From 5af42889db9a85ce615460bfc9af3b49406f73b0 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Sun, 28 Jul 2024 18:35:32 -0400
Subject: [PATCH] IDA test problem requests specific time points.

---
 .../smoke/SimID_1298727889_0_.ida.expected    | 119 ------------------
 ...deInput => SimID_1489333437_0_.cvodeInput} |   3 +-
 ...unctions => SimID_1489333437_0_.functions} |   2 +-
 .../smoke/SimID_1489333437_0_.ida.expected    |   9 ++
 ...8727889_0_.log => SimID_1489333437_0_.log} |   3 +-
 ....xml => SimID_1489333437_0__0.simtask.xml} |   4 +-
 .../tests/smoke/simpleModel_Network_orig.vcml |  10 +-
 IDAWin/tests/smoke/smoke.sh                   |   6 +-
 8 files changed, 23 insertions(+), 133 deletions(-)
 delete mode 100644 IDAWin/tests/smoke/SimID_1298727889_0_.ida.expected
 rename IDAWin/tests/smoke/{SimID_1298727889_0_.cvodeInput => SimID_1489333437_0_.cvodeInput} (81%)
 rename IDAWin/tests/smoke/{SimID_1298727889_0_.functions => SimID_1489333437_0_.functions} (88%)
 create mode 100644 IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected
 rename IDAWin/tests/smoke/{SimID_1298727889_0_.log => SimID_1489333437_0_.log} (54%)
 rename IDAWin/tests/smoke/{SimID_1298727889_0__0.simtask.xml => SimID_1489333437_0__0.simtask.xml} (93%)

diff --git a/IDAWin/tests/smoke/SimID_1298727889_0_.ida.expected b/IDAWin/tests/smoke/SimID_1298727889_0_.ida.expected
deleted file mode 100644
index 2dbc8cbc..00000000
--- a/IDAWin/tests/smoke/SimID_1298727889_0_.ida.expected
+++ /dev/null
@@ -1,119 +0,0 @@
-t:s2:s4:
-0.00000000000000000E+00	4.00000000000000000E+00	0.00000000000000000E+00
-1.48651441805552199E-05	3.99997027324676591E+00	0.00000000000000000E+00
-2.97302883611104398E-05	3.99994055002821147E+00	0.00000000000000000E+00
-7.03106428215170950E-05	3.99985942617623413E+00	0.00000000000000000E+00
-1.10890997281923754E-04	3.99977832572827419E+00	0.00000000000000000E+00
-1.51471351742330412E-04	3.99969725062747017E+00	0.00000000000000000E+00
-1.92051706202737071E-04	3.99961620151555541E+00	0.00000000000000000E+00
-2.74093820841242409E-04	3.99945242312521154E+00	0.00000000000000000E+00
-4.23421345978895161E-04	3.99915460021103986E+00	0.00000000000000000E+00
-7.13707415631975399E-04	3.99857666180608273E+00	0.00000000000000000E+00
-1.25048298686421104E-03	3.99751150465873417E+00	0.00000000000000000E+00
-1.78725855809644656E-03	3.99645090736035824E+00	0.00000000000000000E+00
-2.32403412932868231E-03	3.99539485021374796E+00	0.00000000000000000E+00
-2.86080970056091805E-03	3.99434331293374800E+00	0.00000000000000000E+00
-3.41939153934100971E-03	3.99325383810517343E+00	0.00000000000000000E+00
-3.97797337812110137E-03	3.99216921527774415E+00	0.00000000000000000E+00
-4.53655521690119346E-03	3.99108941996223487E+00	0.00000000000000000E+00
-5.74213315960114649E-03	3.98877526015485628E+00	0.00000000000000000E+00
-6.94771110230109866E-03	3.98648325034444317E+00	0.00000000000000000E+00
-8.15328904500105082E-03	3.98421316501310141E+00	0.00000000000000000E+00
-9.35886698770100299E-03	3.98196478241938001E+00	0.00000000000000000E+00
-1.05644449304009552E-02	3.97973788336407264E+00	0.00000000000000000E+00
-1.17700228731009073E-02	3.97753225090277418E+00	0.00000000000000000E+00
-1.29756008158008595E-02	3.97534767037113479E+00	0.00000000000000000E+00
-1.67234253004214344E-02	3.96868855030449730E+00	0.00000000000000000E+00
-1.89337197523741334E-02	3.96485319172153172E+00	0.00000000000000000E+00
-2.11440142043268324E-02	3.96108446456472141E+00	0.00000000000000000E+00
