Merge pull request #325 from zhangsp8/master

Code optimization & reorganize files.

include/Makeoptions

@@ -1 +1 @@
-Makeoptions.gnu
+Makeoptions.github

include/Makeoptions.SYSU-BaiduBoat.gnu

@@ -0,0 +1,39 @@
+# ==========================================================
+# mpif90 - gnu 
+
+#   please "source /share/home/dq089/soft/gnu-env" first.
+
+FF = mpif90
+
+NETCDF_LIB = /share/home/dq089/soft/netcdf-fortran-4.6.1-gnu/lib         
+NETCDF_INC = /share/home/dq089/soft/netcdf-fortran-4.6.1-gnu/include     
+
+MOD_CMD = -J
+
+FOPTS = -fdefault-real-8 -ffree-form -C -g -u -xcheck=stkovf \
+        -ffpe-trap=invalid,zero,overflow -fbounds-check \
+        -mcmodel=medium -fbacktrace -fdump-core -cpp \
+        -ffree-line-length-0
+
+INCLUDE_DIR = -I../include -I../share -I../mksrfdata -I../mkinidata -I../main -I$(NETCDF_INC)
+LDFLAGS = -L${NETCDF_LIB} -lnetcdff -llapack -L/share/home/dq089/soft/lib -lblas.gnu
+
+#============================================================
+# CaMa-Flood Mkinclude (for Linux, gfortran)
+
+RM = /bin/rm -f
+CP = /bin/cp
+#----
+# Pre-Prosessing options
+# DMPI=-DUseMPI: activate when MPI parallelization is used
+# DCDF=-DUseCDF: activate when using netCDF, comment out when not needed
+# DATM=-DNoAtom: activate when OMP ATOMIC calculation should be avoided (bit identical simulation)
+#----
+#DMPI=-DUseMPI
+DCDF=-DUseCDF
+#DATM=-DNoAtom
+CFLAGS=$(DMPI) $(DCDF) $(DATM)
+#----
+FCMP = gfortran -fopenmp
+FC   = gfortran 
+FFLAGS = -O3 -Wall -cpp -free -fimplicit-none -fbounds-check -fbacktrace 

include/Makeoptions.SYSU-BaiduBoat.intel

@@ -0,0 +1,46 @@
+# =======================================================
+# mpif90 - intel
+
+#   please "source /share/home/dq089/soft/intel-env" first.
+
+FF = mpif90
+
+NETCDF_LIB = /share/home/dq089/soft/netcdf-fortran-4.6.1-intel/lib     
+NETCDF_INC = /share/home/dq089/soft/netcdf-fortran-4.6.1-intel/include 
+
+MOD_CMD = -module  
+
+#<<<<<<< HEAD
+#FOPTS = -qopenmp -g -traceback -r8 -free -check uninit 
+       # -r8 -free -O0 -check uninit -check bounds -check pointers \
+       # -traceback  -assume byterecl -pthread -heap-arrays #-nogen-interface
+
+#INCLUDE_DIR = -I../include -I../share -I../mksrfdata \
+#               -I../mkinidata -I../main -I../hydro -I${NETCDF_INC}
+#LDFLAGS = -L${NETCDF_LIB} -lnetcdff
+
+
+ FOPTS = -qopenmp -O2 -traceback -r8 -free -check uninit -check bounds
+
+ LDFLAGS = -L${NETCDF_LIB} -lnetcdff -llapack -L/share/home/dq089/soft/lib -lgfortran -lblas.intel
+
+#============================================================
+# CaMa-Flood Mkinclude (for Linux, gfortran)
+
+RM = /bin/rm -f
+CP = /bin/cp
+#----
+# Pre-Prosessing options
+# DMPI=-DUseMPI: activate when MPI parallelization is used
+# DCDF=-DUseCDF: activate when using netCDF, comment out when not needed
+# DATM=-DNoAtom: activate when OMP ATOMIC calculation should be avoided (bit identical simulation)
+#----
+#DMPI=-DUseMPI
+DCDF=-DUseCDF
+#DATM=-DNoAtom
+CFLAGS=$(DMPI) $(DCDF) $(DATM)
+#----
+FCMP = ifort -qopenmp
+FC = ifort
+LFLAGS =
+FFLAGS = -O3 -warn all -fpp -free -assume byterecl -heap-arrays -nogen-interface -lpthread -static-intel

