SBML_ODESOLVER_API integratorInstance_t *IntegratorInstance_create(odeModel_t *om, cvodeSettings_t *opt)
{
cvodeData_t *data;
integratorInstance_t *engine;
data = CvodeData_create(om);
RETURN_ON_FATALS_WITH(NULL);
CvodeData_initialize(data, opt, om);
RETURN_ON_FATALS_WITH(NULL);
return IntegratorInstance_allocate(data, opt, om);
}
int main(void)
{
int i, j, neq;
char *formula;
variableIndex_t *vi = NULL;
variableIndex_t *vj = NULL;
const ASTNode_t *f = NULL;
cvodeData_t *data = NULL;
cvodeSettings_t *set;
integratorInstance_t *iI;
/* first load an SBML model and directly construct the
internal odeModel from it */
odeModel_t *odeModel = ODEModel_createFromFile("MAPK.xml");
if ( ODEModel_constructSensitivity(odeModel) &&
ODEModel_getNeq(odeModel) ) {
printf("\n\nSuccessfully constructed the parametric matrix S ");
printf("as used for CVODES sensitivity analysis\n\n");
printf("We might be interested in the `sparsity' of S,\n");
printf("... we can just evaluate the parametric entries:\n\n");
/* we need cvodeData for evaluating formulas */
data = CvodeData_create(odeModel);
printf("... how many parametric entries: %d\n\n",
ODEModel_getNsens(odeModel));
/* now take a look at a all entries of S: */
for ( i=0; i<ODEModel_getNeq(odeModel); i++ ) {
vi = ODEModel_getOdeVariableIndex(odeModel, i);
printf("\nODE VARIABLE %d: %s\n", i+1,
ODEModel_getVariableName(odeModel, vi));
f = ODEModel_getOde(odeModel, vi);
formula = SBML_formulaToString(f);
printf("dY/dt = %s \n", formula);
free(formula);
for ( j=0; j<ODEModel_getNsens(odeModel); j++ ) {
vj = ODEModel_getSensParamIndexByNum(odeModel, j);
printf(" Parameter %d: %s ", j,
ODEModel_getVariableName(odeModel, vj));
f = ODEModel_getSensIJEntry(odeModel, i, j);
formula = SBML_formulaToString(f);
printf(" S[%d][%d] = %s \n", i, j, formula);
free(formula);
VariableIndex_free(vj);
}
VariableIndex_free(vi);
}
printf("\n\n");
printf("Sensitivity: parametric matrix with initial conditions:\n");
printSensiMatrix(odeModel, data);
/* we must free this cvodeData structure */
CvodeData_free(data);
printf("Thx and good bye!\n");
}
else {
SolverError_dumpAndClearErrors();
printf("Sorry, for this system we couldn't generate the Parametric.\n");
printf("Sensitivity can still be run with internal approximation.\n");
}
ODEModel_free(odeModel);
return 1;
}
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");
}
int main(void)
{
char *formula;
variableIndex_t *vi = NULL;
variableIndex_t *vj = NULL;
const ASTNode_t *f = NULL;
cvodeData_t *data = NULL;
cvodeSettings_t *set;
integratorInstance_t *iI;
/* first load an SBML model and directly construct the
internal odeModel from it */
odeModel_t *odeModel = ODEModel_createFromFile("MAPK.xml");
if ( ODEModel_constructJacobian(odeModel) && ODEModel_getNeq(odeModel) ) {
printf("\n\nSuccessfully constructed the jacobian matrix J\n\n");
printf("We might be interested in the `sparsity' of J,\n");
printf("... we can just evaluate the jacobian entries:\n\n");
/* we need cvodeData for evaluating formulas */
data = CvodeData_create(odeModel);
/* ! IMPORTANT : initialize values */
CvodeData_initializeValues(data);
printf("Jacobian with initial conditions:\n");
printJacobian(odeModel, data);
/* we must free this cvodeData structure */
CvodeData_free(data);
printf("Does it change after integration?\n\n");
/* creating settings and integrate */
set = CvodeSettings_create();
CvodeSettings_setTime(set, 1000, 1);
iI = IntegratorInstance_create(odeModel, set);
IntegratorInstance_integrate(iI);
/* get cvodeData from integratorInstance, it contains
the values at the last time point,
and just do the same as above */
data = IntegratorInstance_getData(iI);
printf("Jacobian at time %g:\n", IntegratorInstance_getTime(iI));
printJacobian(odeModel, data);
printf("J[6,4] changed its sign. Let's take a look at the equations:\n\n");
vi = ODEModel_getOdeVariableIndex(odeModel, 6);
vj = ODEModel_getOdeVariableIndex(odeModel, 4);
f = ODEModel_getOde(odeModel, vi);
formula = SBML_formulaToString(f);
printf("The ODE d%s/dt = \n%s \n\n",
ODEModel_getVariableName(odeModel, vi),
formula);
free(formula);
f = ODEModel_getJacobianEntry(odeModel, vi, vj);
formula = SBML_formulaToString(f);
printf("The jacobian entry (d%s/dt)/d%s = \n%s \n\n",
ODEModel_getVariableName(odeModel, vi),
ODEModel_getVariableName(odeModel, vj),
formula);
free(formula);
VariableIndex_free(vi);
VariableIndex_free(vj);
printf("MAPK_P is both a substrate and a product of MKK_PP ");
printf("in different reactions.\nTherefor the corresponding ");
printf("entry in the jacobian can change its sign, depending ");
printf("on concentrations!\n");
/* finally draw a `species interaction graph' of the jacobian' */
drawJacoby(data, "jacobian", "gif");
printf("Take a look at jacobian interaction graph in");
printf("file jacobian_jm.gif that has just been constructed.\n");
printf("If you have compiled w/o graphviz, you just have a textfile");
printf(" jacobian.dot\n");
printf("Thx and good bye!\n");
/* note that this cvodeData MUST NOT be freed, it stays with and
will be freed together with integratorInstance */
IntegratorInstance_free(iI);
CvodeSettings_free(set);
}
else {
SolverError_dumpAndClearErrors();
printf("Sorry, for this system we couldn't generate the Jacobian.\n");
printf("Integration can still be run with internal approximation.\n");
}
ODEModel_free(odeModel);
return 1;
}
