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add smoke test for CVODE solver
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@jcschaff
jcschaff committed Jul 28, 2024
1 parent b9988df commit cf41797
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Showing 11 changed files with 1,538 additions and 13 deletions.
11 changes: 11 additions & 0 deletions IDAWin/CMakeLists.txt
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Expand Up @@ -35,6 +35,17 @@ install(TARGETS IDAWin ARCHIVE DESTINATION bin)

enable_testing()

if (MINGW)
set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE}.exe)
else (MINGW)
set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE})
endif (MINGW)
set(test_dir ${CMAKE_CURRENT_SOURCE_DIR}/tests/smoke)

# smoke test as a bash script, for python test example, see NFsim/tests/smoke
add_test(NAME ${EXE_FILE}_smoke COMMAND bash -c "${test_dir}/smoke.sh ${test_sundials_exe}" WORKING_DIRECTORY ${test_dir})


add_executable(
hello_test
hello_test.cpp
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13 changes: 13 additions & 0 deletions IDAWin/tests/smoke/SimID_1298727889_0_.cvodeInput
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SOLVER CVODE
STARTING_TIME 0.0
ENDING_TIME 1.0
RELATIVE_TOLERANCE 1.0E-9
ABSOLUTE_TOLERANCE 1.0E-9
MAX_TIME_STEP 1.0
KEEP_EVERY 1
NUM_EQUATIONS 2
ODE s2 INIT 4.0;
RATE - ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2))));
ODE s4 INIT 0.0;
RATE 0.0;

10 changes: 10 additions & 0 deletions IDAWin/tests/smoke/SimID_1298727889_0_.functions
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##---------------------------------------------
## /Users/jimschaff/.vcell/simdata/temp/SimID_1298727889_0_.functions
##---------------------------------------------

Compartment::J_r0; ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2)))); ; Nonspatial_VariableType; false
Compartment::J_r1; 0.0; ; Nonspatial_VariableType; false
Compartment::s0; (2.0 * (-1.0 + (0.5 * s2))); ; Nonspatial_VariableType; false
Compartment::s1; (2.0 * (3.5 - (0.5 * s2))); ; Nonspatial_VariableType; false
Compartment::s3; - s4; ; Nonspatial_VariableType; false

119 changes: 119 additions & 0 deletions IDAWin/tests/smoke/SimID_1298727889_0_.ida.expected
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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
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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
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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
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2.99851920121376285E-02 3.94665189325195254E+00 0.00000000000000000E+00
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1.00000000000000000E+00 3.74179783640909713E+00 0.00000000000000000E+00
4 changes: 4 additions & 0 deletions IDAWin/tests/smoke/SimID_1298727889_0_.log
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IDAData logfile
IDAData text format version 1
SimID_1298727889_0_.ida
KeepMost 1000
76 changes: 76 additions & 0 deletions IDAWin/tests/smoke/SimID_1298727889_0__0.simtask.xml
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<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
<MathDescription Name="Application0_generated">
<Constant Name="_F_">96485.3321</Constant>
<Constant Name="_F_nmol_">9.64853321E-5</Constant>
<Constant Name="_K_GHK_">1.0E-9</Constant>
<Constant Name="_N_pmol_">6.02214179E11</Constant>
<Constant Name="_PI_">3.141592653589793</Constant>
<Constant Name="_R_">8314.46261815</Constant>
<Constant Name="_T_">300.0</Constant>
<Constant Name="K_millivolts_per_volt">1000.0</Constant>
<Constant Name="Kf_r0">1.0</Constant>
<Constant Name="Kf_r1">0.0</Constant>
<Constant Name="KMOLE">0.001660538783162726</Constant>
<Constant Name="Kr_r0">2.0</Constant>
<Constant Name="Kr_r1">0.0</Constant>
<Constant Name="s0_init_uM">2.0</Constant>
<Constant Name="s1_init_uM">3.0</Constant>
<Constant Name="s2_init_uM">4.0</Constant>
<Constant Name="s3_init_uM">0.0</Constant>
<Constant Name="s4_init_uM">0.0</Constant>
<Constant Name="Size_c0">0.5</Constant>
<VolumeVariable Name="s2" Domain="Compartment" />
<VolumeVariable Name="s4" Domain="Compartment" />
<Function Name="J_r0" Domain="Compartment">(((Kf_r0 * s0) * s2) - (Kr_r0 * s1))</Function>
<Function Name="J_r1" Domain="Compartment">((Kf_r1 * s3) - (Kr_r1 * s4))</Function>
<Function Name="K_s0_total" Domain="Compartment">((Size_c0 * s0_init_uM) - (Size_c0 * s2_init_uM))</Function>
<Function Name="K_s1_total" Domain="Compartment">((Size_c0 * s1_init_uM) + (Size_c0 * s2_init_uM))</Function>
<Function Name="K_s3_total" Domain="Compartment">((Size_c0 * s3_init_uM) + (Size_c0 * s4_init_uM))</Function>
<Function Name="s0" Domain="Compartment">((K_s0_total + (Size_c0 * s2)) / Size_c0)</Function>
<Function Name="s1" Domain="Compartment">((K_s1_total - (Size_c0 * s2)) / Size_c0)</Function>
<Function Name="s3" Domain="Compartment">((K_s3_total - (Size_c0 * s4)) / Size_c0)</Function>
<CompartmentSubDomain Name="Compartment">
<BoundaryType Boundary="Xm" Type="Value" />
<BoundaryType Boundary="Xp" Type="Value" />
<BoundaryType Boundary="Ym" Type="Value" />
<BoundaryType Boundary="Yp" Type="Value" />
<BoundaryType Boundary="Zm" Type="Value" />
<BoundaryType Boundary="Zp" Type="Value" />
<OdeEquation Name="s2" SolutionType="Unknown">
<Rate>- J_r0</Rate>
<Initial>s2_init_uM</Initial>
</OdeEquation>
<OdeEquation Name="s4" SolutionType="Unknown">
<Rate>J_r1</Rate>
<Initial>s4_init_uM</Initial>
</OdeEquation>
</CompartmentSubDomain>
<Version Name="Application0_generated" KeyValue="95705054" BranchId="95705055" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
<Owner Name="schaff" Identifier="17" />
<GroupAccess Type="1" />
</Version>
</MathDescription>
<Simulation Name="Simulation0">
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
<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" />
<NumberProcessors>1</NumberProcessors>
</SolverTaskDescription>
<MathOverrides />
<Version Name="temp simulation" KeyValue="1298727889" BranchId="1" Archived="1" Date="28-Jul-2024 16:41:38" FromVersionable="false">
<Owner Name="temp" Identifier="123" />
<GroupAccess Type="1" />
</Version>
</Simulation>
<Geometry Name="non-spatial420951543" Dimension="0">
<Extent X="10.0" Y="10.0" Z="10.0" />
<Origin X="0.0" Y="0.0" Z="0.0" />
<SubVolume Name="Compartment" Handle="0" Type="Compartmental" KeyValue="95705043" />
<Version Name="non-spatial420951543" KeyValue="95705039" BranchId="95705040" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
<Owner Name="schaff" Identifier="17" />
<GroupAccess Type="1" />
</Version>
</Geometry>
</SimulationTask>
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