SBML_ODESOLVER_API cvodeSettings_t *CvodeSettings_clone(cvodeSettings_t *set)
{
int i;
cvodeSettings_t *clone;
ASSIGN_NEW_MEMORY(clone, struct cvodeSettings, NULL);
/* Setting SBML ODE Solver integration parameters */
CvodeSettings_setErrors(clone, set->Error, set->RError, set->Mxstep);
CvodeSettings_setSwitches(clone, set->UseJacobian, set->Indefinitely,
set->HaltOnEvent, set->SteadyState,
set->StoreResults,
set->Sensitivity, set->SensMethod);
CvodeSettings_setMethod(clone, set->CvodeMethod, set->MaxOrder);
CvodeSettings_setIterMethod(clone, set->IterMethod);
/* Unless indefinite integration is chosen, generate a TimePoints array */
if ( !clone->Indefinitely ) {
ASSIGN_NEW_MEMORY_BLOCK(clone->TimePoints,clone->PrintStep+1,double,NULL);
/* copy TimePoint array */
for ( i=0; i<=clone->PrintStep; i++ ) {
clone->TimePoints[i] = set->TimePoints[i];
}
}
SBML_ODESOLVER_API cvodeSettings_t *CvodeSettings_createWith(double Time, int PrintStep, double Error, double RError, int Mxstep, int UseJacobian, int Indefinitely, int HaltOnEvent, int SteadyState, int StoreResults, int Sensitivity, int SensMethod)
{
cvodeSettings_t *set;
ASSIGN_NEW_MEMORY(set, struct cvodeSettings, NULL);
/* 1. Setting SBML ODE Solver integration parameters */
CvodeSettings_setErrors(set, Error, RError, Mxstep);
/* set non-linear solver defaults (BDF, Newton, max.order 5*/
set->CvodeMethod = 0;
set->IterMethod = 0;
set->MaxOrder = 5;
CvodeSettings_setSwitches(set, UseJacobian, Indefinitely,
HaltOnEvent, SteadyState, StoreResults,
Sensitivity, SensMethod);
/* 2. Setting Requested Time Series */
/* Unless indefinite integration, generate a TimePoints array */
if ( !Indefinitely ) {
/* ... generate default TimePoint array */
CvodeSettings_setTime(set, Time, PrintStep);
}
return set;
}
int
main (int argc, char *argv[]){
int i, j;
char *model, *parameter, *reaction;
double start, end, steps, value;
double time ;
double printstep;
/* libSBML types */
SBMLDocument_t *d;
SBMLReader_t *sr;
/* SOSlib types */
cvodeSettings_t *set;
varySettings_t *vs;
SBMLResultsMatrix_t *resM;
SBMLResults_t *results;
/* parsing command-line arguments */
if (argc < 8 ) {
fprintf(stderr,
"usage %s sbml-model-file simulation-time time-steps"
" start-value end-value step-number parameter-id"
" [optional reaction-id]\n",
argv[0]);
exit(EXIT_FAILURE);
}
model = argv[1];
time = atof(argv[2]);
printstep = atoi(argv[3]);
parameter = argv[7];
start = atof(argv[4]);
end = atof(argv[5]);
steps = atoi(argv[6]);
if ( argc > 8 ) {
reaction = argv[8];
}
else{
reaction = NULL;
}
printf("### Varying parameter %s (reaction %s) from %f to %f in %f steps\n",
parameter, reaction, start, end, steps);
/* parsing the SBML model with libSBML */
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, model);
SBMLReader_free(sr);
/* Setting SBML ODE Solver integration parameters with default values */
set = CvodeSettings_create();
/* resetting the values we need */
CvodeSettings_setTime(set, time, printstep);
CvodeSettings_setErrors(set, 1e-18, 1e-10, 10000);
CvodeSettings_setSwitches(set, 1, 0, 1, 1, 1, 0, 0);
CvodeSettings_setSteadyState(set, 1);
/* Setting SBML Ode Solver batch integration parameters */
vs = VarySettings_allocate(1, steps+1);
VarySettings_addParameter(vs, parameter, reaction, start, end);
VarySettings_dump(vs);
/* calling the SBML ODE Solver Batch function,
and retrieving SBMLResults */
resM = SBML_odeSolverBatch(d, set, vs);
if ( resM == NULL ) {
printf("### Parameter variation not succesful!\n");
return(0);
}
/* we don't need these anymore */
CvodeSettings_free(set);
SBMLDocument_free(d);
VarySettings_free(vs);
results = resM->results[0][0];
for ( i=0; i<resM->i; i++ ) {
for ( j=0; j<resM->j; j++ ) {
results = SBMLResultsMatrix_getResults(resM, i, j);
printf("### RESULTS Parameter %d, Step %d \n", i+1, j+1);
/* printing results only for species*/
