend, ztodt, tend)
     ! Check energy integrals
-    call check_energy_chng(state, tend, "lunar_tides", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "lunar_tides", nstep, ztodt, zero, zero, zero, zero)
 
     ! Ion drag calculation
     call t_startf ( 'iondrag' )
@@ -2351,7 +2351,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     endif
 
     ! Check energy integrals
-    call check_energy_chng(state, tend, "iondrag", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "iondrag", nstep, ztodt, zero, zero, zero, zero)
 
     call t_stopf  ( 'iondrag' )
 
@@ -2366,7 +2366,7 @@ subroutine tphysac (ztodt,   cam_in,  &
         call outfld( 'VTEND_NDG', ptend%v, pcols, lchnk)
       end if
       call physics_update(state,ptend,ztodt,tend)
-      call check_energy_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
+      call check_energy_cam_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
     endif
 
     !-------------- Energy budget checks vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
@@ -2517,7 +2517,8 @@ subroutine tphysbc (ztodt, state,  &
     use convect_deep,    only: convect_deep_tend
     use time_manager,    only: is_first_step, get_nstep
     use convect_diagnostics,only: convect_diagnostics_calc
-    use check_energy,    only: check_energy_chng, check_energy_fix
+    use check_energy_cam,only: check_energy_cam_chng
+    use check_energy,    only: check_energy_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
@@ -2701,7 +2702,7 @@ subroutine tphysbc (ztodt, state,  &
     if (.not.dycore_is('EUL')) then
        call check_energy_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
-       call check_energy_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
+       call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
     end if
 
@@ -2831,7 +2832,7 @@ subroutine tphysbc (ztodt, state,  &
     ! Check energy integrals, including "reserved liquid"
     flx_cnd(:ncol) = prec_dp(:ncol) + rliq(:ncol)
     snow_dp(:ncol) = snow_dp(:ncol) + rice(:ncol)
-    call check_energy_chng(state, tend, "convect_deep", nstep, ztodt, zero, flx_cnd, snow_dp, zero)
+    call check_energy_cam_chng(state, tend, "convect_deep", nstep, ztodt, zero, flx_cnd, snow_dp, zero)
     snow_dp(:ncol) = snow_dp(:ncol) - rice(:ncol)
 
     !===================================================
diff --git a/src/physics/simple/physpkg.F90 b/src/physics/simple/physpkg.F90
index 8c9c1586ef..22f1171351 100644
--- a/src/physics/simple/physpkg.F90
+++ b/src/physics/simple/physpkg.F90
@@ -503,7 +503,7 @@ subroutine tphysac (ztodt, cam_in, cam_out, state, tend, pbuf)
     use air_composition, only: cpairv, cp_or_cv_dycore
     use time_manager,    only: get_nstep
     use nudging,         only: Nudge_Model, Nudge_ON, nudging_timestep_tend
-    use check_energy,    only: check_energy_chng
+    use check_energy_cam,only: check_energy_cam_chng
 
     ! Arguments
     !
@@ -595,7 +595,7 @@ subroutine tphysac (ztodt, cam_in, cam_out, state, tend, pbuf)
     if (Nudge_Model .and. Nudge_ON) then
       call nudging_timestep_tend(state,ptend)
       call physics_update(state, ptend, ztodt, tend)
-      call check_energy_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
+      call check_energy_cam_chng(state, tend, "nudging", nstep, ztodt, zero, zero, zero, zero)
     endif
 
     call tot_energy_phys(state, 'phAP')
@@ -728,7 +728,8 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     use cam_diagnostics,   only: diag_conv_tend_ini, diag_conv, diag_export
     use cam_history,       only: outfld
     use time_manager,      only: get_nstep
-    use check_energy,      only: check_energy_chng, check_energy_fix, check_energy_timestep_init
+    use check_energy_cam,  only: check_energy_cam_chng
+    use check_energy,      only: check_energy_fix, check_energy_timestep_init
     use check_energy,      only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,      only: tot_energy_phys
     use chemistry,         only: chem_is_active, chem_timestep_tend
@@ -833,7 +834,7 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     if (adiabatic .and. (.not. dycore_is('EUL'))) then
       call check_energy_fix(state, ptend, nstep, flx_heat)
       call physics_update(state, ptend, ztodt, tend)
-      call check_energy_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
+      call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
       call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
     end if
 
@@ -968,7 +969,7 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     ! surface flux is computed and supplied as an argument to
     ! check_energy_chng to account for how the simplified physics forcings are
     ! changing the total exnergy.
-    call check_energy_chng(state, tend, "tphysidl", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "tphysidl", nstep, ztodt, zero, zero, zero, zero)
 
     if (chem_is_active()) then
       call t_startf('simple_chem')
diff --git a/src/physics/spcam/crm_physics.F90 b/src/physics/spcam/crm_physics.F90
index a1d9d2560d..735d6c3630 100644
--- a/src/physics/spcam/crm_physics.F90
+++ b/src/physics/spcam/crm_physics.F90
@@ -750,7 +750,7 @@ subroutine crm_physics_tend(ztodt, state, tend, ptend, pbuf, cam_in)
    use crmx_crm_module,     only: crm
    use crmx_microphysics,   only: nmicro_fields
    use physconst,           only: latvap
-   use check_energy,        only: check_energy_chng
+   use check_energy_cam,    only: check_energy_cam_chng
    use phys_grid,           only: get_rlat_all_p, get_rlon_all_p, get_lon_all_p, get_lat_all_p
    use modal_aero_calcsize, only: modal_aero_calcsize_sub
    use micro_pumas_utils,      only: size_dist_param_liq, mg_liq_props, mincld, qsmall
@@ -2152,7 +2152,7 @@ subroutine crm_physics_tend(ztodt, state, tend, ptend, pbuf, cam_in)
        end if
 
        ! check water and energy conservation
-       call check_energy_chng(state_loc, tend_loc, "crm_tend", nstep, ztodt, zero, &
+       call check_energy_cam_chng(state_loc, tend_loc, "crm_tend", nstep, ztodt, zero, &
                 prec_dp(:ncol)+(qli_hydro(:ncol,2)-qli_hydro(:ncol,1))/ztodt/1000._r8,  &
                 snow_dp(:ncol)+(qi_hydro(:ncol,2)-qi_hydro(:ncol,1))/ztodt/1000._r8, radflux)
 
diff --git a/src/physics/spcam/spcam_drivers.F90 b/src/physics/spcam/spcam_drivers.F90
index ebe6507607..00ab2448bd 100644
--- a/src/physics/spcam/spcam_drivers.F90
+++ b/src/physics/spcam/spcam_drivers.F90
@@ -300,7 +300,8 @@ subroutine tphysbc_spcam (ztodt, state,   &
     use cam_history,     only: outfld
     use constituents,    only: pcnst, qmin, cnst_get_ind
     use time_manager,    only: get_nstep
-    use check_energy,    only: check_energy_chng, check_energy_fix
+    use check_energy_cam,only: check_energy_cam_chng
+    use check_energy,    only: check_energy_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use dycore,          only: dycore_is
     use radiation,       only: radiation_tend
@@ -443,7 +444,7 @@ subroutine tphysbc_spcam (ztodt, state,   &
     if (dycore_is('LR') .or. dycore_is('SE'))  then
        call check_energy_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
-       call check_energy_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
+       call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld('EFIX', flx_heat, pcols,lchnk)
     end if
     ! Save state for convective tendency calculations.
@@ -557,7 +558,7 @@ subroutine tphysbc_spcam (ztodt, state,   &
 
     call physics_update(state, ptend, ztodt, tend)
 
-    call check_energy_chng(state, tend, "spradheat", nstep, ztodt, zero, zero, zero, zero)
+    call check_energy_cam_chng(state, tend, "spradheat", nstep, ztodt, zero, zero, zero, zero)
 
     call t_stopf('radiation')
 

From 03209f0918ce253ea326963a9ee56eab1e2bd89c Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 10 Sep 2024 00:16:43 -0400
Subject: [PATCH 15/53] Add missing USE in physbc

---
 src/physics/cam/physpkg.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/physics/cam/physpkg.F90 b/src/physics/cam/physpkg.F90
index 21e693fa17..bab29327b2 100644
--- a/src/physics/cam/physpkg.F90
+++ b/src/physics/cam/physpkg.F90
@@ -1392,6 +1392,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     use carma_flags_mod,    only: carma_do_aerosol, carma_do_emission
     use check_energy,       only: tot_energy_phys
     use check_energy,       only: check_tracers_data, check_tracers_init, check_tracers_chng
+    use check_energy_cam,   only: check_energy_cam_chng
     use time_manager,       only: get_nstep
     use cam_abortutils,     only: endrun
     use dycore,             only: dycore_is

From 3cc3c3e33cc026cf3148a29a988b59a6d868cf81 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 10 Sep 2024 19:34:41 -0400
Subject: [PATCH 16/53] Fix array oob pcols

---
 src/physics/cam/check_energy_cam.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
index d5ae76ca48..7e1c289b96 100644
--- a/src/physics/cam/check_energy_cam.F90
+++ b/src/physics/cam/check_energy_cam.F90
@@ -49,7 +49,7 @@ subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
     ! handling inside this shim module. (hplin, 9/9/24)
     if(state%psetcols == pcols) then
         ! No subcolumns
-        local_cp_phys(:,:) = cpairv(:,:,lchnk)
+        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
         local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
     else if (state%psetcols > pcols) then
         ! Subcolumns code
@@ -148,10 +148,10 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
 
     if(state%psetcols == pcols) then
         ! No subcolumns
-        local_cp_phys(:,:) = cpairv(:,:,lchnk)
+        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
         local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
 
-        scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
     elseif(state%psetcols > pcols) then
         ! Subcolumns
         if(.not. all(cpairv(:,:,:) == cpair)) then
@@ -164,14 +164,14 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         if (vc_dycore == vc_height) then
             ! compute cv if vertical coordinate is height: cv = cp - R
             local_cp_or_cv_dycore(:ncol,:) = cpair-rair
-            scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
         else if (vc_dycore == vc_dry_pressure) then
             ! SE specific hydrostatic energy
             local_cp_or_cv_dycore(:ncol,:) = cpair
             scaling_dycore(:ncol,:) = 1.0_r8
         else
             ! Moist pressure... use phys formula
-            local_cp_or_cv_dycore(:,:) = local_cp_phys(:,:)
+            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:)
             scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
         end if
     endif

From f7f4139a6f1333eb80375d6adcfb8a34247b22e3 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 7 Oct 2024 10:56:11 -0600
Subject: [PATCH 17/53] Update atmos_phys to check_energy version

---
 .gitmodules                          |   4 +-
 src/atmos_phys                       |   2 +-
 src/physics/cam/cam_diagnostics.F90  |   2 +-
 src/physics/cam/check_energy.F90     | 164 ++-------------------------
 src/physics/cam/check_energy_cam.F90 | 164 ++++++++++++++++++++++++++-
 src/physics/cam/physpkg.F90          |   6 +-
 src/physics/cam7/physpkg.F90         |   7 +-
 src/physics/simple/physpkg.F90       |   8 +-
 src/physics/spcam/spcam_drivers.F90  |   5 +-
 9 files changed, 184 insertions(+), 178 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 224ee10052..e295d8fec1 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -35,8 +35,8 @@
 
 [submodule "atmos_phys"]
 	path = src/atmos_phys
-	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = atmos_phys0_05_001
+	url = https://github.com/jimmielin/atmospheric_physics
+        fxtag = df80b9c1
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index f8ce60bf40..df80b9c1e7 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit f8ce60bf40f800623f8eb3065021ec5dfa9e6b45
+Subproject commit df80b9c1e73064f9a0196282a92b66a2041f6a57
diff --git a/src/physics/cam/cam_diagnostics.F90 b/src/physics/cam/cam_diagnostics.F90
index 97dad2ba01..00d6859a84 100644
--- a/src/physics/cam/cam_diagnostics.F90
+++ b/src/physics/cam/cam_diagnostics.F90
@@ -2019,7 +2019,7 @@ subroutine diag_phys_tend_writeout_dry(state, pbuf,  tend, ztodt)
     !
     !---------------------------------------------------------------
 
-    use check_energy,    only: check_energy_get_integrals
+    use check_energy_cam,only: check_energy_get_integrals
     use physconst,       only: cpair
 
     ! Arguments
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 5e1df3a967..d71f3df8f6 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -24,13 +24,11 @@ module check_energy
   use ppgrid,          only: pcols, pver, begchunk, endchunk
   use spmd_utils,      only: masterproc
 
-  use gmean_mod,       only: gmean
   use physconst,       only: gravit, rga, latvap, latice, cpair, rair
   use air_composition, only: cpairv, cp_or_cv_dycore
-  use physics_types,   only: physics_state, physics_tend, physics_ptend, physics_ptend_init
+  use physics_types,   only: physics_state
   use constituents,    only: cnst_get_ind, pcnst, cnst_name, cnst_get_type_byind
   use cam_logfile,     only: iulog
-  use scamMod,         only: single_column, use_camiop, heat_glob_scm
   use cam_history,     only: outfld, write_camiop
 
   implicit none
@@ -42,10 +40,7 @@ module check_energy
 ! Public methods
   public :: check_energy_readnl    ! read namelist values
   public :: check_energy_register  ! register fields in physics buffer
-  public :: check_energy_get_integrals ! get energy integrals computed in check_energy_gmean
   public :: check_energy_init      ! initialization of module
-  public :: check_energy_gmean     ! global means of physics input and output total energy
-  public :: check_energy_fix       ! add global mean energy difference as a heating
   public :: check_tracers_init      ! initialize tracer integrals and cumulative boundary fluxes
   public :: check_tracers_chng      ! check changes in integrals against cumulative boundary fluxes
 
@@ -55,13 +50,6 @@ module check_energy
 
   logical  :: print_energy_errors = .false.
 
-  real(r8) :: teout_glob           ! global mean energy of output state
-  real(r8) :: teinp_glob           ! global mean energy of input state
-  real(r8) :: tedif_glob           ! global mean energy difference
-  real(r8) :: psurf_glob           ! global mean surface pressure
-  real(r8) :: ptopb_glob           ! global mean top boundary pressure
-  real(r8) :: heat_glob            ! global mean heating rate
-
 ! Physics buffer indices
 
   integer, public  :: teout_idx  = 0       ! teout index in physics buffer
@@ -88,6 +76,9 @@ subroutine check_energy_readnl(nlfile)
    use spmd_utils,      only: mpicom, mstrid=>masterprocid, mpi_logical
    use cam_abortutils,  only: endrun
 
+   ! update the CCPP-ized namelist option
+   use check_energy_chng, only: check_energy_chng_init
+
    character(len=*), intent(in) :: nlfile  ! filepath for file containing namelist input
 
    ! Local variables
@@ -120,6 +111,9 @@ subroutine check_energy_readnl(nlfile)
       write(iulog,*) '  print_energy_errors =', print_energy_errors
    end if
 
+   ! update the CCPP-ized namelist option
+   call check_energy_chng_init(print_energy_errors_in=print_energy_errors)
+
 end subroutine check_energy_readnl
 
 !===============================================================================
@@ -154,28 +148,6 @@ subroutine check_energy_register()
 
   end subroutine check_energy_register
 
-!===============================================================================
-
-subroutine check_energy_get_integrals( tedif_glob_out, heat_glob_out )
-
-!-----------------------------------------------------------------------
-! Purpose: Return energy integrals
-!-----------------------------------------------------------------------
-
-     real(r8), intent(out), optional :: tedif_glob_out
-     real(r8), intent(out), optional :: heat_glob_out
-
-!-----------------------------------------------------------------------
-
-   if ( present(tedif_glob_out) ) then
-      tedif_glob_out = tedif_glob
-   endif
-   if ( present(heat_glob_out) ) then
-      heat_glob_out = heat_glob
-   endif
-
-end subroutine check_energy_get_integrals
-
 !================================================================================================
 
   subroutine check_energy_init()
@@ -214,128 +186,6 @@ subroutine check_energy_init()
 
   end subroutine check_energy_init
 
-!===============================================================================
-
-  subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
-
-    use physics_buffer, only : physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
-    use physics_types,   only: dyn_te_idx
-    use cam_history,     only: write_camiop
-!-----------------------------------------------------------------------
-! Compute global mean total energy of physics input and output states
-! computed consistently with dynamical core vertical coordinate
-! (under hydrostatic assumption)
-!-----------------------------------------------------------------------
-!------------------------------Arguments--------------------------------
-
-    type(physics_state), intent(in   ), dimension(begchunk:endchunk) :: state
-    type(physics_buffer_desc),    pointer    :: pbuf2d(:,:)
-
-    real(r8), intent(in) :: dtime        ! physics time step
-    integer , intent(in) :: nstep        ! current timestep number
-
-!---------------------------Local storage-------------------------------
-    integer :: ncol                      ! number of active columns
-    integer :: lchnk                     ! chunk index
-
-    real(r8) :: te(pcols,begchunk:endchunk,4)
-                                         ! total energy of input/output states (copy)
-    real(r8) :: te_glob(4)               ! global means of total energy
-    real(r8), pointer :: teout(:)
-!-----------------------------------------------------------------------
-
-    ! Copy total energy out of input and output states
-    do lchnk = begchunk, endchunk
-       ncol = state(lchnk)%ncol
-       ! input energy using dynamical core energy formula
-       te(:ncol,lchnk,1) = state(lchnk)%te_ini(:ncol,dyn_te_idx)
-       ! output energy
-       call pbuf_get_field(pbuf_get_chunk(pbuf2d,lchnk),teout_idx, teout)
-
-       te(:ncol,lchnk,2) = teout(1:ncol)
-       ! surface pressure for heating rate
-       te(:ncol,lchnk,3) = state(lchnk)%pint(:ncol,pver+1)
-       ! model top pressure for heating rate (not constant for z-based vertical coordinate!)
-       te(:ncol,lchnk,4) = state(lchnk)%pint(:ncol,1)
-    end do
-
-    ! Compute global means of input and output energies and of
-    ! surface pressure for heating rate (assume uniform ptop)
-    call gmean(te, te_glob, 4)
-
-    if (begchunk .le. endchunk) then
-       teinp_glob = te_glob(1)
-       teout_glob = te_glob(2)
-       psurf_glob = te_glob(3)
-       ptopb_glob = te_glob(4)
-
-       ! Global mean total energy difference
-       tedif_glob =  teinp_glob - teout_glob
-       heat_glob  = -tedif_glob/dtime * gravit / (psurf_glob - ptopb_glob)
-       if (masterproc) then
-          write(iulog,'(1x,a9,1x,i8,5(1x,e25.17))') "nstep, te", nstep, teinp_glob, teout_glob, &
-               heat_glob, psurf_glob, ptopb_glob
-       end if
-    else
-       heat_glob = 0._r8
-    end if  !  (begchunk .le. endchunk)
-
-  end subroutine check_energy_gmean
-
-!===============================================================================
-  subroutine check_energy_fix(state, ptend, nstep, eshflx)
-
-!-----------------------------------------------------------------------
-! Add heating rate required for global mean total energy conservation
-!-----------------------------------------------------------------------
-!------------------------------Arguments--------------------------------
-
-    type(physics_state), intent(in   ) :: state
-    type(physics_ptend), intent(out)   :: ptend
-
-    integer , intent(in   ) :: nstep          ! time step number
-    real(r8), intent(out  ) :: eshflx(pcols)  ! effective sensible heat flux
-
-!---------------------------Local storage-------------------------------
-    integer  :: i                        ! column
-    integer  :: ncol                     ! number of atmospheric columns in chunk
-    integer  :: lchnk                    ! chunk number
-    real(r8) :: heat_out(pcols)
-!-----------------------------------------------------------------------
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    call physics_ptend_init(ptend, state%psetcols, 'chkenergyfix', ls=.true.)
-
-#if ( defined OFFLINE_DYN )
-    ! disable the energy fix for offline driver
-    heat_glob = 0._r8
-#endif
-
-    ! Special handling of energy fix for SCAM - supplied via CAMIOP - zero's for normal IOPs
-    if (single_column) then
-       if ( use_camiop) then
-          heat_glob = heat_glob_scm(1)
-       else
-          heat_glob = 0._r8
-       endif
-    endif
-    ptend%s(:ncol,:pver) = heat_glob
-
-    if (nstep > 0 .and. write_camiop) then
-      heat_out(:ncol) = heat_glob
-      call outfld('heat_glob',  heat_out(:ncol), pcols, lchnk)
-    endif
-
-! compute effective sensible heat flux
-    do i = 1, ncol
-       eshflx(i) = heat_glob * (state%pint(i,pver+1) - state%pint(i,1)) * rga
-    end do
-
-    return
-  end subroutine check_energy_fix
-
-
 !===============================================================================
   subroutine check_tracers_init(state, tracerint)
 
diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
index 7e1c289b96..6931cfb3ee 100644
--- a/src/physics/cam/check_energy_cam.F90
+++ b/src/physics/cam/check_energy_cam.F90
@@ -1,4 +1,4 @@
-! Shim for CCPP-ized check_energy routines in CAM
+! CAM interface for CCPP-ized check_energy routines in CAM
 module check_energy_cam
   use shr_kind_mod,    only: r8 => shr_kind_r8
   use ppgrid,          only: pcols, pver
@@ -8,9 +8,23 @@ module check_energy_cam
   implicit none
   private
 
-  public :: check_energy_cam_chng      ! check changes in integrals against cumulative boundary fluxes
+  public :: check_energy_cam_chng           ! check changes in integrals against cumulative boundary fluxes
   public :: check_energy_cam_timestep_init  ! timestep initialization of energy integrals and cumulative boundary fluxes
 
+  public :: check_energy_cam_fix            ! add heating rate required for global mean total energy conservation
+
+  ! These subroutines cannot be CCPP-ized and replicated from check_energy
+  public :: check_energy_gmean              ! global means of physics input and output total energy
+  public :: check_energy_get_integrals      ! get energy integrals computed in check_energy_gmean
+
+  ! Module variables used for check_energy_gmean
+  real(r8) :: teout_glob   ! global mean energy of output state
+  real(r8) :: teinp_glob   ! global mean energy of input state
+  real(r8) :: tedif_glob   ! global mean energy difference
+  real(r8) :: psurf_glob   ! global mean surface pressure
+  real(r8) :: ptopb_glob   ! global mean top boundary pressure
+  real(r8) :: heat_glob    ! global mean heating rate
+
 contains
   ! Compute initial values of energy and water integrals,
   ! zero cumulative tendencies
@@ -215,4 +229,148 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
     )
 
   end subroutine check_energy_cam_chng
-end module check_energy_cam
\ No newline at end of file
+
+  ! Add heating rate required for global mean total energy conservation
+  subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
+    use physics_types,    only: physics_ptend, physics_ptend_init
+    use physconst,        only: rga
+
+    ! SCAM support
+    use scamMod,          only: single_column, use_camiop, heat_glob_scm
+
+    ! CCPP-ized subroutine
+    use check_energy_fix, only: check_energy_fix_run
+
+    type(physics_state), intent(in)    :: state
+    type(physics_ptend), intent(out)   :: ptend
+
+    integer , intent(in)  :: nstep          ! time step number
+    real(r8), intent(out) :: eshflx(pcols)  ! effective sensible heat flux
+
+    integer     :: ncol                     ! number of atmospheric columns in chunk
+    integer     :: lchnk                    ! chunk number
+    real(r8)    :: heat_out(pcols)
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    call physics_ptend_init(ptend, state%psetcols, 'chkenergyfix', ls=.true.)
+
+#if ( defined OFFLINE_DYN )
+    ! disable the energy fix for offline driver
+    heat_glob = 0._r8
+#endif
+
+    ! Special handling of energy fix for SCAM - supplied via CAMIOP - zero's for normal IOPs
+    if (single_column) then
+       if (use_camiop) then
+          heat_glob = heat_glob_scm(1)
+       else
+          heat_glob = 0._r8
+       endif
+    endif
+
+    if (nstep > 0 .and. write_camiop) then
+      heat_out(:ncol) = heat_glob
+      call outfld('heat_glob',  heat_out(:ncol), pcols, lchnk)
+    endif
+
+    ! Call the CCPP-ized subroutine (for non-SCAM)
+    ! to compute the effective sensible heat flux and save to ptend%s
+    call check_energy_fix_run( &
+        ncol      = ncol, &
+        pver      = pver, &
+        pint      = state%pint(:ncol,:), &
+        rga       = rga, &
+        heat_glob = heat_glob. &
+        ptend_s   = ptend%s(:ncol,:), &
+        eshflx    = eshflx(:ncol) &
+    )
+
+  end subroutine check_energy_cam_fix
+
+  ! Compute global mean total energy of physics input and output states
+  ! computed consistently with dynamical core vertical coordinate
+  ! (under hydrostatic assumption)
+  !
+  ! This subroutine cannot use the CCPP-ized equivalent because
+  ! it is dependent on chunks.
+  subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
+    use physics_buffer,  only: physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
+    use physics_types,   only: dyn_te_idx
+    use cam_history,     only: write_camiop
+    use ppgrid,          only: begchunk, endchunk
+    use spmd_utils,      only: masterproc
+    use cam_logfile,     only: iulog
+    use gmean_mod,       only: gmean
+    use physconst,       only: gravit
+
+    ! To remove, pbuf indices in check_energy
+    use check_energy,    only: teout_idx
+
+    type(physics_state), intent(in), dimension(begchunk:endchunk) :: state
+    type(physics_buffer_desc), pointer                            :: pbuf2d(:,:)
+
+    real(r8), intent(in) :: dtime        ! physics time step
+    integer , intent(in) :: nstep        ! current timestep number
+
+    integer :: ncol                      ! number of active columns
+    integer :: lchnk                     ! chunk index
+
+    real(r8) :: te(pcols,begchunk:endchunk,4)
+                                         ! total energy of input/output states (copy)
+    real(r8) :: te_glob(4)               ! global means of total energy
+    real(r8), pointer :: teout(:)
+
+    ! Copy total energy out of input and output states
+    do lchnk = begchunk, endchunk
+       ncol = state(lchnk)%ncol
+       ! input energy using dynamical core energy formula
+       te(:ncol,lchnk,1) = state(lchnk)%te_ini(:ncol,dyn_te_idx)
+       ! output energy
+       call pbuf_get_field(pbuf_get_chunk(pbuf2d,lchnk),teout_idx, teout)
+
+       te(:ncol,lchnk,2) = teout(1:ncol)
+       ! surface pressure for heating rate
+       te(:ncol,lchnk,3) = state(lchnk)%pint(:ncol,pver+1)
+       ! model top pressure for heating rate (not constant for z-based vertical coordinate!)
+       te(:ncol,lchnk,4) = state(lchnk)%pint(:ncol,1)
+    end do
+
+    ! Compute global means of input and output energies and of
+    ! surface pressure for heating rate (assume uniform ptop)
+    call gmean(te, te_glob, 4)
+
+    if (begchunk .le. endchunk) then
+       teinp_glob = te_glob(1)
+       teout_glob = te_glob(2)
+       psurf_glob = te_glob(3)
+       ptopb_glob = te_glob(4)
+
+       ! Global mean total energy difference
+       tedif_glob =  teinp_glob - teout_glob
+       heat_glob  = -tedif_glob/dtime * gravit / (psurf_glob - ptopb_glob)
+       if (masterproc) then
+          write(iulog,'(1x,a9,1x,i8,5(1x,e25.17))') "nstep, te", nstep, teinp_glob, teout_glob, &
+               heat_glob, psurf_glob, ptopb_glob
+       end if
+    else
+       heat_glob = 0._r8
+    end if  !  (begchunk .le. endchunk)
+
+  end subroutine check_energy_gmean
+
+  ! Return energy integrals (module variables)
+  subroutine check_energy_get_integrals(tedif_glob_out, heat_glob_out)
+     real(r8), intent(out), optional :: tedif_glob_out
+     real(r8), intent(out), optional :: heat_glob_out
+
+   if ( present(tedif_glob_out) ) then
+      tedif_glob_out = tedif_glob
+   endif
+
+   if ( present(heat_glob_out) ) then
+      heat_glob_out = heat_glob
+   endif
+  end subroutine check_energy_get_integrals
+end module check_energy_cam
diff --git a/src/physics/cam/physpkg.F90 b/src/physics/cam/physpkg.F90
index bab29327b2..25f46c3a45 100644
--- a/src/physics/cam/physpkg.F90
+++ b/src/physics/cam/physpkg.F90
@@ -1065,7 +1065,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,   only: get_nstep
     use cam_diagnostics,only: diag_allocate, diag_physvar_ic
-    use check_energy,   only: check_energy_gmean
+    use check_energy_cam, only: check_energy_gmean
     use phys_control,   only: phys_getopts
     use spcam_drivers,  only: tphysbc_spcam
     use spmd_utils,     only: mpicom
@@ -2046,7 +2046,7 @@ subroutine tphysbc (ztodt, state,  &
     use time_manager,    only: is_first_step, get_nstep
     use convect_shallow, only: convect_shallow_tend
     use check_energy_cam,only: check_energy_cam_timestep_init, check_energy_cam_chng
-    use check_energy,    only: check_energy_fix
+    use check_energy_cam,only: check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
@@ -2256,7 +2256,7 @@ subroutine tphysbc (ztodt, state,  &
     call tot_energy_phys(state, 'phBF')
     call tot_energy_phys(state, 'dyBF',vc=vc_dycore)
     if (.not.dycore_is('EUL')) then
-       call check_energy_fix(state, ptend, nstep, flx_heat)
+       call check_energy_cam_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
        call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
diff --git a/src/physics/cam7/physpkg.F90 b/src/physics/cam7/physpkg.F90
index b31a3fcd04..1ce28d3a93 100644
--- a/src/physics/cam7/physpkg.F90
+++ b/src/physics/cam7/physpkg.F90
@@ -1056,7 +1056,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,   only: get_nstep
     use cam_diagnostics,only: diag_allocate, diag_physvar_ic
-    use check_energy,   only: check_energy_gmean
+    use check_energy_cam, only: check_energy_gmean
     use spmd_utils,     only: mpicom
     use physics_buffer, only: physics_buffer_desc, pbuf_get_chunk, pbuf_allocate
     use cam_history,    only: outfld, write_camiop
@@ -2517,8 +2517,7 @@ subroutine tphysbc (ztodt, state,  &
     use convect_deep,    only: convect_deep_tend
     use time_manager,    only: is_first_step, get_nstep
     use convect_diagnostics,only: convect_diagnostics_calc
-    use check_energy_cam,only: check_energy_cam_chng
-    use check_energy,    only: check_energy_fix
+    use check_energy_cam,only: check_energy_cam_chng, check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
@@ -2700,7 +2699,7 @@ subroutine tphysbc (ztodt, state,  &
     call tot_energy_phys(state, 'dyBF',vc=vc_dycore)
 
     if (.not.dycore_is('EUL')) then
-       call check_energy_fix(state, ptend, nstep, flx_heat)
+       call check_energy_cam_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
        call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
diff --git a/src/physics/simple/physpkg.F90 b/src/physics/simple/physpkg.F90
index 22f1171351..3e594d9073 100644
--- a/src/physics/simple/physpkg.F90
+++ b/src/physics/simple/physpkg.F90
@@ -305,7 +305,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,    only: get_nstep
     use cam_diagnostics, only: diag_allocate, diag_physvar_ic
-    use check_energy,    only: check_energy_gmean
+    use check_energy_cam, only: check_energy_gmean
 
     use physics_buffer,  only: physics_buffer_desc, pbuf_get_chunk, pbuf_allocate
     !
@@ -728,8 +728,8 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     use cam_diagnostics,   only: diag_conv_tend_ini, diag_conv, diag_export
     use cam_history,       only: outfld
     use time_manager,      only: get_nstep
-    use check_energy_cam,  only: check_energy_cam_chng
-    use check_energy,      only: check_energy_fix, check_energy_timestep_init
+    use check_energy_cam,  only: check_energy_cam_chng, check_energy_cam_fix
+    use check_energy,      only: check_energy_timestep_init
     use check_energy,      only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,      only: tot_energy_phys
     use chemistry,         only: chem_is_active, chem_timestep_tend
@@ -832,7 +832,7 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     call t_startf('energy_fixer')
 
     if (adiabatic .and. (.not. dycore_is('EUL'))) then
-      call check_energy_fix(state, ptend, nstep, flx_heat)
+      call check_energy_cam_fix(state, ptend, nstep, flx_heat)
       call physics_update(state, ptend, ztodt, tend)
       call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
       call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
diff --git a/src/physics/spcam/spcam_drivers.F90 b/src/physics/spcam/spcam_drivers.F90
index 00ab2448bd..cd7d3f6370 100644
--- a/src/physics/spcam/spcam_drivers.F90
+++ b/src/physics/spcam/spcam_drivers.F90
@@ -300,8 +300,7 @@ subroutine tphysbc_spcam (ztodt, state,   &
     use cam_history,     only: outfld
     use constituents,    only: pcnst, qmin, cnst_get_ind
     use time_manager,    only: get_nstep
-    use check_energy_cam,only: check_energy_cam_chng
-    use check_energy,    only: check_energy_fix
+    use check_energy_cam,only: check_energy_cam_chng, check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use dycore,          only: dycore_is
     use radiation,       only: radiation_tend
@@ -442,7 +441,7 @@ subroutine tphysbc_spcam (ztodt, state,   &
     call t_startf('energy_fixer')
 
     if (dycore_is('LR') .or. dycore_is('SE'))  then
-       call check_energy_fix(state, ptend, nstep, flx_heat)
+       call check_energy_cam_fix(state, ptend, nstep, flx_heat)
        call physics_update(state, ptend, ztodt, tend)
        call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld('EFIX', flx_heat, pcols,lchnk)