-2.33543086562795314E-02	3.95738115285649039E+00	0.00000000000000000E+00
-2.55646031082322304E-02	3.95374206395657302E+00	0.00000000000000000E+00
-2.77748975601849295E-02	3.95016602693239616E+00	0.00000000000000000E+00
-2.99851920121376285E-02	3.94665189325195254E+00	0.00000000000000000E+00
-3.39049650973853797E-02	3.94056863534787771E+00	0.00000000000000000E+00
-3.78247381826331344E-02	3.93467043053284460E+00	0.00000000000000000E+00
-4.17445112678808891E-02	3.92895138505977526E+00	0.00000000000000000E+00
-4.56642843531286438E-02	3.92340580883081591E+00	0.00000000000000000E+00
-4.95840574383763985E-02	3.91802820674839003E+00	0.00000000000000000E+00
-5.35038305236241532E-02	3.91281327107547749E+00	0.00000000000000000E+00
-5.74236036088719079E-02	3.90775587446059802E+00	0.00000000000000000E+00
-6.13433766941196626E-02	3.90285106322542541E+00	0.00000000000000000E+00
-6.84728229020150347E-02	3.89430562565290339E+00	0.00000000000000000E+00
-7.37428199410849750E-02	3.88828712325357273E+00	0.00000000000000000E+00
-7.90128169801549152E-02	3.88251029559613814E+00	0.00000000000000000E+00
-8.42828140192248554E-02	3.87696509848465487E+00	0.00000000000000000E+00
-8.95528110582947956E-02	3.87164192979062172E+00	0.00000000000000000E+00
-9.48228080973647358E-02	3.86653161204979012E+00	0.00000000000000000E+00
-1.03895507740910858E-01	3.85820715640567258E+00	0.00000000000000000E+00
-1.12968207384456981E-01	3.85044556500262702E+00	0.00000000000000000E+00
-1.22040907028003104E-01	3.84320776397366703E+00	0.00000000000000000E+00
-1.31113606671549227E-01	3.83645751934507606E+00	0.00000000000000000E+00
-1.40186306315095349E-01	3.83016121349890604E+00	0.00000000000000000E+00
-1.49259005958641472E-01	3.82428764594274551E+00	0.00000000000000000E+00
-1.58331705602187595E-01	3.81880784918148475E+00	0.00000000000000000E+00
-1.67404405245733717E-01	3.81369491665000870E+00	0.00000000000000000E+00
-1.76477104889279840E-01	3.80892384475510415E+00	0.00000000000000000E+00
-1.85549804532825963E-01	3.80447138986503042E+00	0.00000000000000000E+00
-1.94622504176372085E-01	3.80031593806204171E+00	0.00000000000000000E+00
-2.03695203819918208E-01	3.79643738500637262E+00	0.00000000000000000E+00
-2.12767903463464331E-01	3.79281702477258964E+00	0.00000000000000000E+00
-2.21840603107010453E-01	3.78943744750896849E+00	0.00000000000000000E+00
-2.30913302750556576E-01	3.78628244550990312E+00	0.00000000000000000E+00
-2.39986002394102699E-01	3.78333692677324018E+00	0.00000000000000000E+00
-2.49058702037648821E-01	3.78058683512230864E+00	0.00000000000000000E+00
-2.58131401681194972E-01	3.77801907631750922E+00	0.00000000000000000E+00
-2.67204101324741095E-01	3.77562144978565639E+00	0.00000000000000000E+00
-2.76276800968287217E-01	3.77338258555965789E+00	0.00000000000000000E+00
-2.85349500611833340E-01	3.77129188596279263E+00	0.00000000000000000E+00
-2.94422200255379463E-01	3.76933947156831506E+00	0.00000000000000000E+00
-3.03494899898925585E-01	3.76751613113105677E+00	0.00000000000000000E+00
-3.12567599542471708E-01	3.76581327519609887E+00	0.00000000000000000E+00
-3.21640299186017831E-01	3.76422289308732960E+00	0.00000000000000000E+00
-3.30712998829563953E-01	3.76273751299914583E+00	0.00000000000000000E+00
-3.39785698473110076E-01	3.76135016494949248E+00	0.00000000000000000E+00
-3.48858398116656199E-01	3.76005434638016833E+00	0.00000000000000000E+00
-3.57931097760202321E-01	3.75884399020569138E+00	0.00000000000000000E+00
-3.67003797403748444E-01	3.75771343512392031E+00	0.00000000000000000E+00
-3.76076497047294567E-01	3.75665739801656251E+00	0.00000000000000000E+00