include/Makeoptions.github

@@ -0,0 +1,52 @@
+# =======================================================
+# mpif90 - gfortran 
+# 
+
+  FF = mpif90 -fopenmp
+
+  NETCDF_LIB = /usr/lib/x86_64-linux-gnu
+  NETCDF_INC = /usr/include
+
+  MOD_CMD = -J
+
+# determine the gfortran version
+  GCC_VERSION := "`gcc -dumpversion`"
+  IS_GCC_ABOVE_10 := $(shell expr "$(GCC_VERSION)" ">=" "10")
+  ifeq "$(IS_GCC_ABOVE_10)" "1" 
+     FOPTS = -fdefault-real-8 -ffree-form -C -g -u -xcheck=stkovf \
+           -ffpe-trap=invalid,zero,overflow -fbounds-check \
+           -mcmodel=medium -fbacktrace -fdump-core -cpp \
+           -ffree-line-length-0 -fallow-argument-mismatch 
+  else
+     FOPTS = -fdefault-real-8 -ffree-form -C -g -u -xcheck=stkovf \
+           -ffpe-trap=invalid,zero,overflow -fbounds-check \
+           -mcmodel=medium -fbacktrace -fdump-core -cpp \
+           -ffree-line-length-0
+  endif
+
+  INCLUDE_DIR = -I../include -I../share -I../mksrfdata -I../mkinidata -I../main -I$(NETCDF_INC)
+  LDFLAGS = -L$(NETCDF_LIB) -lnetcdff -lnetcdf -llapack -lblas 
+
+
+
+#============================================================
+# CaMa-Flood Mkinclude (for Linux, gfortran)
+
+RM = /bin/rm -f
+CP = /bin/cp
+#----
+# Pre-Prosessing options
+# DMPI=-DUseMPI: activate when MPI parallelization is used
+# DCDF=-DUseCDF: activate when using netCDF, comment out when not needed
+# DATM=-DNoAtom: activate when OMP ATOMIC calculation should be avoided (bit identical simulation)
+#----
+#DMPI=-DUseMPI
+DCDF=-DUseCDF -DUseCDF_CMF
+#DATM=-DNoAtom
+CFLAGS=$(DMPI) $(DCDF) $(DATM) 
+#----
+FCMP = /usr/bin/gfortran -fopenmp
+FC   = /usr/bin/gfortran 
+
+LFLAGS =
+FFLAGS = -O3 -Wall -cpp -free -fimplicit-none -fbounds-check -fbacktrace 

include/Makeoptions.gnu → include/Makeoptions.land.gnu

@@ -4,11 +4,8 @@
 
   FF = mpif90 -fopenmp
 
-NETCDF_LIB = /usr/lib/x86_64-linux-gnu
-NETCDF_INC = /usr/include
-
-#  NETCDF_LIB = /opt/netcdf-c-4.9.2-fortran-4.6.0-gnu/lib
-#  NETCDF_INC = /opt/netcdf-c-4.9.2-fortran-4.6.0-gnu/include
+  NETCDF_LIB = /opt/netcdf-c-4.9.2-fortran-4.6.0-gnu/lib
+  NETCDF_INC = /opt/netcdf-c-4.9.2-fortran-4.6.0-gnu/include
 
   MOD_CMD = -J
 

main/MOD_LAIReadin.F90

@@ -114,7 +114,7 @@ SUBROUTINE LAI_readin (year, time, dir_landdata)
 #ifdef URBAN_MODEL
                IF(m == URBAN) CYCLE
 #endif
-               IF( m == 0 )THEN
+               IF(m == 0 .or. m == WATERBODY)THEN
                   fveg(npatch)  = 0.
                   tlai(npatch)  = 0.
                   tsai(npatch)  = 0.