From f6f464bb6b73aa52c2850cdb4595ab4148774fc4 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Thu, 10 Oct 2024 16:26:34 -0600
Subject: [PATCH 18/53] Fix build errors -- does not include bld/configure
 atmos_phys path updates

---
 src/physics/cam/check_energy.F90     |  2 +-
 src/physics/cam/check_energy_cam.F90 | 12 ++++++++----
 src/physics/simple/physpkg.F90       |  2 +-
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index d71f3df8f6..9f9faa10fe 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -29,7 +29,7 @@ module check_energy
   use physics_types,   only: physics_state
   use constituents,    only: cnst_get_ind, pcnst, cnst_name, cnst_get_type_byind
   use cam_logfile,     only: iulog
-  use cam_history,     only: outfld, write_camiop
+  use cam_history,     only: outfld
 
   implicit none
   private
diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
index 6931cfb3ee..e1f143c0c2 100644
--- a/src/physics/cam/check_energy_cam.F90
+++ b/src/physics/cam/check_energy_cam.F90
@@ -50,6 +50,7 @@ subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
 
     real(r8)  :: local_cp_phys(state%psetcols,pver)
     real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
+    real(r8)  :: teout(state%ncol) ! dummy teout argument
     integer   :: lchnk     ! chunk identifier
     integer   :: ncol      ! number of atmospheric columns
     character(len=512) :: errmsg
@@ -91,6 +92,7 @@ subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
         ncol            = ncol, &
         pver            = pver, &
         pcnst           = pcnst, &
+        is_first_timestep = is_first_step(), &
         q               = state%q(1:ncol,1:pver,1:pcnst), &
         pdel            = state%pdel(1:ncol,1:pver), &
         u               = state%u(1:ncol,1:pver), &
@@ -99,8 +101,6 @@ subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
         pintdry         = state%pintdry(1:ncol,1:pver), &
         phis            = state%phis(1:ncol), &
         zm              = state%zm(1:ncol,:), &
-        temp_ini        = state%temp_ini(:ncol,:), &
-        z_ini           = state%z_ini(:ncol,:), &
         cp_phys         = local_cp_phys(1:ncol,:), &
         cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:), &
         te_ini_phys     = state%te_ini(1:ncol,phys_te_idx), &
@@ -111,7 +111,10 @@ subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
         tw_cur          = state%tw_cur(1:ncol),             &
         tend_te_tnd     = tend%te_tnd(1:ncol),              &
         tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
+        temp_ini        = state%temp_ini(:ncol,:), &
+        z_ini           = state%z_ini(:ncol,:), &
         count           = state%count,                      &
+        teout           = teout(1:ncol),                    & ! dummy argument - actual teout written to pbuf directly below
         vc_physics      = vc_physics, &
         vc_dycore       = vc_dycore, &
         errmsg          = errmsg, &
@@ -237,6 +240,8 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
 
     ! SCAM support
     use scamMod,          only: single_column, use_camiop, heat_glob_scm
+    use cam_history,      only: write_camiop
+    use cam_history,      only: outfld
 
     ! CCPP-ized subroutine
     use check_energy_fix, only: check_energy_fix_run
@@ -282,7 +287,7 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
         pver      = pver, &
         pint      = state%pint(:ncol,:), &
         rga       = rga, &
-        heat_glob = heat_glob. &
+        heat_glob = heat_glob, &
         ptend_s   = ptend%s(:ncol,:), &
         eshflx    = eshflx(:ncol) &
     )
@@ -298,7 +303,6 @@ end subroutine check_energy_cam_fix
   subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
     use physics_buffer,  only: physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
     use physics_types,   only: dyn_te_idx
-    use cam_history,     only: write_camiop
     use ppgrid,          only: begchunk, endchunk
     use spmd_utils,      only: masterproc
     use cam_logfile,     only: iulog
diff --git a/src/physics/simple/physpkg.F90 b/src/physics/simple/physpkg.F90
index 3e594d9073..eaea0ff1dd 100644
--- a/src/physics/simple/physpkg.F90
+++ b/src/physics/simple/physpkg.F90
@@ -729,7 +729,7 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     use cam_history,       only: outfld
     use time_manager,      only: get_nstep
     use check_energy_cam,  only: check_energy_cam_chng, check_energy_cam_fix
-    use check_energy,      only: check_energy_timestep_init
+    use check_energy_cam,  only: check_energy_cam_timestep_init
     use check_energy,      only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,      only: tot_energy_phys
     use chemistry,         only: chem_is_active, chem_timestep_tend

From 2ffa522d8403f73aba0f306a2c35dd50319c33a5 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 14 Oct 2024 12:16:26 -0400
Subject: [PATCH 19/53] Move back to check_energy.F90 for FV3 external
 compatibility

---
 src/dynamics/eul/dp_coupling.F90     |   4 +-
 src/dynamics/fv/dp_coupling.F90      |   4 +-
 src/dynamics/mpas/dp_coupling.F90    |   4 +-
 src/dynamics/se/dp_coupling.F90      |   4 +-
 src/physics/cam/cam_diagnostics.F90  |   2 +-
 src/physics/cam/check_energy.F90     | 390 ++++++++++++++++++++++++++-
 src/physics/cam/check_energy_cam.F90 | 380 --------------------------
 src/physics/cam/physpkg.F90          |  12 +-
 src/physics/cam7/physpkg.F90         |   8 +-
 src/physics/simple/physpkg.F90       |   8 +-
 src/physics/spcam/crm_physics.F90    |   2 +-
 src/physics/spcam/spcam_drivers.F90  |   2 +-
 12 files changed, 403 insertions(+), 417 deletions(-)
 delete mode 100644 src/physics/cam/check_energy_cam.F90

diff --git a/src/dynamics/eul/dp_coupling.F90 b/src/dynamics/eul/dp_coupling.F90
index 8e3eb64a21..bc900e2d0e 100644
--- a/src/dynamics/eul/dp_coupling.F90
+++ b/src/dynamics/eul/dp_coupling.F90
@@ -14,7 +14,7 @@ module dp_coupling
    use physconst,         only: cpair, gravit, rair, zvir
    use air_composition,   only: rairv
    use geopotential,      only: geopotential_t
-   use check_energy_cam,  only: check_energy_cam_timestep_init
+   use check_energy,      only: check_energy_timestep_init
 #if (defined SPMD)
    use spmd_dyn,          only: buf1, buf1win, buf2, buf2win, &
                                 spmdbuf_siz, local_dp_map, &
@@ -291,7 +291,7 @@ subroutine d_p_coupling(ps, t3, u3, v3, q3, &
 
 ! Compute energy and water integrals of input state
        pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-       call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk )
+       call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk )
 
     end do
 
diff --git a/src/dynamics/fv/dp_coupling.F90 b/src/dynamics/fv/dp_coupling.F90
index af2d13b12e..fc02821471 100644
--- a/src/dynamics/fv/dp_coupling.F90
+++ b/src/dynamics/fv/dp_coupling.F90
@@ -12,7 +12,7 @@ module dp_coupling
    use physconst,         only: gravit, zvir
    use air_composition,   only: cpairv, rairv
    use geopotential,      only: geopotential_t
-   use check_energy_cam,  only: check_energy_cam_timestep_init
+   use check_energy,      only: check_energy_timestep_init
    use dynamics_vars,     only: T_FVDYCORE_GRID, t_fvdycore_state
    use dyn_internal_state,only: get_dyn_state
    use dyn_comp,          only: dyn_import_t, dyn_export_t, fv_print_dpcoup_warn
@@ -621,7 +621,7 @@ subroutine d_p_coupling(grid, phys_state, phys_tend,  pbuf2d, dyn_out)
 ! Compute energy and water integrals of input state
 
        pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-       call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+       call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
     end do
     call t_stopf('derived_fields')
diff --git a/src/dynamics/mpas/dp_coupling.F90 b/src/dynamics/mpas/dp_coupling.F90
index c312f1e2f9..10d75b4b8c 100644
--- a/src/dynamics/mpas/dp_coupling.F90
+++ b/src/dynamics/mpas/dp_coupling.F90
@@ -413,7 +413,7 @@ subroutine derived_phys(phys_state, phys_tend, pbuf2d)
    ! MPAS prognostic fields.
 
    use geopotential,    only: geopotential_t
-   use check_energy_cam,  only: check_energy_cam_timestep_init
+   use check_energy,    only: check_energy_timestep_init
    use shr_vmath_mod,   only: shr_vmath_log
    use phys_control,    only: waccmx_is
    use cam_thermo,      only: cam_thermo_dry_air_update, cam_thermo_water_update
@@ -564,7 +564,7 @@ subroutine derived_phys(phys_state, phys_tend, pbuf2d)
 
       ! Compute energy and water integrals of input state
       pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-      call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+      call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
    end do
 
diff --git a/src/dynamics/se/dp_coupling.F90 b/src/dynamics/se/dp_coupling.F90
index 9de31132a2..919b7f3510 100644
--- a/src/dynamics/se/dp_coupling.F90
+++ b/src/dynamics/se/dp_coupling.F90
@@ -546,7 +546,7 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
    use phys_control,    only: waccmx_is
    use geopotential,    only: geopotential_t
    use static_energy,   only: update_dry_static_energy_run
-   use check_energy_cam,only: check_energy_cam_timestep_init
+   use check_energy,    only: check_energy_timestep_init
    use hycoef,          only: hyai, ps0
    use shr_vmath_mod,   only: shr_vmath_log
    use qneg_module,     only: qneg3
@@ -707,7 +707,7 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
                                         cpairv(1:ncol,:,lchnk), errflg, errmsg)
       ! Compute energy and water integrals of input state
       pbuf_chnk => pbuf_get_chunk(pbuf2d, lchnk)
-      call check_energy_cam_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
+      call check_energy_timestep_init(phys_state(lchnk), phys_tend(lchnk), pbuf_chnk)
 
 
    end do  ! lchnk
diff --git a/src/physics/cam/cam_diagnostics.F90 b/src/physics/cam/cam_diagnostics.F90
index 00d6859a84..97dad2ba01 100644
--- a/src/physics/cam/cam_diagnostics.F90
+++ b/src/physics/cam/cam_diagnostics.F90
@@ -2019,7 +2019,7 @@ subroutine diag_phys_tend_writeout_dry(state, pbuf,  tend, ztodt)
     !
     !---------------------------------------------------------------
 
-    use check_energy_cam,only: check_energy_get_integrals
+    use check_energy,    only: check_energy_get_integrals
     use physconst,       only: cpair
 
     ! Arguments
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 9f9faa10fe..f318cb51e1 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -21,37 +21,52 @@ module check_energy
 !---------------------------------------------------------------------------------
 
   use shr_kind_mod,    only: r8 => shr_kind_r8
-  use ppgrid,          only: pcols, pver, begchunk, endchunk
+  use ppgrid,          only: pcols, pver
   use spmd_utils,      only: masterproc
 
-  use physconst,       only: gravit, rga, latvap, latice, cpair, rair
+  use physconst,       only: rga
   use air_composition, only: cpairv, cp_or_cv_dycore
   use physics_types,   only: physics_state
   use constituents,    only: cnst_get_ind, pcnst, cnst_name, cnst_get_type_byind
   use cam_logfile,     only: iulog
-  use cam_history,     only: outfld
 
   implicit none
   private
 
-! Public types:
+  ! Public types:
   public check_tracers_data
 
-! Public methods
-  public :: check_energy_readnl    ! read namelist values
-  public :: check_energy_register  ! register fields in physics buffer
-  public :: check_energy_init      ! initialization of module
-  public :: check_tracers_init      ! initialize tracer integrals and cumulative boundary fluxes
-  public :: check_tracers_chng      ! check changes in integrals against cumulative boundary fluxes
+  ! Public methods - not CCPP-ized
+  public :: check_tracers_init              ! initialize tracer integrals and cumulative boundary fluxes
+  public :: check_tracers_chng              ! check changes in integrals against cumulative boundary fluxes
+  public :: tot_energy_phys                 ! calculate and output total energy and axial angular momentum diagnostics
 
-  public :: tot_energy_phys ! calculate and output total energy and axial angular momentum diagnostics
+  ! These subroutines cannot be CCPP-ized
+  public :: check_energy_readnl             ! read namelist values
+  public :: check_energy_register           ! register fields in physics buffer
+  public :: check_energy_init               ! initialization of module
+  public :: check_energy_gmean              ! global means of physics input and output total energy
+  public :: check_energy_get_integrals      ! get energy integrals computed in check_energy_gmean
 
-! Private module data
+  ! Public methods - CAM interfaces to CCPP version:
+  public :: check_energy_cam_chng           ! check changes in integrals against cumulative boundary fluxes
+  public :: check_energy_timestep_init      ! timestep initialization of energy integrals and cumulative boundary fluxes
+                                            ! name is retained for FV3 compatibility
 
+  public :: check_energy_cam_fix            ! add heating rate required for global mean total energy conservation
+
+  ! Private module data
   logical  :: print_energy_errors = .false.
 
-! Physics buffer indices
+  ! used for check_energy_gmean
+  real(r8) :: teout_glob   ! global mean energy of output state
+  real(r8) :: teinp_glob   ! global mean energy of input state
+  real(r8) :: tedif_glob   ! global mean energy difference
+  real(r8) :: psurf_glob   ! global mean surface pressure
+  real(r8) :: ptopb_glob   ! global mean top boundary pressure
+  real(r8) :: heat_glob    ! global mean heating rate
 
+  ! Physics buffer indices
   integer, public  :: teout_idx  = 0       ! teout index in physics buffer
   integer, public  :: dtcore_idx = 0       ! dtcore index in physics buffer
   integer, public  :: dqcore_idx = 0       ! dqcore index in physics buffer
@@ -542,5 +557,354 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
 
   end subroutine tot_energy_phys
 
+  ! Compute global mean total energy of physics input and output states
+  ! computed consistently with dynamical core vertical coordinate
+  ! (under hydrostatic assumption)
+  !
+  ! This subroutine cannot use the CCPP-ized equivalent because
+  ! it is dependent on chunks.
+  subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
+    use physics_buffer,  only: physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
+    use physics_types,   only: dyn_te_idx
+    use ppgrid,          only: begchunk, endchunk
+    use spmd_utils,      only: masterproc
+    use cam_logfile,     only: iulog
+    use gmean_mod,       only: gmean
+    use physconst,       only: gravit
+
+    type(physics_state), intent(in), dimension(begchunk:endchunk) :: state
+    type(physics_buffer_desc), pointer                            :: pbuf2d(:,:)
+
+    real(r8), intent(in) :: dtime        ! physics time step
+    integer , intent(in) :: nstep        ! current timestep number
+
+    integer :: ncol                      ! number of active columns
+    integer :: lchnk                     ! chunk index
+
+    real(r8) :: te(pcols,begchunk:endchunk,4)
+                                         ! total energy of input/output states (copy)
+    real(r8) :: te_glob(4)               ! global means of total energy
+    real(r8), pointer :: teout(:)
+
+    ! Copy total energy out of input and output states
+    do lchnk = begchunk, endchunk
+       ncol = state(lchnk)%ncol
+       ! input energy using dynamical core energy formula
+       te(:ncol,lchnk,1) = state(lchnk)%te_ini(:ncol,dyn_te_idx)
+       ! output energy
+       call pbuf_get_field(pbuf_get_chunk(pbuf2d,lchnk),teout_idx, teout)
+
+       te(:ncol,lchnk,2) = teout(1:ncol)
+       ! surface pressure for heating rate
+       te(:ncol,lchnk,3) = state(lchnk)%pint(:ncol,pver+1)
+       ! model top pressure for heating rate (not constant for z-based vertical coordinate!)
+       te(:ncol,lchnk,4) = state(lchnk)%pint(:ncol,1)
+    end do
+
+    ! Compute global means of input and output energies and of
+    ! surface pressure for heating rate (assume uniform ptop)
+    call gmean(te, te_glob, 4)
+
+    if (begchunk .le. endchunk) then
+       teinp_glob = te_glob(1)
+       teout_glob = te_glob(2)
+       psurf_glob = te_glob(3)
+       ptopb_glob = te_glob(4)
+
+       ! Global mean total energy difference
+       tedif_glob =  teinp_glob - teout_glob
+       heat_glob  = -tedif_glob/dtime * gravit / (psurf_glob - ptopb_glob)
+       if (masterproc) then
+          write(iulog,'(1x,a9,1x,i8,5(1x,e25.17))') "nstep, te", nstep, teinp_glob, teout_glob, &
+               heat_glob, psurf_glob, ptopb_glob
+       end if
+    else
+       heat_glob = 0._r8
+    end if  !  (begchunk .le. endchunk)
+
+  end subroutine check_energy_gmean
+
+  ! Return energy integrals (module variables)
+  subroutine check_energy_get_integrals(tedif_glob_out, heat_glob_out)
+     real(r8), intent(out), optional :: tedif_glob_out
+     real(r8), intent(out), optional :: heat_glob_out
+
+   if ( present(tedif_glob_out) ) then
+      tedif_glob_out = tedif_glob
+   endif
+
+   if ( present(heat_glob_out) ) then
+      heat_glob_out = heat_glob
+   endif
+  end subroutine check_energy_get_integrals
+
+  ! Compute initial values of energy and water integrals,
+  ! zero cumulative tendencies
+  subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
+    use physics_buffer,  only: physics_buffer_desc, pbuf_set_field
+    use cam_abortutils,  only: endrun
+    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
+    use physics_types,   only: physics_tend
+    use physics_types,   only: phys_te_idx, dyn_te_idx
+    use time_manager,    only: is_first_step
+    use physconst,       only: cpair, rair
+    use air_composition, only: cpairv, cp_or_cv_dycore
+
+    ! CCPP-ized subroutine
+    use check_energy_chng, only: check_energy_chng_timestep_init
+
+    type(physics_state),   intent(inout)    :: state
+    type(physics_tend ),   intent(inout)    :: tend
+    type(physics_buffer_desc), pointer      :: pbuf(:)
+    integer, optional                       :: col_type  ! Flag indicating whether using grid or subcolumns
+
+    real(r8)  :: local_cp_phys(state%psetcols,pver)
+    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
+    real(r8)  :: teout(state%ncol) ! dummy teout argument
+    integer   :: lchnk     ! chunk identifier
+    integer   :: ncol      ! number of atmospheric columns
+    character(len=512) :: errmsg
+    integer            :: errflg
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    ! The code below is split into not-subcolumns and subcolumns code, as there is different handling of the
+    ! cp passed into the hydrostatic energy call. CAM-SIMA does not support subcolumns, so we keep this special
+    ! handling inside this shim module. (hplin, 9/9/24)
+    if(state%psetcols == pcols) then
+        ! No subcolumns
+        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
+        local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
+    else if (state%psetcols > pcols) then
+        ! Subcolumns code
+        ! Subcolumns specific error handling
+        if(.not. all(cpairv(:,:,lchnk) == cpair)) then
+            call endrun('check_energy_timestep_init: cpairv is not allowed to vary when subcolumns are turned on')
+        endif
+
+        local_cp_phys(1:ncol,:) = cpair
+
+        if (vc_dycore == vc_height) then
+            ! MPAS specific hydrostatic energy computation (internal energy)
+            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
+        else if(vc_dycore == vc_dry_pressure) then
+            ! SE specific hydrostatic energy (enthalpy)
+            local_cp_or_cv_dycore(:ncol,:) = cpair
+        else
+            ! cp_or_cv is not used in the underlying subroutine, zero it out to be sure
+            local_cp_or_cv_dycore(:ncol,:) = 0.0_r8
+        endif
+    end if
+
+    ! Call CCPP-ized underlying subroutine.
+    call check_energy_chng_timestep_init( &
+        ncol            = ncol, &
+        pver            = pver, &
+        pcnst           = pcnst, &
+        is_first_timestep = is_first_step(), &
+        q               = state%q(1:ncol,1:pver,1:pcnst), &
+        pdel            = state%pdel(1:ncol,1:pver), &
+        u               = state%u(1:ncol,1:pver), &
+        v               = state%v(1:ncol,1:pver), &
+        T               = state%T(1:ncol,1:pver), &
+        pintdry         = state%pintdry(1:ncol,1:pver), &
+        phis            = state%phis(1:ncol), &
+        zm              = state%zm(1:ncol,:), &
+        cp_phys         = local_cp_phys(1:ncol,:), &
+        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:), &
+        te_ini_phys     = state%te_ini(1:ncol,phys_te_idx), &
+        te_ini_dyn      = state%te_ini(1:ncol,dyn_te_idx),  &
+        tw_ini          = state%tw_ini(1:ncol),             &
+        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
+        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
+        tw_cur          = state%tw_cur(1:ncol),             &
+        tend_te_tnd     = tend%te_tnd(1:ncol),              &
+        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
+        temp_ini        = state%temp_ini(:ncol,:), &
+        z_ini           = state%z_ini(:ncol,:), &
+        count           = state%count,                      &
+        teout           = teout(1:ncol),                    & ! dummy argument - actual teout written to pbuf directly below
+        vc_physics      = vc_physics, &
+        vc_dycore       = vc_dycore, &
+        errmsg          = errmsg, &
+        errflg          = errflg  &
+    )
+
+    ! initialize physics buffer
+    if (is_first_step()) then
+       call pbuf_set_field(pbuf, teout_idx, state%te_ini(:,dyn_te_idx), col_type=col_type)
+    end if
+
+  end subroutine check_energy_timestep_init
+
+  ! Check that the energy and water change matches the boundary fluxes
+  subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
+       flx_vap, flx_cnd, flx_ice, flx_sen)
+    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
+    use cam_abortutils,  only: endrun
+    use physics_types,   only: phys_te_idx, dyn_te_idx
+    use physics_types,   only: physics_tend
+    use physconst,       only: cpair, rair, latice, latvap
+    use air_composition, only: cpairv, cp_or_cv_dycore
+
+    ! CCPP-ized subroutine
+    use check_energy_chng, only: check_energy_chng_run
+
+    type(physics_state), intent(inout) :: state
+    type(physics_tend ), intent(inout) :: tend
+    character*(*),intent(in) :: name               ! parameterization name for fluxes
+    integer , intent(in) :: nstep                  ! current timestep number
+    real(r8), intent(in) :: ztodt                  ! 2 delta t (model time increment)
+    real(r8), intent(in) :: flx_vap(:)             ! (pcols) - boundary flux of vapor         (kg/m2/s)
+    real(r8), intent(in) :: flx_cnd(:)             ! (pcols) -boundary flux of liquid+ice    (m/s) (precip?)
+    real(r8), intent(in) :: flx_ice(:)             ! (pcols) -boundary flux of ice           (m/s) (snow?)
+    real(r8), intent(in) :: flx_sen(:)             ! (pcols) -boundary flux of sensible heat (w/m2)
 