-3.85149196690840689E-01	3.75567094828400894E+00	0.00000000000000000E+00
-3.94221896334386812E-01	3.75474948397272268E+00	0.00000000000000000E+00
-4.03294595977932935E-01	3.75388870956413268E+00	0.00000000000000000E+00
-4.12367295621479057E-01	3.75308461530349158E+00	0.00000000000000000E+00
-4.21439995265025180E-01	3.75233345795667939E+00	0.00000000000000000E+00
-4.30512694908571303E-01	3.75163174289208223E+00	0.00000000000000000E+00
-4.44159393104912537E-01	3.75066225727547398E+00	0.00000000000000000E+00
-4.57806091301253770E-01	3.74978710730619946E+00	0.00000000000000000E+00
-4.71452789497595004E-01	3.74899709401433023E+00	0.00000000000000000E+00
-4.85099487693936238E-01	3.74828391848170916E+00	0.00000000000000000E+00
-4.98746185890277471E-01	3.74764009455926406E+00	0.00000000000000000E+00
-5.12392884086618761E-01	3.74705886856906956E+00	0.00000000000000000E+00
-5.26039582282959994E-01	3.74653414626810255E+00	0.00000000000000000E+00
-5.39686280479301228E-01	3.74606042778060777E+00	0.00000000000000000E+00
-5.53332978675642462E-01	3.74563274969380977E+00	0.00000000000000000E+00
-5.66979676871983695E-01	3.74524663281769499E+00	0.00000000000000000E+00
-5.80626375068324929E-01	3.74489803471053317E+00	0.00000000000000000E+00
-5.94273073264666163E-01	3.74458330675762285E+00	0.00000000000000000E+00
-6.07919771461007397E-01	3.74429915562765103E+00	0.00000000000000000E+00
-6.21566469657348630E-01	3.74404260864832494E+00	0.00000000000000000E+00
-6.35213167853689864E-01	3.74381098255801570E+00	0.00000000000000000E+00
-6.48859866050031098E-01	3.74360185524668188E+00	0.00000000000000000E+00
-6.62506564246372331E-01	3.74341304024822019E+00	0.00000000000000000E+00
-6.76153262442713565E-01	3.74324256376294118E+00	0.00000000000000000E+00
-6.89799960639054799E-01	3.74308864395120899E+00	0.00000000000000000E+00
-7.03446658835396033E-01	3.74294967224440933E+00	0.00000000000000000E+00
-7.17093357031737266E-01	3.74282419646718356E+00	0.00000000000000000E+00
-7.30740055228078500E-01	3.74271090560538200E+00	0.00000000000000000E+00
-7.44386753424419734E-01	3.74260861606723871E+00	0.00000000000000000E+00
-7.58033451620760967E-01	3.74251625928863207E+00	0.00000000000000000E+00
-7.78504463495302002E-01	3.74239425897741995E+00	0.00000000000000000E+00
-7.98975475369843036E-01	3.74228959135233685E+00	0.00000000000000000E+00
-8.19446487244384070E-01	3.74219979287007698E+00	0.00000000000000000E+00
-8.39917499118925104E-01	3.74212274979894621E+00	0.00000000000000000E+00
-8.60388510993466138E-01	3.74205664985144182E+00	0.00000000000000000E+00
-8.80859522868007172E-01	3.74199993902022765E+00	0.00000000000000000E+00
-9.01330534742548206E-01	3.74195128387593856E+00	0.00000000000000000E+00
-9.21801546617089240E-01	3.74190953994056041E+00	0.00000000000000000E+00
-9.42272558491630274E-01	3.74187372523816819E+00	0.00000000000000000E+00
-9.62743570366171308E-01	3.74184299751532601E+00	0.00000000000000000E+00
-9.83214582240712343E-01	3.74181663430575906E+00	0.00000000000000000E+00
-1.00000000000000000E+00	3.74179783640909713E+00	0.00000000000000000E+00
diff --git a/IDAWin/tests/smoke/SimID_1298727889_0_.cvodeInput b/IDAWin/tests/smoke/SimID_1489333437_0_.cvodeInput
similarity index 81%
rename from IDAWin/tests/smoke/SimID_1298727889_0_.cvodeInput
rename to IDAWin/tests/smoke/SimID_1489333437_0_.cvodeInput
index 3e30f775..7afffdd1 100644
--- a/IDAWin/tests/smoke/SimID_1298727889_0_.cvodeInput
+++ b/IDAWin/tests/smoke/SimID_1489333437_0_.cvodeInput
@@ -4,7 +4,8 @@ ENDING_TIME 1.0
