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Merge pull request #982 from sys-bio/reduce-step-size
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Add methods for getting and setting mDiffStepSize to C API
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@luciansmith
luciansmith committed Apr 18, 2022
2 parents 08e9381 + 523a6ab commit a4acf43
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Showing 7 changed files with 200 additions and 36 deletions.
6 changes: 3 additions & 3 deletions source/rrRoadRunner.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,7 @@ namespace rr {
bool simulatedSinceReset = false;

RoadRunnerImpl(const std::string &uriOrSBML, const Dictionary *dict) :
mDiffStepSize(0.05),
mDiffStepSize(0.02),
mSteadyStateThreshold(1.E-2),
simulationResult(),
integrator(0),
Expand All @@ -268,7 +268,7 @@ namespace rr {
}

RoadRunnerImpl(const std::istream &in) :
mDiffStepSize(0.05),
mDiffStepSize(0.02),
mSteadyStateThreshold(1.E-2),
simulationResult(),
integrator(NULL),
Expand All @@ -287,7 +287,7 @@ namespace rr {

RoadRunnerImpl(const std::string &_compiler, const std::string &_tempDir,
const std::string &_supportCodeDir) :
mDiffStepSize(0.05),
mDiffStepSize(0.02),
mSteadyStateThreshold(1.E-2),
simulationResult(),
integrator(NULL),
Expand Down
56 changes: 56 additions & 0 deletions test/c_api_core/CAPICoreTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -269,4 +269,60 @@ TEST_F(CAPICoreTest, CheckRK4WorksFromC) {
for (int k = 0; k < cvode->CSize(); k++) {
EXPECT_NEAR((*cvode)(cvode->RSize() - 1, k), (*rk4)(rk4->RSize() - 1, k), 1e-6);
}
}

TEST_F(CAPICoreTest, SetAndGetMDiffStepSize) {
string xml = getFileContent((testModelFilePath.string()));
RRHandle rr = createRRInstance();
EXPECT_TRUE(loadSBML(rr, xml.c_str()));

double mDiffStepSize;
EXPECT_TRUE(getDiffStepSize(rr, &mDiffStepSize));
EXPECT_EQ(mDiffStepSize, 0.02);

EXPECT_TRUE(setDiffStepSize(rr, 0.06));

EXPECT_TRUE(getDiffStepSize(rr, &mDiffStepSize));
EXPECT_EQ(mDiffStepSize, 0.06);

freeRRInstance(rr);
}

TEST_F(CAPICoreTest, CheckGetCC) {

RRHandle rrH = createRRInstance();
EXPECT_TRUE(loadSBMLFromFileE(rrH, (cAPICoreModelsDir / path("steadystate.xml")).string().c_str(), true));

double K = 0.8;
double ss_val;
double prev_AP;
double AP;
EXPECT_TRUE(steadyState(rrH, &ss_val));
EXPECT_TRUE(getCC(rrH, "AP", "K", &prev_AP));

bool found_local_max = false;
bool success = true;
for (int i = 1; i < 20; i++) {
K = K + 0.01;
EXPECT_TRUE(setValue(rrH, "K", K));
EXPECT_TRUE(steadyState(rrH, &ss_val));
EXPECT_TRUE(getCC(rrH, "AP", "K", &AP));
if (!found_local_max) {
if (AP < prev_AP) {
found_local_max = true;
}
}
else {
if (AP > prev_AP) {
success = false;
break;
}
}
prev_AP = AP;
}

EXPECT_TRUE(success);

delete rrH;

}
2 changes: 1 addition & 1 deletion test/model_analysis/model_analysis.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ TEST_F(ModelAnalysisTests, checkUCCForSet) {
//Behind the scenes, we get and then set various values to calculate ucc, and
// have to ensure that we don't worry about setting something that's already set.
double val = rr.getValue("ucc(P0_to_P1, V_mT)");
EXPECT_NEAR(val, 7.78235, 0.001);
EXPECT_NEAR(val, 7.84724, 0.001);
}