+    integer :: lchnk                               ! chunk identifier
+    integer :: ncol                                ! number of atmospheric columns
+    real(r8)  :: local_cp_phys(state%psetcols,pver)
+    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
+    real(r8)  :: scaling_dycore(state%ncol,pver)
+    character(len=512) :: errmsg
+    integer            :: errflg
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    if(state%psetcols == pcols) then
+        ! No subcolumns
+        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
+
+        ! Only if vertical coordinate is vc_height or vc_dry_pressure, cp_or_cv_dycore
+        ! is nonzero.
+        if(vc_dycore == vc_height .or. vc_dycore == vc_dry_pressure) then
+            local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
+
+            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        endif
+    elseif(state%psetcols > pcols) then
+        ! Subcolumns
+        if(.not. all(cpairv(:,:,:) == cpair)) then
+            call endrun('check_energy_chng: cpairv is not allowed to vary when subcolumns are turned on')
+        endif
+
+        local_cp_phys(:,:) = cpair
+
+        ! Note: cp_or_cv set above for pressure coordinate
+        if (vc_dycore == vc_height) then
+            ! compute cv if vertical coordinate is height: cv = cp - R
+            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
+            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        else if (vc_dycore == vc_dry_pressure) then
+            ! SE specific hydrostatic energy
+            local_cp_or_cv_dycore(:ncol,:) = cpair
+            scaling_dycore(:ncol,:) = 1.0_r8
+        else
+            ! Moist pressure... use phys formula
+            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:)
+            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+        end if
+    endif
+
+    ! Call CCPP-ized underlying subroutine.
+    call check_energy_chng_run( &
+        ncol            = ncol, &
+        pver            = pver, &
+        pcnst           = pcnst, &
+        q               = state%q(1:ncol,1:pver,1:pcnst), &
+        pdel            = state%pdel(1:ncol,1:pver), &
+        u               = state%u(1:ncol,1:pver), &
+        v               = state%v(1:ncol,1:pver), &
+        T               = state%T(1:ncol,1:pver), &
+        pintdry         = state%pintdry(1:ncol,1:pver), &
+        phis            = state%phis(1:ncol), &
+        zm              = state%zm(1:ncol,:), &
+        cp_phys         = local_cp_phys(1:ncol,:), &
+        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:),  &
+        scaling_dycore  = scaling_dycore(1:ncol,:),         &
+        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
+        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
+        tw_cur          = state%tw_cur(1:ncol),             &
+        tend_te_tnd     = tend%te_tnd(1:ncol),              &
+        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
+        temp_ini        = state%temp_ini(:ncol,:),          &
+        z_ini           = state%z_ini(:ncol,:),             &
+        count           = state%count,                      &
+        ztodt           = ztodt,                            &
+        latice          = latice, &
+        latvap          = latvap, &
+        vc_physics      = vc_physics, &
+        vc_dycore       = vc_dycore,  &
+        name            = name,       &
+        flx_vap         = flx_vap,    &
+        flx_cnd         = flx_cnd,    &
+        flx_ice         = flx_ice,    &
+        flx_sen         = flx_sen,    &
+        errmsg          = errmsg, &
+        errflg          = errflg  &
+    )
+
+  end subroutine check_energy_cam_chng
+
+  ! Add heating rate required for global mean total energy conservation
+  subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
+    use physics_types,    only: physics_ptend, physics_ptend_init
+    use physconst,        only: rga
+
+    ! SCAM support
+    use scamMod,          only: single_column, use_camiop, heat_glob_scm
+    use cam_history,      only: write_camiop
+    use cam_history,      only: outfld
+
+    ! CCPP-ized subroutine
+    use check_energy_fix, only: check_energy_fix_run
+
+    type(physics_state), intent(in)    :: state
+    type(physics_ptend), intent(out)   :: ptend
+
+    integer , intent(in)  :: nstep          ! time step number
+    real(r8), intent(out) :: eshflx(pcols)  ! effective sensible heat flux
+
+    integer     :: ncol                     ! number of atmospheric columns in chunk
+    integer     :: lchnk                    ! chunk number
+    real(r8)    :: heat_out(pcols)
+
+    lchnk = state%lchnk
+    ncol  = state%ncol
+
+    call physics_ptend_init(ptend, state%psetcols, 'chkenergyfix', ls=.true.)
+
+#if ( defined OFFLINE_DYN )
+    ! disable the energy fix for offline driver
+    heat_glob = 0._r8
+#endif
+
+    ! Special handling of energy fix for SCAM - supplied via CAMIOP - zero's for normal IOPs
+    if (single_column) then
+       if (use_camiop) then
+          heat_glob = heat_glob_scm(1)
+       else
+          heat_glob = 0._r8
+       endif
+    endif
+
+    if (nstep > 0 .and. write_camiop) then
+      heat_out(:ncol) = heat_glob
+      call outfld('heat_glob',  heat_out(:ncol), pcols, lchnk)
+    endif
+
+    ! Call the CCPP-ized subroutine (for non-SCAM)
+    ! to compute the effective sensible heat flux and save to ptend%s
+    call check_energy_fix_run( &
+        ncol      = ncol, &
+        pver      = pver, &
+        pint      = state%pint(:ncol,:), &
+        rga       = rga, &
+        heat_glob = heat_glob, &
+        ptend_s   = ptend%s(:ncol,:), &
+        eshflx    = eshflx(:ncol) &
+    )
+
+  end subroutine check_energy_cam_fix
 end module check_energy
diff --git a/src/physics/cam/check_energy_cam.F90 b/src/physics/cam/check_energy_cam.F90
deleted file mode 100644
index e1f143c0c2..0000000000
--- a/src/physics/cam/check_energy_cam.F90
+++ /dev/null
@@ -1,380 +0,0 @@
-! CAM interface for CCPP-ized check_energy routines in CAM
-module check_energy_cam
-  use shr_kind_mod,    only: r8 => shr_kind_r8
-  use ppgrid,          only: pcols, pver
-  use constituents,    only: pcnst
-  use physics_types,   only: physics_state, physics_tend
-
-  implicit none
-  private
-
-  public :: check_energy_cam_chng           ! check changes in integrals against cumulative boundary fluxes
-  public :: check_energy_cam_timestep_init  ! timestep initialization of energy integrals and cumulative boundary fluxes
-
-  public :: check_energy_cam_fix            ! add heating rate required for global mean total energy conservation
-
-  ! These subroutines cannot be CCPP-ized and replicated from check_energy
-  public :: check_energy_gmean              ! global means of physics input and output total energy
-  public :: check_energy_get_integrals      ! get energy integrals computed in check_energy_gmean
-
-  ! Module variables used for check_energy_gmean
-  real(r8) :: teout_glob   ! global mean energy of output state
-  real(r8) :: teinp_glob   ! global mean energy of input state
-  real(r8) :: tedif_glob   ! global mean energy difference
-  real(r8) :: psurf_glob   ! global mean surface pressure
-  real(r8) :: ptopb_glob   ! global mean top boundary pressure
-  real(r8) :: heat_glob    ! global mean heating rate
-
-contains
-  ! Compute initial values of energy and water integrals,
-  ! zero cumulative tendencies
-  subroutine check_energy_cam_timestep_init(state, tend, pbuf, col_type)
-    use physics_buffer,  only: physics_buffer_desc, pbuf_set_field
-    use cam_abortutils,  only: endrun
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
-    use physics_types,   only: phys_te_idx, dyn_te_idx
-    use time_manager,    only: is_first_step
-    use physconst,       only: cpair, rair
-    use air_composition, only: cpairv, cp_or_cv_dycore
-
-    ! To remove, pbuf indices in check_energy
-    use check_energy,    only: teout_idx
-
-    ! CCPP-ized subroutine
-    use check_energy_chng, only: check_energy_chng_timestep_init
-
-    type(physics_state),   intent(inout)    :: state
-    type(physics_tend ),   intent(inout)    :: tend
-    type(physics_buffer_desc), pointer      :: pbuf(:)
-    integer, optional                       :: col_type  ! Flag indicating whether using grid or subcolumns
-
-    real(r8)  :: local_cp_phys(state%psetcols,pver)
-    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
-    real(r8)  :: teout(state%ncol) ! dummy teout argument
-    integer   :: lchnk     ! chunk identifier
-    integer   :: ncol      ! number of atmospheric columns
-    character(len=512) :: errmsg
-    integer            :: errflg
-
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    ! The code below is split into not-subcolumns and subcolumns code, as there is different handling of the
-    ! cp passed into the hydrostatic energy call. CAM-SIMA does not support subcolumns, so we keep this special
-    ! handling inside this shim module. (hplin, 9/9/24)
-    if(state%psetcols == pcols) then
-        ! No subcolumns
-        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
-        local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-    else if (state%psetcols > pcols) then
-        ! Subcolumns code
-        ! Subcolumns specific error handling
-        if(.not. all(cpairv(:,:,lchnk) == cpair)) then
-            call endrun('check_energy_timestep_init: cpairv is not allowed to vary when subcolumns are turned on')
-        endif
-
-        local_cp_phys(1:ncol,:) = cpair
-
-        if (vc_dycore == vc_height) then
-            ! MPAS specific hydrostatic energy computation (internal energy)
-            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
-        else if(vc_dycore == vc_dry_pressure) then
-            ! SE specific hydrostatic energy (enthalpy)
-            local_cp_or_cv_dycore(:ncol,:) = cpair
-        else
-            ! cp_or_cv is not used in the underlying subroutine, zero it out to be sure
-            local_cp_or_cv_dycore(:ncol,:) = 0.0_r8
-        endif
-    end if
-
-    ! Call CCPP-ized underlying subroutine.
-    call check_energy_chng_timestep_init( &
-        ncol            = ncol, &
-        pver            = pver, &
-        pcnst           = pcnst, &
-        is_first_timestep = is_first_step(), &
-        q               = state%q(1:ncol,1:pver,1:pcnst), &
-        pdel            = state%pdel(1:ncol,1:pver), &
-        u               = state%u(1:ncol,1:pver), &
-        v               = state%v(1:ncol,1:pver), &
-        T               = state%T(1:ncol,1:pver), &
-        pintdry         = state%pintdry(1:ncol,1:pver), &
-        phis            = state%phis(1:ncol), &
-        zm              = state%zm(1:ncol,:), &
-        cp_phys         = local_cp_phys(1:ncol,:), &
-        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:), &
-        te_ini_phys     = state%te_ini(1:ncol,phys_te_idx), &
-        te_ini_dyn      = state%te_ini(1:ncol,dyn_te_idx),  &
-        tw_ini          = state%tw_ini(1:ncol),             &
-        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
-        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
-        tw_cur          = state%tw_cur(1:ncol),             &
-        tend_te_tnd     = tend%te_tnd(1:ncol),              &
-        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
-        temp_ini        = state%temp_ini(:ncol,:), &
-        z_ini           = state%z_ini(:ncol,:), &
-        count           = state%count,                      &
-        teout           = teout(1:ncol),                    & ! dummy argument - actual teout written to pbuf directly below
-        vc_physics      = vc_physics, &
-        vc_dycore       = vc_dycore, &
-        errmsg          = errmsg, &
-        errflg          = errflg  &
-    )
-
-    ! initialize physics buffer
-    if (is_first_step()) then
-       call pbuf_set_field(pbuf, teout_idx, state%te_ini(:,dyn_te_idx), col_type=col_type)
-    end if
-
-  end subroutine check_energy_cam_timestep_init
-
-  ! Check that the energy and water change matches the boundary fluxes
-  subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
-       flx_vap, flx_cnd, flx_ice, flx_sen)
-    use cam_thermo,      only: get_hydrostatic_energy
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
-    use cam_abortutils,  only: endrun
-    use physics_types,   only: phys_te_idx, dyn_te_idx
-    use physconst,       only: cpair, rair, latice, latvap
-    use air_composition, only: cpairv, cp_or_cv_dycore
-
-    ! CCPP-ized subroutine
-    use check_energy_chng, only: check_energy_chng_run
-
-    type(physics_state), intent(inout) :: state
-    type(physics_tend ), intent(inout) :: tend
-    character*(*),intent(in) :: name               ! parameterization name for fluxes
-    integer , intent(in) :: nstep                  ! current timestep number
-    real(r8), intent(in) :: ztodt                  ! 2 delta t (model time increment)
-    real(r8), intent(in) :: flx_vap(:)             ! (pcols) - boundary flux of vapor         (kg/m2/s)
-    real(r8), intent(in) :: flx_cnd(:)             ! (pcols) -boundary flux of liquid+ice    (m/s) (precip?)
-    real(r8), intent(in) :: flx_ice(:)             ! (pcols) -boundary flux of ice           (m/s) (snow?)
-    real(r8), intent(in) :: flx_sen(:)             ! (pcols) -boundary flux of sensible heat (w/m2)
-
-    integer :: lchnk                               ! chunk identifier
-    integer :: ncol                                ! number of atmospheric columns
-    integer :: i                                   ! column index
-    real(r8)  :: local_cp_phys(state%psetcols,pver)
-    real(r8)  :: local_cp_or_cv_dycore(state%psetcols,pver)
-    real(r8)  :: scaling_dycore(state%ncol,pver)
-    character(len=512) :: errmsg
-    integer            :: errflg
-
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    if(state%psetcols == pcols) then
-        ! No subcolumns
-        local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
-        local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
-
-        scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
-    elseif(state%psetcols > pcols) then
-        ! Subcolumns
-        if(.not. all(cpairv(:,:,:) == cpair)) then
-            call endrun('check_energy_chng: cpairv is not allowed to vary when subcolumns are turned on')
-        endif
-
-        local_cp_phys(:,:) = cpair
-
-        ! Note: cp_or_cv set above for pressure coordinate
-        if (vc_dycore == vc_height) then
-            ! compute cv if vertical coordinate is height: cv = cp - R
-            local_cp_or_cv_dycore(:ncol,:) = cpair-rair
-            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
-        else if (vc_dycore == vc_dry_pressure) then
-            ! SE specific hydrostatic energy
-            local_cp_or_cv_dycore(:ncol,:) = cpair
-            scaling_dycore(:ncol,:) = 1.0_r8
-        else
-            ! Moist pressure... use phys formula
-            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:)
-            scaling_dycore(:ncol,:)  = cpairv(:,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
-        end if
-    endif
-
-    ! Call CCPP-ized underlying subroutine.
-    call check_energy_chng_run( &
-        ncol            = ncol, &
-        pver            = pver, &
-        pcnst           = pcnst, &
-        q               = state%q(1:ncol,1:pver,1:pcnst), &
-        pdel            = state%pdel(1:ncol,1:pver), &
-        u               = state%u(1:ncol,1:pver), &
-        v               = state%v(1:ncol,1:pver), &
-        T               = state%T(1:ncol,1:pver), &
-        pintdry         = state%pintdry(1:ncol,1:pver), &
-        phis            = state%phis(1:ncol), &
-        zm              = state%zm(1:ncol,:), &
-        cp_phys         = local_cp_phys(1:ncol,:), &
-        cp_or_cv_dycore = local_cp_or_cv_dycore(1:ncol,:),  &
-        scaling_dycore  = scaling_dycore(1:ncol,:),         &
-        te_cur_phys     = state%te_cur(1:ncol,phys_te_idx), &
-        te_cur_dyn      = state%te_cur(1:ncol,dyn_te_idx),  &
-        tw_cur          = state%tw_cur(1:ncol),             &
-        tend_te_tnd     = tend%te_tnd(1:ncol),              &
-        tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
-        temp_ini        = state%temp_ini(:ncol,:),          &
-        z_ini           = state%z_ini(:ncol,:),             &
-        count           = state%count,                      &
-        ztodt           = ztodt,                            &
-        latice          = latice, &
-        latvap          = latvap, &
-        vc_physics      = vc_physics, &
-        vc_dycore       = vc_dycore,  &
-        name            = name,       &
-        flx_vap         = flx_vap,    &
-        flx_cnd         = flx_cnd,    &
-        flx_ice         = flx_ice,    &
-        flx_sen         = flx_sen,    &
-        errmsg          = errmsg, &
-        errflg          = errflg  &
-    )
-
-  end subroutine check_energy_cam_chng
-
-  ! Add heating rate required for global mean total energy conservation
-  subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
-    use physics_types,    only: physics_ptend, physics_ptend_init
-    use physconst,        only: rga
-
-    ! SCAM support
-    use scamMod,          only: single_column, use_camiop, heat_glob_scm
-    use cam_history,      only: write_camiop
-    use cam_history,      only: outfld
-
-    ! CCPP-ized subroutine
-    use check_energy_fix, only: check_energy_fix_run
-
-    type(physics_state), intent(in)    :: state
-    type(physics_ptend), intent(out)   :: ptend
-
-    integer , intent(in)  :: nstep          ! time step number
-    real(r8), intent(out) :: eshflx(pcols)  ! effective sensible heat flux
-
-    integer     :: ncol                     ! number of atmospheric columns in chunk
-    integer     :: lchnk                    ! chunk number
-    real(r8)    :: heat_out(pcols)
-
-    lchnk = state%lchnk
-    ncol  = state%ncol
-
-    call physics_ptend_init(ptend, state%psetcols, 'chkenergyfix', ls=.true.)
-
-#if ( defined OFFLINE_DYN )
-    ! disable the energy fix for offline driver
-    heat_glob = 0._r8
-#endif
-
-    ! Special handling of energy fix for SCAM - supplied via CAMIOP - zero's for normal IOPs
-    if (single_column) then
-       if (use_camiop) then
-          heat_glob = heat_glob_scm(1)
-       else
-          heat_glob = 0._r8
-       endif
-    endif
-
-    if (nstep > 0 .and. write_camiop) then
-      heat_out(:ncol) = heat_glob
-      call outfld('heat_glob',  heat_out(:ncol), pcols, lchnk)
-    endif
-
-    ! Call the CCPP-ized subroutine (for non-SCAM)
-    ! to compute the effective sensible heat flux and save to ptend%s
-    call check_energy_fix_run( &
-        ncol      = ncol, &
-        pver      = pver, &
-        pint      = state%pint(:ncol,:), &
-        rga       = rga, &
-        heat_glob = heat_glob, &
-        ptend_s   = ptend%s(:ncol,:), &
-        eshflx    = eshflx(:ncol) &
-    )
-
-  end subroutine check_energy_cam_fix
-
-  ! Compute global mean total energy of physics input and output states
-  ! computed consistently with dynamical core vertical coordinate
-  ! (under hydrostatic assumption)
-  !
-  ! This subroutine cannot use the CCPP-ized equivalent because
-  ! it is dependent on chunks.
-  subroutine check_energy_gmean(state, pbuf2d, dtime, nstep)
-    use physics_buffer,  only: physics_buffer_desc, pbuf_get_field, pbuf_get_chunk
-    use physics_types,   only: dyn_te_idx
-    use ppgrid,          only: begchunk, endchunk
-    use spmd_utils,      only: masterproc
-    use cam_logfile,     only: iulog
-    use gmean_mod,       only: gmean
-    use physconst,       only: gravit
-
-    ! To remove, pbuf indices in check_energy
-    use check_energy,    only: teout_idx
-
-    type(physics_state), intent(in), dimension(begchunk:endchunk) :: state
-    type(physics_buffer_desc), pointer                            :: pbuf2d(:,:)
-
-    real(r8), intent(in) :: dtime        ! physics time step
-    integer , intent(in) :: nstep        ! current timestep number
-
-    integer :: ncol                      ! number of active columns
-    integer :: lchnk                     ! chunk index
-
-    real(r8) :: te(pcols,begchunk:endchunk,4)
-                                         ! total energy of input/output states (copy)
-    real(r8) :: te_glob(4)               ! global means of total energy
-    real(r8), pointer :: teout(:)
-
-    ! Copy total energy out of input and output states
-    do lchnk = begchunk, endchunk
-       ncol = state(lchnk)%ncol
-       ! input energy using dynamical core energy formula
-       te(:ncol,lchnk,1) = state(lchnk)%te_ini(:ncol,dyn_te_idx)
-       ! output energy
-       call pbuf_get_field(pbuf_get_chunk(pbuf2d,lchnk),teout_idx, teout)
-
-       te(:ncol,lchnk,2) = teout(1:ncol)
-       ! surface pressure for heating rate
-       te(:ncol,lchnk,3) = state(lchnk)%pint(:ncol,pver+1)
-       ! model top pressure for heating rate (not constant for z-based vertical coordinate!)
-       te(:ncol,lchnk,4) = state(lchnk)%pint(:ncol,1)
-    end do
-
-    ! Compute global means of input and output energies and of
-    ! surface pressure for heating rate (assume uniform ptop)
-    call gmean(te, te_glob, 4)
-
-    if (begchunk .le. endchunk) then
-       teinp_glob = te_glob(1)
-       teout_glob = te_glob(2)
-       psurf_glob = te_glob(3)
-       ptopb_glob = te_glob(4)
-
-       ! Global mean total energy difference
-       tedif_glob =  teinp_glob - teout_glob
-       heat_glob  = -tedif_glob/dtime * gravit / (psurf_glob - ptopb_glob)
-       if (masterproc) then
-          write(iulog,'(1x,a9,1x,i8,5(1x,e25.17))') "nstep, te", nstep, teinp_glob, teout_glob, &
-               heat_glob, psurf_glob, ptopb_glob
-       end if
-    else
-       heat_glob = 0._r8
-    end if  !  (begchunk .le. endchunk)
-
-  end subroutine check_energy_gmean
-
-  ! Return energy integrals (module variables)
-  subroutine check_energy_get_integrals(tedif_glob_out, heat_glob_out)
-     real(r8), intent(out), optional :: tedif_glob_out
-     real(r8), intent(out), optional :: heat_glob_out
-
-   if ( present(tedif_glob_out) ) then
-      tedif_glob_out = tedif_glob
-   endif
-
-   if ( present(heat_glob_out) ) then
-      heat_glob_out = heat_glob
-   endif
-  end subroutine check_energy_get_integrals
-end module check_energy_cam
diff --git a/src/physics/cam/physpkg.F90 b/src/physics/cam/physpkg.F90
index 25f46c3a45..1d431b2dbb 100644
--- a/src/physics/cam/physpkg.F90
+++ b/src/physics/cam/physpkg.F90
@@ -1065,7 +1065,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,   only: get_nstep
     use cam_diagnostics,only: diag_allocate, diag_physvar_ic
-    use check_energy_cam, only: check_energy_gmean
+    use check_energy,   only: check_energy_gmean
     use phys_control,   only: phys_getopts
     use spcam_drivers,  only: tphysbc_spcam
     use spmd_utils,     only: mpicom
@@ -1392,7 +1392,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     use carma_flags_mod,    only: carma_do_aerosol, carma_do_emission
     use check_energy,       only: tot_energy_phys
     use check_energy,       only: check_tracers_data, check_tracers_init, check_tracers_chng
-    use check_energy_cam,   only: check_energy_cam_chng
+    use check_energy,       only: check_energy_cam_chng
     use time_manager,       only: get_nstep
     use cam_abortutils,     only: endrun
     use dycore,             only: dycore_is
@@ -2045,8 +2045,8 @@ subroutine tphysbc (ztodt, state,  &
     use convect_deep,    only: convect_deep_tend, convect_deep_tend_2, deep_scheme_does_scav_trans
     use time_manager,    only: is_first_step, get_nstep
     use convect_shallow, only: convect_shallow_tend
-    use check_energy_cam,only: check_energy_cam_timestep_init, check_energy_cam_chng
-    use check_energy_cam,only: check_energy_cam_fix
+    use check_energy,    only: check_energy_timestep_init, check_energy_cam_chng
+    use check_energy,    only: check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
@@ -2257,7 +2257,9 @@ subroutine tphysbc (ztodt, state,  &
     call tot_energy_phys(state, 'dyBF',vc=vc_dycore)
     if (.not.dycore_is('EUL')) then
        call check_energy_cam_fix(state, ptend, nstep, flx_heat)
+
        call physics_update(state, ptend, ztodt, tend)
+
        call check_energy_cam_chng(state, tend, "chkengyfix", nstep, ztodt, zero, zero, zero, flx_heat)
        call outfld( 'EFIX', flx_heat    , pcols, lchnk   )
     end if
@@ -2632,7 +2634,7 @@ subroutine tphysbc (ztodt, state,  &
              call subcol_gen(state, tend, state_sc, tend_sc, pbuf)
 
              !Initialize check energy for subcolumns
-             call check_energy_cam_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
+             call check_energy_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
           end if
 
           if (trim(cam_take_snapshot_before) == "microp_section") then
diff --git a/src/physics/cam7/physpkg.F90 b/src/physics/cam7/physpkg.F90
index 1ce28d3a93..ead4935939 100644
--- a/src/physics/cam7/physpkg.F90
+++ b/src/physics/cam7/physpkg.F90
@@ -1056,7 +1056,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,   only: get_nstep
     use cam_diagnostics,only: diag_allocate, diag_physvar_ic
-    use check_energy_cam, only: check_energy_gmean
+    use check_energy,   only: check_energy_gmean
     use spmd_utils,     only: mpicom
     use physics_buffer, only: physics_buffer_desc, pbuf_get_chunk, pbuf_allocate
     use cam_history,    only: outfld, write_camiop
@@ -1366,7 +1366,7 @@ subroutine tphysac (ztodt,   cam_in,  &
     use aoa_tracers,        only: aoa_tracers_timestep_tend
     use physconst,          only: rhoh2o
     use aero_model,         only: aero_model_drydep
-    use check_energy_cam,   only: check_energy_cam_timestep_init, check_energy_cam_chng
+    use check_energy,       only: check_energy_timestep_init, check_energy_cam_chng
     use check_energy,       only: tot_energy_phys
     use check_energy,       only: check_tracers_data, check_tracers_init, check_tracers_chng
     use time_manager,       only: get_nstep
@@ -1775,7 +1775,7 @@ subroutine tphysac (ztodt,   cam_in,  &
              call subcol_gen(state, tend, state_sc, tend_sc, pbuf)
 
              !Initialize check energy for subcolumns
-             call check_energy_cam_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
+             call check_energy_timestep_init(state_sc, tend_sc, pbuf, col_type_subcol)
           end if
 
           if (trim(cam_take_snapshot_before) == "microp_section") then
@@ -2517,7 +2517,7 @@ subroutine tphysbc (ztodt, state,  &
     use convect_deep,    only: convect_deep_tend
     use time_manager,    only: is_first_step, get_nstep
     use convect_diagnostics,only: convect_diagnostics_calc
-    use check_energy_cam,only: check_energy_cam_chng, check_energy_cam_fix
+    use check_energy,    only: check_energy_cam_chng, check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use check_energy,    only: tot_energy_phys
     use dycore,          only: dycore_is
diff --git a/src/physics/simple/physpkg.F90 b/src/physics/simple/physpkg.F90
index eaea0ff1dd..c236f7f021 100644
--- a/src/physics/simple/physpkg.F90
+++ b/src/physics/simple/physpkg.F90
@@ -305,7 +305,7 @@ subroutine phys_run1(phys_state, ztodt, phys_tend, pbuf2d,  cam_in, cam_out)
     !-----------------------------------------------------------------------
     use time_manager,    only: get_nstep
     use cam_diagnostics, only: diag_allocate, diag_physvar_ic
-    use check_energy_cam, only: check_energy_gmean
+    use check_energy,    only: check_energy_gmean
 
     use physics_buffer,  only: physics_buffer_desc, pbuf_get_chunk, pbuf_allocate
     !
@@ -503,7 +503,7 @@ subroutine tphysac (ztodt, cam_in, cam_out, state, tend, pbuf)
     use air_composition, only: cpairv, cp_or_cv_dycore
     use time_manager,    only: get_nstep
     use nudging,         only: Nudge_Model, Nudge_ON, nudging_timestep_tend
-    use check_energy_cam,only: check_energy_cam_chng
+    use check_energy,    only: check_energy_cam_chng
 
     ! Arguments
     !
@@ -728,8 +728,8 @@ subroutine tphysbc (ztodt, state, tend, pbuf, cam_out, cam_in )
     use cam_diagnostics,   only: diag_conv_tend_ini, diag_conv, diag_export
     use cam_history,       only: outfld
     use time_manager,      only: get_nstep
-    use check_energy_cam,  only: check_energy_cam_chng, check_energy_cam_fix
-    use check_energy_cam,  only: check_energy_cam_timestep_init
+    use check_energy,      only: check_energy_cam_chng, check_energy_cam_fix
+    use check_energy,      only: check_energy_timestep_init
     use check_energy,      only: check_tracers_data, check_tracers_init, check_tracers_chng
     use check_energy,      only: tot_energy_phys
     use chemistry,         only: chem_is_active, chem_timestep_tend
diff --git a/src/physics/spcam/crm_physics.F90 b/src/physics/spcam/crm_physics.F90
index 735d6c3630..8812d2be72 100644
--- a/src/physics/spcam/crm_physics.F90
+++ b/src/physics/spcam/crm_physics.F90
@@ -750,7 +750,7 @@ subroutine crm_physics_tend(ztodt, state, tend, ptend, pbuf, cam_in)
    use crmx_crm_module,     only: crm
    use crmx_microphysics,   only: nmicro_fields
    use physconst,           only: latvap
-   use check_energy_cam,    only: check_energy_cam_chng
+   use check_energy,        only: check_energy_cam_chng
    use phys_grid,           only: get_rlat_all_p, get_rlon_all_p, get_lon_all_p, get_lat_all_p
    use modal_aero_calcsize, only: modal_aero_calcsize_sub
    use micro_pumas_utils,      only: size_dist_param_liq, mg_liq_props, mincld, qsmall
diff --git a/src/physics/spcam/spcam_drivers.F90 b/src/physics/spcam/spcam_drivers.F90
index cd7d3f6370..b9f7a596cc 100644
--- a/src/physics/spcam/spcam_drivers.F90
+++ b/src/physics/spcam/spcam_drivers.F90
@@ -300,7 +300,7 @@ subroutine tphysbc_spcam (ztodt, state,   &
     use cam_history,     only: outfld
     use constituents,    only: pcnst, qmin, cnst_get_ind
     use time_manager,    only: get_nstep
-    use check_energy_cam,only: check_energy_cam_chng, check_energy_cam_fix
+    use check_energy,    only: check_energy_cam_chng, check_energy_cam_fix
     use check_energy,    only: check_tracers_data, check_tracers_init
     use dycore,          only: dycore_is
     use radiation,       only: radiation_tend

From 4b6de4306cce342c6eab46333004e63d4afcb989 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 15 Oct 2024 12:47:16 -0400
Subject: [PATCH 20/53] Fix subcol test with FV dycore

---
 src/physics/cam/check_energy.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index f318cb51e1..998fbb9e18 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -801,9 +801,9 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
             local_cp_or_cv_dycore(:ncol,:) = cpair
             scaling_dycore(:ncol,:) = 1.0_r8
         else
-            ! Moist pressure... use phys formula
-            local_cp_or_cv_dycore(:ncol,:) = local_cp_phys(:ncol,:)
-            scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
+            ! Moist pressure... use phys formula, cp_or_cv_dycore is unused. Reset for safety
+            local_cp_or_cv_dycore(:ncol,:) = 0.0_r8
+            scaling_dycore(:ncol,:)  = 0.0_r8
         end if
     endif
 

From d924e4e434929aa47a89d875e80b7974ce1cdee5 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Wed, 23 Oct 2024 13:19:24 -0400
Subject: [PATCH 21/53] Update atmos_phys; move energy formula to
 cam_thermo_formula; write cp_or_cv_dycore to snapshot

---
 .gitmodules                         |  2 +-
 src/atmos_phys                      |  2 +-
 src/control/cam_snapshot_common.F90 |  9 ++++-
 src/physics/cam/check_energy.F90    | 56 +++++++++++++++--------------
 src/utils/cam_thermo_formula.F90    | 14 ++++++++
 5 files changed, 53 insertions(+), 30 deletions(-)
 create mode 100644 src/utils/cam_thermo_formula.F90

diff --git a/.gitmodules b/.gitmodules
index e295d8fec1..0edbb78972 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/jimmielin/atmospheric_physics
-        fxtag = df80b9c1
+        fxtag = 952ebdd
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index df80b9c1e7..952ebddfa2 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit df80b9c1e73064f9a0196282a92b66a2041f6a57
+Subproject commit 952ebddfa22dd796578fba8d73db6128c8db88c1
diff --git a/src/control/cam_snapshot_common.F90 b/src/control/cam_snapshot_common.F90
index ffae561370..fa558b3ad2 100644
--- a/src/control/cam_snapshot_common.F90
+++ b/src/control/cam_snapshot_common.F90
@@ -81,7 +81,7 @@ module cam_snapshot_common
 integer :: cam_snapshot_before_num, cam_snapshot_after_num
 
 ! Note the maximum number of variables for each type
-type (snapshot_type)    ::  state_snapshot(29)
+type (snapshot_type)    ::  state_snapshot(30)
 type (snapshot_type)    ::  cnst_snapshot(pcnst)
 type (snapshot_type)    ::  tend_snapshot(6)
 type (snapshot_type)    ::  cam_in_snapshot(30)
@@ -283,6 +283,9 @@ subroutine cam_state_snapshot_init(cam_snapshot_before_num_in, cam_snapshot_afte
    call snapshot_addfld( nstate_var, state_snapshot,  cam_snapshot_before_num, cam_snapshot_after_num, &
      'state%te_cur_dyn',  'state_te_cur_dyn',   'unset',            horiz_only)
 
