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jcschaffjcschaff
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add smoke test for CVODE solver
1 parent b9988df commit 42fec0f

13 files changed

+1462
-13
lines changed

‎.gitignore‎

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NFsim_v1.11/tests/smoke/SimID_273069657_0_.gdat
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NFsim_v1.11/tests/smoke/SimID_273069657_0_.species
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IDAWin/tests/smoke/SimID_1489333437_0_.ida

‎IDAWin/CMakeLists.txt‎

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enable_testing()
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if (MINGW)
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set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE}.exe)
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set(python_cmd py)
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else (MINGW)
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set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE})
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set(python_cmd python3)
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endif (MINGW)
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set(test_dir ${CMAKE_CURRENT_SOURCE_DIR}/tests/smoke)
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# smoke test as a python script, for bash test example, see NFsim/tests/smoke
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add_test(NAME ${EXE_FILE}_smoke COMMAND ${python_cmd} ${test_dir}/smoke.py ${test_sundials_exe} WORKING_DIRECTORY ${test_dir})
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add_executable(
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hello_test
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hello_test.cpp

‎IDAWin/SundialsSolverStandalone.cpp‎

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break;
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}
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}
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#ifdef USE_MESSAGING
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// should only happen during testing for solver compiled with messaging but run locally.
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if (SimulationMessaging::getInstVar() == nullptr) {
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SimulationMessaging::create();
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}
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#endif
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if (solver.empty()) {
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throw "Solver not defined ";

‎IDAWin/tests/smoke/SimID_1489333437_0_.cvodeInput‎

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SOLVER CVODE
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STARTING_TIME 0.0
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ENDING_TIME 1.0
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RELATIVE_TOLERANCE 1.0E-9
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ABSOLUTE_TOLERANCE 1.0E-9
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MAX_TIME_STEP 1.0
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OUTPUT_TIMES 8
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0.0 1.0E-5 1.0E-4 0.001 0.01 0.1 0.5 1.0
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NUM_EQUATIONS 2
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ODE s2 INIT 4.0;
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RATE - ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2))));
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ODE s4 INIT 0.0;
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RATE 0.0;
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‎IDAWin/tests/smoke/SimID_1489333437_0_.functions‎

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##---------------------------------------------
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## /Users/jimschaff/.vcell/simdata/temp/SimID_1489333437_0_.functions
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##---------------------------------------------
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Compartment::J_r0; ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2)))); ; Nonspatial_VariableType; false
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Compartment::J_r1; 0.0; ; Nonspatial_VariableType; false
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Compartment::s0; (2.0 * (-1.0 + (0.5 * s2))); ; Nonspatial_VariableType; false
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Compartment::s1; (2.0 * (3.5 - (0.5 * s2))); ; Nonspatial_VariableType; false
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Compartment::s3; - s4; ; Nonspatial_VariableType; false
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‎IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected‎

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t:s2:s4:
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0.00000000000000000E+00 4.00000000000000000E+00 0.00000000000000000E+00
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1.00000000000000008E-05 3.99998000095349759E+00 0.00000000000000000E+00
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1.00000000000000005E-04 3.99980008070643711E+00 0.00000000000000000E+00
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1.00000000000000002E-03 3.99800797408532871E+00 0.00000000000000000E+00
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1.00000000000000002E-02 3.98077784306128457E+00 0.00000000000000000E+00
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1.00000000000000006E-01 3.86170998966032331E+00 0.00000000000000000E+00
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5.00000000000000000E-01 3.74758417187014503E+00 0.00000000000000000E+00
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1.00000000000000000E+00 3.74179783773998942E+00 0.00000000000000000E+00

‎IDAWin/tests/smoke/SimID_1489333437_0_.log‎

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IDAData logfile
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IDAData text format version 1
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SimID_1489333437_0_.ida

