void printSpecies(Model_t *m, FILE *f) { int i, j; Species_t *s; Compartment_t *c; fprintf(f, "\n"); fprintf(f, "# Initial Conditions for Species and Compartments:\n"); for ( i=0; i<Model_getNumCompartments(m); i++ ) { if ( i== 0 ) fprintf(f, "# Compartments:\n"); c = Model_getCompartment(m,i); if(Compartment_isSetId(c)) fprintf(f, "%s ", Compartment_getId(c)); if(Compartment_isSetName(c)) fprintf(f, "(%s) ", Compartment_getName(c)); if ( Compartment_isSetVolume(c) ) fprintf(f, "= %g; ", Compartment_getSize(c)); fprintf(f, "%s", Compartment_getConstant(c) ? "" : "variable; "); if(Compartment_isSetOutside(c)) fprintf(f, "outside %s; ", Compartment_getOutside(c)); /* fprintf(f, "\n"); */ fprintf(f, "dimensions %d; ", Compartment_getSpatialDimensions(c)); if(Compartment_isSetUnits(c)) fprintf(f, "[%s]; ", Compartment_getUnits(c)); fprintf(f, "\n"); fprintf(f, "# Species concentrations in `compartment' %s\n", Compartment_getId(c)); for(j=0;j<Model_getNumSpecies(m);j++){ s = Model_getSpecies(m,j); if(strcmp(Species_getCompartment(s), Compartment_getId(c))==0){ fprintf(f, "%s ", Species_getId(s)); if(Species_isSetName(s)) fprintf(f, "(%s) ", Species_getName(s)); if ( Species_isSetInitialAmount(s) ) fprintf(f, "= %g/%g; ", Species_getInitialAmount(s), Compartment_getSize(c)); else if ( Species_isSetInitialConcentration(s) ) fprintf(f, "= %g; ", Species_getInitialConcentration(s)); else fprintf(f, "# no initial value;"); fprintf(f, "%s", Species_getBoundaryCondition(s) ? "boundary;" : ""); fprintf(f, "%s", Species_getConstant(s) ? "constant;" : ""); if(Species_isSetCharge(s)) fprintf(f, "charge = %d; ", Species_getCharge(s)); fprintf(f, "\n"); } } fprintf(f, "\n"); } }
SBML_ODESOLVER_API void CvodeData_initializeValues(cvodeData_t *data) { int i; Parameter_t *p; Species_t *s; Compartment_t *c; odeModel_t *om = data->model; Model_t *ode = om->simple; /* First, fill cvodeData_t structure with data from the derived SBML model */ for ( i=0; i<data->nvalues; i++ ) { if ( (s = Model_getSpeciesById(ode, om->names[i])) ) data->value[i] = Species_getInitialConcentration(s); else if ( (c = Model_getCompartmentById(ode, om->names[i])) ) data->value[i] = Compartment_getSize(c); else if ((p = Model_getParameterById(ode, om->names[i])) ) data->value[i] = Parameter_getValue(p); } /* initialize assigned parameters */ for ( i=0; i<om->nass; i++ ) data->value[om->neq+i] = evaluateAST(om->assignment[i],data); /* set current time to 0 */ data->currenttime = 0.0; }
END_TEST START_TEST (test_L3_Compartment_size) { double size = 0.2; fail_unless( !Compartment_isSetSize(C)); fail_unless( util_isNaN(Compartment_getSize(C))); Compartment_setSize(C, size); fail_unless( Compartment_getSize(C) == size ); fail_unless( Compartment_isSetSize(C) ); Compartment_unsetSize(C); fail_unless( !Compartment_isSetSize(C) ); fail_unless( util_isNaN(Compartment_getSize(C))); }
END_TEST START_TEST (test_Compartment_unsetSize) { Compartment_setSize(C, 0.2); fail_unless( Compartment_getSize(C) == 0.2 ); fail_unless( Compartment_isSetSize(C) ); Compartment_unsetSize(C); fail_unless( !Compartment_isSetSize(C) ); }
END_TEST START_TEST (test_Compartment_setSize1) { int i = Compartment_setSize(C, 2.0); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Compartment_getSize(C) == 2.0 ); i = Compartment_unsetSize(C); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); }
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_Compartment_setSize2) { Compartment_t *c = Compartment_create(2, 2); int i = Compartment_setSize(c, 4); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Compartment_getSize(c) == 4 ); fail_unless( Compartment_isSetSize(c)); i = Compartment_unsetSize(c); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( !Compartment_isSetSize(c)); Compartment_free(c); }
END_TEST START_TEST (test_L3_Compartment_initDefaults) { Compartment_t *c = Compartment_create(3, 1); Compartment_setId(c, "A"); fail_unless( Compartment_isSetId (c) ); fail_unless( !Compartment_isSetName (c) ); fail_unless( !Compartment_isSetSize (c) ); fail_unless( !Compartment_isSetVolume (c) ); fail_unless( !Compartment_isSetUnits (c) ); fail_unless( !Compartment_isSetConstant (c) ); fail_unless( !Compartment_isSetSpatialDimensions (c) ); Compartment_initDefaults(c); fail_unless( !strcmp(Compartment_getId (c), "A")); fail_unless( Compartment_getName (c) == NULL ); fail_unless( !strcmp(Compartment_getUnits(c), "litre") ); fail_unless( Compartment_getSpatialDimensions(c) == 3 ); fail_unless( Compartment_getSize(c) == 1 ); fail_unless( Compartment_getConstant (c) == 1 ); fail_unless( Compartment_isSetId (c) ); fail_unless( !Compartment_isSetName (c) ); fail_unless( !Compartment_isSetSize (c) ); fail_unless( !Compartment_isSetVolume (c) ); fail_unless( Compartment_isSetUnits (c) ); fail_unless( Compartment_isSetConstant (c) ); fail_unless( Compartment_isSetSpatialDimensions (c) ); Compartment_free(c); }