+   call snapshot_addfld( nstate_var, state_snapshot,  cam_snapshot_before_num, cam_snapshot_after_num, &
+     'air_composition_cp_or_cv_dycore',  'cp_or_cv_dycore',   'J kg-1 K-1',  'lev')
+
 end subroutine cam_state_snapshot_init
 
 subroutine cam_cnst_snapshot_init(cam_snapshot_before_num, cam_snapshot_after_num)
@@ -741,6 +744,7 @@ end subroutine snapshot_addfld
 subroutine state_snapshot_all_outfld(lchnk, file_num, state)
 
    use physics_types,    only: phys_te_idx, dyn_te_idx
+   use air_composition,  only: cp_or_cv_dycore
 
    integer,              intent(in)  :: lchnk
    integer,              intent(in)  :: file_num
@@ -843,6 +847,9 @@ subroutine state_snapshot_all_outfld(lchnk, file_num, state)
       case ('state%te_cur_dyn')
          call outfld(state_snapshot(i)%standard_name, state%te_cur(:, dyn_te_idx), pcols, lchnk)
 
+      case ('air_composition_cp_or_cv_dycore')
+         call outfld(state_snapshot(i)%standard_name, cp_or_cv_dycore(:,:,lchnk), pcols, lchnk)
+
       case default
          call endrun('ERROR in state_snapshot_all_outfld: no match found for '//trim(state_snapshot(i)%ddt_string))
 
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 998fbb9e18..774764c563 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -415,7 +415,8 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
     use cam_thermo,      only: get_hydrostatic_energy,thermo_budget_num_vars,thermo_budget_vars, &
                                wvidx,wlidx,wiidx,seidx,poidx,keidx,moidx,mridx,ttidx,teidx
     use cam_history,     only: outfld
-    use dyn_tests_utils, only: vc_physics, vc_height, vc_dry_pressure
+    use dyn_tests_utils, only: vc_physics
+    use cam_thermo_formula, only: ENERGY_FORMULA_DYCORE_SE, ENERGY_FORMULA_DYCORE_MPAS
 
     use cam_abortutils,  only: endrun
     use cam_history_support, only: max_fieldname_len
@@ -467,7 +468,7 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
     end if
 
     if (state%psetcols == pcols) then
-      if (vc_loc == vc_height .or. vc_loc == vc_dry_pressure) then
+      if (vc_loc == ENERGY_FORMULA_DYCORE_MPAS .or. vc_loc == ENERGY_FORMULA_DYCORE_SE) then
         cp_or_cv(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
       else
         cp_or_cv(:ncol,:) = cpairv(:ncol,:,lchnk)
@@ -476,7 +477,7 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
       call endrun('tot_energy_phys: energy diagnostics not implemented/tested for subcolumns')
     end if
 
-    if (vc_loc == vc_height .or. vc_loc == vc_dry_pressure) then
+    if (vc_loc == ENERGY_FORMULA_DYCORE_MPAS .or. vc_loc == ENERGY_FORMULA_DYCORE_SE) then
       scaling(:ncol,:) = cpairv(:ncol,:,lchnk)/cp_or_cv(:ncol,:)!scaling for energy consistency
     else
       scaling(:ncol,:) = 1.0_r8 !internal energy / enthalpy same as CAM physics
@@ -643,7 +644,8 @@ end subroutine check_energy_get_integrals
   subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
     use physics_buffer,  only: physics_buffer_desc, pbuf_set_field
     use cam_abortutils,  only: endrun
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
+    use dyn_tests_utils, only: vc_physics, vc_dycore
+    use cam_thermo_formula, only: ENERGY_FORMULA_DYCORE_SE, ENERGY_FORMULA_DYCORE_MPAS
     use physics_types,   only: physics_tend
     use physics_types,   only: phys_te_idx, dyn_te_idx
     use time_manager,    only: is_first_step
@@ -671,7 +673,7 @@ subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
 
     ! The code below is split into not-subcolumns and subcolumns code, as there is different handling of the
     ! cp passed into the hydrostatic energy call. CAM-SIMA does not support subcolumns, so we keep this special
-    ! handling inside this shim module. (hplin, 9/9/24)
+    ! handling inside this CAM interface. (hplin, 9/9/24)
     if(state%psetcols == pcols) then
         ! No subcolumns
         local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
@@ -685,10 +687,10 @@ subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
 
         local_cp_phys(1:ncol,:) = cpair
 
-        if (vc_dycore == vc_height) then
+        if (vc_dycore == ENERGY_FORMULA_DYCORE_MPAS) then
             ! MPAS specific hydrostatic energy computation (internal energy)
             local_cp_or_cv_dycore(:ncol,:) = cpair-rair
-        else if(vc_dycore == vc_dry_pressure) then
+        else if(vc_dycore == ENERGY_FORMULA_DYCORE_SE) then
             ! SE specific hydrostatic energy (enthalpy)
             local_cp_or_cv_dycore(:ncol,:) = cpair
         else
@@ -721,12 +723,12 @@ subroutine check_energy_timestep_init(state, tend, pbuf, col_type)
         tw_cur          = state%tw_cur(1:ncol),             &
         tend_te_tnd     = tend%te_tnd(1:ncol),              &
         tend_tw_tnd     = tend%tw_tnd(1:ncol),              &
-        temp_ini        = state%temp_ini(:ncol,:), &
-        z_ini           = state%z_ini(:ncol,:), &
+        temp_ini        = state%temp_ini(:ncol,:),          &
+        z_ini           = state%z_ini(:ncol,:),             &
         count           = state%count,                      &
         teout           = teout(1:ncol),                    & ! dummy argument - actual teout written to pbuf directly below
-        vc_physics      = vc_physics, &
-        vc_dycore       = vc_dycore, &
+        energy_formula_physics = vc_physics,                &
+        energy_formula_dycore  = vc_dycore,                 &
         errmsg          = errmsg, &
         errflg          = errflg  &
     )
@@ -741,15 +743,16 @@ end subroutine check_energy_timestep_init
   ! Check that the energy and water change matches the boundary fluxes
   subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
        flx_vap, flx_cnd, flx_ice, flx_sen)
-    use dyn_tests_utils, only: vc_physics, vc_dycore, vc_height, vc_dry_pressure
-    use cam_abortutils,  only: endrun
-    use physics_types,   only: phys_te_idx, dyn_te_idx
-    use physics_types,   only: physics_tend
-    use physconst,       only: cpair, rair, latice, latvap
-    use air_composition, only: cpairv, cp_or_cv_dycore
+    use dyn_tests_utils,    only: vc_physics, vc_dycore
+    use cam_thermo_formula, only: ENERGY_FORMULA_DYCORE_SE, ENERGY_FORMULA_DYCORE_MPAS
+    use cam_abortutils,     only: endrun
+    use physics_types,      only: phys_te_idx, dyn_te_idx
+    use physics_types,      only: physics_tend
+    use physconst,          only: cpair, rair, latice, latvap
+    use air_composition,    only: cpairv, cp_or_cv_dycore
 
     ! CCPP-ized subroutine
-    use check_energy_chng, only: check_energy_chng_run
+    use check_energy_chng,  only: check_energy_chng_run
 
     type(physics_state), intent(inout) :: state
     type(physics_tend ), intent(inout) :: tend
@@ -776,9 +779,8 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         ! No subcolumns
         local_cp_phys(:ncol,:) = cpairv(:ncol,:,lchnk)
 
-        ! Only if vertical coordinate is vc_height or vc_dry_pressure, cp_or_cv_dycore
-        ! is nonzero.
-        if(vc_dycore == vc_height .or. vc_dycore == vc_dry_pressure) then
+        ! Only if using MPAS or SE energy formula cp_or_cv_dycore is nonzero.
+        if(vc_dycore == ENERGY_FORMULA_DYCORE_MPAS .or. vc_dycore == ENERGY_FORMULA_DYCORE_SE) then
             local_cp_or_cv_dycore(:ncol,:) = cp_or_cv_dycore(:ncol,:,lchnk)
 
             scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
@@ -792,11 +794,11 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         local_cp_phys(:,:) = cpair
 
         ! Note: cp_or_cv set above for pressure coordinate
-        if (vc_dycore == vc_height) then
+        if (vc_dycore == ENERGY_FORMULA_DYCORE_MPAS) then
             ! compute cv if vertical coordinate is height: cv = cp - R
             local_cp_or_cv_dycore(:ncol,:) = cpair-rair
             scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
-        else if (vc_dycore == vc_dry_pressure) then
+        else if (vc_dycore == ENERGY_FORMULA_DYCORE_SE) then
             ! SE specific hydrostatic energy
             local_cp_or_cv_dycore(:ncol,:) = cpair
             scaling_dycore(:ncol,:) = 1.0_r8
@@ -832,10 +834,10 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         z_ini           = state%z_ini(:ncol,:),             &
         count           = state%count,                      &
         ztodt           = ztodt,                            &
-        latice          = latice, &
-        latvap          = latvap, &
-        vc_physics      = vc_physics, &
-        vc_dycore       = vc_dycore,  &
+        latice          = latice,                           &
+        latvap          = latvap,                           &
+        energy_formula_physics = vc_physics,                &
+        energy_formula_dycore  = vc_dycore,                 &
         name            = name,       &
         flx_vap         = flx_vap,    &
         flx_cnd         = flx_cnd,    &
diff --git a/src/utils/cam_thermo_formula.F90 b/src/utils/cam_thermo_formula.F90
new file mode 100644
index 0000000000..7781e9da9c
--- /dev/null
+++ b/src/utils/cam_thermo_formula.F90
@@ -0,0 +1,14 @@
+module cam_thermo_formula
+
+   implicit none
+   private
+   save
+
+   ! energy_formula options for use by CCPPized check_energy
+   integer, public, parameter :: ENERGY_FORMULA_DYCORE_FV   = 0  ! vc_moist_pressure
+   integer, public, parameter :: ENERGY_FORMULA_DYCORE_SE   = 1  ! vc_dry_pressure
+   integer, public, parameter :: ENERGY_FORMULA_DYCORE_MPAS = 2  ! vc_height
+
+   !REMOVECAM: in CAM, energy_formula_physics and energy_formula_dycore still uses vc_physics
+   ! and vc_dycore in dyn_tests_utils. The values are the same.
+end module cam_thermo_formula

From 46b82279c76644b410979b327dabb813afee01a7 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 28 Oct 2024 11:09:15 -0400
Subject: [PATCH 22/53] Update external to fix bug; ChangeLog draft

---
 .gitmodules    |  2 +-
 doc/ChangeLog  | 72 +++++++++++++++++++++++++++++++++++++++++++++++---
 src/atmos_phys |  2 +-
 3 files changed, 71 insertions(+), 5 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 0edbb78972..e74baf681e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/jimmielin/atmospheric_physics
-        fxtag = 952ebdd
+        fxtag = 44d724d
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 8294c223f2..f9aded72d5 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,5 +1,71 @@
 ===============================================================
 
+Tag name:
+Originator(s): jimmielin
+Date: 25 Oct 2024
+One-line Summary: Implement CCPPized check_energy_chng and check_energy_fix
+Github PR URL: https://github.com/ESCOMP/CAM/pull/1180
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+- CCPPize check_energy_chng and check_energy_fix (https://github.com/ESCOMP/CAM/issues/1138)
+  CAM interfaces have been kept in check_energy.F90 instead of a new module because check_tracers is not yet CCPPized, there are other non-CCPPized routines in module, and for compatibility with FV3 external calls
+- Save air_composition cp_or_cv_dycore into state snapshot
+- Separate out "energy_formula_physics"/"energy_formula_dycore" definitions used in get_hydrostatic_energy from dyn_tests_utils "vcoord" for an eventual change in SIMA.
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by:
+
+List all files eliminated: N/A
+
+List all files added and what they do:
+- separate out energy formula definitions used in get_hydrostatic_energy from dyn_tests_utils "vcoord"
+A       src/utils/cam_thermo_formula.F90
+
+List all existing files that have been modified, and describe the changes:
+
+Update atmos_phys external with CCPPized check_energy
+M       .gitmodules
+M       bld/configure
+M       src/atmos_phys
+
+Save cp_or_cv_dycore in state snapshot
+M       src/control/cam_snapshot_common.F90
+
+New CAM interfaces to CCPPized routines, when avaialble
+M       src/physics/cam/check_energy.F90
+
+Update calls to CCPPized routines, when available
+M       src/physics/cam/physpkg.F90
+M       src/physics/cam/zm_conv_intr.F90
+M       src/physics/cam7/physpkg.F90
+M       src/physics/simple/physpkg.F90
+M       src/physics/spcam/crm_physics.F90
+M       src/physics/spcam/spcam_drivers.F90
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+derecho/intel/aux_cam:
+
+derecho/nvhpc/aux_cam:
+
+izumi/nag/aux_cam:
+
+izumi/gnu/aux_cam:
+
+Summarize any changes to answers: B4B
+
+===============================================================
+
 Tag name: cam6_4_043
 Originator(s): eaton
 Date: 25 Oct 2024
@@ -31,12 +97,12 @@ Describe any changes made to the namelist:
 . change default value of seasalt_emis_scale to 0.75 for cam7 (both lt and mt)
   This is a cam7 tuning mod from issue #1143
 
-. update ubc_file_path for cam7 (lt only) to 
+. update ubc_file_path for cam7 (lt only) to
   atm/cam/chem/ubc/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensAvg123.cam.h0zm.H2O.1849-2014_c240604.nc
 
 List any changes to the defaults for the boundary datasets:
 
-. update ubc_file_path for cam7 (lt only) to 
+. update ubc_file_path for cam7 (lt only) to
   atm/cam/chem/ubc/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensAvg123.cam.h0zm.H2O.1849-2014_c240604.nc
 
 Describe any substantial timing or memory changes: none
@@ -64,7 +130,7 @@ bld/namelist_files/namelist_defaults_cam.xml
   This is a cam7 tuning mod from issue #1143
 
 bld/namelist_files/use_cases/1850_cam_lt.xml
-. update ubc_file_path to 
+. update ubc_file_path to
   atm/cam/chem/ubc/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensAvg123.cam.h0zm.H2O.1849-2014_c240604.nc
 
 cime_config/testdefs/testlist_cam.xml
diff --git a/src/atmos_phys b/src/atmos_phys
index 952ebddfa2..44d724d8e8 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit 952ebddfa22dd796578fba8d73db6128c8db88c1
+Subproject commit 44d724d8e88ab0b910543a9fdecd24fea9ca62f7

From ba1e652c92e1127ea3cdc3a61654c38959062ef9 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Mon, 28 Oct 2024 15:01:44 -0600
Subject: [PATCH 23/53] fix filename for instantaneous monthly files

---
 src/control/cam_history.F90 | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index 867c84eaea..d8346ec22f 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -309,6 +309,7 @@ module cam_history
   !
   character(len=max_string_len) :: rhfilename_spec = '%c.cam.rh%t.%y-%m-%d-%s.nc' ! history restart
   character(len=max_string_len) :: hfilename_spec(ptapes) = (/ (' ', idx=1, ptapes) /) ! filename specifyer
+  logical                       :: default_monthly_filename(ptapes) = .false.
   ! Flag for if there are accumulated fields specified for a given tape
   logical                       :: hfile_accum(ptapes) = .false.
 
@@ -812,6 +813,7 @@ subroutine history_readnl(nlfile)
           if ( nhtfrq(t) == 0 )then
             ! Monthly files
             hfilename_spec(t) = '%c.cam' // trim(inst_suffix) // '.h%t%f.%y-%m.nc'
+            default_monthly_filename(t) = .true.
           else
             hfilename_spec(t) = '%c.cam' // trim(inst_suffix) // '.h%t%f.%y-%m-%d-%s.nc'
           end if
@@ -880,6 +882,7 @@ subroutine history_readnl(nlfile)
     call mpi_bcast(write_nstep0,1, mpi_logical, masterprocid, mpicom, ierr)
     call mpi_bcast(avgflag_pertape, ptapes, mpi_character, masterprocid, mpicom, ierr)
     call mpi_bcast(hfilename_spec, len(hfilename_spec(1))*ptapes, mpi_character, masterprocid, mpicom, ierr)
+    call mpi_bcast(default_monthly_filename, ptapes, mpi_logical, masterprocid, mpicom, ierr)
     call mpi_bcast(fincl, len(fincl (1,1))*pflds*ptapes, mpi_character, masterprocid, mpicom, ierr)
     call mpi_bcast(fexcl, len(fexcl (1,1))*pflds*ptapes, mpi_character, masterprocid, mpicom, ierr)
 
@@ -5613,6 +5616,7 @@ subroutine wshist (rgnht_in)
     character(len=max_string_len) :: fname ! Filename
     character(len=max_string_len) :: fname_inst ! Filename for instantaneous tape
     character(len=max_string_len) :: fname_acc ! Filename for accumulated tape
+    character(len=max_string_len) :: inst_filename_spec ! Filename specifier override for monthly inst. files
     logical :: prev              ! Label file with previous date rather than current
     logical :: duplicate         ! Flag for duplicate file name
     integer :: ierr
@@ -5726,7 +5730,14 @@ subroutine wshist (rgnht_in)
           else
             fname_acc = interpret_filename_spec( hfilename_spec(t), number=(t-1), &
                  prev=prev, flag_spec='a' )
-            fname_inst = interpret_filename_spec( hfilename_spec(t), number=(t-1), &
+            ! If this is a monthly instantaneous file, override to default timestamp
+            !  unless the user input a filename specifier
+            if (default_monthly_filename(t)) then
+               inst_filename_spec = '%c.cam' // trim(inst_suffix) // '.h%t%f.%y-%m-%d-%s.nc'
+            else
+               inst_filename_spec = hfilename_spec(t)
+            end if
+            fname_inst = interpret_filename_spec( inst_filename_spec, number=(t-1), &
                  prev=prev, flag_spec='i' )
           end if
           !

From 2ec915a42c5fa25f3a9fc2815db14e64bbb08be4 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 10 Sep 2024 08:31:19 -0600
Subject: [PATCH 24/53] add timestamp to rpointer files

---
 src/control/cam_comp.F90         | 14 +++++++++++---
 src/control/cam_initfiles.F90    | 27 +++++++++++++++++----------
 src/control/cam_restart.F90      | 32 +++++++++++++++++++-------------
 src/control/runtime_opts.F90     |  6 +++---
 src/cpl/nuopc/atm_comp_nuopc.F90 |  3 +++
 5 files changed, 53 insertions(+), 29 deletions(-)

diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
index a040762067..561129c3db 100644
--- a/src/control/cam_comp.F90
+++ b/src/control/cam_comp.F90
@@ -16,7 +16,7 @@ module cam_comp
 use spmd_utils,        only: masterproc, mpicom
 use cam_control_mod,   only: cam_ctrl_init, cam_ctrl_set_orbit
 use runtime_opts,      only: read_namelist
-use time_manager,      only: timemgr_init, get_nstep
+use time_manager,      only: timemgr_init, get_nstep, get_curr_date
 use camsrfexch,        only: cam_out_t, cam_in_t
 use ppgrid,            only: begchunk, endchunk
 use physics_types,     only: physics_state, physics_tend
@@ -122,11 +122,11 @@ subroutine cam_init(                                             &
    integer,           intent(in) :: stop_tod              ! Stop time of day (sec)
    integer,           intent(in) :: ref_ymd               ! Reference date (YYYYMMDD)
    integer,           intent(in) :: ref_tod               ! Reference time of day (sec)
-
    type(cam_out_t),   pointer    :: cam_out(:)       ! Output from CAM to surface
    type(cam_in_t) ,   pointer    :: cam_in(:)        ! Merged input state to CAM
 
    ! Local variables
+   integer           :: yr, mon, day, tod
    character(len=cs) :: filein      ! Input namelist filename
    !-----------------------------------------------------------------------
 
@@ -152,7 +152,15 @@ subroutine cam_init(                                             &
 
    ! Read CAM namelists.
    filein = "atm_in" // trim(inst_suffix)
-   call read_namelist(filein, single_column, scmlat, scmlon)
+   call get_curr_date(yr, mon, day, tod)
+   if(len_trim(inst_suffix) > 0) then
+      restart_pointer_file = interpret_filename_spec("rpointer.cam."//trim(inst_suffix)//".%y-%m-%d-%s", &
+              yr=yr_spec, mon=mon_spec, day=day_spec, tod= sec_spec )
+   else
+      restart_pointer_file = interpret_filename_spec("rpointer.cam.%y-%m-%d-%s", &
+              yr=yr_spec, mon=mon_spec, day=day_spec, tod= sec_spec )
+   endif
+   call read_namelist(filein, single_column, scmlat, scmlon, restart_pointer_file=restart_pointer_file)
 
    ! Open initial or restart file, and topo file if specified.
    call cam_initfiles_open()
diff --git a/src/control/cam_initfiles.F90 b/src/control/cam_initfiles.F90
index 3b48f1ab0e..6c67125c8d 100644
--- a/src/control/cam_initfiles.F90
+++ b/src/control/cam_initfiles.F90
@@ -42,10 +42,6 @@ module cam_initfiles
 
 real(r8), public, protected :: scale_dry_air_mass = 0.0_r8 ! Toggle and target avg air mass for MPAS dycore
 
-! The restart pointer file contains name of most recently written primary restart file.
-! The contents of this file are updated by cam_write_restart as new restart files are written.
-character(len=cl), public, protected :: rest_pfile
-
 ! Filename for initial restart file.
 character(len=cl) :: restart_file = ' '
 
@@ -61,7 +57,7 @@ module cam_initfiles
 contains
 !========================================================================================
 
-subroutine cam_initfiles_readnl(nlfile)
+subroutine cam_initfiles_readnl(nlfile, restart_pointer_file)
 
    use namelist_utils,  only: find_group_name
    use units,           only: getunit, freeunit
@@ -70,7 +66,7 @@ subroutine cam_initfiles_readnl(nlfile)
    use cam_instance,    only: inst_suffix
 
    character(len=*), intent(in) :: nlfile  ! filepath for file containing namelist input
-
+   character(len=*), optional, intent(in) :: restart_pointer_file
    ! Local variables
    integer :: unitn, ierr
 
@@ -78,6 +74,10 @@ subroutine cam_initfiles_readnl(nlfile)
    logical                  :: filefound
    integer                  :: xtype
    integer(pio_offset_kind) :: slen
+   logical                  :: found
+
+   ! The restart pointer file contains name of most recently written primary restart file.
+   character(len=cl)       :: rest_pfile
 
    character(len=*), parameter :: sub = 'cam_initfiles_readnl'
 
@@ -112,18 +112,25 @@ subroutine cam_initfiles_readnl(nlfile)
    call mpi_bcast(scale_dry_air_mass, 1, mpir8, mstrid, mpicom, ierr)
    if (ierr /= 0) call endrun(sub//": ERROR: mpi_bcast: scale_dry_air_mass")
 
-   ! Set pointer file name based on instance suffix
-   rest_pfile = './rpointer.atm' // trim(inst_suffix)
-
+   if(present(restart_pointer_file)) then
+      rest_pfile = restart_pointer_file
+   else
+      ! Set pointer file name based on instance suffix
+      rest_pfile = './rpointer.atm' // trim(inst_suffix)
+   endif
    ! Set name of primary restart file
    if (restart_run) then
       ! Read name of restart file from pointer file
       if (masterproc) then
+         inquire(file=trim(rest_pfile),exist=found)
+         if(.not. found) then
+            call endrun(sub // ': ERROR: rpointer file: '//trim(rest_pfile) // ' not found')
+         endif
          unitn = getunit()
          call opnfil(rest_pfile, unitn, 'f', status="old")
          read (unitn, '(a)', iostat=ierr) restart_file
          if (ierr /= 0) then
-            call endrun(sub // ': ERROR: reading rpointer file')
+            call endrun(sub // ': ERROR: reading rpointer file: '//trim(rest_pfile))
          end if
          close(unitn)
          call freeunit(unitn)
diff --git a/src/control/cam_restart.F90 b/src/control/cam_restart.F90
index 124cf3b4b5..41463c71f9 100644
--- a/src/control/cam_restart.F90
+++ b/src/control/cam_restart.F90
@@ -132,38 +132,44 @@ subroutine cam_write_restart(cam_in, cam_out, dyn_out, pbuf2d, &
    call ionosphere_write_restart(fh)
    call write_restart_physics(fh, cam_in, cam_out, pbuf2d)
 
-   if (present(yr_spec).and.present(mon_spec).and.&
-      present(day_spec).and.present(sec_spec)) then
-      call write_restart_history(fh, yr_spec=yr_spec, mon_spec=mon_spec, &
-                                 day_spec=day_spec, sec_spec= sec_spec )
-   else
-      call write_restart_history(fh)
-   end if
+   call write_restart_history(fh, yr_spec=yr_spec, mon_spec=mon_spec, &
+        day_spec=day_spec, sec_spec= sec_spec )
 
    ! Close the primary restart file
    call pio_closefile(fh)
 
    ! Update the restart pointer file
-   call write_rest_pfile(fname)
+   call write_rest_pfile(fname, yr_spec=yr_spec, mon_spec=mon_spec, &
+                                 day_spec=day_spec, sec_spec= sec_spec )
 
 end subroutine cam_write_restart
 
 !========================================================================================
 
-subroutine write_rest_pfile(restart_file)
+subroutine write_rest_pfile(restart_file, yr_spec, mon_spec, day_spec, sec_spec)
 
    ! Write the restart pointer file
-
-   use cam_initfiles, only: rest_pfile
-
+   use cam_instance,     only: inst_suffix
+   use filenames,        only: interpret_filename_spec
    character(len=*), intent(in) :: restart_file
+   integer,       optional, intent(in) :: yr_spec         ! Simulation year
+   integer,       optional, intent(in) :: mon_spec        ! Simulation month
+   integer,       optional, intent(in) :: day_spec        ! Simulation day
+   integer,       optional, intent(in) :: sec_spec        ! Seconds into current simulation day
 
    integer :: nsds, ierr
+   character(len=CL) :: rest_pfile
    character(len=*), parameter :: sub='write_rest_pfile'
    !---------------------------------------------------------------------------
 
    if (masterproc) then
-
+      if(inst_suffix .ne. "") then
+         rest_pfile = interpret_filename_spec('rpointer.cpl.%y-%m-%d-%s',&
+              yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
+      else
+         rest_pfile = interpret_filename_spec('rpointer.cpl.'//trim(inst_suffix)//'.'//'%y-%m-%d-%s',&
+              yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
+      endif
       nsds = getunit()
       call opnfil(rest_pfile, nsds, 'f')
       rewind nsds
diff --git a/src/control/runtime_opts.F90 b/src/control/runtime_opts.F90
index 915664cdb9..0a8c48b509 100644
--- a/src/control/runtime_opts.F90
+++ b/src/control/runtime_opts.F90
@@ -19,7 +19,7 @@ module runtime_opts
 contains
 !=======================================================================
 
-subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
+subroutine read_namelist(nlfilename, single_column, scmlat, scmlon, restart_pointer_file)
 
    use cam_initfiles,       only: cam_initfiles_readnl
    use constituents,        only: cnst_readnl
@@ -109,7 +109,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
    logical,          intent(in) :: single_column
    real(r8),         intent(in) :: scmlat
    real(r8),         intent(in) :: scmlon
-
+   character(len=*), optional, intent(in) :: restart_pointer_file
    !---------------------------Local variables-----------------------------
    character(len=*), parameter ::  subname = "read_namelist"
 
@@ -133,7 +133,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
 !++bee 13 Oct 2015, need to fix the pbuf_global_allocate functionality, then
 !                   can uncomment the pbuf_readnl line
 !   call pbuf_readnl(nlfilename)
-   call cam_initfiles_readnl(nlfilename)
+   call cam_initfiles_readnl(nlfilename, restart_pointer_file=restart_pointer_file)
    call cnst_readnl(nlfilename)
    call history_readnl(nlfilename)
    call chem_surfvals_readnl(nlfilename)
diff --git a/src/cpl/nuopc/atm_comp_nuopc.F90 b/src/cpl/nuopc/atm_comp_nuopc.F90
index 8b2ba903d0..927a300bae 100644
--- a/src/cpl/nuopc/atm_comp_nuopc.F90
+++ b/src/cpl/nuopc/atm_comp_nuopc.F90
@@ -1976,6 +1976,9 @@ subroutine cam_write_clockrest( clock, yr_spec, mon_spec, day_spec, sec_spec, rc
          yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
 
     if (masterproc) then
+       restart_pfile = interpret_filename_spec('rpointer.cpl.%y-%m-%d-%s',&
+            yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
+
        write(iulog,*) " In this configuration, there is no mediator"
        write(iulog,*) " Normally, the mediator restart file provides the restart time info"
        write(iulog,*) " In this case, CAM will create the rpointer.cpl and cpl restart file"

From 230a84a552e7c4add07ec21f32e4d68ff109b61e Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 10 Sep 2024 15:23:27 -0600
Subject: [PATCH 25/53] add rpointer timestamp to cam

---
 src/control/cam_comp.F90    | 13 ++++++++-----
 src/control/cam_restart.F90 |  6 +++---
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
index 561129c3db..66adf3b614 100644
--- a/src/control/cam_comp.F90
+++ b/src/control/cam_comp.F90
@@ -16,7 +16,7 @@ module cam_comp
 use spmd_utils,        only: masterproc, mpicom
 use cam_control_mod,   only: cam_ctrl_init, cam_ctrl_set_orbit
 use runtime_opts,      only: read_namelist
-use time_manager,      only: timemgr_init, get_nstep, get_curr_date
+use time_manager,      only: timemgr_init, get_nstep, get_prev_date
 use camsrfexch,        only: cam_out_t, cam_in_t
 use ppgrid,            only: begchunk, endchunk
 use physics_types,     only: physics_state, physics_tend
@@ -87,7 +87,7 @@ subroutine cam_init(                                             &
    use cam_snapshot_common, only: cam_snapshot_deactivate
    use air_composition,  only: air_composition_init
    use phys_grid_ctem,   only: phys_grid_ctem_reg
-
+   use filenames,        only: interpret_filename_spec
    ! Arguments
    character(len=cl), intent(in) :: caseid                ! case ID
    character(len=cl), intent(in) :: ctitle                ! case title
@@ -126,6 +126,7 @@ subroutine cam_init(                                             &
    type(cam_in_t) ,   pointer    :: cam_in(:)        ! Merged input state to CAM
 