 RELATIVE_TOLERANCE 1.0E-9
 ABSOLUTE_TOLERANCE 1.0E-9
 MAX_TIME_STEP 1.0
-KEEP_EVERY 1
+OUTPUT_TIMES 8
+0.0 1.0E-5 1.0E-4 0.001 0.01 0.1 0.5 1.0
 NUM_EQUATIONS 2
 ODE s2 INIT 4.0;
 	 RATE  - ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2))));
diff --git a/IDAWin/tests/smoke/SimID_1298727889_0_.functions b/IDAWin/tests/smoke/SimID_1489333437_0_.functions
similarity index 88%
rename from IDAWin/tests/smoke/SimID_1298727889_0_.functions
rename to IDAWin/tests/smoke/SimID_1489333437_0_.functions
index 27b36be6..bb726212 100644
--- a/IDAWin/tests/smoke/SimID_1298727889_0_.functions
+++ b/IDAWin/tests/smoke/SimID_1489333437_0_.functions
@@ -1,5 +1,5 @@
 ##---------------------------------------------
-##  /Users/jimschaff/.vcell/simdata/temp/SimID_1298727889_0_.functions
+##  /Users/jimschaff/.vcell/simdata/temp/SimID_1489333437_0_.functions
 ##---------------------------------------------
 
 Compartment::J_r0; ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2)))); ; Nonspatial_VariableType; false
diff --git a/IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected b/IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected
new file mode 100644
index 00000000..eb40f12d
--- /dev/null
+++ b/IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected
@@ -0,0 +1,9 @@
+t:s2:s4:
+0.00000000000000000E+00	4.00000000000000000E+00	0.00000000000000000E+00
+1.00000000000000008E-05	3.99998000095349759E+00	0.00000000000000000E+00
+1.00000000000000005E-04	3.99980008070643711E+00	0.00000000000000000E+00
+1.00000000000000002E-03	3.99800797408532871E+00	0.00000000000000000E+00
+1.00000000000000002E-02	3.98077784306128457E+00	0.00000000000000000E+00
+1.00000000000000006E-01	3.86170998966032331E+00	0.00000000000000000E+00
+5.00000000000000000E-01	3.74758417187014503E+00	0.00000000000000000E+00
+1.00000000000000000E+00	3.74179783773998942E+00	0.00000000000000000E+00
diff --git a/IDAWin/tests/smoke/SimID_1298727889_0_.log b/IDAWin/tests/smoke/SimID_1489333437_0_.log
similarity index 54%
rename from IDAWin/tests/smoke/SimID_1298727889_0_.log
rename to IDAWin/tests/smoke/SimID_1489333437_0_.log
index fc9fb11d..ad570edb 100644
--- a/IDAWin/tests/smoke/SimID_1298727889_0_.log
+++ b/IDAWin/tests/smoke/SimID_1489333437_0_.log
@@ -1,4 +1,3 @@
 IDAData logfile
 IDAData text format version 1
-SimID_1298727889_0_.ida
-KeepMost 1000
+SimID_1489333437_0_.ida
diff --git a/IDAWin/tests/smoke/SimID_1298727889_0__0.simtask.xml b/IDAWin/tests/smoke/SimID_1489333437_0__0.simtask.xml
similarity index 93%
rename from IDAWin/tests/smoke/SimID_1298727889_0__0.simtask.xml
rename to IDAWin/tests/smoke/SimID_1489333437_0__0.simtask.xml
index 22ca720f..d173c8bc 100644
--- a/IDAWin/tests/smoke/SimID_1298727889_0__0.simtask.xml
+++ b/IDAWin/tests/smoke/SimID_1489333437_0__0.simtask.xml
@@ -55,11 +55,11 @@
       <TimeBound StartTime="0.0" EndTime="1.0" />
       <TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
       <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
-      <OutputOptions KeepEvery="1" KeepAtMost="1000" />
+      <OutputOptions OutputTimes="0.0,1.0E-5,1.0E-4,0.001,0.01,0.1,0.5,1.0" />
       <NumberProcessors>1</NumberProcessors>
     </SolverTaskDescription>
     <MathOverrides />
-    <Version Name="temp simulation" KeyValue="1298727889" BranchId="1" Archived="1" Date="28-Jul-2024 16:41:38" FromVersionable="false">
+    <Version Name="temp simulation" KeyValue="1489333437" BranchId="1" Archived="1" Date="28-Jul-2024 18:28:21" FromVersionable="false">
