SBML_ODESOLVER_API int IntegratorInstance_updateModel(integratorInstance_t *engine)
{
int i;
Species_t *s;
Compartment_t *c;
Parameter_t *p;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeResults_t *results = engine->results;
int nout = results->nout;
int nvalues = data->nvalues;
Model_t *m = om->m;
for ( i=0; i<nvalues; i++ ) {
if ( (s = Model_getSpeciesById(m, om->names[i]))
!= NULL ) {
Species_setInitialConcentration(s, results->value[i][nout]);
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) != NULL ) {
Compartment_setSize(c, results->value[i][nout]);
}
else if ( (p = Model_getParameterById(m, om->names[i])) != NULL ) {
Parameter_setValue(p, results->value[i][nout]);
}
else
return 0;
}
return 1;
}
END_TEST
START_TEST (test_Species_setInitialConcentration1)
{
int i = Species_setInitialConcentration(C, 2.0);
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
fail_unless( !Species_isSetInitialConcentration(C) );
}
END_TEST
START_TEST (test_Species_setInitialConcentration)
{
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( !Species_isSetInitialConcentration(S) );
Species_setInitialConcentration(S, 3.4);
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( Species_isSetInitialConcentration(S) );
fail_unless( Species_getInitialConcentration(S) == 3.4 );
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Concentration)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c =
Compartment_create(2, 1);
Species_t *s =
Species_create(2, 1);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Model_addCompartment( m, c );
Species_setId ( s, "s" );
Species_setCompartment ( s, sid );
Species_setInitialConcentration( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL);
/**
* These tests will fail under Cygwin because of a minimal
* setlocale() implementation (see setlocale manpage).
*/
#ifndef CYGWIN
fail_unless( Species_getInitialAmount(Model_getSpecies(m, 0)) == 2.808, NULL );
#endif
Species_t * s1 = Model_getSpecies(m, 0);
fail_unless (s1 != NULL);
fail_unless (!strcmp(Species_getCompartment(s1), "C"));
fail_unless(Compartment_getSize(Model_getCompartmentById(m, "C")) == 1.2);
fail_unless(Species_getInitialConcentration(s1) == 2.34);
fail_unless(Species_isSetInitialConcentration(s1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_L3_Species_initialConcentration)
{
double initialConcentration = 0.2;
fail_unless( !Species_isSetInitialConcentration(S));
fail_unless( util_isNaN(Species_getInitialConcentration(S)));
Species_setInitialConcentration(S, initialConcentration);
fail_unless( Species_getInitialConcentration(S) == initialConcentration );
fail_unless( Species_isSetInitialConcentration(S) );
Species_unsetInitialConcentration(S);
fail_unless( !Species_isSetInitialConcentration(S) );
fail_unless( util_isNaN(Species_getInitialConcentration(S)));
}
END_TEST
START_TEST (test_Species_setInitialConcentration2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setInitialConcentration(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialConcentration(c) == 4 );
fail_unless( Species_isSetInitialConcentration(c));
i = Species_unsetInitialConcentration(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialConcentration(c));
Species_free(c);
}
/*
setValues: the user can enter a species name and
change its initial condition (amount or concentration)
*/
static void setValues(Model_t *m) {
char *species;
char *newIA;
char *newIC;
Species_t *s;
printf("Please enter the id of the species to change: ");
species = get_line(stdin);
species = util_trim(species);
if ( (s = Model_getSpeciesById(m,species) ) ) {
printf("\n");
printf("Id: %s\n", Species_getId(s));
if ( Species_isSetName(s) ) {
printf("Name: %s\n", Species_getName(s));
}
if ( Species_isSetInitialAmount(s) ) {
printf("Initial Amount: %g", Species_getInitialAmount(s));
}
else if (Species_isSetInitialConcentration(s) ) {
printf("Initial Concentration: %g", Species_getInitialConcentration(s));
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
} else {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
if ( Species_isSetSpatialSizeUnits(s) ) {
printf("%s%s", "/", Species_getSpatialSizeUnits(s));
}
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
printf(" (has only substance units)");
}
printf("\n");
if ( Species_isSetCharge(s) ) {
printf("Charge: %-10d", Species_getCharge(s));
}
printf("\n");
printf("%s ", Species_getBoundaryCondition(s) ?
"Species is a Boundary\n" : "\n");
printf("%s ", Species_getConstant(s) ?
"Species is set constant" : "\n");
printf("\n");
if ( Species_isSetInitialAmount(s) ) {
printf("Please enter new initial Amount: ");
newIA = get_line(stdin);
newIA = util_trim(newIA);
Species_setInitialAmount(s, (float) atof(newIA));
}
else if ( Species_isSetInitialConcentration(s) ) {
printf("Please enter new initial Concentration: ");
newIC = get_line(stdin);
newIC = util_trim(newIC);
Species_setInitialConcentration(s, (float) atof(newIC));
}
}
else {
printf("%s not found.\n", species);
}
}