    ! Local variables
+   character(len=cl) :: restart_pointer_file
    integer           :: yr, mon, day, tod
    character(len=cs) :: filein      ! Input namelist filename
    !-----------------------------------------------------------------------
@@ -152,14 +153,16 @@ subroutine cam_init(                                             &
 
    ! Read CAM namelists.
    filein = "atm_in" // trim(inst_suffix)
-   call get_curr_date(yr, mon, day, tod)
+   call get_prev_date(yr, mon, day, tod)
    if(len_trim(inst_suffix) > 0) then
       restart_pointer_file = interpret_filename_spec("rpointer.cam."//trim(inst_suffix)//".%y-%m-%d-%s", &
-              yr=yr_spec, mon=mon_spec, day=day_spec, tod= sec_spec )
+              yr_spec=yr, mon_spec=mon, day_spec=day, sec_spec=tod )
    else
       restart_pointer_file = interpret_filename_spec("rpointer.cam.%y-%m-%d-%s", &
-              yr=yr_spec, mon=mon_spec, day=day_spec, tod= sec_spec )
+              yr_spec=yr, mon_spec=mon, day_spec=day, sec_spec=tod )
+
    endif
+   print *,__FILE__,__LINE__,trim(restart_pointer_file)
    call read_namelist(filein, single_column, scmlat, scmlon, restart_pointer_file=restart_pointer_file)
 
    ! Open initial or restart file, and topo file if specified.
diff --git a/src/control/cam_restart.F90 b/src/control/cam_restart.F90
index 41463c71f9..02cb97b8c5 100644
--- a/src/control/cam_restart.F90
+++ b/src/control/cam_restart.F90
@@ -163,11 +163,11 @@ subroutine write_rest_pfile(restart_file, yr_spec, mon_spec, day_spec, sec_spec)
    !---------------------------------------------------------------------------
 
    if (masterproc) then
-      if(inst_suffix .ne. "") then
-         rest_pfile = interpret_filename_spec('rpointer.cpl.%y-%m-%d-%s',&
+      if(len_trim(inst_suffix) > 0) then
+         rest_pfile = interpret_filename_spec('rpointer.cam.'//trim(inst_suffix)//'.'//'%y-%m-%d-%s',&
               yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
       else
-         rest_pfile = interpret_filename_spec('rpointer.cpl.'//trim(inst_suffix)//'.'//'%y-%m-%d-%s',&
+         rest_pfile = interpret_filename_spec('rpointer.cam.%y-%m-%d-%s',&
               yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
       endif
       nsds = getunit()

From e00353cf02df9e0957b0a515fef024454ab5773d Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 12 Sep 2024 07:27:50 -0600
Subject: [PATCH 26/53] simplify rpointer naming

---
 src/control/cam_comp.F90      | 15 ++-------------
 src/control/cam_initfiles.F90 | 22 +++++++++++-----------
 src/control/cam_restart.F90   | 17 ++++-------------
 src/control/runtime_opts.F90  |  5 ++---
 4 files changed, 19 insertions(+), 40 deletions(-)

diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
index 66adf3b614..3eb94f041a 100644
--- a/src/control/cam_comp.F90
+++ b/src/control/cam_comp.F90
@@ -16,7 +16,7 @@ module cam_comp
 use spmd_utils,        only: masterproc, mpicom
 use cam_control_mod,   only: cam_ctrl_init, cam_ctrl_set_orbit
 use runtime_opts,      only: read_namelist
-use time_manager,      only: timemgr_init, get_nstep, get_prev_date
+use time_manager,      only: timemgr_init, get_nstep
 use camsrfexch,        only: cam_out_t, cam_in_t
 use ppgrid,            only: begchunk, endchunk
 use physics_types,     only: physics_state, physics_tend
@@ -126,8 +126,6 @@ subroutine cam_init(                                             &
    type(cam_in_t) ,   pointer    :: cam_in(:)        ! Merged input state to CAM
 
    ! Local variables
-   character(len=cl) :: restart_pointer_file
-   integer           :: yr, mon, day, tod
    character(len=cs) :: filein      ! Input namelist filename
    !-----------------------------------------------------------------------
 
@@ -153,17 +151,8 @@ subroutine cam_init(                                             &
 
    ! Read CAM namelists.
    filein = "atm_in" // trim(inst_suffix)
-   call get_prev_date(yr, mon, day, tod)
-   if(len_trim(inst_suffix) > 0) then
-      restart_pointer_file = interpret_filename_spec("rpointer.cam."//trim(inst_suffix)//".%y-%m-%d-%s", &
-              yr_spec=yr, mon_spec=mon, day_spec=day, sec_spec=tod )
-   else
-      restart_pointer_file = interpret_filename_spec("rpointer.cam.%y-%m-%d-%s", &
-              yr_spec=yr, mon_spec=mon, day_spec=day, sec_spec=tod )
 
-   endif
-   print *,__FILE__,__LINE__,trim(restart_pointer_file)
-   call read_namelist(filein, single_column, scmlat, scmlon, restart_pointer_file=restart_pointer_file)
+   call read_namelist(filein, single_column, scmlat, scmlon)
 
    ! Open initial or restart file, and topo file if specified.
    call cam_initfiles_open()
diff --git a/src/control/cam_initfiles.F90 b/src/control/cam_initfiles.F90
index 6c67125c8d..d44d5030e1 100644
--- a/src/control/cam_initfiles.F90
+++ b/src/control/cam_initfiles.F90
@@ -57,19 +57,19 @@ module cam_initfiles
 contains
 !========================================================================================
 
-subroutine cam_initfiles_readnl(nlfile, restart_pointer_file)
+subroutine cam_initfiles_readnl(nlfile)
 
    use namelist_utils,  only: find_group_name
    use units,           only: getunit, freeunit
    use spmd_utils,      only: mpicom, mstrid=>masterprocid, mpir8=>mpi_real8, &
                               mpichar=>mpi_character, mpi_logical
    use cam_instance,    only: inst_suffix
-
+   use filenames,       only: interpret_filename_spec
+   
    character(len=*), intent(in) :: nlfile  ! filepath for file containing namelist input
-   character(len=*), optional, intent(in) :: restart_pointer_file
+
    ! Local variables
    integer :: unitn, ierr
-
    character(len=cl)        :: locfn
    logical                  :: filefound
    integer                  :: xtype
@@ -112,19 +112,19 @@ subroutine cam_initfiles_readnl(nlfile, restart_pointer_file)
    call mpi_bcast(scale_dry_air_mass, 1, mpir8, mstrid, mpicom, ierr)
    if (ierr /= 0) call endrun(sub//": ERROR: mpi_bcast: scale_dry_air_mass")
 
-   if(present(restart_pointer_file)) then
-      rest_pfile = restart_pointer_file
-   else
-      ! Set pointer file name based on instance suffix
-      rest_pfile = './rpointer.atm' // trim(inst_suffix)
-   endif
    ! Set name of primary restart file
    if (restart_run) then
       ! Read name of restart file from pointer file
       if (masterproc) then
+         rest_pfile = interpret_filename_spec("rpointer.cam"//trim(inst_suffix)//".%y-%m-%d-%s", prev=.true.)
          inquire(file=trim(rest_pfile),exist=found)
          if(.not. found) then
-            call endrun(sub // ': ERROR: rpointer file: '//trim(rest_pfile) // ' not found')
+            write(iulog, "Warning : rpointer file "//trim(rest_pfile)//" not found.")
+            rest_pfile = "rpointer.cam"//trim(inst_suffix)
+            inquire(file=trim(rest_pfile),exist=found)
+            if(.not. found) then
+               call endrun(sub // ': ERROR: rpointer file: '//trim(rest_pfile) // ' not found')
+            endif
          endif
          unitn = getunit()
          call opnfil(rest_pfile, unitn, 'f', status="old")
diff --git a/src/control/cam_restart.F90 b/src/control/cam_restart.F90
index 02cb97b8c5..35087aa89b 100644
--- a/src/control/cam_restart.F90
+++ b/src/control/cam_restart.F90
@@ -106,12 +106,8 @@ subroutine cam_write_restart(cam_in, cam_out, dyn_out, pbuf2d, &
    ! (%c = caseid, $y = year, $m = month, $d = day, $s = seconds in day, %t = number)
    rfilename_spec = '%c.cam' // trim(inst_suffix) //'.r.%y-%m-%d-%s.nc'
 
-   if (present(yr_spec).and.present(mon_spec).and.present(day_spec).and.present(sec_spec)) then
-      fname = interpret_filename_spec( rfilename_spec, &
-              yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
-   else
-      fname = interpret_filename_spec( rfilename_spec )
-   end if
+   fname = interpret_filename_spec( rfilename_spec, &
+        yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
 
    call cam_pio_createfile(fh, trim(fname), 0)
    ierr = cam_pio_set_fill(fh)
@@ -163,13 +159,8 @@ subroutine write_rest_pfile(restart_file, yr_spec, mon_spec, day_spec, sec_spec)
    !---------------------------------------------------------------------------
 
    if (masterproc) then
-      if(len_trim(inst_suffix) > 0) then
-         rest_pfile = interpret_filename_spec('rpointer.cam.'//trim(inst_suffix)//'.'//'%y-%m-%d-%s',&
-              yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
-      else
-         rest_pfile = interpret_filename_spec('rpointer.cam.%y-%m-%d-%s',&
-              yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
-      endif
+      rest_pfile = interpret_filename_spec('rpointer.cam'//trim(inst_suffix)//'.'//'%y-%m-%d-%s',&
+           yr_spec=yr_spec, mon_spec=mon_spec, day_spec=day_spec, sec_spec= sec_spec )
       nsds = getunit()
       call opnfil(rest_pfile, nsds, 'f')
       rewind nsds
diff --git a/src/control/runtime_opts.F90 b/src/control/runtime_opts.F90
index 0a8c48b509..19cff5c884 100644
--- a/src/control/runtime_opts.F90
+++ b/src/control/runtime_opts.F90
@@ -19,7 +19,7 @@ module runtime_opts
 contains
 !=======================================================================
 
-subroutine read_namelist(nlfilename, single_column, scmlat, scmlon, restart_pointer_file)
+subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
 
    use cam_initfiles,       only: cam_initfiles_readnl
    use constituents,        only: cnst_readnl
@@ -109,7 +109,6 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon, restart_poin
    logical,          intent(in) :: single_column
    real(r8),         intent(in) :: scmlat
    real(r8),         intent(in) :: scmlon
-   character(len=*), optional, intent(in) :: restart_pointer_file
    !---------------------------Local variables-----------------------------
    character(len=*), parameter ::  subname = "read_namelist"
 
@@ -133,7 +132,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon, restart_poin
 !++bee 13 Oct 2015, need to fix the pbuf_global_allocate functionality, then
 !                   can uncomment the pbuf_readnl line
 !   call pbuf_readnl(nlfilename)
-   call cam_initfiles_readnl(nlfilename, restart_pointer_file=restart_pointer_file)
+   call cam_initfiles_readnl(nlfilename)
    call cnst_readnl(nlfilename)
    call history_readnl(nlfilename)
    call chem_surfvals_readnl(nlfilename)

From e67008e34f1d9aa5789b38975fda7f8ad4a80bb7 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Mon, 30 Sep 2024 15:51:08 -0600
Subject: [PATCH 27/53] update from utils to status for newer cime versions

---
 src/cpl/nuopc/atm_comp_nuopc.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cpl/nuopc/atm_comp_nuopc.F90 b/src/cpl/nuopc/atm_comp_nuopc.F90
index 927a300bae..5b16968c44 100644
--- a/src/cpl/nuopc/atm_comp_nuopc.F90
+++ b/src/cpl/nuopc/atm_comp_nuopc.F90
@@ -1967,8 +1967,8 @@ subroutine cam_write_clockrest( clock, yr_spec, mon_spec, day_spec, sec_spec, rc
     call shr_cal_ymd2date(yy,mm,dd,start_ymd)
 
     call ESMF_TimeGet( nextTime, yy=yy, mm=mm, dd=dd, s=curr_tod, rc=rc )
-   !call ESMF_TimeGet( currTime, yy=yy, mm=mm, dd=dd, s=curr_tod, rc=rc )
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
     call shr_cal_ymd2date(yy,mm,dd,curr_ymd)
 
     ! Open clock info restart dataset

From 880dd3e70c35905414412dc9ebbed07263c4be46 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 3 Oct 2024 11:48:28 -0600
Subject: [PATCH 28/53] remove whitespace changes, correct issue in
 atm_comp_nuopc

---
 src/control/cam_comp.F90         | 4 ++--
 src/control/cam_initfiles.F90    | 3 ++-
 src/control/runtime_opts.F90     | 1 +
 src/cpl/nuopc/atm_comp_nuopc.F90 | 2 +-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
index 3eb94f041a..a040762067 100644
--- a/src/control/cam_comp.F90
+++ b/src/control/cam_comp.F90
@@ -87,7 +87,7 @@ subroutine cam_init(                                             &
    use cam_snapshot_common, only: cam_snapshot_deactivate
    use air_composition,  only: air_composition_init
    use phys_grid_ctem,   only: phys_grid_ctem_reg
-   use filenames,        only: interpret_filename_spec
+
    ! Arguments
    character(len=cl), intent(in) :: caseid                ! case ID
    character(len=cl), intent(in) :: ctitle                ! case title
@@ -122,6 +122,7 @@ subroutine cam_init(                                             &
    integer,           intent(in) :: stop_tod              ! Stop time of day (sec)
    integer,           intent(in) :: ref_ymd               ! Reference date (YYYYMMDD)
    integer,           intent(in) :: ref_tod               ! Reference time of day (sec)
+
    type(cam_out_t),   pointer    :: cam_out(:)       ! Output from CAM to surface
    type(cam_in_t) ,   pointer    :: cam_in(:)        ! Merged input state to CAM
 
@@ -151,7 +152,6 @@ subroutine cam_init(                                             &
 
    ! Read CAM namelists.
    filein = "atm_in" // trim(inst_suffix)
-
    call read_namelist(filein, single_column, scmlat, scmlon)
 
    ! Open initial or restart file, and topo file if specified.
diff --git a/src/control/cam_initfiles.F90 b/src/control/cam_initfiles.F90
index d44d5030e1..08de6340ad 100644
--- a/src/control/cam_initfiles.F90
+++ b/src/control/cam_initfiles.F90
@@ -119,8 +119,9 @@ subroutine cam_initfiles_readnl(nlfile)
          rest_pfile = interpret_filename_spec("rpointer.cam"//trim(inst_suffix)//".%y-%m-%d-%s", prev=.true.)
          inquire(file=trim(rest_pfile),exist=found)
          if(.not. found) then
-            write(iulog, "Warning : rpointer file "//trim(rest_pfile)//" not found.")
+            write(iulog, "INFO : rpointer file "//trim(rest_pfile)//" not found.")
             rest_pfile = "rpointer.cam"//trim(inst_suffix)
+            write(iulog, "  Try looking for "//trim(rest_pfile)//" ...")
             inquire(file=trim(rest_pfile),exist=found)
             if(.not. found) then
                call endrun(sub // ': ERROR: rpointer file: '//trim(rest_pfile) // ' not found')
diff --git a/src/control/runtime_opts.F90 b/src/control/runtime_opts.F90
index 19cff5c884..915664cdb9 100644
--- a/src/control/runtime_opts.F90
+++ b/src/control/runtime_opts.F90
@@ -109,6 +109,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
    logical,          intent(in) :: single_column
    real(r8),         intent(in) :: scmlat
    real(r8),         intent(in) :: scmlon
+
    !---------------------------Local variables-----------------------------
    character(len=*), parameter ::  subname = "read_namelist"
 
diff --git a/src/cpl/nuopc/atm_comp_nuopc.F90 b/src/cpl/nuopc/atm_comp_nuopc.F90
index 5b16968c44..8faf60fc79 100644
--- a/src/cpl/nuopc/atm_comp_nuopc.F90
+++ b/src/cpl/nuopc/atm_comp_nuopc.F90
@@ -1985,7 +1985,7 @@ subroutine cam_write_clockrest( clock, yr_spec, mon_spec, day_spec, sec_spec, rc
        write(iulog,*) " containing this information"
        write(iulog,*) " writing rpointer file for driver clock info, rpointer.cpl"
        write(iulog,*) " writing restart clock info for driver= "//trim(restart_file)
-       open(newunit=unitn, file='rpointer.cpl', form='FORMATTED')
+       open(newunit=unitn, file=trim(restart_pfile), form='FORMATTED')
        write(unitn,'(a)') trim(restart_file)
        close(unitn)
     endif

From 0007c77f803399c58080c4b4b640c528ab6f5b75 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Thu, 17 Oct 2024 12:53:00 -0600
Subject: [PATCH 29/53] reverse alarm initialization to support alarm_restart
 at end of run

---
 src/cpl/nuopc/atm_comp_nuopc.F90 | 44 ++++++++++++++++----------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/src/cpl/nuopc/atm_comp_nuopc.F90 b/src/cpl/nuopc/atm_comp_nuopc.F90
index 8faf60fc79..bfde73912d 100644
--- a/src/cpl/nuopc/atm_comp_nuopc.F90
+++ b/src/cpl/nuopc/atm_comp_nuopc.F90
@@ -1296,51 +1296,51 @@ subroutine ModelSetRunClock(gcomp, rc)
        call ESMF_LogWrite(subname//'setting alarms for' // trim(name), ESMF_LOGMSG_INFO)
 
        !----------------
-       ! Restart alarm
+       ! Stop alarm
        !----------------
-       call NUOPC_CompAttributeGet(gcomp, name="restart_option", value=restart_option, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="stop_option", value=stop_option, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call NUOPC_CompAttributeGet(gcomp, name="restart_n", value=cvalue, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) restart_n
+       read(cvalue,*) stop_n
 
-       call NUOPC_CompAttributeGet(gcomp, name="restart_ymd", value=cvalue, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) restart_ymd
+       read(cvalue,*) stop_ymd
 
-       call alarmInit(mclock, restart_alarm, restart_option, &
-            opt_n   = restart_n,           &
-            opt_ymd = restart_ymd,         &
+       call alarmInit(mclock, stop_alarm, stop_option, &
+            opt_n   = stop_n,           &
+            opt_ymd = stop_ymd,         &
             RefTime = mcurrTime,           &
-            alarmname = 'alarm_restart', rc=rc)
+            alarmname = 'alarm_stop', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call ESMF_AlarmSet(restart_alarm, clock=mclock, rc=rc)
+       call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
        !----------------
-       ! Stop alarm
+       ! Restart alarm
        !----------------
-       call NUOPC_CompAttributeGet(gcomp, name="stop_option", value=stop_option, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="restart_option", value=restart_option, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="restart_n", value=cvalue, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) stop_n
+       read(cvalue,*) restart_n
 
-       call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc)
+       call NUOPC_CompAttributeGet(gcomp, name="restart_ymd", value=cvalue, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) stop_ymd
+       read(cvalue,*) restart_ymd
 
-       call alarmInit(mclock, stop_alarm, stop_option, &
-            opt_n   = stop_n,           &
-            opt_ymd = stop_ymd,         &
+       call alarmInit(mclock, restart_alarm, restart_option, &
+            opt_n   = restart_n,           &
+            opt_ymd = restart_ymd,         &
             RefTime = mcurrTime,           &
-            alarmname = 'alarm_stop', rc=rc)
+            alarmname = 'alarm_restart', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc)
+       call ESMF_AlarmSet(restart_alarm, clock=mclock, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     end if

From 2f59d18a1604dc761ea42d5f8d1f87084bd7d464 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Tue, 29 Oct 2024 17:01:21 -0600
Subject: [PATCH 30/53] add sampled_on_subcycle argument for missing subcycle
 fields

---
 src/physics/cam/check_energy.F90        | 12 ++--
 src/physics/cam/clubb_intr.F90          | 15 +++--
 src/physics/cam/hetfrz_classnuc_cam.F90 | 68 +++++++++++-----------
 src/physics/cam/ndrop.F90               | 26 ++++-----
 src/physics/cam/ndrop_bam.F90           | 14 ++---
 src/physics/cam/nucleate_ice_cam.F90    | 56 +++++++++---------
 src/physics/cam/subcol_SILHS.F90        | 76 ++++++++++++-------------
 7 files changed, 136 insertions(+), 131 deletions(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 94ef9a05e1..9c569387e0 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -201,12 +201,12 @@ subroutine check_energy_init()
                        history_waccm_out = history_waccm )
 
 ! register history variables
-    call addfld('TEINP',  horiz_only,  'A', 'J/m2', 'Total energy of physics input', sampled_on_subcycle=.true.)
-    call addfld('TEOUT',  horiz_only,  'A', 'J/m2', 'Total energy of physics output', sampled_on_subcycle=.true.)
-    call addfld('TEFIX',  horiz_only,  'A', 'J/m2', 'Total energy after fixer', sampled_on_subcycle=.true.)
-    call addfld('EFIX',   horiz_only,  'A', 'W/m2', 'Effective sensible heat flux due to energy fixer', sampled_on_subcycle=.true.)
-    call addfld('DTCORE', (/ 'lev' /), 'A', 'K/s' , 'T tendency due to dynamical core', sampled_on_subcycle=.true.)
-    call addfld('DQCORE', (/ 'lev' /), 'A', 'kg/kg/s' , 'Water vapor tendency due to dynamical core', sampled_on_subcycle=.true.)
+    call addfld('TEINP',  horiz_only,  'A', 'J/m2', 'Total energy of physics input')
+    call addfld('TEOUT',  horiz_only,  'A', 'J/m2', 'Total energy of physics output')
+    call addfld('TEFIX',  horiz_only,  'A', 'J/m2', 'Total energy after fixer')
+    call addfld('EFIX',   horiz_only,  'A', 'W/m2', 'Effective sensible heat flux due to energy fixer')
+    call addfld('DTCORE', (/ 'lev' /), 'A', 'K/s' , 'T tendency due to dynamical core')
+    call addfld('DQCORE', (/ 'lev' /), 'A', 'kg/kg/s' , 'Water vapor tendency due to dynamical core')
 
     if ( history_budget ) then
        call add_default ('DTCORE', history_budget_histfile_num, ' ')
diff --git a/src/physics/cam/clubb_intr.F90 b/src/physics/cam/clubb_intr.F90
index 872bbc4963..41580cc2c7 100644
--- a/src/physics/cam/clubb_intr.F90
+++ b/src/physics/cam/clubb_intr.F90
@@ -5115,7 +5115,8 @@ subroutine stats_init_clubb( l_stats_in, stats_tsamp_in, stats_tout_in, &
 
         call addfld( trim(sub), (/ 'ilev' /), 'A', &
                      trim(stats_zt(1)%file%grid_avg_var(i)%units), &
-                     trim(stats_zt(1)%file%grid_avg_var(i)%description) )
+                     trim(stats_zt(1)%file%grid_avg_var(i)%description), &
+                     sampled_on_subcycle=.true. )
     enddo
 
     do i = 1, stats_zm(1)%num_output_fields
@@ -5126,7 +5127,8 @@ subroutine stats_init_clubb( l_stats_in, stats_tsamp_in, stats_tout_in, &
 
        call addfld( trim(sub), (/ 'ilev' /), 'A', &
                     trim(stats_zm(1)%file%grid_avg_var(i)%units), &
-                    trim(stats_zm(1)%file%grid_avg_var(i)%description) )
+                    trim(stats_zm(1)%file%grid_avg_var(i)%description), &
+                    sampled_on_subcycle=.true. )
     enddo
 
     if (stats_metadata%l_output_rad_files) then
@@ -5137,7 +5139,8 @@ subroutine stats_init_clubb( l_stats_in, stats_tsamp_in, stats_tout_in, &
           if (len(temp1) > max_fieldname_len) sub = temp1(1:max_fieldname_len)
           call addfld( trim(sub), (/ 'ilev' /), 'A', &
                        trim(stats_rad_zt(1)%file%grid_avg_var(i)%units), &
-                       trim(stats_rad_zt(1)%file%grid_avg_var(i)%description) )
+                       trim(stats_rad_zt(1)%file%grid_avg_var(i)%description), &
+                       sampled_on_subcycle=.true. )
        enddo
 
        do i = 1, stats_rad_zm(1)%num_output_fields
@@ -5146,7 +5149,8 @@ subroutine stats_init_clubb( l_stats_in, stats_tsamp_in, stats_tout_in, &
           if (len(temp1) > max_fieldname_len) sub = temp1(1:max_fieldname_len)
           call addfld( trim(sub), (/ 'ilev' /), 'A', &
                        trim(stats_rad_zm(1)%file%grid_avg_var(i)%units), &
-                       trim(stats_rad_zm(1)%file%grid_avg_var(i)%description) )
+                       trim(stats_rad_zm(1)%file%grid_avg_var(i)%description), &
+                       sampled_on_subcycle=.true. )
        enddo
     endif
 
@@ -5156,7 +5160,8 @@ subroutine stats_init_clubb( l_stats_in, stats_tsamp_in, stats_tout_in, &
        if (len(temp1) > max_fieldname_len) sub = temp1(1:max_fieldname_len)
        call addfld( trim(sub), horiz_only, 'A', &
                     trim(stats_sfc(1)%file%grid_avg_var(i)%units), &
-                    trim(stats_sfc(1)%file%grid_avg_var(i)%description) )
+                    trim(stats_sfc(1)%file%grid_avg_var(i)%description), &
+                    sampled_on_subcycle=.true. )
     enddo
 
 
diff --git a/src/physics/cam/hetfrz_classnuc_cam.F90 b/src/physics/cam/hetfrz_classnuc_cam.F90
index 2f6d11787b..175ba8cfbb 100644
--- a/src/physics/cam/hetfrz_classnuc_cam.F90
+++ b/src/physics/cam/hetfrz_classnuc_cam.F90
@@ -228,23 +228,23 @@ subroutine hetfrz_classnuc_cam_init(mincld_in, aero_props)
             wactfac_hnames(cnt) = trim(tmpstr)//'_wactfac'
 
             call addfld(tot_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'total '//trim(tmpstr)//' number density' )
+                 'total '//trim(tmpstr)//' number density', sampled_on_subcycle=.true.)
             call addfld(cld_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'cloud borne '//trim(tmpstr)//' number density' )
+                 'cloud borne '//trim(tmpstr)//' number density', sampled_on_subcycle=.true.)
             call addfld(cldfn_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'cloud borne '//trim(tmpstr)//' number density derived from fn' )
+                 'cloud borne '//trim(tmpstr)//' number density derived from fn', sampled_on_subcycle=.true.)
             call addfld(amb_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'ambient '//trim(tmpstr)//' number density' )
+                 'ambient '//trim(tmpstr)//' number density', sampled_on_subcycle=.true.)
             call addfld(coated_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'coated '//trim(tmpstr)//' number density' )
+                 'coated '//trim(tmpstr)//' number density', sampled_on_subcycle=.true.)
             call addfld(uncoated_dens_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'uncoated '//trim(tmpstr)//' number density' )
+                 'uncoated '//trim(tmpstr)//' number density', sampled_on_subcycle=.true.)
             call addfld(coated_frac_hnames(cnt),(/ 'lev' /), 'A', '#/cm3', &
-                 'coated '//trim(tmpstr)//' fraction' )
+                 'coated '//trim(tmpstr)//' fraction', sampled_on_subcycle=.true.)
             call addfld(radius_hnames(cnt),(/ 'lev' /), 'A', 'm', &
-                 'ambient '//trim(tmpstr)//' radius' )
+                 'ambient '//trim(tmpstr)//' radius', sampled_on_subcycle=.true.)
             call addfld(wactfac_hnames(cnt),(/ 'lev' /), 'A', ' ', &
-                 trim(tmpstr)//' water activity mass factor' )
+                 trim(tmpstr)//' water activity mass factor', sampled_on_subcycle=.true.)
 
          end if
       end do
@@ -261,49 +261,49 @@ subroutine hetfrz_classnuc_cam_init(mincld_in, aero_props)
    ! pbuf fields used by hetfrz_classnuc
    ast_idx      = pbuf_get_index('AST')
 
-   call addfld('FRZIMM', (/ 'lev' /), 'A', ' ', 'immersion  freezing')
-   call addfld('FRZCNT', (/ 'lev' /), 'A', ' ', 'contact    freezing')
-   call addfld('FRZDEP', (/ 'lev' /), 'A', ' ', 'deposition freezing')
-   call addfld('FREQIMM', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of immersion  freezing')
-   call addfld('FREQCNT', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of contact    freezing')
-   call addfld('FREQDEP', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of deposition freezing')
-   call addfld('FREQMIX', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of mixed-phase clouds' )
+   call addfld('FRZIMM', (/ 'lev' /), 'A', ' ', 'immersion  freezing', sampled_on_subcycle=.true.)
+   call addfld('FRZCNT', (/ 'lev' /), 'A', ' ', 'contact    freezing', sampled_on_subcycle=.true.)
+   call addfld('FRZDEP', (/ 'lev' /), 'A', ' ', 'deposition freezing', sampled_on_subcycle=.true.)
+   call addfld('FREQIMM', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of immersion  freezing', sampled_on_subcycle=.true.)
+   call addfld('FREQCNT', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of contact    freezing', sampled_on_subcycle=.true.)
+   call addfld('FREQDEP', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of deposition freezing', sampled_on_subcycle=.true.)
+   call addfld('FREQMIX', (/ 'lev' /), 'A', 'fraction', 'Fractional occurance of mixed-phase clouds' , sampled_on_subcycle=.true.)
 
-   call addfld('DSTFREZIMM', (/ 'lev' /), 'A', 'm-3s-1', 'dust immersion  freezing rate')
-   call addfld('DSTFREZCNT', (/ 'lev' /), 'A', 'm-3s-1', 'dust contact    freezing rate')
-   call addfld('DSTFREZDEP', (/ 'lev' /), 'A', 'm-3s-1', 'dust deposition freezing rate')
+   call addfld('DSTFREZIMM', (/ 'lev' /), 'A', 'm-3s-1', 'dust immersion  freezing rate', sampled_on_subcycle=.true.)
+   call addfld('DSTFREZCNT', (/ 'lev' /), 'A', 'm-3s-1', 'dust contact    freezing rate', sampled_on_subcycle=.true.)
+   call addfld('DSTFREZDEP', (/ 'lev' /), 'A', 'm-3s-1', 'dust deposition freezing rate', sampled_on_subcycle=.true.)
 