       <Owner Name="temp" Identifier="123" />
       <GroupAccess Type="1" />
     </Version>
diff --git a/IDAWin/tests/smoke/simpleModel_Network_orig.vcml b/IDAWin/tests/smoke/simpleModel_Network_orig.vcml
index 7b16957d..75d2470a 100644
--- a/IDAWin/tests/smoke/simpleModel_Network_orig.vcml
+++ b/IDAWin/tests/smoke/simpleModel_Network_orig.vcml
@@ -159,11 +159,11 @@
           <TimeBound StartTime="0.0" EndTime="1.0" />
           <TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
           <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
-          <OutputOptions KeepEvery="1" KeepAtMost="1000" />
+          <OutputOptions OutputTimes="0.0,1.0E-5,1.0E-4,0.001,0.01,0.1,0.5,1.0" />
           <NumberProcessors>1</NumberProcessors>
         </SolverTaskDescription>
         <MathOverrides />
-        <Version Name="Simulation0" KeyValue="95705119" BranchId="95705120" Archived="0" Date="06-Aug-2015 13:27:30" FromVersionable="false">
+        <Version Name="Simulation0" KeyValue="273319284" BranchId="95705120" Archived="0" Date="28-Jul-2024 22:26:56" FromVersionable="false">
           <Owner Name="schaff" Identifier="17" />
           <GroupAccess Type="1" />
         </Version>
@@ -566,7 +566,7 @@
             <ParticleDriftZ>0.0</ParticleDriftZ>
           </ParticleProperties>
         </CompartmentSubDomain>
-        <Version Name="Application2_generated" KeyValue="273069957" BranchId="95705061" Archived="0" Date="24-Jul-2024 14:17:07" FromVersionable="false">
+        <Version Name="Application2_generated" KeyValue="273319272" BranchId="95705061" Archived="0" Date="28-Jul-2024 22:26:56" FromVersionable="false">
           <Owner Name="schaff" Identifier="17" />
           <GroupAccess Type="1" />
         </Version>
@@ -593,7 +593,7 @@
           <GroupAccess Type="1" />
         </Version>
       </Simulation>
-      <Version Name="nfsim" KeyValue="273069959" BranchId="95705109" Archived="0" Date="24-Jul-2024 14:17:07" FromVersionable="false">
+      <Version Name="nfsim" KeyValue="273319274" BranchId="95705109" Archived="0" Date="28-Jul-2024 22:26:56" FromVersionable="false">
         <Owner Name="schaff" Identifier="17" />
         <GroupAccess Type="1" />
       </Version>
@@ -601,7 +601,7 @@
         <ConvolutionKernel Type="ProjectionZKernel" />
       </MicroscopeMeasurement>
     </SimulationSpec>
-    <Version Name="simpleModel_Network_orig" KeyValue="273069969" BranchId="95705129" Archived="0" Date="24-Jul-2024 14:17:07" FromVersionable="false">
+    <Version Name="simpleModel_Network_orig" KeyValue="273319286" BranchId="95705129" Archived="0" Date="28-Jul-2024 22:26:56" FromVersionable="false">
       <Owner Name="schaff" Identifier="17" />
       <GroupAccess Type="1" />
     </Version>
diff --git a/IDAWin/tests/smoke/smoke.sh b/IDAWin/tests/smoke/smoke.sh
index f3c44e73..6eeb6722 100755
--- a/IDAWin/tests/smoke/smoke.sh
+++ b/IDAWin/tests/smoke/smoke.sh
@@ -7,9 +7,9 @@ echo "Running SundialsSolverStandalone_x64 solver with smoke.sh $EXE"
 # get the directory of this script
 TEST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
-INPUT="${TEST_DIR}/SimID_1298727889_0_.cvodeInput"
-OUTPUT="${TEST_DIR}/SimID_1298727889_0_.ida"
-EXPECTED_OUTPUT="${TEST_DIR}/SimID_1298727889_0_.ida.expected"
+INPUT="${TEST_DIR}/SimID_1489333437_0_.cvodeInput"
+OUTPUT="${TEST_DIR}/SimID_1489333437_0_.ida"
+EXPECTED_OUTPUT="${TEST_DIR}/SimID_1489333437_0_.ida.expected"
 
 if [ ! -f "$EXE" ]; then
     echo "NFsim executable $EXE not found. Exiting..."