mkinidata/MOD_IniTimeVariable.F90

@@ -333,9 +333,9 @@ SUBROUTINE IniTimeVar(ipatch, patchtype&
       IF(patchtype <= 5)THEN ! land grid
 
          ! (1) SOIL temperature, water and SNOW
-         ! Variables: t_soisno, wliq_soisno, wice_soisno
-         !            snowdp, sag, scv, fsno, snl, z_soisno, dz_soisno
+         ! Variables: t_soisno, wliq_soisno, wice_soisno, wa, zwt
          IF (use_soilini) THEN
+            ! (1.1) all temperature, water and zwt from data.
 
             zi_soi_a(:) = (/0., zi_soi/)
 
@@ -408,9 +408,36 @@ SUBROUTINE IniTimeVar(ipatch, patchtype&
                wa = wa + 5000.
             ENDIF
 
+         ELSEIF (use_wtd) THEN
+            ! (1.2) only zwt is from data.
+
+            DO j = 1, nl_soil
+               IF(patchtype==3)THEN !land ice
+                  t_soisno(j) = 253.
+                  wliq_soisno(j) = 0.
+                  wice_soisno(j) = dz_soisno(j)*denice
+               ELSE
+                  t_soisno(j) = 283.
+                  wliq_soisno(j) = dz_soisno(j)*porsl(j)*denh2o
+                  wice_soisno(j) = 0.
+               ENDIF
+            ENDDO 
+
+            IF (patchtype <= 1) THEN
+               CALL get_water_equilibrium_state (zwtmm, nl_soil, wliq_soisno(1:nl_soil), smp, hk, wa, &
+                  zc_soimm, zi_soimm, porsl, vliq_r, psi0, hksati, nprms, prms)
+            ELSE
+               wa  = 0.
+               zwt = 0.
+            ENDIF
+
+            IF (.not. DEF_USE_VariablySaturatedFlow) THEN
+               wa = wa + 5000.
+            ENDIF
+
          ELSE
+            ! (1.3) cold start
 
-            ! soil temperature, water content
             DO j = 1, nl_soil
                IF(patchtype==3)THEN !land ice
                   t_soisno(j) = 253.
@@ -423,8 +450,21 @@ SUBROUTINE IniTimeVar(ipatch, patchtype&
                ENDIF
             ENDDO
 
+            IF (DEF_USE_VariablySaturatedFlow) THEN
+               wa  = 0.
+               zwt = zi_soimm(nl_soil)/1000.
+            ELSE
+               ! water table depth (initially at 1.0 m below the model bottom; wa when zwt
+               !                    is below the model bottom zi(nl_soil)
+               wa  = 4800.                             !assuming aquifer capacity is 5000 mm
+               zwt = (25. + z_soisno(nl_soil))+dz_soisno(nl_soil)/2. - wa/1000./0.2 !to result in zwt = zi(nl_soil) + 1.0 m
+            ENDIF
+
          ENDIF
 
+
+         ! (2) snow initialization
+         !     variables: snowdp, sag, scv, fsno, snl, z_soisno, dz_soisno
          z0m = htop * z0mr
 #if (defined LULC_IGBP_PFT || defined LULC_IGBP_PC)
          IF(patchtype==0)THEN
@@ -500,34 +540,6 @@ SUBROUTINE IniTimeVar(ipatch, patchtype&
 