-   call addfld('BCFREZIMM', (/ 'lev' /), 'A', 'm-3s-1', 'bc immersion  freezing rate')
-   call addfld('BCFREZCNT', (/ 'lev' /), 'A', 'm-3s-1', 'bc contact    freezing rate')
-   call addfld('BCFREZDEP', (/ 'lev' /), 'A', 'm-3s-1', 'bc deposition freezing rate')
+   call addfld('BCFREZIMM', (/ 'lev' /), 'A', 'm-3s-1', 'bc immersion  freezing rate', sampled_on_subcycle=.true.)
+   call addfld('BCFREZCNT', (/ 'lev' /), 'A', 'm-3s-1', 'bc contact    freezing rate', sampled_on_subcycle=.true.)
+   call addfld('BCFREZDEP', (/ 'lev' /), 'A', 'm-3s-1', 'bc deposition freezing rate', sampled_on_subcycle=.true.)
 
    call addfld('NIMIX_IMM', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to het immersion freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to het immersion freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('NIMIX_CNT', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to het contact freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to het contact freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('NIMIX_DEP', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to het deposition freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to het deposition freezing in Mixed Clouds', sampled_on_subcycle=.true.)
 
    call addfld('DSTNIDEP', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to dst dep freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to dst dep freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('DSTNICNT', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to dst cnt freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to dst cnt freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('DSTNIIMM', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to dst imm freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to dst imm freezing in Mixed Clouds', sampled_on_subcycle=.true.)
 
    call addfld('BCNIDEP', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to bc dep freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to bc dep freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('BCNICNT', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to bc cnt freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to bc cnt freezing in Mixed Clouds', sampled_on_subcycle=.true.)
    call addfld('BCNIIMM', (/ 'lev' /), 'A', '#/m3', &
-               'Activated Ice Number Concentration due to bc imm freezing in Mixed Clouds')
+               'Activated Ice Number Concentration due to bc imm freezing in Mixed Clouds', sampled_on_subcycle=.true.)
 
    call addfld('NUMICE10s', (/ 'lev' /), 'A', '#/m3', &
-               'Ice Number Concentration due to het freezing in Mixed Clouds during 10-s period')
+               'Ice Number Concentration due to het freezing in Mixed Clouds during 10-s period', sampled_on_subcycle=.true.)
    call addfld('NUMIMM10sDST', (/ 'lev' /), 'A', '#/m3', &
-               'Ice Number Concentration due to imm freezing by dst in Mixed Clouds during 10-s period')
+               'Ice Number Concentration due to imm freezing by dst in Mixed Clouds during 10-s period', sampled_on_subcycle=.true.)
    call addfld('NUMIMM10sBC', (/ 'lev' /), 'A', '#/m3', &
-               'Ice Number Concentration due to imm freezing by bc in Mixed Clouds during 10-s period')
+               'Ice Number Concentration due to imm freezing by bc in Mixed Clouds during 10-s period', sampled_on_subcycle=.true.)
 
    if (hist_hetfrz_classnuc) then
 
diff --git a/src/physics/cam/ndrop.F90 b/src/physics/cam/ndrop.F90
index 9eea87d218..ea3d7522da 100644
--- a/src/physics/cam/ndrop.F90
+++ b/src/physics/cam/ndrop.F90
@@ -135,10 +135,10 @@ subroutine ndrop_init(aero_props)
 
          ! Add tendency fields to the history only when prognostic MAM is enabled.
          long_name = trim(tmpname) // ' dropmixnuc mixnuc column tendency'
-         call addfld(fieldname(mm),    horiz_only, 'A', unit, long_name)
+         call addfld(fieldname(mm),    horiz_only, 'A', unit, long_name, sampled_on_subcycle=.true.)
 
          long_name = trim(tmpname_cw) // ' dropmixnuc mixnuc column tendency'
-         call addfld(fieldname_cw(mm), horiz_only, 'A', unit, long_name)
+         call addfld(fieldname_cw(mm), horiz_only, 'A', unit, long_name, sampled_on_subcycle=.true.)
 
          if (history_aerosol) then
             call add_default(fieldname(mm), 1, ' ')
@@ -148,19 +148,19 @@ subroutine ndrop_init(aero_props)
       end do
    end do
 
-   call addfld('CCN1',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.02%')
-   call addfld('CCN2',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.05%')
-   call addfld('CCN3',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.1%')
-   call addfld('CCN4',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.2%')
-   call addfld('CCN5',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.5%')
-   call addfld('CCN6',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=1.0%')
+   call addfld('CCN1',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.02%', sampled_on_subcycle=.true.)
+   call addfld('CCN2',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.05%', sampled_on_subcycle=.true.)
+   call addfld('CCN3',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.1%',  sampled_on_subcycle=.true.)
+   call addfld('CCN4',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.2%',  sampled_on_subcycle=.true.)
+   call addfld('CCN5',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.5%',  sampled_on_subcycle=.true.)
+   call addfld('CCN6',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=1.0%',  sampled_on_subcycle=.true.)
 
 
-   call addfld('WTKE',     (/ 'lev' /), 'A', 'm/s', 'Standard deviation of updraft velocity')
-   call addfld('NDROPMIX', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number mixing')
-   call addfld('NDROPSRC', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number source')
-   call addfld('NDROPSNK', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number loss by microphysics')
-   call addfld('NDROPCOL', horiz_only,  'A', '#/m2', 'Column droplet number')
+   call addfld('WTKE',     (/ 'lev' /), 'A', 'm/s', 'Standard deviation of updraft velocity', sampled_on_subcycle=.true.)
+   call addfld('NDROPMIX', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number mixing', sampled_on_subcycle=.true.)
+   call addfld('NDROPSRC', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number source', sampled_on_subcycle=.true.)
+   call addfld('NDROPSNK', (/ 'lev' /), 'A', '#/kg/s', 'Droplet number loss by microphysics', sampled_on_subcycle=.true.)
+   call addfld('NDROPCOL', horiz_only,  'A', '#/m2', 'Column droplet number', sampled_on_subcycle=.true.)
 
    ! set the add_default fields
    if (history_amwg) then
diff --git a/src/physics/cam/ndrop_bam.F90 b/src/physics/cam/ndrop_bam.F90
index 6cd8231356..01ab3b5856 100644
--- a/src/physics/cam/ndrop_bam.F90
+++ b/src/physics/cam/ndrop_bam.F90
@@ -112,7 +112,7 @@ subroutine ndrop_bam_init
       if (trim(aername(iaer)) == 'SULFATE') idxsul   = iaer
 
       ! aerosol number concentration
-      call addfld(trim(aername(iaer))//'_m3', (/ 'lev' /), 'A', 'm-3', 'aerosol number concentration')
+      call addfld(trim(aername(iaer))//'_m3', (/ 'lev' /), 'A', 'm-3', 'aerosol number concentration', sampled_on_subcycle=.true.)
 
    end do
 
@@ -129,12 +129,12 @@ subroutine ndrop_bam_init
       end if
    end if
 
-   call addfld ('CCN1',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.02%')
-   call addfld ('CCN2',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.05%')
-   call addfld ('CCN3',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.1%')
-   call addfld ('CCN4',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.2%')
-   call addfld ('CCN5',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.5%')
-   call addfld ('CCN6',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=1.0%')
+   call addfld ('CCN1',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.02%', sampled_on_subcycle=.true.)
+   call addfld ('CCN2',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.05%', sampled_on_subcycle=.true.)
+   call addfld ('CCN3',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.1%',  sampled_on_subcycle=.true.)
+   call addfld ('CCN4',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.2%',  sampled_on_subcycle=.true.)
+   call addfld ('CCN5',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=0.5%',  sampled_on_subcycle=.true.)
+   call addfld ('CCN6',(/ 'lev' /), 'A','#/cm3','CCN concentration at S=1.0%',  sampled_on_subcycle=.true.)
 
    if (history_amwg) then
       call add_default('CCN3', 1, ' ')
diff --git a/src/physics/cam/nucleate_ice_cam.F90 b/src/physics/cam/nucleate_ice_cam.F90
index 7dff84f529..41cea58b38 100644
--- a/src/physics/cam/nucleate_ice_cam.F90
+++ b/src/physics/cam/nucleate_ice_cam.F90
@@ -263,52 +263,52 @@ subroutine nucleate_ice_cam_init(mincld_in, bulk_scale_in, pbuf2d, aero_props)
 
    if (cam_physpkg_is("cam7")) then
       ! Updates for PUMAS v1.21+
-      call addfld('NIHFTEN',  (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to homogenous freezing')
-      call addfld('NIDEPTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to deposition nucleation')
-      call addfld('NIIMMTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to immersion freezing')
-      call addfld('NIMEYTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to meyers deposition')
+      call addfld('NIHFTEN',  (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to homogenous freezing', sampled_on_subcycle=.true.)
+      call addfld('NIDEPTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to deposition nucleation', sampled_on_subcycle=.true.)
+      call addfld('NIIMMTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to immersion freezing', sampled_on_subcycle=.true.)
+      call addfld('NIMEYTEN', (/ 'lev' /), 'A', '1/m3/s', 'Activated Ice Number Concentration tendency due to meyers deposition', sampled_on_subcycle=.true.)
    else
-      call addfld('NIHF',  (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to homogenous freezing')
-      call addfld('NIDEP', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to deposition nucleation')
-      call addfld('NIIMM', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to immersion freezing')
-      call addfld('NIMEY', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to meyers deposition')
+      call addfld('NIHF',  (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to homogenous freezing', sampled_on_subcycle=.true.)
+      call addfld('NIDEP', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to deposition nucleation', sampled_on_subcycle=.true.)
+      call addfld('NIIMM', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to immersion freezing', sampled_on_subcycle=.true.)
+      call addfld('NIMEY', (/ 'lev' /), 'A', '1/m3', 'Activated Ice Number Concentration due to meyers deposition', sampled_on_subcycle=.true.)
    endif
 
-   call addfld('NIREGM',(/ 'lev' /), 'A', 'C', 'Ice Nucleation Temperature Threshold for Regime')
-   call addfld('NISUBGRID',(/ 'lev' /), 'A', '', 'Ice Nucleation subgrid saturation factor')
-   call addfld('NITROP_PD',(/ 'lev' /), 'A', '', 'Chemical Tropopause probability')
+   call addfld('NIREGM',(/ 'lev' /), 'A', 'C', 'Ice Nucleation Temperature Threshold for Regime', sampled_on_subcycle=.true.)
+   call addfld('NISUBGRID',(/ 'lev' /), 'A', '', 'Ice Nucleation subgrid saturation factor', sampled_on_subcycle=.true.)
+   call addfld('NITROP_PD',(/ 'lev' /), 'A', '', 'Chemical Tropopause probability', sampled_on_subcycle=.true.)
    if ( history_cesm_forcing ) then
       call add_default('NITROP_PD',8,' ')
    endif
 
    if (use_preexisting_ice) then
-      call addfld('fhom',      (/ 'lev' /), 'A','fraction', 'Fraction of cirrus where homogeneous freezing occur'   )
-      call addfld ('WICE',     (/ 'lev' /), 'A','m/s','Vertical velocity Reduction caused by preexisting ice'  )
-      call addfld ('WEFF',     (/ 'lev' /), 'A','m/s','Effective Vertical velocity for ice nucleation' )
+      call addfld('fhom',      (/ 'lev' /), 'A','fraction', 'Fraction of cirrus where homogeneous freezing occur', sampled_on_subcycle=.true.)
+      call addfld ('WICE',     (/ 'lev' /), 'A','m/s','Vertical velocity Reduction caused by preexisting ice', sampled_on_subcycle=.true.)
+      call addfld ('WEFF',     (/ 'lev' /), 'A','m/s','Effective Vertical velocity for ice nucleation', sampled_on_subcycle=.true.)
 
       if (cam_physpkg_is("cam7")) then
          ! Updates for PUMAS v1.21+
-         call addfld ('INnso4TEN',   (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency so4 (in) to ice_nucleation')
-         call addfld ('INnbcTEN',    (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency bc  (in) to ice_nucleation')
-         call addfld ('INndustTEN',  (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency dust (in) ice_nucleation')
-         call addfld ('INondustTEN',  (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency dust (out) from ice_nucleation')
+         call addfld ('INnso4TEN',   (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency so4 (in) to ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INnbcTEN',    (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency bc  (in) to ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INndustTEN',  (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency dust (in) ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INondustTEN',  (/ 'lev' /), 'A','1/m3/s','Number Concentration tendency dust (out) from ice_nucleation', sampled_on_subcycle=.true.)
          call addfld ('INhetTEN',    (/ 'lev' /), 'A','1/m3/s', &
-              'Tendency for contribution for in-cloud ice number density increase by het nucleation in ice cloud')
+              'Tendency for contribution for in-cloud ice number density increase by het nucleation in ice cloud', sampled_on_subcycle=.true.)
          call addfld ('INhomTEN',    (/ 'lev' /), 'A','1/m3/s', &
-              'Tendency for contribution for in-cloud ice number density increase by hom nucleation in ice cloud')
+              'Tendency for contribution for in-cloud ice number density increase by hom nucleation in ice cloud', sampled_on_subcycle=.true.)
       else
-         call addfld ('INnso4',   (/ 'lev' /), 'A','1/m3','Number Concentration so4 (in) to ice_nucleation')
-         call addfld ('INnbc',    (/ 'lev' /), 'A','1/m3','Number Concentration bc  (in) to ice_nucleation')
-         call addfld ('INndust',  (/ 'lev' /), 'A','1/m3','Number Concentration dust (in) ice_nucleation')
-         call addfld ('INondust',  (/ 'lev' /), 'A','1/m3','Number Concentration dust (out) from ice_nucleation')
+         call addfld ('INnso4',   (/ 'lev' /), 'A','1/m3','Number Concentration so4 (in) to ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INnbc',    (/ 'lev' /), 'A','1/m3','Number Concentration bc  (in) to ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INndust',  (/ 'lev' /), 'A','1/m3','Number Concentration dust (in) ice_nucleation', sampled_on_subcycle=.true.)
+         call addfld ('INondust',  (/ 'lev' /), 'A','1/m3','Number Concentration dust (out) from ice_nucleation', sampled_on_subcycle=.true.)
          call addfld ('INhet',    (/ 'lev' /), 'A','1/m3', &
-              'contribution for in-cloud ice number density increase by het nucleation in ice cloud')
+              'contribution for in-cloud ice number density increase by het nucleation in ice cloud', sampled_on_subcycle=.true.)
          call addfld ('INhom',    (/ 'lev' /), 'A','1/m3', &
-              'contribution for in-cloud ice number density increase by hom nucleation in ice cloud')
+              'contribution for in-cloud ice number density increase by hom nucleation in ice cloud', sampled_on_subcycle=.true.)
       endif
 
-      call addfld ('INFrehom', (/ 'lev' /), 'A','frequency','hom IN frequency ice cloud')
-      call addfld ('INFreIN',  (/ 'lev' /), 'A','frequency','frequency of ice nucleation occur')
+      call addfld ('INFrehom', (/ 'lev' /), 'A','frequency','hom IN frequency ice cloud', sampled_on_subcycle=.true.)
+      call addfld ('INFreIN',  (/ 'lev' /), 'A','frequency','frequency of ice nucleation occur', sampled_on_subcycle=.true.)
 
       if (hist_preexisting_ice) then
          call add_default ('WSUBI   ', 1, ' ')  ! addfld/outfld calls are in microp_aero
diff --git a/src/physics/cam/subcol_SILHS.F90 b/src/physics/cam/subcol_SILHS.F90
index c373ed6b3e..05653b9f03 100644
--- a/src/physics/cam/subcol_SILHS.F90
+++ b/src/physics/cam/subcol_SILHS.F90
@@ -489,80 +489,80 @@ subroutine subcol_init_SILHS(pbuf2d)
       ! Register output fields from SILHS
       !-------------------------------
       call addfld('SILHS_NCLD_SCOL', (/'psubcols', 'ilev    '/), 'I', 'm^-3', &
-           'Subcolumn Cloud Number Concentration', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Cloud Number Concentration', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_NRAIN_SCOL', (/'psubcols', 'ilev    '/), 'I', 'm^-3', &
-           'Subcolumn Number Concentration of Rain from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Number Concentration of Rain from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_OMEGA_SCOL', (/'psubcols', 'ilev    '/), 'I', 'Pa/s', &
-           'Subcolumn vertical pressure velocity', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn vertical pressure velocity', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_RCM_SCOL', (/'psubcols', 'ilev    '/), 'I', 'kg/kg', &
-           'Subcolumn Cloud Liquid Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Cloud Liquid Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_RICLD_SCOL', (/'psubcols', 'ilev    '/), 'I', 'kg/kg', &
-           'Subcolumn Cloud Ice Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Cloud Ice Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_NICLD_SCOL', (/'psubcols', 'ilev    '/), 'I', 'kg/kg', &
-           'Subcolumn Cloud Ice Number Conc from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Cloud Ice Number Conc from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_RRAIN_SCOL', (/'psubcols', 'ilev    '/), 'I', 'kg/kg', &
-           'Subcolumn Precipitating Liquid Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Precipitating Liquid Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_RT_SCOL', (/'psubcols', 'ilev    '/), 'I', 'kg/kg ', &
-           'Subcolumn Total Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn Total Water from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_THLM_SCOL', (/'psubcols', 'ilev    '/), 'I', 'K', &
-           'Subcolumn liquid water pot temperature', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn liquid water pot temperature', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_WEIGHT_SCOL', (/'psubcols'/), 'I', 'frac', &
-           'Weights for each subcolumn', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Weights for each subcolumn', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
       call addfld('SILHS_WM_SCOL', (/'psubcols', 'ilev    '/), 'I', 'm/s', &
-           'Subcolumn vertical velocity from SILHS', flag_xyfill=.true., fill_value=1.e30_r8)
+           'Subcolumn vertical velocity from SILHS', flag_xyfill=.true., fill_value=1.e30_r8, sampled_on_subcycle=.true.)
 
       call addfld('NR_IN_LH', (/ 'lev' /), 'I', 'm^-3', &
-                  'Num Rain Conc as input to SILHS')
+                  'Num Rain Conc as input to SILHS', sampled_on_subcycle=.true.)
      call addfld('SILHS_RTM', (/ 'ilev' /), 'I', 'kg/kg', &
-                  'Input total water mixing ratio')
+                  'Input total water mixing ratio', sampled_on_subcycle=.true.)
      call addfld('SILHS_THLM', (/ 'ilev' /), 'I', 'K', &
-                  'Input liquid water potential temperature')
+                  'Input liquid water potential temperature', sampled_on_subcycle=.true.)
      call addfld('SILHS_QC_IN', (/ 'lev' /), 'I', 'kg/kg', &
-                  'Input cloud water mixing ratio')
+                  'Input cloud water mixing ratio', sampled_on_subcycle=.true.)
      call addfld('SILHS_QI_IN', (/ 'lev' /), 'I', 'kg/kg', &
-                  'Input cloud ice mixing ratio')
+                  'Input cloud ice mixing ratio', sampled_on_subcycle=.true.)
      call addfld('SILHS_NC_IN', (/ 'lev' /), 'I', '#/kg', &
-                  'Input cloud water number concentration')
+                  'Input cloud water number concentration', sampled_on_subcycle=.true.)
      call addfld('SILHS_NI_IN', (/ 'lev' /), 'I', '#/kg', &
-                  'Input cloud ice number concentration')
+                  'Input cloud ice number concentration', sampled_on_subcycle=.true.)
      call addfld('AKM_CLUBB', (/ 'ilev' /), 'I', '(kg/kg)/s', &
-                  'Exact Kessler autoconversion')
+                  'Exact Kessler autoconversion', sampled_on_subcycle=.true.)
      call addfld('AKM_LH_CLUBB', (/ 'ilev' /), 'I', '(kg/kg)/s', &
-                  'Monte Carlo estimate of Kessler autoconversion')
+                  'Monte Carlo estimate of Kessler autoconversion', sampled_on_subcycle=.true.)
      call addfld('INVS_EXNER', (/ 'lev' /), 'I', 'none', &
-                  'inverse EXNER function from state in subcol_SILHS')
+                  'inverse EXNER function from state in subcol_SILHS', sampled_on_subcycle=.true.)
      call addfld('SILHS_ZTODT', horiz_only, 'I', 's', & 
-                  'Length of Physics timestep (for debugging)')
+                  'Length of Physics timestep (for debugging)', sampled_on_subcycle=.true.)
      if ( subcol_SILHS_constrainmn ) then
         call addfld('SILHS_MSC_CLDICE', (/ 'lev' /), 'A', 'kg/kg', &
-                    'Mean Cloud Ice across subcolumns')
+                    'Mean Cloud Ice across subcolumns', sampled_on_subcycle=.true.)
         call addfld('SILHS_STDSC_CLDICE', (/ 'lev' /), 'A', 'kg/kg', &
-                    'Standard deviation of Ice across subcolumns')
+                    'Standard deviation of Ice across subcolumns', sampled_on_subcycle=.true.)
         if ( ixsnow > 0 ) then
            call addfld('SILHS_MSC_CLDLIQ', (/ 'lev' /), 'A', 'kg/kg', &
-                       'Mean Cloud Liquid across subcolumns')
+                       'Mean Cloud Liquid across subcolumns', sampled_on_subcycle=.true.)
            call addfld('SILHS_STDSC_CLDLIQ', (/ 'lev' /), 'A', 'kg/kg', &
-                       'Standard deviation of Liquid across subcolumns')
+                       'Standard deviation of Liquid across subcolumns', sampled_on_subcycle=.true.)
            call addfld('SILHS_MSC_Q', (/ 'lev' /), 'A', 'kg/kg', &
-                       'Mean water vapor across subcolumns')
+                       'Mean water vapor across subcolumns', sampled_on_subcycle=.true.)
            call addfld('SILHS_STDSC_Q', (/ 'lev' /), 'A', 'kg/kg', &
-                       'Standard deviation of water vapor across subcolumns')
+                       'Standard deviation of water vapor across subcolumns', sampled_on_subcycle=.true.)
         endif ! ixsnow > 0
      endif ! subcol_SILHS_constrainmn
      call addfld('SILHS_EFF_CLDFRAC', (/ 'lev' /), 'A', 'frac', &
-                  'Calculated cloud fraction from subcolumn liq or ice') 
+                  'Calculated cloud fraction from subcolumn liq or ice', sampled_on_subcycle=.true.)
 
      call addfld('SILHS_CLUBB_PRECIP_FRAC', (/ 'lev' /), 'A', 'frac', &
-                  'Precipitation fraction from CLUBB (set_up_pdf_params_incl_hydromet)')
+                  'Precipitation fraction from CLUBB (set_up_pdf_params_incl_hydromet)', sampled_on_subcycle=.true.)
      call addfld('SILHS_CLUBB_ICE_SS_FRAC', (/ 'lev' /), 'A', 'frac', &
-                  'Ice supersaturation fraction from CLUBB')
-
-     call addfld ('QVHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Water vapor mixing ratio tendency from hole filling')
-     call addfld ('QCHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud water mixing ratio tendency from hole filling')
-     call addfld ('QRHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Rain water mixing ratio tendency from hole filling')
-     call addfld ('QIHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud ice mixing ratio tendency from hole filling')
-     call addfld ('QSHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from hole filling')
-     call addfld ('THFTEN', (/ 'lev' /), 'A', 'K/s', 'Temperature tendency from hole filling')
+                  'Ice supersaturation fraction from CLUBB', sampled_on_subcycle=.true.)
+
+     call addfld ('QVHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Water vapor mixing ratio tendency from hole filling', sampled_on_subcycle=.true.)
+     call addfld ('QCHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud water mixing ratio tendency from hole filling', sampled_on_subcycle=.true.)
+     call addfld ('QRHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Rain water mixing ratio tendency from hole filling', sampled_on_subcycle=.true.)
+     call addfld ('QIHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Cloud ice mixing ratio tendency from hole filling', sampled_on_subcycle=.true.)
+     call addfld ('QSHFTEN', (/ 'lev' /), 'A', 'kg/kg/s', 'Snow mixing ratio tendency from hole filling', sampled_on_subcycle=.true.)
+     call addfld ('THFTEN', (/ 'lev' /), 'A', 'K/s', 'Temperature tendency from hole filling', sampled_on_subcycle=.true.)
 
 #endif
 #endif

From f820ab62a28ba9b9e39633e6a480af52d86c0776 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Mon, 4 Nov 2024 15:30:33 -0700
Subject: [PATCH 31/53] remove "prev" argument for inst files; move open file
 logging to before pio call

---
 src/control/cam_history.F90 | 2 +-
 src/utils/cam_pio_utils.F90 | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/control/cam_history.F90 b/src/control/cam_history.F90
index d8346ec22f..81659ec12a 100644
--- a/src/control/cam_history.F90
+++ b/src/control/cam_history.F90
@@ -5738,7 +5738,7 @@ subroutine wshist (rgnht_in)
                inst_filename_spec = hfilename_spec(t)
             end if
             fname_inst = interpret_filename_spec( inst_filename_spec, number=(t-1), &
-                 prev=prev, flag_spec='i' )
+                 flag_spec='i' )
           end if
           !
           ! Check that this new filename isn't the same as a previous or current filename
diff --git a/src/utils/cam_pio_utils.F90 b/src/utils/cam_pio_utils.F90
index 350c421539..7fd58b13cd 100644
--- a/src/utils/cam_pio_utils.F90
+++ b/src/utils/cam_pio_utils.F90
@@ -1133,12 +1133,14 @@ subroutine cam_pio_openfile(file, fname, mode)
 
     integer :: ierr
 
+    if(pio_iotask_rank(pio_subsystem) == 0) then
+       write(iulog,*) 'Opening existing file ', trim(fname), file%fh
+    end if
+
     ierr = pio_openfile(pio_subsystem, file, pio_iotype, fname, mode)
 
     if(ierr/= PIO_NOERR) then
        call endrun('Failed to open '//trim(fname)//' to read')
-    else if(pio_iotask_rank(pio_subsystem) == 0) then
-       write(iulog,*) 'Opened existing file ', trim(fname), file%fh
     end if
 
   end subroutine cam_pio_openfile

From 03c0a0f8798ec46a439d8fccaec84774208dec0c Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Mon, 11 Nov 2024 13:44:43 -0700
Subject: [PATCH 32/53] initial changelog

---
 doc/ChangeLog | 97 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index fdc0c4aa65..aad083f035 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,5 +1,102 @@
 ===============================================================
 
+Tag name: cam6_4_047
+Originator(s): peverwhee
+Date: 12 November 2024
+One-line Summary: History bugfixes
+Github PR URL: https://github.com/ESCOMP/CAM/pull/1163
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+- Issue #1149: cam history always chooses first averaging flag when using duplicate fields
+- Issue #1150: CAM history erroneously overrides averaging flags for nhtfrq=1
+- Issue #1166: time_bounds array should not be present in history files containing instantaneous output
+- Issue #1167: Time shown in history file names is incorrect for instantaneous data
+- Issue #1183: Suggested improvement for openfile
+- Updates git-fleximod to v0.9.2
+
+Describe any changes made to build system:
+M   bld/namelist_files/use_cases/sd_waccm_sulfur.xml
+ - Remove bad XML comment line
+
+Describe any changes made to the namelist: none
+
+List any changes to the defaults for the boundary datasets: none
+
+Describe any substantial timing or memory changes: none
+
+Code reviewed by: brian-eaton
+
+List all files eliminated: none
+
+List all files added and what they do: none
+
+List all existing files that have been modified, and describe the changes:
+
+M   .lib/git-fleximod/*
+ - updates to move git-fleximod to v0.9.2
+
+M   src/control/cam_history.F90
+ - remove nhtfrq=1 accumulation flag override if sampled_on_subcyle=.true.
+ - modify list_index routine to optionally check for duplicates/compatibility
+ - endrun with message including all duplicates found (if flags differ)
+ - remove time_bounds from instantaneous history files
+ - override instantaneous file name for monthly files to include full timestep
+   - also report correct timestamp on inst. files (don't use prev timestamp as
+   in accumulated files)
+
+M   src/control/cam_history_support.F90
+ - add sampled_on_subcycle to field_info object
+
+M   src/physics/cam/cam_diagnostics.F90
+M   src/physics/cam/clubb_intr.F90
+M   src/physics/cam/hetfrz_classnuc_cam.F90
+M   src/physics/cam/macrop_driver.F90
+M   src/physics/cam/micro_pumas_cam.F90
+M   src/physics/cam/microp_aero.F90
+M   src/physics/cam/ndrop.F90
+M   src/physics/cam/ndrop_bam.F90
+M   src/physics/cam/nucleate_ice_cam.F90
+M   src/physics/cam/subcol_SILHS.F90
+M   src/physics/cam7/micro_pumas_cam.F90
+M   src/physics/cam7/stochastic_emulated_cam.F90
+M   src/physics/cam7/stochastic_tau_cam.F90
+ - add sampled_on_subcycle=.true. argument to addflds calls for history fields
+   that are outfld-ed in the macmic loop
+
+M   src/utils/cam_pio_utils.F90
+ - move filename logging to before pio call
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+derecho/intel/aux_cam:
+
+SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: FAIL)
+SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL)
+ - pre-existing failures due to build-namelist error requiring CLM/CTSM external update.
+
+ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL)
+SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF)
+ - pre-existing failure due to HEMCO not having reproducible results issues #1018 and #856
+
+derecho/nvhpc/aux_cam:
+
+izumi/nag/aux_cam:
+
+DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
+ - pre-existing failure -- issue #670
+
+izumi/gnu/aux_cam:
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers: none
+
+===============================================================
+
 Tag name: cam6_4_046
 Originator(s): sjsprecious
 Date: 06 November 2024

From cdcbea521b4d1319fa9ae116c1d3d3fa051c0e90 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Tue, 12 Nov 2024 13:39:18 -0700
Subject: [PATCH 33/53] update archive_baseline script to modify read
 permissions on izumi

