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);
}