          ENDIF
 
-         ! (2) SOIL aquifer and water table
-         ! Variables: wa, zwt
-         IF (.not. use_wtd) THEN
-
-            IF (.not. use_soilini) THEN
-               IF (DEF_USE_VariablySaturatedFlow) THEN
-                  wa  = 0.
-                  zwt = zi_soimm(nl_soil)/1000.
-               ELSE
-                  ! water table depth (initially at 1.0 m below the model bottom; wa when zwt
-                  !                    is below the model bottom zi(nl_soil)
-                  wa  = 4800.                             !assuming aquifer capacity is 5000 mm
-                  zwt = (25. + z_soisno(nl_soil))+dz_soisno(nl_soil)/2. - wa/1000./0.2 !to result in zwt = zi(nl_soil) + 1.0 m
-               ENDIF
-            ENDIF
-         ELSE
-            IF (patchtype <= 1) THEN
-               CALL get_water_equilibrium_state (zwtmm, nl_soil, wliq_soisno(1:nl_soil), smp, hk, wa, &
-                  zc_soimm, zi_soimm, porsl, vliq_r, psi0, hksati, nprms, prms)
-            ELSE
-               wa  = 0.
-               zwt = 0.
-            ENDIF
-
-            IF (.not. DEF_USE_VariablySaturatedFlow) THEN
-               wa = wa + 5000.
-            ENDIF
-         ENDIF
 
          ! (3) soil matrix potential hydraulic conductivity
          ! Variables: smp, hk

mksrfdata/Aggregation_PercentagesPFT.F90

@@ -203,10 +203,12 @@ SUBROUTINE Aggregation_PercentagesPFT (gland, dir_rawdata, dir_model_landdata, l
          -1.0e36_r8, lndname, 'pct_crop_patch', compress = 1, write_mode = 'one')
 #endif
 #else
-      allocate (SITE_croptyp(numpatch))
-      allocate (SITE_pctcrop(numpatch))
-      SITE_croptyp = cropclass
-      SITE_pctcrop = pctshrpch
+      IF (.not. USE_SITE_pctcrop) THEN
+         allocate (SITE_croptyp(numpatch))
+         allocate (SITE_pctcrop(numpatch))
+         SITE_croptyp = cropclass
+         SITE_pctcrop = pctshrpch
+      ENDIF
 #endif
 #endif
 

mksrfdata/MOD_LandCrop.F90

@@ -150,6 +150,8 @@ SUBROUTINE landcrop_build (lc_year)
 
       CALL pixelsetshared_build (landpatch, gcrop, cropdata, N_CFT, cropfilter, &
          pctshrpch, cropclass, fracin = pctshared)
+
+      cropclass = cropclass + N_PFT - 1
 
       numpatch = landpatch%nset
 

mksrfdata/MOD_LandPFT.F90

@@ -126,7 +126,7 @@ SUBROUTINE landpft_build (lc_year)
 #ifdef CROP
             ELSEIF (landpatch%settyp(1) == CROPLAND) THEN
                DO ipft = 1, numpft
-                  landpft%settyp(ipft) = cropclass(ipft) + N_PFT - 1
+                  landpft%settyp(ipft) = cropclass(ipft)
                   pft2patch   (ipft) = ipft
                   patch_pft_s (ipft) = ipft
                   patch_pft_e (ipft) = ipft
@@ -273,7 +273,7 @@ SUBROUTINE landpft_build (lc_year)
                      landpft%eindex(npft) = landpatch%eindex(ipatch)
                      landpft%ipxstt(npft) = landpatch%ipxstt(ipatch)
                      landpft%ipxend(npft) = landpatch%ipxend(ipatch)
-                     landpft%settyp(npft) = cropclass(ipatch) + N_PFT - 1
+                     landpft%settyp(npft) = cropclass(ipatch)
 
                      landpft%pctshared(npft) = landpatch%pctshared(ipatch)
 

mksrfdata/MOD_SingleSrfdata.F90

@@ -24,7 +24,7 @@ MODULE MOD_SingleSrfdata
 #endif
 
 #ifdef CROP
-   real(r8), allocatable :: SITE_croptyp (:)
+   integer,  allocatable :: SITE_croptyp (:)
    real(r8), allocatable :: SITE_pctcrop (:)
 #endif