---
 test/system/archive_baseline.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/system/archive_baseline.sh b/test/system/archive_baseline.sh
index f64561dc4d..ef836a8131 100755
--- a/test/system/archive_baseline.sh
+++ b/test/system/archive_baseline.sh
@@ -68,6 +68,7 @@ case $hostname in
     test_file_list="tests_pretag_izumi_${CAM_FC,,}"
     cam_tag=$1_${CAM_FC,,}
     baselinedir="/fs/cgd/csm/models/atm/cam/pretag_bl/$cam_tag"
+    chmod_cmd="chmod -R a+r ${baselinedir}"
   ;;
 
   de*)
@@ -78,6 +79,7 @@ case $hostname in
     test_file_list="tests_pretag_derecho_${CAM_FC,,}"
     cam_tag=$1_${CAM_FC,,}
     baselinedir="/glade/campaign/cesm/community/amwg/cam_baselines/$cam_tag"
+    chmod_cmd=""
   ;;
 
   * ) echo "ERROR: machine $hostname not currently supported"; exit 1 ;;
@@ -97,6 +99,7 @@ if [ -n "$CESM_TESTDIR" ]; then
     if [ -d $CESM_TESTDIR/baselines ]; then
       echo "Using cp to archive baselines."
       cp -r $CESM_TESTDIR/baselines/. $root_baselinedir/$cam_tag
+      eval ${chmod_cmd}
     else
       echo "Using bless_test_results to archive baselines."
       ../../cime/CIME/Tools/bless_test_results -p -t '' -c '' -r $CESM_TESTDIR --baseline-root $root_baselinedir -b $cam_tag -f -s

From 7244285a9702f8ec99478bc5dc9d6991a634826a Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 18 Nov 2024 11:26:46 -0500
Subject: [PATCH 34/53] Update build issues; atmos_phys external to head of PR

---
 .gitmodules                      | 2 +-
 src/atmos_phys                   | 2 +-
 src/physics/cam/check_energy.F90 | 5 +++--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 195d003bc2..c478c0c686 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/jimmielin/atmospheric_physics
-        fxtag = 7b188e35
+        fxtag = b1e2c2a9
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index 7b188e35fe..b1e2c2a9d1 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit 7b188e35fe26247289d3bdbbbdd902cde382765a
+Subproject commit b1e2c2a9d188172f888b0b5c903c5a12a741f30e
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 774764c563..9fbc2d592c 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -814,6 +814,7 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
         ncol            = ncol, &
         pver            = pver, &
         pcnst           = pcnst, &
+        iulog           = iulog, &
         q               = state%q(1:ncol,1:pver,1:pcnst), &
         pdel            = state%pdel(1:ncol,1:pver), &
         u               = state%u(1:ncol,1:pver), &
@@ -852,7 +853,7 @@ end subroutine check_energy_cam_chng
   ! Add heating rate required for global mean total energy conservation
   subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
     use physics_types,    only: physics_ptend, physics_ptend_init
-    use physconst,        only: rga
+    use physconst,        only: gravit
 
     ! SCAM support
     use scamMod,          only: single_column, use_camiop, heat_glob_scm
@@ -902,7 +903,7 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
         ncol      = ncol, &
         pver      = pver, &
         pint      = state%pint(:ncol,:), &
-        rga       = rga, &
+        gravit    = gravit, &
         heat_glob = heat_glob, &
         ptend_s   = ptend%s(:ncol,:), &
         eshflx    = eshflx(:ncol) &

From e3e6a131208feaf72360d5fa5767ddf638ecc3c9 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 18 Nov 2024 11:52:16 -0500
Subject: [PATCH 35/53] Update check_energy_cam_fix interface

---
 src/physics/cam/check_energy.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 9fbc2d592c..592faeab00 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -872,6 +872,7 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
     integer     :: ncol                     ! number of atmospheric columns in chunk
     integer     :: lchnk                    ! chunk number
     real(r8)    :: heat_out(pcols)
+    character(len=64) :: dummy_scheme_name  ! dumy scheme name for CCPP-ized scheme
 
     lchnk = state%lchnk
     ncol  = state%ncol
@@ -906,7 +907,8 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
         gravit    = gravit, &
         heat_glob = heat_glob, &
         ptend_s   = ptend%s(:ncol,:), &
-        eshflx    = eshflx(:ncol) &
+        eshflx    = eshflx(:ncol), &
+        scheme_name = dummy_scheme_name
     )
 
   end subroutine check_energy_cam_fix

From a10a9557acc06679839e64682c9c3f5f4b96663b Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 18 Nov 2024 13:15:13 -0500
Subject: [PATCH 36/53] Update check_energy_cam_fix interface (2)

---
 src/physics/cam/check_energy.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 592faeab00..3f203bae2c 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -872,7 +872,7 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
     integer     :: ncol                     ! number of atmospheric columns in chunk
     integer     :: lchnk                    ! chunk number
     real(r8)    :: heat_out(pcols)
-    character(len=64) :: dummy_scheme_name  ! dumy scheme name for CCPP-ized scheme
+    character(len=64) :: dummy_scheme_name  ! dummy scheme name for CCPP-ized scheme
 
     lchnk = state%lchnk
     ncol  = state%ncol
@@ -908,7 +908,7 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
         heat_glob = heat_glob, &
         ptend_s   = ptend%s(:ncol,:), &
         eshflx    = eshflx(:ncol), &
-        scheme_name = dummy_scheme_name
+        scheme_name = dummy_scheme_name &
     )
 
   end subroutine check_energy_cam_fix

From 902c495ebb7ec85b107ed7cba8bf003136b9ca04 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 19 Nov 2024 12:26:51 -0500
Subject: [PATCH 37/53] Update atmos_phys to atmos_phys0_07_000

---
 .gitmodules    | 4 ++--
 src/atmos_phys | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index c478c0c686..40e189dab5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -35,8 +35,8 @@
 
 [submodule "atmos_phys"]
 	path = src/atmos_phys
-	url = https://github.com/jimmielin/atmospheric_physics
-        fxtag = b1e2c2a9
+	url = https://github.com/ESCOMP/atmospheric_physics
+        fxtag = atmos_phys0_07_000
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index b1e2c2a9d1..e10f81151e 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit b1e2c2a9d188172f888b0b5c903c5a12a741f30e
+Subproject commit e10f81151ecef5416462472ef0e52810dc82e412

From a9441a893bbaa2db6eb15087c13edc4ec7ff2348 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Wed, 20 Nov 2024 09:37:50 -0700
Subject: [PATCH 38/53] update git-fleximod to 0.9.3

---
 .lib/git-fleximod/git_fleximod/cli.py         | 38 ++++++++++---------
 .../git-fleximod/git_fleximod/git_fleximod.py |  2 +-
 .lib/git-fleximod/git_fleximod/submodule.py   |  2 +-
 .lib/git-fleximod/poetry.lock                 |  6 +--
 .lib/git-fleximod/pyproject.toml              |  2 +-
 .lib/git-fleximod/tbump.toml                  |  2 +-
 .lib/git-fleximod/tests/conftest.py           |  4 +-
 doc/ChangeLog                                 | 10 +++--
 test/system/archive_baseline.sh               |  4 +-
 9 files changed, 38 insertions(+), 32 deletions(-)

diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
index 208bc04684..ac9493cfc3 100644
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ b/.lib/git-fleximod/git_fleximod/cli.py
@@ -2,27 +2,31 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree
     which contains a file called filename """
-    d = Path.cwd()
-    root = Path(d.root)
-    dirlist = []
-    dl = d
-    while dl != root:
-        dirlist.append(dl)
-        dl = dl.parent
-    dirlist.append(root)
-    dirlist.reverse()
-
-    for dl in dirlist:
-        attempt = dl / filename
-        if attempt.is_file():
-            return str(dl)
-    return None
-
+    try:
+        root = utils.execute_subprocess(["git","rev-parse", "--show-toplevel"],
+                                        output_to_caller=True ).rstrip()
+    except:
+        d = Path.cwd()
+        root = Path(d.root)
+        dirlist = []
+        dl = d
+        while dl != root:
+            dirlist.append(dl)
+            dl = dl.parent
+        dirlist.append(root)
+        dirlist.reverse()
+
+        for dl in dirlist:
+            attempt = dl / filename
+            if attempt.is_file():
+                return str(dl)
+        return None
+    return Path(root)
 
 def get_parser():
     description = """
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
index 0851e9d095..13f35df959 100755
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ b/.lib/git-fleximod/git_fleximod/git_fleximod.py
@@ -342,7 +342,7 @@ def main():
         excludelist=excludelist,
     )
     if not gitmodules.sections():
-        sys.exit("No submodule components found")
+        sys.exit(f"No submodule components found, root_dir={root_dir}")
     retval = 0
     if action == "update":
         submodules_update(gitmodules, root_dir, fxrequired, force)
diff --git a/.lib/git-fleximod/git_fleximod/submodule.py b/.lib/git-fleximod/git_fleximod/submodule.py
index c939d54bc9..75d9dd4eb9 100644
--- a/.lib/git-fleximod/git_fleximod/submodule.py
+++ b/.lib/git-fleximod/git_fleximod/submodule.py
@@ -221,7 +221,7 @@ def sparse_checkout(self):
         if superroot:
             gitroot = superroot.strip()
         else:
-            gitroot = self.root_dir.strip()
+            gitroot = self.root_dir
         # Now need to move the .git dir to the submodule location
         rootdotgit = os.path.join(self.root_dir, ".git")
         while os.path.isfile(rootdotgit):
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
index 3a74effcd1..ac82fb0d97 100644
--- a/.lib/git-fleximod/poetry.lock
+++ b/.lib/git-fleximod/poetry.lock
@@ -30,13 +30,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
index 619cdabe3b..1d0419ad20 100644
--- a/.lib/git-fleximod/pyproject.toml
+++ b/.lib/git-fleximod/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.9.2"
+version = "0.9.3"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
index 920ff0591c..b432206a54 100644
--- a/.lib/git-fleximod/tbump.toml
+++ b/.lib/git-fleximod/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.9.2"
+current = "0.9.3"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
index 81edbe713e..1dd1b86f34 100644
--- a/.lib/git-fleximod/tests/conftest.py
+++ b/.lib/git-fleximod/tests/conftest.py
@@ -32,7 +32,7 @@ def logger():
      "submodule_name": "test_optional",
      "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
      "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)",
+     "status3" : "test_optional not checked out, out of sync at tag MPIserial_2.5.1, expected tag is MPIserial_2.4.0 (optional)",
      "status4" : "test_optional at tag MPIserial_2.4.0",
      "gitmodules_content": """
      [submodule "test_optional"]
@@ -46,7 +46,7 @@ def logger():
      "submodule_name": "test_alwaysoptional",
      "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
      "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "out of sync at tag None, expected tag is e5cf35c",
+     "status3" : "out of sync at tag MPIserial_2.5.1, expected tag is e5cf35c",
      "status4" : "test_alwaysoptional at hash e5cf35c",
      "gitmodules_content": """
     [submodule "test_alwaysoptional"]
diff --git a/doc/ChangeLog b/doc/ChangeLog
index aad083f035..ef811a5bc6 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,8 +1,8 @@
 ===============================================================
 
-Tag name: cam6_4_047
+Tag name: cam6_4_049
 Originator(s): peverwhee
-Date: 12 November 2024
+Date:  November 2024
 One-line Summary: History bugfixes
 Github PR URL: https://github.com/ESCOMP/CAM/pull/1163
 
@@ -12,7 +12,8 @@ Purpose of changes (include the issue number and title text for each relevant Gi
 - Issue #1166: time_bounds array should not be present in history files containing instantaneous output
 - Issue #1167: Time shown in history file names is incorrect for instantaneous data
 - Issue #1183: Suggested improvement for openfile
-- Updates git-fleximod to v0.9.2
+- Update git-fleximod to v0.9.3
+- Update archive_baseline.sh modify read permissions on izumi
 
 Describe any changes made to build system:
 M   bld/namelist_files/use_cases/sd_waccm_sulfur.xml
@@ -66,6 +67,9 @@ M   src/physics/cam7/stochastic_tau_cam.F90
 M   src/utils/cam_pio_utils.F90
  - move filename logging to before pio call
 
+M   test/system/archive_baseline.sh
+ - make all baseline files globally readable on izumi
+
 If there were any failures reported from running test_driver.sh on any test
 platform, and checkin with these failures has been OK'd by the gatekeeper,
 then copy the lines from the td.*.status files for the failed tests to the
diff --git a/test/system/archive_baseline.sh b/test/system/archive_baseline.sh
index ef836a8131..99a1003fb0 100755
--- a/test/system/archive_baseline.sh
+++ b/test/system/archive_baseline.sh
@@ -68,7 +68,6 @@ case $hostname in
     test_file_list="tests_pretag_izumi_${CAM_FC,,}"
     cam_tag=$1_${CAM_FC,,}
     baselinedir="/fs/cgd/csm/models/atm/cam/pretag_bl/$cam_tag"
-    chmod_cmd="chmod -R a+r ${baselinedir}"
   ;;
 
   de*)
@@ -79,7 +78,6 @@ case $hostname in
     test_file_list="tests_pretag_derecho_${CAM_FC,,}"
     cam_tag=$1_${CAM_FC,,}
     baselinedir="/glade/campaign/cesm/community/amwg/cam_baselines/$cam_tag"
-    chmod_cmd=""
   ;;
 
   * ) echo "ERROR: machine $hostname not currently supported"; exit 1 ;;
@@ -99,7 +97,7 @@ if [ -n "$CESM_TESTDIR" ]; then
     if [ -d $CESM_TESTDIR/baselines ]; then
       echo "Using cp to archive baselines."
       cp -r $CESM_TESTDIR/baselines/. $root_baselinedir/$cam_tag
-      eval ${chmod_cmd}
+      chmod -R a+r ${baselinedir}
     else
       echo "Using bless_test_results to archive baselines."
       ../../cime/CIME/Tools/bless_test_results -p -t '' -c '' -r $CESM_TESTDIR --baseline-root $root_baselinedir -b $cam_tag -f -s

From bc5428f4eaaf55641176b61034a1a71363a943cd Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Wed, 20 Nov 2024 21:41:42 -0500
Subject: [PATCH 39/53] Address review comments

---
 src/control/cam_snapshot_common.F90 |  2 ++
 src/physics/cam/check_energy.F90    | 15 +++++++++------
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/control/cam_snapshot_common.F90 b/src/control/cam_snapshot_common.F90
index fa558b3ad2..0f49d27a02 100644
--- a/src/control/cam_snapshot_common.F90
+++ b/src/control/cam_snapshot_common.F90
@@ -848,6 +848,8 @@ subroutine state_snapshot_all_outfld(lchnk, file_num, state)
          call outfld(state_snapshot(i)%standard_name, state%te_cur(:, dyn_te_idx), pcols, lchnk)
 
       case ('air_composition_cp_or_cv_dycore')
+         ! this field is not part of physics state (it is in air_composition)
+         ! but describes the atmospheric thermodynamic state and thus saved within the snapshot
          call outfld(state_snapshot(i)%standard_name, cp_or_cv_dycore(:,:,lchnk), pcols, lchnk)
 
       case default
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 3f203bae2c..5350371cef 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -461,6 +461,9 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
     lchnk = state%lchnk
     ncol  = state%ncol
 
+    ! The "vertical coordinate" parameter is equivalent to the dynamical core
+    ! energy formula parameter, which controls the dycore energy formula used
+    ! by get_hydrostatic_energy.
     if (present(vc)) then
       vc_loc = vc
     else
@@ -758,11 +761,11 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
     type(physics_tend ), intent(inout) :: tend
     character*(*),intent(in) :: name               ! parameterization name for fluxes
     integer , intent(in) :: nstep                  ! current timestep number
-    real(r8), intent(in) :: ztodt                  ! 2 delta t (model time increment)
-    real(r8), intent(in) :: flx_vap(:)             ! (pcols) - boundary flux of vapor         (kg/m2/s)
-    real(r8), intent(in) :: flx_cnd(:)             ! (pcols) -boundary flux of liquid+ice    (m/s) (precip?)
-    real(r8), intent(in) :: flx_ice(:)             ! (pcols) -boundary flux of ice           (m/s) (snow?)
-    real(r8), intent(in) :: flx_sen(:)             ! (pcols) -boundary flux of sensible heat (w/m2)
+    real(r8), intent(in) :: ztodt                  ! physics timestep (s)
+    real(r8), intent(in) :: flx_vap(:)             ! (pcols) - boundary flux of vapor (kg/m2/s)
+    real(r8), intent(in) :: flx_cnd(:)             ! (pcols) - boundary flux of lwe liquid+ice (m/s)
+    real(r8), intent(in) :: flx_ice(:)             ! (pcols) - boundary flux of lwe ice (m/s)
+    real(r8), intent(in) :: flx_sen(:)             ! (pcols) - boundary flux of sensible heat (W/m2)
 
     integer :: lchnk                               ! chunk identifier
     integer :: ncol                                ! number of atmospheric columns
@@ -785,7 +788,7 @@ subroutine check_energy_cam_chng(state, tend, name, nstep, ztodt,        &
 
             scaling_dycore(:ncol,:)  = cpairv(:ncol,:,lchnk)/local_cp_or_cv_dycore(:ncol,:) ! cp/cv scaling
         endif
-    elseif(state%psetcols > pcols) then
+    else if(state%psetcols > pcols) then
         ! Subcolumns
         if(.not. all(cpairv(:,:,:) == cpair)) then
             call endrun('check_energy_chng: cpairv is not allowed to vary when subcolumns are turned on')

From c0b9d8bc47d2a7b658d1b45a31e723f5ca7055a3 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Thu, 21 Nov 2024 08:51:05 -0500
Subject: [PATCH 40/53] Update comment for tot_energy_phys vc parameter

---
 src/physics/cam/check_energy.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 5350371cef..7af3a32bda 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -425,7 +425,7 @@ subroutine tot_energy_phys(state, outfld_name_suffix,vc)
 
     type(physics_state), intent(inout) :: state
     character(len=*),    intent(in)    :: outfld_name_suffix ! suffix for "outfld"
-    integer, optional,   intent(in)    :: vc                 ! vertical coordinate
+    integer, optional,   intent(in)    :: vc                 ! vertical coordinate (controls energy formula to use)
 
 !---------------------------Local storage-------------------------------
     real(r8) :: se(pcols)                          ! Dry Static energy (J/m2)

From 3aa74633894adc742e7e0590a9786d5c8f9be6a4 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Wed, 4 Dec 2024 14:01:54 -0700
Subject: [PATCH 41/53] update to head of cam_development; update cime and
 share externals

---
 .gitmodules | 4 ++--
 cime        | 2 +-
 share       | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 817bb1ff6b..7fed08dbb7 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -151,7 +151,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.41
+fxtag = cime6.1.47
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
@@ -172,7 +172,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.2
+fxtag = share1.1.4
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
diff --git a/cime b/cime
index 1236c0fede..f28506021f 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit 1236c0feded460aef3e5bdba18e4b850f1997346
+Subproject commit f28506021f122fbfab8fea741da35ac48ab875b2
diff --git a/share b/share
index f6f31fd61c..63ae6cc216 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit f6f31fd61cb8f80aee97311fcca64b3e26b0202c
+Subproject commit 63ae6cc216c517d3ced4d3466d3616b4c24107b5

From 5865cd8aed0fb0e6f2ac784ea9f9fe9564fd56bc Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Tue, 17 Dec 2024 10:04:00 -0700
Subject: [PATCH 42/53] update externals; use temp ctsm tag

---
 .gitmodules | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 7fed08dbb7..f72ec58ae7 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -151,14 +151,14 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.47
+fxtag = cime6.1.49
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.22
+fxtag = cmeps1.0.32
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
@@ -172,7 +172,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.4
+fxtag = share1.1.6
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
@@ -192,8 +192,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 
 [submodule "clm"]
 path = components/clm
-url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.3.002
+url = https://github.com/jedwards4b/CTSM
+fxtag = 14aad99fea41c4bef32205494290a675200d3058
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 

From f040c7cf8df27df25950c6c529a16cf273bb4d67 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Tue, 17 Dec 2024 13:57:40 -0700
Subject: [PATCH 43/53] update cdeps external

---
 .gitmodules      | 2 +-
 cime             | 2 +-
 components/cdeps | 2 +-
 components/clm   | 2 +-
 components/cmeps | 2 +-
 share            | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index f72ec58ae7..c1e9973a6a 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -165,7 +165,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.53
+fxtag = cdeps1.0.61
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
diff --git a/cime b/cime
index f28506021f..b2f271b174 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit f28506021f122fbfab8fea741da35ac48ab875b2
+Subproject commit b2f271b1742533715a05701b1bdd80a24bb2ad77
diff --git a/components/cdeps b/components/cdeps
index f6bc97483a..0750c91753 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit f6bc97483a1bfb7352c6c5610a13ed898a86990b
+Subproject commit 0750c9175395d3ba3bf8eba65703dee230d08572
diff --git a/components/clm b/components/clm
index 16cf4ac469..14aad99fea 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit 16cf4ac469614f4b329c7da206c3d6b9b773bb03
+Subproject commit 14aad99fea41c4bef32205494290a675200d3058
diff --git a/components/cmeps b/components/cmeps
index 1355710f04..a91cedfe58 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 1355710f04fa6286a13e8056e35c6736e7250e3d
+Subproject commit a91cedfe58658a9fc391195481137a2d83372c25
diff --git a/share b/share
index 63ae6cc216..a48ff8790a 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit 63ae6cc216c517d3ced4d3466d3616b4c24107b5
+Subproject commit a48ff8790a21d3831873ed9f023a43c606a1ef03

From 2120003618a88ea7642e981a0c1b780b69be60b9 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Thu, 19 Dec 2024 16:39:35 -0700
Subject: [PATCH 44/53] update clm tag

---
 .gitmodules    | 4 ++--
 components/clm | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index c1e9973a6a..0176e8431c 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -192,8 +192,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 
 [submodule "clm"]
 path = components/clm
-url = https://github.com/jedwards4b/CTSM
-fxtag = 14aad99fea41c4bef32205494290a675200d3058
+url = https://github.com/ESCOMP/CTSM
+fxtag = ctsm5.3.016
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
diff --git a/components/clm b/components/clm
index 14aad99fea..f437651ee4 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit 14aad99fea41c4bef32205494290a675200d3058
+Subproject commit f437651ee449789af9325882bb0acc09576c9411

From ee5b5400f28814297bf80a3428bdac30a91d237a Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Thu, 19 Dec 2024 17:18:05 -0700
Subject: [PATCH 45/53] initial changelog

---
 doc/ChangeLog | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 746fead140..7fb8dacc70 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,5 +1,74 @@
 ===============================================================
 
+Tag name: cam6_4_048
+Originator(s): jedwards4b, peverwhee
+Date: 20 December 2024
+One-line Summary: Timestamp in rpointer name
+Github PR URL: https://github.com/ESCOMP/CAM/pull/1147
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+#1146 - Add timestep to rpointer file name
+- Updates to externals, nuopc cap, and cam control code to handle timestamp in
+rpointer file
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: brian-eaton
+
+List all files eliminated: N/A
+
+List all files added and what they do: N/A
+
+List all existing files that have been modified, and describe the changes:
+M  .gitmodules
+- update cmeps, cdeps, cime, share, clm externals
+
+M  src/control/cam_initfiles.F90
+- look for new timestamped rpointer file
+
+M  src/control/cam_restart.F90
+- remove unnecessary conditionals for optional variables
+
+M src/cpl/nuopc/atm_comp_nuopc.F90
+- update variable names coming from coupler
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+derecho/intel/aux_cam:
+
+SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: FAIL)
+SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL)
+ - pre-existing failures due to build-namelist error requiring CLM/CTSM external update.
+
+ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL)
+SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF)
+ - pre-existing failure due to HEMCO not having reproducible results issues #1018 and #856
+
+derecho/nvhpc/aux_cam:
+
+izumi/nag/aux_cam:
+
+DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
+ - pre-existing failure -- issue #670
+
+izumi/gnu/aux_cam:
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers:
+
+===============================================================
+
 Tag name: cam6_4_047
 Originator(s): jedwards4b, fvitt
 Date: 19 November 2024

From 19f0d962144bfc9d8cd41a0fe98d6db79aa67ec1 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Fri, 20 Dec 2024 16:17:21 -0700
Subject: [PATCH 46/53] updated changelog

---
 doc/ChangeLog | 82 ++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 75 insertions(+), 7 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 7fb8dacc70..cf2aa2517d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -27,7 +27,12 @@ List all files added and what they do: N/A
 
 List all existing files that have been modified, and describe the changes:
 M  .gitmodules
-- update cmeps, cdeps, cime, share, clm externals
+- update externals for rpointer mods
+  - cime6.1.49
+  - cmeps1.0.32
+  - cdeps1.0.61
+  - share1.1.6
+  - ctsm5.3.016
 
 M  src/control/cam_initfiles.F90
 - look for new timestamped rpointer file
@@ -45,6 +50,64 @@ appropriate machine below.  All failed tests must be justified.
 
 derecho/intel/aux_cam:
 
+ERC_D_Ln9.f19_f19_mg17.QPC6.derecho_intel.cam-outfrq3s_cosp (Overall: NLFAIL) details:
+ERC_D_Ln9.f19_f19_mg17.QPMOZ.derecho_intel.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.f19_f19_mg17.QPX2000.derecho_intel.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.ne16_ne16_mg17.FADIAB.derecho_intel.cam-terminator (Overall: NLFAIL) details:
+ERC_D_Ln9.ne16_ne16_mg17.QPC5HIST.derecho_intel.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9_P144x1.ne16pg3_ne16pg3_mg17.QPC6HIST.derecho_intel.cam-outfrq3s_ttrac_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9.T42_T42_mg17.FDABIP04.derecho_intel.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9.T42_T42_mg17.FHS94.derecho_intel.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERI_D_Ln18.f45_f45_mg37.QPC41850.derecho_intel.cam-co2rmp_usecase (Overall: NLFAIL) details:
+ERP_D_Ln9.f19_f19_mg17.QPC6.derecho_intel.cam-outfrq9s (Overall: NLFAIL) details:
+ERP_D_Ln9_P64x2.f09_f09_mg17.QSC6.derecho_intel.cam-outfrq9s (Overall: NLFAIL) details:
+ERP_Ld3.f09_f09_mg17.FWHIST.derecho_intel.cam-reduced_hist1d (Overall: NLFAIL) details:
+ERS_Ln9.ne0TESTONLYne5x4_ne0TESTONLYne5x4_mg37.FADIAB.derecho_intel.cam-outfrq3s_refined (Overall: NLFAIL) details:
+SCT_D_Ln7.ne3_ne3_mg37.QPC5.derecho_intel.cam-scm_prep (Overall: NLFAIL) details:
+SCT_D_Ln7.T42_T42_mg17.QPC5.derecho_intel.cam-scm_prep (Overall: NLFAIL) details:
+SMS_D_Ld2.f19_f19_mg17.QPC5HIST.derecho_intel.cam-volc_usecase (Overall: NLFAIL) details:
+SMS_D_Ld5.f19_f19_mg17.PC4.derecho_intel.cam-cam4_port5d (Overall: NLFAIL) details:
+SMS_D_Ln9.f19_f19_mg17.QPC2000climo.derecho_intel.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+SMS_D_Ln9.f19_f19_mg17.QPC5M7.derecho_intel.cam-outfrq9s (Overall: NLFAIL) details:
+SMS_D_Ln9.ne16_ne16_mg17.QPX2000.derecho_intel.cam-outfrq9s (Overall: NLFAIL) details:
+SMS_Ld5.f09_f09_mg17.PC6.derecho_intel.cam-cam6_port_f09 (Overall: NLFAIL) details:
+SMS_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-nudging (Overall: NLFAIL) details:
+SMS_Ln9.f09_f09_mg17.FW1850.derecho_intel.cam-reduced_hist3s (Overall: NLFAIL) details:
+SMS_Ln9.f19_f19.F2000climo.derecho_intel.cam-silhs (Overall: NLFAIL) details:
+ - NL diffs due to CMEPS & CTSM external updates
+
+ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ld3.ne30pg3_ne30pg3_mg17.FHISTC_MTt4s.derecho_intel.cam-outfrq1d_aoa (Overall: DIFF) details:
+ERP_Lh12.f19_f19_mg17.FW4madSD.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+ERP_Ln9.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 (Overall: DIFF) details:
+ERP_Ln9.f09_f09_mg17.F1850.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.f09_f09_mg17.F2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.f09_f09_mg17.FHIST_BDRD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.f19_f19_mg17.FWsc1850.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.ne30pg3_ne30pg3_mg17.FCnudged.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9.f09_f09_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9.f19_f19_mg17.FSPCAMS.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9.f19_f19_mg17.FXSD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9_P288x1.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 (Overall: DIFF) details:
+SMS_D_Ln9.f09_f09_mg17.FCts2nudged.derecho_intel.cam-outfrq9s_leapday (Overall: DIFF) details:
+SMS_D_Ln9.f09_f09_mg17.FCvbsxHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9.f09_f09_mg17.FSD.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s_waccm_ma_mam4 (Overall: DIFF) details:
+SMS_D_Ln9.ne16pg3_ne16pg3_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_D_Ln9_P1280x1.ne30pg3_ne30pg3_mg17.FHISTC_MTt1s.derecho_intel.cam-outfrq9s_Leung_dust (Overall: DIFF) details:
+SMS_D_Ln9.T42_T42.FSCAMARM97.derecho_intel.cam-outfrq9s (Overall: DIFF) details:
+SMS_Ld1.f09_f09_mg17.FW2000climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+SMS_Ld1.ne30pg3_ne30pg3_mg17.FC2010climo.derecho_intel.cam-outfrq1d (Overall: DIFF) details:
+SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem (Overall: DIFF) details:
+SMS_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_rrtmgp (Overall: DIFF) details:
+ - Diffs due to updated CTSM external
+
 SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: FAIL)
 SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL)
  - pre-existing failures due to build-namelist error requiring CLM/CTSM external update.
@@ -54,18 +117,23 @@ SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF)
  - pre-existing failure due to HEMCO not having reproducible results issues #1018 and #856
 
 derecho/nvhpc/aux_cam:
+ERS_Ln9.ne30pg3_ne30pg3_mg17.F2000dev.derecho_nvhpc.cam-outfrq9s_gpu_default (Overall: DIFF) details:
+ - Diffs due to updated CTSM external
 