‎IDAWin/tests/smoke/SimID_1489333437_0__0.simtask.xml‎

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<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
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<MathDescription Name="Application0_generated">
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_K_GHK_">1.0E-9</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="K_millivolts_per_volt">1000.0</Constant>
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<Constant Name="Kf_r0">1.0</Constant>
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<Constant Name="Kf_r1">0.0</Constant>
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr_r0">2.0</Constant>
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<Constant Name="Kr_r1">0.0</Constant>
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<Constant Name="s0_init_uM">2.0</Constant>
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<Constant Name="s1_init_uM">3.0</Constant>
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<Constant Name="s2_init_uM">4.0</Constant>
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<Constant Name="s3_init_uM">0.0</Constant>
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<Constant Name="s4_init_uM">0.0</Constant>
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<Constant Name="Size_c0">0.5</Constant>
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<VolumeVariable Name="s2" Domain="Compartment" />
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<VolumeVariable Name="s4" Domain="Compartment" />
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<Function Name="J_r0" Domain="Compartment">(((Kf_r0 * s0) * s2) - (Kr_r0 * s1))</Function>
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<Function Name="J_r1" Domain="Compartment">((Kf_r1 * s3) - (Kr_r1 * s4))</Function>
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<Function Name="K_s0_total" Domain="Compartment">((Size_c0 * s0_init_uM) - (Size_c0 * s2_init_uM))</Function>
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<Function Name="K_s1_total" Domain="Compartment">((Size_c0 * s1_init_uM) + (Size_c0 * s2_init_uM))</Function>
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<Function Name="K_s3_total" Domain="Compartment">((Size_c0 * s3_init_uM) + (Size_c0 * s4_init_uM))</Function>
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<Function Name="s0" Domain="Compartment">((K_s0_total + (Size_c0 * s2)) / Size_c0)</Function>
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<Function Name="s1" Domain="Compartment">((K_s1_total - (Size_c0 * s2)) / Size_c0)</Function>
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<Function Name="s3" Domain="Compartment">((K_s3_total - (Size_c0 * s4)) / Size_c0)</Function>
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<CompartmentSubDomain Name="Compartment">
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<BoundaryType Boundary="Xm" Type="Value" />
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<BoundaryType Boundary="Xp" Type="Value" />
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<BoundaryType Boundary="Ym" Type="Value" />
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<BoundaryType Boundary="Yp" Type="Value" />
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<BoundaryType Boundary="Zm" Type="Value" />
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<BoundaryType Boundary="Zp" Type="Value" />
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<OdeEquation Name="s2" SolutionType="Unknown">
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<Rate>- J_r0</Rate>
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<Initial>s2_init_uM</Initial>
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</OdeEquation>
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<OdeEquation Name="s4" SolutionType="Unknown">
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<Rate>J_r1</Rate>
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<Initial>s4_init_uM</Initial>
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</OdeEquation>
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</CompartmentSubDomain>
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<Version Name="Application0_generated" KeyValue="95705054" BranchId="95705055" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
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<Owner Name="schaff" Identifier="17" />
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<GroupAccess Type="1" />
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</Version>
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</MathDescription>
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<Simulation Name="Simulation0">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
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<TimeBound StartTime="0.0" EndTime="1.0" />
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<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
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<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
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<OutputOptions OutputTimes="0.0,1.0E-5,1.0E-4,0.001,0.01,0.1,0.5,1.0" />
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<NumberProcessors>1</NumberProcessors>
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</SolverTaskDescription>
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<MathOverrides />
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<Version Name="temp simulation" KeyValue="1489333437" BranchId="1" Archived="1" Date="28-Jul-2024 18:28:21" FromVersionable="false">
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<Owner Name="temp" Identifier="123" />
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<GroupAccess Type="1" />
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</Version>
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</Simulation>
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<Geometry Name="non-spatial420951543" Dimension="0">
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<Extent X="10.0" Y="10.0" Z="10.0" />
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<Origin X="0.0" Y="0.0" Z="0.0" />
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<SubVolume Name="Compartment" Handle="0" Type="Compartmental" KeyValue="95705043" />
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<Version Name="non-spatial420951543" KeyValue="95705039" BranchId="95705040" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
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<Owner Name="schaff" Identifier="17" />
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<GroupAccess Type="1" />
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</Version>
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</Geometry>
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</SimulationTask>

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