TEST_F(ModelAnalysisTests, getConcentrationRateSimple) {
Expand Down
70 changes: 70 additions & 0 deletions test/models/CAPICore/steadystate.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model metaid="__main" id="__main">
<listOfCompartments>
<compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="A" compartment="default_compartment" initialAmount="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="AP" compartment="default_compartment" initialAmount="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="K" value="0.1" constant="true"/>
<parameter id="Vm1" value="5" constant="true"/>
<parameter id="Km1" value="0.08" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="_J0" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="AP" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> K </ci>
<ci> Vm1 </ci>
<ci> A </ci>
</apply>
<apply>
<plus/>
<ci> Km1 </ci>
<ci> A </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="_J1" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="AP" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> Vm1 </ci>
<ci> AP </ci>
</apply>
<apply>
<plus/>
<ci> Km1 </ci>
<ci> AP </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
64 changes: 32 additions & 32 deletions test/python/test_python_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ def test_removeSpecies(self):
)

def test_diffstep_getter(self):
self.assertEqual(self.rr._diffstep_getter(), 0.05)
self.assertEqual(self.rr._diffstep_getter(), 0.02)

def test_diffstep_stter(self):
self.rr._diffstep_stter(0.01)
Expand Down Expand Up @@ -244,7 +244,7 @@ def test_default_compartment(self):
self.assertEqual(self.rr.default_compartment, 1)

def test_diffstep(self):
self.assertEqual(self.rr.diffstep, 0.05)
self.assertEqual(self.rr.diffstep, 0.02)

@unittest.skip("This API is unclear. ")
def test_ensureSolversRegistered(self):
Expand All @@ -265,7 +265,7 @@ def test_getBoundarySpeciesConcentrationsNamedArray(self):
self.assertEqual(bs["S1"], 20)

def test_getCC(self):
self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090752242926029)
self.assertAlmostEqual(self.rr.getCC("_J0", "kf"), 0.009090905110435235)

def test_getCompiler(self):
compiler_string = str(self.rr.getCompiler())
Expand Down Expand Up @@ -311,7 +311,7 @@ def test_getDependentRatesOfChangeNamedArray(self):
self.assertTrue(callable(self.rr.getDependentRatesOfChangeNamedArray))

def test_getDiffStepSize(self):
self.assertEqual(0.05, self.rr.getDiffStepSize())
self.assertEqual(0.02, self.rr.getDiffStepSize())

def test_getEE(self):
self.assertAlmostEqual(self.rr.getEE("_J0", "kf"), 1.0000000000000024)
Expand Down Expand Up @@ -662,7 +662,7 @@ def test_getUnscaledParameterElasticity(self):

def test_getUnscaledSpeciesElasticity(self):
self.assertEqual(
0.09999999999999994,
0.10000000000000007,
self.rr.getUnscaledSpeciesElasticity(0, 0),
)

Expand All @@ -674,7 +674,7 @@ def test_getValue(self):

def test_getuCC(self):
self.assertAlmostEqual(
0.09090752242926028,
0.09090905110435235,
self.rr.getuCC("_J0", "kf"),
)