-izumi/nag/aux_cam:
+izumi/nag/aux_cam: !!due to izumi being down and the desire to make a CESM alpha
+tag, the izumi tests were not run!! this changelog entry will be updated once
+the tests are run
 
-DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
- - pre-existing failure -- issue #670
-
-izumi/gnu/aux_cam:
+izumi/gnu/aux_cam: !!due to izumi being down and the desire to make a CESM alpha
+tag, the izumi tests were not run!! this changelog entry will be updated once
+the tests are run
 
 CAM tag used for the baseline comparison tests if different than previous
 tag:
 
-Summarize any changes to answers:
+Summarize any changes to answers: answer changes thanks to updated CTSM tag
+- ran derecho intel & nvhpc tests on head of cam_development with ctsm5.3.015 vs baselines for
+this tag and confirmed that there were no DIFFs
 
 ===============================================================
 

From 3548dcfb3925d57026391c9aedb72611414606c8 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Sat, 21 Dec 2024 21:05:44 -0700
Subject: [PATCH 47/53] update submodules

---
 cime             | 2 +-
 components/cdeps | 2 +-
 components/clm   | 2 +-
 components/cmeps | 2 +-
 share            | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/cime b/cime
index 1236c0fede..b2f271b174 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit 1236c0feded460aef3e5bdba18e4b850f1997346
+Subproject commit b2f271b1742533715a05701b1bdd80a24bb2ad77
diff --git a/components/cdeps b/components/cdeps
index f6bc97483a..0750c91753 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit f6bc97483a1bfb7352c6c5610a13ed898a86990b
+Subproject commit 0750c9175395d3ba3bf8eba65703dee230d08572
diff --git a/components/clm b/components/clm
index 16cf4ac469..f437651ee4 160000
--- a/components/clm
+++ b/components/clm
@@ -1 +1 @@
-Subproject commit 16cf4ac469614f4b329c7da206c3d6b9b773bb03
+Subproject commit f437651ee449789af9325882bb0acc09576c9411
diff --git a/components/cmeps b/components/cmeps
index 1355710f04..a91cedfe58 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 1355710f04fa6286a13e8056e35c6736e7250e3d
+Subproject commit a91cedfe58658a9fc391195481137a2d83372c25
diff --git a/share b/share
index f6f31fd61c..a48ff8790a 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit f6f31fd61cb8f80aee97311fcca64b3e26b0202c
+Subproject commit a48ff8790a21d3831873ed9f023a43c606a1ef03

From d60dbc20f4cfe039657b766b641f311296b988cc Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Fri, 27 Dec 2024 10:11:31 -0700
Subject: [PATCH 48/53] update cime tag to fix restarts issue

---
 .gitmodules | 2 +-
 cime        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 0176e8431c..305d3c828a 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -151,7 +151,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.49
+fxtag = cime6.1.55
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
diff --git a/cime b/cime
index b2f271b174..85922c028f 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit b2f271b1742533715a05701b1bdd80a24bb2ad77
+Subproject commit 85922c028ff8a5b9f5573888f4240cdc4b8104a3

From 2d12f78b9b7e261d5b4da13f9c50dbd7c92b65b8 Mon Sep 17 00:00:00 2001
From: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
Date: Mon, 30 Dec 2024 14:04:25 -0700
Subject: [PATCH 49/53] update cime

---
 .gitmodules | 2 +-
 cime        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 305d3c828a..d8c01f79d2 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -151,7 +151,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.55
+fxtag = cime6.1.56
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
diff --git a/cime b/cime
index 85922c028f..ac8e583108 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit 85922c028ff8a5b9f5573888f4240cdc4b8104a3
+Subproject commit ac8e583108b1ce1f592a6f6436c71d6dc087f447

From c3c9ed2ed02afd4338d0e0aa4865583a930b6d83 Mon Sep 17 00:00:00 2001
From: peverwhee <courtneyp@ucar.edu>
Date: Mon, 30 Dec 2024 17:23:02 -0700
Subject: [PATCH 50/53] final changelog

---
 doc/ChangeLog | 223 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 215 insertions(+), 8 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5c8757c219..43712d490b 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -2,7 +2,7 @@
 
 Tag name: cam6_4_049
 Originator(s): peverwhee
-Date:  23 December 2024
+Date:  30 December 2024
 One-line Summary: History bugfixes
 Github PR URL: https://github.com/ESCOMP/CAM/pull/1163
 
@@ -14,6 +14,7 @@ Purpose of changes (include the issue number and title text for each relevant Gi
 - Issue #1183: Suggested improvement for openfile
 - Update git-fleximod to v0.9.3
 - Update archive_baseline.sh modify read permissions on izumi
+- Update CIME tag to cime6.1.56 to fix restart issue in CAM
 
 Describe any changes made to build system:
 M   bld/namelist_files/use_cases/sd_waccm_sulfur.xml
@@ -33,8 +34,11 @@ List all files added and what they do: none
 
 List all existing files that have been modified, and describe the changes:
 
+M   .gitmodules
+ - update CIME tag to cime6.1.56
+
 M   .lib/git-fleximod/*
- - updates to move git-fleximod to v0.9.2
+ - updates to move git-fleximod to v0.9.3
 
 M   src/control/cam_history.F90
  - remove nhtfrq=1 accumulation flag override if sampled_on_subcyle=.true.
@@ -77,6 +81,63 @@ appropriate machine below.  All failed tests must be justified.
 
 derecho/intel/aux_cam:
 
+ERC_D_Ln9.f19_f19_mg17.QPC6.derecho_intel.cam-outfrq3s_cosp (Overall: DIFF)
+ERC_D_Ln9.f19_f19_mg17.QPMOZ.derecho_intel.cam-outfrq3s (Overall: DIFF)
+ERC_D_Ln9.f19_f19_mg17.QPX2000.derecho_intel.cam-outfrq3s (Overall: DIFF)
+ERC_D_Ln9.ne16_ne16_mg17.FADIAB.derecho_intel.cam-terminator (Overall: DIFF)
+ERC_D_Ln9.ne16_ne16_mg17.QPC5HIST.derecho_intel.cam-outfrq3s_usecase (Overall: DIFF)
+ERC_D_Ln9_P144x1.ne16pg3_ne16pg3_mg17.QPC6HIST.derecho_intel.cam-outfrq3s_ttrac_usecase (Overall: DIFF)
+ERC_D_Ln9.T42_T42_mg17.FDABIP04.derecho_intel.cam-outfrq3s_usecase (Overall: DIFF)
+ERC_D_Ln9.T42_T42_mg17.FHS94.derecho_intel.cam-outfrq3s_usecase (Overall: DIFF)
+ERI_D_Ln18.f45_f45_mg37.QPC41850.derecho_intel.cam-co2rmp_usecase (Overall: DIFF)
+ERP_D_Ln9.f19_f19_mg17.QPC6.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_D_Ln9_P64x2.f09_f09_mg17.QSC6.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ld3.f09_f09_mg17.FWHIST.derecho_intel.cam-reduced_hist1d (Overall: DIFF)
+ERP_Ld3.ne30pg3_ne30pg3_mg17.FHISTC_MTt4s.derecho_intel.cam-outfrq1d_aoa (Overall: DIFF)
+ERP_Lh12.f19_f19_mg17.FW4madSD.derecho_intel.cam-outfrq3h (Overall: DIFF)
+ERP_Ln9.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 (Overall: DIFF)
+ERP_Ln9.f09_f09_mg17.F1850.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.f09_f09_mg17.F2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.f09_f09_mg17.FHIST_BDRD.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.f19_f19_mg17.FWsc1850.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.ne30pg3_ne30pg3_mg17.FCnudged.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERP_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERS_Ln9.f09_f09_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERS_Ln9.f19_f19_mg17.FSPCAMS.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERS_Ln9.f19_f19_mg17.FXSD.derecho_intel.cam-outfrq9s (Overall: DIFF)
+ERS_Ln9.ne0TESTONLYne5x4_ne0TESTONLYne5x4_mg37.FADIAB.derecho_intel.cam-outfrq3s_refined (Overall: DIFF)
+ERS_Ln9_P288x1.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 (Overall: DIFF)
+SCT_D_Ln7.ne3_ne3_mg37.QPC5.derecho_intel.cam-scm_prep (Overall: DIFF)
+SCT_D_Ln7.T42_T42_mg17.QPC5.derecho_intel.cam-scm_prep (Overall: DIFF)
+SMS_D_Ld2.f19_f19_mg17.QPC5HIST.derecho_intel.cam-volc_usecase (Overall: DIFF)
+SMS_D_Ld5.f19_f19_mg17.PC4.derecho_intel.cam-cam4_port5d (Overall: DIFF)
+SMS_D_Ln9.f09_f09_mg17.FCts2nudged.derecho_intel.cam-outfrq9s_leapday (Overall: DIFF)
+SMS_D_Ln9.f09_f09_mg17.FCvbsxHIST.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.f09_f09_mg17.FSD.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.f19_f19_mg17.FWma2000climo.derecho_intel.cam-outfrq9s_waccm_ma_mam4 (Overall: DIFF)
+SMS_D_Ln9.f19_f19_mg17.QPC2000climo.derecho_intel.cam-outfrq3s_usecase (Overall: DIFF)
+SMS_D_Ln9.f19_f19_mg17.QPC5M7.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.ne16_ne16_mg17.QPX2000.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.ne16pg3_ne16pg3_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9_P1280x1.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.FHIST.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_D_Ln9_P1280x1.ne30pg3_ne30pg3_mg17.FHISTC_MTt1s.derecho_intel.cam-outfrq9s_Leung_dust (Overall: DIFF)
+SMS_D_Ln9.T42_T42.FSCAMARM97.derecho_intel.cam-outfrq9s (Overall: DIFF)
+SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF)
+SMS_Ld1.f09_f09_mg17.FW2000climo.derecho_intel.cam-outfrq1d (Overall: DIFF)
+SMS_Ld1.ne30pg3_ne30pg3_mg17.FC2010climo.derecho_intel.cam-outfrq1d (Overall: DIFF)
+SMS_Ld5.f09_f09_mg17.PC6.derecho_intel.cam-cam6_port_f09 (Overall: DIFF)
+SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF)
+SMS_Ln9.f09_f09_mg17.F2010climo.derecho_intel.cam-nudging (Overall: DIFF)
+SMS_Ln9.f09_f09_mg17.FW1850.derecho_intel.cam-reduced_hist3s (Overall: DIFF)
+SMS_Ln9.f19_f19.F2000climo.derecho_intel.cam-silhs (Overall: DIFF) details:
+SMS_Ln9.f19_f19_mg17.FHIST.derecho_intel.cam-outfrq9s_nochem (Overall: DIFF)
+SMS_Ln9.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_rrtmgp (Overall: DIFF)
+ - fieldlist differences due to removal of time_bounds field from instantaneous file
+
 SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: FAIL)
 SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL)
  - pre-existing failures due to build-namelist error requiring CLM/CTSM external update.
@@ -87,13 +148,87 @@ SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: DIFF)
 
 derecho/nvhpc/aux_cam:
 
+ERS_Ln9.ne30pg3_ne30pg3_mg17.F2000dev.derecho_nvhpc.cam-outfrq9s_gpu_default (Overall: DIFF)
+ - fieldlist differences due to removal of time_bounds field from instantaneous file
+
 izumi/nag/aux_cam:
 
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-carma_sea_salt (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_cosp (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_subcol (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_am (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_cospsathist (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPWmaC6.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QSPCAMS.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+ERC_D_Ln9.mpasa480z32_mpasa480.FHS94.izumi_nag.cam-outfrq3s_usecase (Overall: DIFF) details:
+ERC_D_Ln9.ne16_ne16_mg17.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: DIFF) details:
+ERC_D_Ln9.ne16pg3_ne16pg3_mg17.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: DIFF) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-outfrq3s_ttrac (Overall: DIFF) details:
+ERC_D_Ln9.T5_T5_mg37.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: DIFF) details:
+ERI_D_Ln18.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_eoyttrac (Overall: DIFF) details:
+ERI_D_Ln18.f19_f19_mg17.QPC6.izumi_nag.cam-ghgrmp_e8 (Overall: DIFF) details:
+ERI_D_Ln18.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s_bwic (Overall: DIFF) details:
+ERI_D_Ln18.ne5pg3_ne5pg3_mg37.FADIAB.izumi_nag.cam-outfrq3s_bwic (Overall: DIFF) details:
+ERP_Ln9.ne5pg3_ne5pg3_mg37.QPC6.izumi_nag.cam-outfrq9s_clubbmf (Overall: DIFF) details:
+ERS_Ln27.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq9s (Overall: DIFF) details:
+PEM_D_Ln9.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal0 (Overall: DIFF) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal1 (Overall: DIFF) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal3 (Overall: DIFF) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal0 (Overall: DIFF) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal1 (Overall: DIFF) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal3 (Overall: DIFF) details:
+SMS_D_Ld2.f45_f45_mg37.PC5.izumi_nag.cam-outfrq24h_port (Overall: DIFF) details:
+SMS_D_Ln3.ne5pg3_ne5pg3_mg37.QPX2000.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+SMS_D_Ln6.ne5_ne5_mg37.QPWmaC4.izumi_nag.cam-outfrq3s_physgrid_tem (Overall: DIFF) details:
+SMS_D_Ln7.T42_T42_mg17.QPSCAMC5.izumi_nag.cam-scmarm (Overall: DIFF) details:
+SMS_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-rad_diag_mam (Overall: DIFF) details:
+SMS_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_ba (Overall: DIFF) details:
+SMS_D_Ln9_P1x1.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+SMS_P48x1_D_Ln3.f09_f09_mg17.QPC6HIST.izumi_nag.cam-outfrq3s_co2cycle_usecase (Overall: DIFF) details:
+SUB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s (Overall: DIFF) details:
+TMC_D.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_eoyttrac (Overall: DIFF) details:
+TMC_D.T5_T5_mg37.QPC5.izumi_nag.cam-ghgrmp_e8 (Overall: DIFF) details:
+ - fieldlist differences due to removal of time_bounds field from instantaneous file
+
 DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
  - pre-existing failure -- issue #670
 
 izumi/gnu/aux_cam:
 
+ERC_D_Ln9.f10_f10_mg37.FADIAB.izumi_gnu.cam-terminator (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC4.izumi_gnu.cam-outfrq3s_diags (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_gnu.cam-outfrq3s_unicon (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_gnu.cam-rad_diag (Overall: DIFF) details:
+ERC_D_Ln9.f10_f10_mg37.QPSPCAMM.izumi_gnu.cam-outfrq3s (Overall: DIFF) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC4.izumi_gnu.cam-outfrq3s_nudging_ne5_L26 (Overall: DIFF) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC5.izumi_gnu.cam-outfrq3s_ba (Overall: DIFF) details:
+ERC_D_Ln9.ne5pg2_ne5pg2_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: DIFF) details:
+ERC_D_Ln9.ne5pg3_ne5pg3_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: DIFF) details:
+ERI_D_Ln18.T5_T5_mg37.QPC4.izumi_gnu.cam-co2rmp (Overall: DIFF) details:
+ERP_D_Ln9.C48_C48_mg17.QPC6.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ERP_D_Ln9.ne3pg3_ne3pg3_mg37.FLTHIST.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ERP_D_Ln9.ne3pg3_ne3pg3_mg37.QPC6.izumi_gnu.cam-outfrq9s_rrtmgp (Overall: DIFF) details:
+ERP_Ln9.ne5_ne5_mg37.FHS94.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9.ne5_ne5_mg37.QPC5.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ERP_Ln9_P24x2.f45_f45_mg37.QPWmaC6.izumi_gnu.cam-outfrq9s_mee_fluxes (Overall: DIFF) details:
+ERS_Ln9_P24x1.mpasa480_mpasa480.F2000climo.izumi_gnu.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+PEM_D_Ln9.ne5pg3_ne5pg3_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: DIFF) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal0 (Overall: DIFF) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal1 (Overall: DIFF) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal3 (Overall: DIFF) details:
+SCT_D_Ln7.ne3_ne3_mg37.QPC6.izumi_gnu.cam-scm_prep_c6 (Overall: DIFF) details:
+SCT_D_Ln7.T42_T42_mg17.QPC4.izumi_gnu.cam-scm_prep (Overall: DIFF) details:
+SCT_D_Ln7.T42_T42_mg17.QPC6.izumi_gnu.cam-scm_prep_c6 (Overall: DIFF) details:
+SMS_D_Ln3.f10_f10_mg37.QPMOZ.izumi_gnu.cam-outfrq3s_chemproc (Overall: DIFF) details:
+SMS_D_Ln9.f10_f10_mg37.QPWmaC4.izumi_gnu.cam-outfrq9s_apmee (Overall: DIFF) details:
+SMS_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-outfrq3s_ttrac (Overall: DIFF) details:
+SMS_Ld5.f09_f09_mg17.PC6.izumi_gnu.cam-cam6_port_f09_rrtmgp (Overall: DIFF) details:
+SMS_P48x1_D_Ln9.f19_f19_mg17.FW4madSD.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ - fieldlist differences due to removal of time_bounds field from instantaneous file
+
 CAM tag used for the baseline comparison tests if different than previous
 tag:
 
@@ -221,13 +356,85 @@ derecho/nvhpc/aux_cam:
 ERS_Ln9.ne30pg3_ne30pg3_mg17.F2000dev.derecho_nvhpc.cam-outfrq9s_gpu_default (Overall: DIFF) details:
  - Diffs due to updated CTSM external
 
-izumi/nag/aux_cam: !!due to izumi being down and the desire to make a CESM alpha
-tag, the izumi tests were not run!! this changelog entry will be updated once
-the tests are run
+izumi/nag/aux_cam: izumi tests run 12/21/2024
+
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-carma_sea_salt (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_cosp (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_subcol (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_am (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_cospsathist (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPWmaC6.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QSPCAMS.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.mpasa480z32_mpasa480.FHS94.izumi_nag.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9.ne16_ne16_mg17.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9.ne16pg3_ne16pg3_mg17.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-outfrq3s_ttrac (Overall: NLFAIL) details:
+ERC_D_Ln9.T5_T5_mg37.QPC4.izumi_nag.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ERI_D_Ln18.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_eoyttrac (Overall: NLFAIL) details:
+ERI_D_Ln18.f19_f19_mg17.QPC6.izumi_nag.cam-ghgrmp_e8 (Overall: NLFAIL) details:
+ERI_D_Ln18.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s_bwic (Overall: NLFAIL) details:
+ERI_D_Ln18.ne5pg3_ne5pg3_mg37.FADIAB.izumi_nag.cam-outfrq3s_bwic (Overall: NLFAIL) details:
+ERP_Ln9.ne5pg3_ne5pg3_mg37.QPC6.izumi_nag.cam-outfrq9s_clubbmf (Overall: NLFAIL) details:
+ERS_Ln27.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s (Overall: NLFAIL) details:
+ERS_Ln9.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq9s (Overall: NLFAIL) details:
+PEM_D_Ln9.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal0 (Overall: NLFAIL) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal1 (Overall: NLFAIL) details:
+PLB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-ttrac_loadbal3 (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal0 (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal1 (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5_ne5_mg37.QPC5.izumi_nag.cam-ttrac_loadbal3 (Overall: NLFAIL) details:
+SMS_D_Ld2.f45_f45_mg37.PC5.izumi_nag.cam-outfrq24h_port (Overall: NLFAIL) details:
+SMS_D_Ln3.ne5pg3_ne5pg3_mg37.QPX2000.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+SMS_D_Ln6.ne5_ne5_mg37.QPWmaC4.izumi_nag.cam-outfrq3s_physgrid_tem (Overall: NLFAIL) details:
+SMS_D_Ln7.T42_T42_mg17.QPSCAMC5.izumi_nag.cam-scmarm (Overall: NLFAIL) details:
+SMS_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-rad_diag_mam (Overall: NLFAIL) details:
+SMS_D_Ln9.f10_f10_mg37.QPC6.izumi_nag.cam-outfrq3s_ba (Overall: NLFAIL) details:
+MS_D_Ln9_P1x1.ne5_ne5_mg37.FADIAB.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+SMS_P48x1_D_Ln3.f09_f09_mg17.QPC6HIST.izumi_nag.cam-outfrq3s_co2cycle_usecase (Overall: NLFAIL) details:
+SUB_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s (Overall: NLFAIL) details:
+TMC_D.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_eoyttrac (Overall: NLFAIL) details:
+TMC_D.T5_T5_mg37.QPC5.izumi_nag.cam-ghgrmp_e8 (Overall: NLFAIL) details:
+ - NL diffs due to CMEPS & CTSM external updates
+
+DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
+ - pre-existing failure -- issue #670
+
+izumi/gnu/aux_cam: izumi tests run 12/21/2024
+
+ERC_D_Ln9.f10_f10_mg37.FADIAB.izumi_gnu.cam-terminator (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC4.izumi_gnu.cam-outfrq3s_diags (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_gnu.cam-outfrq3s_unicon (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_gnu.cam-rad_diag (Overall: NLFAIL) details:
+ERC_D_Ln9.f10_f10_mg37.QPSPCAMM.izumi_gnu.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC4.izumi_gnu.cam-outfrq3s_nudging_ne5_L26 (Overall: NLFAIL) details:
+ERC_D_Ln9.ne5_ne5_mg37.QPC5.izumi_gnu.cam-outfrq3s_ba (Overall: NLFAIL) details:
+ERC_D_Ln9.ne5pg2_ne5pg2_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: NLFAIL) details:
+ERC_D_Ln9.ne5pg3_ne5pg3_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: NLFAIL) details:
+ERI_D_Ln18.T5_T5_mg37.QPC4.izumi_gnu.cam-co2rmp (Overall: NLFAIL) details:
+ERP_D_Ln9.C48_C48_mg17.QPC6.izumi_gnu.cam-outfrq9s (Overall: NLFAIL) details:
+ERP_D_Ln9.ne3pg3_ne3pg3_mg37.QPC6.izumi_gnu.cam-outfrq9s_rrtmgp (Overall: NLFAIL) details:
+ERP_Ln9.ne5_ne5_mg37.FHS94.izumi_gnu.cam-outfrq9s (Overall: NLFAIL) details:
+ERP_Ln9.ne5_ne5_mg37.QPC5.izumi_gnu.cam-outfrq9s (Overall: NLFAIL) details:
+ERP_Ln9_P24x2.f45_f45_mg37.QPWmaC6.izumi_gnu.cam-outfrq9s_mee_fluxes (Overall: NLFAIL) details:
+PEM_D_Ln9.ne5pg3_ne5pg3_mg37.FADIAB.izumi_gnu.cam-outfrq3s (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal0 (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal1 (Overall: NLFAIL) details:
+PLB_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-ttrac_loadbal3 (Overall: NLFAIL) details:
+SCT_D_Ln7.ne3_ne3_mg37.QPC6.izumi_gnu.cam-scm_prep_c6 (Overall: NLFAIL) details:
+SCT_D_Ln7.T42_T42_mg17.QPC4.izumi_gnu.cam-scm_prep (Overall: NLFAIL) details:
+SCT_D_Ln7.T42_T42_mg17.QPC6.izumi_gnu.cam-scm_prep_c6 (Overall: NLFAIL) details:
+SMS_D_Ln3.f10_f10_mg37.QPMOZ.izumi_gnu.cam-outfrq3s_chemproc (Overall: NLFAIL) details:
+SMS_D_Ln9.f10_f10_mg37.QPWmaC4.izumi_gnu.cam-outfrq9s_apmee (Overall: NLFAIL) details:
+SMS_D_Ln9.ne5pg3_ne5pg3_mg37.QPC5.izumi_gnu.cam-outfrq3s_ttrac (Overall: NLFAIL) details:
+SMS_Ld5.f09_f09_mg17.PC6.izumi_gnu.cam-cam6_port_f09_rrtmgp (Overall: NLFAIL) details:
+ - NL diffs due to CMEPS & CTSM external updates
 
-izumi/gnu/aux_cam: !!due to izumi being down and the desire to make a CESM alpha
-tag, the izumi tests were not run!! this changelog entry will be updated once
-the tests are run
+ERP_D_Ln9.ne3pg3_ne3pg3_mg37.FLTHIST.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ERS_Ln9_P24x1.mpasa480_mpasa480.F2000climo.izumi_gnu.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+SMS_P48x1_D_Ln9.f19_f19_mg17.FW4madSD.izumi_gnu.cam-outfrq9s (Overall: DIFF) details:
+ - Diffs due to updated CTSM external
 
 CAM tag used for the baseline comparison tests if different than previous
 tag:

From bdb3b768da79bebb4154a8e1a4597883de700261 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Mon, 30 Dec 2024 23:54:15 -0500
Subject: [PATCH 51/53] Update to head of atmos_phys with check_energy_fix_run
 arguments

---
 .gitmodules                      |  2 +-
 src/atmos_phys                   |  2 +-
 src/physics/cam/check_energy.F90 | 21 +++++++++++++--------
 3 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 91690771e1..d07d5f8ac5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = atmos_phys0_07_000
+        fxtag = 8e3d0bdff98ff70a4e815160ebd13a150c662a12
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index e10f81151e..8e3d0bdff9 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit e10f81151ecef5416462472ef0e52810dc82e412
+Subproject commit 8e3d0bdff98ff70a4e815160ebd13a150c662a12
diff --git a/src/physics/cam/check_energy.F90 b/src/physics/cam/check_energy.F90
index 7af3a32bda..d1d59e173f 100644
--- a/src/physics/cam/check_energy.F90
+++ b/src/physics/cam/check_energy.F90
@@ -877,6 +877,9 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
     real(r8)    :: heat_out(pcols)
     character(len=64) :: dummy_scheme_name  ! dummy scheme name for CCPP-ized scheme
 
+    integer            :: errflg
+    character(len=512) :: errmsg
+
     lchnk = state%lchnk
     ncol  = state%ncol
 
@@ -904,14 +907,16 @@ subroutine check_energy_cam_fix(state, ptend, nstep, eshflx)
     ! Call the CCPP-ized subroutine (for non-SCAM)
     ! to compute the effective sensible heat flux and save to ptend%s
     call check_energy_fix_run( &
-        ncol      = ncol, &
-        pver      = pver, &
-        pint      = state%pint(:ncol,:), &
-        gravit    = gravit, &
-        heat_glob = heat_glob, &
-        ptend_s   = ptend%s(:ncol,:), &
-        eshflx    = eshflx(:ncol), &
-        scheme_name = dummy_scheme_name &
+        ncol        = ncol, &
+        pver        = pver, &
+        pint        = state%pint(:ncol,:), &
+        gravit      = gravit, &
+        heat_glob   = heat_glob, &
+        ptend_s     = ptend%s(:ncol,:), &
+        eshflx      = eshflx(:ncol), &
+        scheme_name = dummy_scheme_name, &
+        errmsg      = errmsg, &
+        errflg      = errflg  &
     )
 
   end subroutine check_energy_cam_fix

From 0881a22bde02cf059f3d383f0de13cf35a492108 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 31 Dec 2024 09:57:33 -0500
Subject: [PATCH 52/53] Update to atmos_phys0_07_001

---
 .gitmodules    | 2 +-
 src/atmos_phys | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 29c2e7bdac..1809a94e55 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -36,7 +36,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = 8e3d0bdff98ff70a4e815160ebd13a150c662a12
+        fxtag = atmos_phys0_07_001
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
diff --git a/src/atmos_phys b/src/atmos_phys
index 8e3d0bdff9..c3de8468f7 160000
--- a/src/atmos_phys
+++ b/src/atmos_phys
@@ -1 +1 @@
-Subproject commit 8e3d0bdff98ff70a4e815160ebd13a150c662a12
+Subproject commit c3de8468f7b245a939448f4ca6d3ef386584e92d

From b7b4c3cfad202facbb6064e33f607c26f1988f03 Mon Sep 17 00:00:00 2001
From: Haipeng Lin <hplin@ucar.edu>
Date: Tue, 31 Dec 2024 14:02:57 -0500
Subject: [PATCH 53/53] Finalize ChangeLog for cam6_4_050.

---
 doc/ChangeLog | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/doc/ChangeLog b/doc/ChangeLog
index dcc4560393..8ae657fda9 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,7 +1,7 @@
 ===============================================================
-Tag name:
+Tag name: cam6_4_050
 Originator(s): jimmielin
-Date: 30 Dec 2024
+Date: 31 Dec 2024
 One-line Summary: Implement CCPPized check_energy_chng and check_energy_fix
 Github PR URL: https://github.com/ESCOMP/CAM/pull/1180
 
@@ -37,7 +37,7 @@ M       src/atmos_phys
 Save cp_or_cv_dycore in state snapshot
 M       src/control/cam_snapshot_common.F90
 
-New CAM interfaces to CCPPized routines, when avaialble
+New CAM interfaces to CCPPized routines, when available
 M       src/physics/cam/check_energy.F90
 
 Update calls to CCPPized routines, when available
@@ -55,11 +55,22 @@ appropriate machine below.  All failed tests must be justified.
 
 derecho/intel/aux_cam:
 
-derecho/nvhpc/aux_cam:
+SMS_D_Ln9.f19_f19_mg17.FXHIST.derecho_intel.cam-outfrq9s_amie (Overall: FAIL)
+SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s (Overall: FAIL)
+ - pre-existing failures due to build-namelist error requiring CLM/CTSM external update.
+
+ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL)
+SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d (Overall: PASS)
+ - pre-existing failure due to HEMCO not having reproducible results issues #1018 and #856
+
+derecho/nvhpc/aux_cam: All PASS
 
 izumi/nag/aux_cam:
 
-izumi/gnu/aux_cam:
+DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL)
+ - pre-existing failure -- issue #670
+
+izumi/gnu/aux_cam: All PASS
 
 Summarize any changes to answers: B4B