SBMLResults_dumpSpecies(results);
}
}
/* SolverError_dumpAndClearErrors(); */
SBMLResultsMatrix_free(resM);
return (EXIT_SUCCESS);
}
int doIt(void)
{
int i ;
cvodeSettings_t *settings, *set2;
variableIndex_t *s1, *s2;
integratorInstance_t *integratorInstance;
odeModel_t *model =
ODEModel_createFromFile("basic-model1-forward-l2.xml");
RETURN_ON_ERRORS_WITH(1)
s1 = ODEModel_getVariableIndex(model, "S1");
s2 = ODEModel_getVariableIndex(model, "S2");
/* Creating settings with default values */
settings = CvodeSettings_create();
/* Setting end time to .1, number of time steps to 1 and NULL
instead of an optional predefined time series (double *); due
to Indefinitely == 1, Printstep 5 will be ignored and Time =
0.1 will be used as timestep for infinite integration */
CvodeSettings_setTime(settings, .1, 5);
/* Setting Cvode Parameters: absolute tolerance, relative
tolerance and maximal internal step, respectively */
CvodeSettings_setErrors(settings, 1e-20, 1e-14, 500);
/* Setting Integration Switches */
CvodeSettings_setMethod(settings, 1, 12);
CvodeSettings_setJacobian(settings, 1);
CvodeSettings_setIndefinitely(settings, 1);
CvodeSettings_setHaltOnEvent(settings, 0);
CvodeSettings_setSteadyState(settings, 0);
CvodeSettings_setStoreResults(settings, 0);
CvodeSettings_setSensitivity(settings, 0);
/* first integration run */
printf("\nFIRST INTEGRATION RUN WITH:\n");
CvodeSettings_dump(settings);
integratorInstance = IntegratorInstance_create(model, settings);
RETURN_ON_ERRORS_WITH(1);
/* print variable (ODE, assignments) and constant names */
printf("#time ");
IntegratorInstance_dumpNames(integratorInstance);
/* print initial conditions and parameters */
IntegratorInstance_dumpData(integratorInstance);
for (i=0; i != 12; i++)
{
/* setting the next time step, uncomment the following
function call to see its effect */
/* IntegratorInstance_setNextTimeStep(integratorInstance, 0.2*(i+1)); */
IntegratorInstance_integrateOneStep(integratorInstance);
RETURN_ON_ERRORS_WITH(1);
/* print current data */
IntegratorInstance_dumpData(integratorInstance);
}
/* now, let's try again, with different settings */
set2 = CvodeSettings_create();
/* as Indefinitely will be set to 0, a finite integration
to time 0.24 in 6 steps will be run */
CvodeSettings_setTime(set2, 1.2, 6);
CvodeSettings_setErrors(set2, 1e-16, 1e-14, 500);
/* switches can be set all together, same order as above */
CvodeSettings_setSwitches(set2, 1, 0, 0, 0, 0, 0, 0);
printf("\nNOW, LET'S TRY AGAIN WITH DIFFERENT SETTINGS:\n");
CvodeSettings_dump(set2);
IntegratorInstance_set(integratorInstance, set2);
IntegratorInstance_dumpData(integratorInstance);
while( !IntegratorInstance_timeCourseCompleted(integratorInstance) ) {
IntegratorInstance_integrateOneStep(integratorInstance);
RETURN_ON_ERRORS_WITH(1);
IntegratorInstance_dumpData(integratorInstance);
}
printf("\n\nFINISHED SUCCESSFULLY!\n");
printf("Please, note the different values e.g. at time 1.2.\n");
printf("The values for the first run a more exact, due to the much\n");
printf("lower error tolerances. The error tolerances have to be\n");
printf("adapted to the ranges of each model!!\n\n");
IntegratorInstance_free(integratorInstance);
ODEModel_free(model);
VariableIndex_free(s1);
VariableIndex_free(s2);
CvodeSettings_free(settings);
CvodeSettings_free(set2);
return 0;
}
int doit(void)
{
int i ;
cvodeSettings_t *settings ;
variableIndex_t *s1, *s2;
integratorInstance_t *integratorInstanceA;
integratorInstance_t *integratorInstanceB;
odeModel_t *model = ODEModel_createFromFile("events-2-events-1-assignment-l2.xml");
RETURN_ON_ERRORS_WITH(1);
assert(ODEModel_hasVariable(model, "S1"));
assert(ODEModel_hasVariable(model, "S1"));
assert(!ODEModel_hasVariable(model, "foobar"));
s1 = ODEModel_getVariableIndex(model, "S1");
s2 = ODEModel_getVariableIndex(model, "S2");
/* Creating settings with default values */