Expand Down Expand Up @@ -731,40 +731,40 @@ def test_items(self):
('stoich(S1, _J1)', 1.0),
('stoich(S2, _J0)', 1.0),
('stoich(S2, _J1)', -1.0),
('uec(_J0, S1)', 0.09999999999999994),
('uec(_J0, S1)', 0.10000000000000007),
('uec(_J0, S2)', 0.0),
('uec(_J0, kf)', 10.000000000000023),
('uec(_J0, kf)', 10.000000000000082),
('uec(_J0, kb)', 0.0),
('uec(_J1, S1)', 0.0),
('uec(_J1, S2)', 0.010000000000000007),
('uec(_J1, S2)', 0.009999999999999998),
('uec(_J1, kf)', 0.0),
('uec(_J1, kb)', 1.0000000000000009),
('ec(_J0, S1)', 0.9999999999999993),
('uec(_J1, kb)', 1.0000000000000053),
('ec(_J0, S1)', 1.0000000000000007),
('ec(_J0, S2)', 0.0),
('ec(_J0, kf)', 1.0000000000000024),
('ec(_J0, kf)', 1.0000000000000082),
('ec(_J0, kb)', 0.0),
('ec(_J1, S1)', 0.0),
('ec(_J1, S2)', 1.0000000000000007),
('ec(_J1, S2)', 0.9999999999999998),
('ec(_J1, kf)', 0.0),
('ec(_J1, kb)', 1.0000000000000009),
('ucc(_J0, kf)', 0.09090752242926028),
('ucc(_J0, kb)', 9.090909075384493),
('ucc(_J1, kf)', 0.09090752242926028),
('ucc(_J1, kb)', 9.090909075384475),
('ucc(S1, kf)', -9.090752242926154),
('ucc(S1, kb)', 90.90909075384494),
('ucc(S2, kf)', 9.090752242926213),
('ucc(S2, kb)', -90.90909075384464),
('cc(_J0, kf)', 0.009090752242926029),
('cc(_J0, kb)', 0.09090909075384493),
('cc(_J1, kf)', 0.9090752242926029),
('cc(_J1, kb)', 9.090909075384475),
('cc(S1, kf)', -0.09090752242926155),
('cc(S1, kb)', 0.09090909075384493),
('cc(S2, kf)', 0.9090752242926213),
('cc(S2, kb)', -0.9090909075384463),
('eigen(S1)', (-0.11000000000000017+0j)),
('eigenReal(S1)', -0.11000000000000017),
('ec(_J1, kb)', 1.0000000000000053),
('ucc(_J0, kf)', 0.09090905110435235),
('ucc(_J0, kb)', 9.090909090511781),
('ucc(_J1, kf)', 0.09090905110435235),
('ucc(_J1, kb)', 9.090909090511735),
('ucc(S1, kf)', -9.09090511043516),
('ucc(S1, kb)', 90.90909090511799),
('ucc(S2, kf)', 9.090905110435088),
('ucc(S2, kb)', -90.90909090512392),
('cc(_J0, kf)', 0.009090905110435235),
('cc(_J0, kb)', 0.09090909090511781),
('cc(_J1, kf)', 0.9090905110435236),
('cc(_J1, kb)', 9.090909090511735),
('cc(S1, kf)', -0.09090905110435162),
('cc(S1, kb)', 0.09090909090511799),
('cc(S2, kf)', 0.9090905110435088),
('cc(S2, kb)', -0.9090909090512392),
('eigen(S1)', (-0.10999999999999983+0j)),
('eigenReal(S1)', -0.10999999999999983),
('eigenImag(S1)', 0.0),
('eigen(S2)', 0j),
('eigenReal(S2)', 0.0),
Expand Down
18 changes: 18 additions & 0 deletions wrappers/C/rrc_api.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1302,6 +1302,24 @@ bool rrcCallConv getCC (RRHandle handle, const char* variable, const char* param
catch_bool_macro
}

bool rrcCallConv getDiffStepSize(RRHandle handle, double *value)
{
start_try
RoadRunner* rri = castToRoadRunner(handle);
*value = rri->getDiffStepSize();
return true;
catch_bool_macro
}

bool rrcCallConv setDiffStepSize(RRHandle handle, const double value)
{
start_try
RoadRunner* rri = castToRoadRunner(handle);
rri->setDiffStepSize(value);
return true;
catch_bool_macro
}

bool rrcCallConv getuEE(RRHandle handle, const char* name, const char* species, double* value)
{
start_try
Expand Down
20 changes: 20 additions & 0 deletions wrappers/C/rrc_api.h
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Original file line number Diff line number Diff line change
Expand Up @@ -2816,6 +2816,26 @@ C_DECL_SPEC bool rrcCallConv getuCC (RRHandle handle, const char* variable, cons
*/
C_DECL_SPEC bool rrcCallConv getCC (RRHandle handle, const char* variable, const char* parameter, double* value);

/*!
\brief Retrieve the differential step size used in routines such as getCC
\param[in] handle Handle to a RoadRunner instance
\param[out] value This is the value of the step size returns to the caller
\return Returns true if successful
\ingroup mca
*/
C_DECL_SPEC bool rrcCallConv getDiffStepSize(RRHandle handle, double* value);

/*!
\brief Sets the differential step size used in routines such as getCC
\param[in] handle Handle to a RoadRunner instance
\param[in] value This is the desired step size value
\return Returns true if successful
\ingroup mca
*/
C_DECL_SPEC bool rrcCallConv setDiffStepSize(RRHandle handle, const double value);

/*!
\brief Retrieve a single elasticity coefficient
Expand Down

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