void
AddCoupledSolidKinSpeciesAction::act()
{
mooseDoOnce(printReactions());
std::vector<bool> primary_participation(_primary_species.size(), false);
std::vector<std::string> solid_kin_species(_reactions.size());
std::vector<Real> weight;
// Loop through reactions
for (unsigned int j = 0; j < _reactions.size(); ++j)
{
std::vector<std::string> tokens;
// Parsing each reaction
MooseUtils::tokenize(_reactions[j], tokens, 1, "+=");
if (tokens.size() == 0)
mooseError("Empty reaction specified.");
std::vector<Real> stos(tokens.size() - 1);
std::vector<VariableName> rxn_species(tokens.size() - 1);
for (unsigned int k = 0; k < tokens.size(); ++k)
{
std::vector<std::string> stos_primary_species;
MooseUtils::tokenize(tokens[k], stos_primary_species, 1, "()");
if (stos_primary_species.size() == 2)
{
Real coef;
std::istringstream iss(stos_primary_species[0]);
iss >> coef;
stos[k] = coef;
rxn_species[k] = stos_primary_species[1];
// Check the participation of primary species
for (unsigned int i = 0; i < _primary_species.size(); ++i)
if (rxn_species[k] == _primary_species[i])
primary_participation[i] = true;
}
else
solid_kin_species[j] = stos_primary_species[0];
}
void
interactive() {
char *sbmlFilename;
char *select;
int quit;
SBMLDocument_t *d = NULL;
Model_t *m = NULL;
odeModel_t *om = NULL;
cvodeData_t * data = NULL;
integratorInstance_t *ii = NULL;
cvodeSettings_t *set = NULL;
printf("\n\nWelcome to the simple SBML ODE solver.\n");
printf("You have entered the interactive mode.\n");
printf("All other commandline options have been ignored.\n");
printf("Have fun!\n\n");
initializeOptions();
/* reset steady state */
Opt.SteadyState = 0;
/* activate printing of results to XMGrace */
Opt.Xmgrace = 1;
/* activate printing integrator messages */
Opt.PrintMessage = 1;
/* deactivate on the fly printing of results */
Opt.PrintOnTheFly = 0;
sbmlFilename = concat(Opt.ModelPath, Opt.ModelFile);
if ( (d = parseModelWithArguments(sbmlFilename)) == 0 )
{
Warn(stderr, "%s:%d interactive(): Can't parse Model >%s<",
__FILE__, __LINE__, sbmlFilename);
d = loadFile();
}
/* load models and default settings */
m = SBMLDocument_getModel(d);
om = ODEModel_create(m);
set = CvodeSettings_create();
SolverError_dumpAndClearErrors();
quit = 0;
data = NULL;
while ( quit == 0 ) {
printf("\n");
printf("Press (h) for instructions or (q) to quit.\n");
printf("> ");
select = get_line( stdin );
select = util_trim(select);
printf("\n");
if( strcmp(select,"l") == 0 ) {
/* free all existing structures */
if ( om != NULL )
ODEModel_free(data->model);
if ( d != NULL )
SBMLDocument_free(d);
if ( ii != NULL )
IntegratorInstance_free(ii);
/* load a new file */
d = loadFile();
/* load new models */
m = SBMLDocument_getModel(d);
om = ODEModel_create(m);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"h")==0)
printMenu();
if(strcmp(select,"s")==0)
printModel(m, stdout);
if(strcmp(select,"c")==0)
printSpecies(m, stdout);
if(strcmp(select,"r")==0)
printReactions(m, stdout);
if(strcmp(select,"o")==0)
printODEs(om, stdout);
/* integrate interface functions, asks for time and printsteps */
if(strcmp(select,"i")==0){
ii = callIntegrator(om, set);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"x")==0){
if ( Opt.Xmgrace == 1 ) {
Opt.Xmgrace = 0;
printf(" Printing results to stdout\n");
}
else if ( Opt.Xmgrace == 0 ) {
Opt.Xmgrace = 1;
printf(" Printing results to XMGrace\n");
}
}
if(strcmp(select,"st")==0)
printConcentrationTimeCourse(ii->data, stdout);
if(strcmp(select,"jt")==0)
printJacobianTimeCourse(ii->data, stdout);
if(strcmp(select,"ot")==0)
printOdeTimeCourse(ii->data, stdout);
if(strcmp(select,"rt")==0)
printReactionTimeCourse(ii->data, m, stdout);
if(strcmp(select,"xp")==0)
printPhase(ii->data);
if(strcmp(select,"set")==0)
setValues(m);
if(strcmp(select,"ss")==0){
if ( Opt.SteadyState == 1 ) {
Opt.SteadyState = 0;
printf(" Not checking for steady states during integration.\n");
}
else if ( Opt.SteadyState == 0 ) {
Opt.SteadyState = 1;
printf(" Checking for steady states during integration.\n");
}
}
if(strcmp(select,"uj")==0){
if ( Opt.Jacobian == 1 ) {
Opt.Jacobian = 0;
printf(" Using CVODE's internal approximation\n");
printf(" of the jacobian matrix for integration\n");
}
else if ( Opt.Jacobian == 0 ) {
Opt.Jacobian = 1;
printf(" Using automatically generated\n");
printf(" jacobian matrix for integration\n");
}
}
if(strcmp(select,"gf")==0)
setFormat();
if(strcmp(select,"rg")==0) {
drawModel(m, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"jg")==0){
if ( ii == NULL ) {
data = CvodeData_create(om);
CvodeData_initialize(data, set, om, 0);
drawJacoby(data, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
CvodeData_free(data);
}
else {
drawJacoby(ii->data, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
}
}
if(strcmp(select,"j")==0) {
if ( om->jacob == NULL )
ODEModel_constructJacobian(om);
printJacobian(om, stdout);
}
if(strcmp(select,"q")==0)
quit = 1;
}
if ( ii != NULL )
IntegratorInstance_free(ii);
if ( om != NULL )
ODEModel_free(om);
SBMLDocument_free(d);
SolverError_dumpAndClearErrors();
printf("\n\nGood Bye. Thx for using.\n\n");
}