settings = CvodeSettings_create();
/* Setting end time to .1, number of time steps to 1 and NULL
instead of an optional predefined time series (double *); due
to Indefinitely == 1, Printstep 1 will be ignored and Time =
0.1 will be used as timestep for infinite integration */
CvodeSettings_setTime(settings, .01, 1);
/* Setting Cvode Parameters: absolute and relative tolerances and
maximal internal step */
CvodeSettings_setErrors(settings, 1e-18, 1e-14, 500);
/* Setting Integration Switches: see documentation or
example simpleIntegratorInstance.c for details on
the passed values */
CvodeSettings_setSwitches(settings, 1, 1, 0, 0, 0, 0);
integratorInstanceA = IntegratorInstance_create(model, settings);
RETURN_ON_ERRORS_WITH(1);
integratorInstanceB = IntegratorInstance_create(model, settings);
RETURN_ON_ERRORS_WITH(1);
DumpState(integratorInstanceA, integratorInstanceB, s1, s2);
for (i=0; i != 500; i++)
{
IntegratorInstance_integrateOneStep(integratorInstanceA);
RETURN_ON_ERRORS_WITH(1);
IntegratorInstance_integrateOneStep(integratorInstanceB);
RETURN_ON_ERRORS_WITH(1);
DumpState(integratorInstanceA, integratorInstanceB, s1, s2);
}
IntegratorInstance_free(integratorInstanceA);
IntegratorInstance_free(integratorInstanceB);
VariableIndex_free(s1);
VariableIndex_free(s2);
ODEModel_free(model);
CvodeSettings_free(settings);
return 0;
}
int doit(void)
{
int i ;
double value;
cvodeSettings_t *settings ;
variableIndex_t *s1, *s2;
integratorInstance_t *integratorInstanceA;
integratorInstance_t *integratorInstanceB;
odeModel_t *model = ODEModel_createFromFile("basic-model1-forward-l2.xml");
RETURN_ON_ERRORS_WITH(1);
s1 = ODEModel_getVariableIndex(model, "S1");
s2 = ODEModel_getVariableIndex(model, "S2");
RETURN_ON_ERRORS_WITH(1);
/* Creating settings with default values */
settings = CvodeSettings_create();
/* Setting end time to .1, number of time steps to 1 and NULL
instead of an optional predefined time series (double *); due
to Indefinitely == 1, Printstep 1 will be ignored and Time =
0.1 will be used as timestep for infinite integration */
CvodeSettings_setTime(settings, .1, 1);
/* Setting Cvode Parameters: absolute and relative tolerances and
maximal internal step */
CvodeSettings_setErrors(settings, 1e-18, 1e-14, 500);
/* Setting Integration Switches: see documentation or
example simpleIntegratorInstance.c for details on
the passed values */
CvodeSettings_setSwitches(settings, 1, 1, 0, 0, 0, 0, 0);
/* use compiled model */
CvodeSettings_setCompileFunctions(settings, 0);
/* Generate two independent integrator instances from the same
odeModel and cvodeSettings */
integratorInstanceA = IntegratorInstance_create(model, settings);
RETURN_ON_ERRORS_WITH(1);
integratorInstanceB = IntegratorInstance_create(model, settings);
RETURN_ON_ERRORS_WITH(1);
DumpState(integratorInstanceA, integratorInstanceB, s1, s2);
for (i=0; i != 30; i++)
{
/* run integrations A and B */
IntegratorInstance_integrateOneStep(integratorInstanceA);
RETURN_ON_ERRORS_WITH(1);
IntegratorInstance_integrateOneStep(integratorInstanceB);
RETURN_ON_ERRORS_WITH(1);
/* While variable s1 from integration A is between 1e-15 and
1e-16, set variables s1 and s2 in integration B to some
value. This function also takes care of creating and
freeing CVODE solver structures when ODE variables are
changed!
*/
value = IntegratorInstance_getVariableValue(integratorInstanceA, s1);
if ( value < 1.e-15 && value > 1.e-16 )
{
IntegratorInstance_setVariableValue(integratorInstanceB,
s1,1.5e-15);
IntegratorInstance_setVariableValue(integratorInstanceB,
s2,1.5e-15);
}
DumpState(integratorInstanceA, integratorInstanceB, s1, s2);
}
IntegratorInstance_free(integratorInstanceA);
IntegratorInstance_free(integratorInstanceB);
VariableIndex_free(s1);
VariableIndex_free(s2);
ODEModel_free(model);
CvodeSettings_free(settings);
return 0;
}
