END_TEST
START_TEST(test_IntegratorInstance_integrate)
{
integratorInstance_t *ii;
cvodeSettings_t *cs;
int r;
model = ODEModel_createFromFile(EXAMPLES_FILENAME("MAPK.xml"));
cs = CvodeSettings_create();
ii = IntegratorInstance_create(model, cs);
r = IntegratorInstance_integrate(ii);
ck_assert_int_eq(r, 1);
CHECK_DOUBLE_WITH_TOLERANCE(IntegratorInstance_getTime(ii), 1.0);
ck_assert_int_eq(IntegratorInstance_timeCourseCompleted(ii), 1);
CvodeSettings_free(cs);
IntegratorInstance_free(ii);
}
END_TEST
START_TEST(test_IntegratorInstance_updateModel)
{
integratorInstance_t *ii;
cvodeSettings_t *cs;
int r;
model = ODEModel_createFromFile(EXAMPLES_FILENAME("MAPK.xml"));
cs = CvodeSettings_create();
ii = IntegratorInstance_create(model, cs);
r = IntegratorInstance_integrate(ii);
ck_assert_int_eq(r, 1);
r = IntegratorInstance_updateModel(ii);
ck_assert_int_eq(r, 0); /* TODO: expected? */
CvodeSettings_free(cs);
IntegratorInstance_free(ii);
}
END_TEST
START_TEST(test_IntegratorInstance_getResults)
{
integratorInstance_t *ii;
cvodeSettings_t *cs;
int r;
const cvodeResults_t *cr;
model = ODEModel_createFromFile(EXAMPLES_FILENAME("MAPK.xml"));
cs = CvodeSettings_create();
ii = IntegratorInstance_create(model, cs);
r = IntegratorInstance_integrate(ii);
ck_assert_int_eq(r, 1);
cr = IntegratorInstance_getResults(ii);
ck_assert(ii->results == cr);
CvodeSettings_free(cs);
IntegratorInstance_free(ii);
}
END_TEST
START_TEST(test_IntegratorInstance_printResults)
{
integratorInstance_t *ii;
cvodeSettings_t *cs;
int r;
FILE *fp;
model = ODEModel_createFromFile(EXAMPLES_FILENAME("MAPK.xml"));
cs = CvodeSettings_create();
ii = IntegratorInstance_create(model, cs);
r = IntegratorInstance_integrate(ii);
ck_assert_int_eq(r, 1);
OPEN_TMPFILE_OR_ABORT(fp);
IntegratorInstance_printResults(ii, fp);
/* TODO: check the printed text */
fclose(fp);
CvodeSettings_free(cs);
IntegratorInstance_free(ii);
}
SBML_ODESOLVER_API int IntegratorInstance_handleError(integratorInstance_t *engine)
{
cvodeData_t *data;
cvodeSettings_t *opt;
int errorCode;
if ( SolverError_getNum(ERROR_ERROR_TYPE) == 0 )
return SolverError_getLastCode(WARNING_ERROR_TYPE);
errorCode = SolverError_getLastCode(ERROR_ERROR_TYPE);
data = engine->data;
opt = engine->opt;
/* if (om->algebraic) ?? */
/* if (opt->Sensitivity) ?? */
if ( errorCode ) {
/* on flag CV_CONV_FAILURE
try again, but now with/without generated Jacobian matrix */
if ( errorCode == CV_CONV_FAILURE && data->run == 1 &&
opt->StoreResults) {
SolverError_error(WARNING_ERROR_TYPE,
SOLVER_MESSAGE_RERUN_WITH_OR_WO_JACOBIAN,
"Rerun with %s Jacobian matrix.",
opt->UseJacobian ?
"CVODE's internal approximation of the" :
"automatically generated");
/* integrate again */
opt->UseJacobian = !opt->UseJacobian;
IntegratorInstance_reset(engine);
return IntegratorInstance_integrate(engine);
}
}
return errorCode;
}
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;
}
int
main (int argc, char *argv[]){
int i, j;
odeModel_t *om;
cvodeSettings_t *set;
integratorInstance_t *ii;
cvodeResults_t *results;
variableIndex_t *y, *p;
/* Setting SBML ODE Solver integration parameters */
set = CvodeSettings_create();
CvodeSettings_setTime(set, 300.0, 10);
CvodeSettings_setErrors(set, 1e-9, 1e-4, 1e9);
/* ACTIVATE SENSITIVITY ANALYSIS */
CvodeSettings_setSensitivity(set, 1);
/* 0: simultaneous 1: staggered, 2: staggered1
see CVODES user guide for details */
CvodeSettings_setSensMethod(set, 0);
CvodeSettings_setJacobian(set, 1); /* for testing only */
/* CvodeSettings_dump(set); */
/* creating the odeModel */
om = ODEModel_createFromFile("MAPK.xml");
/* get a parameter for which we will check sensitivities */
p = ODEModel_getVariableIndex(om, "K1");
/* calling the integrator */
ii = IntegratorInstance_create(om, set);
printf("### Printing Sensitivities to %s (%g) on the fly:\n",
ODEModel_getVariableName(om, p),
IntegratorInstance_getVariableValue(ii, p));
printf("#time ");
IntegratorInstance_dumpNames(ii);
IntegratorInstance_dumpPSensitivities(ii, p);
while( !IntegratorInstance_timeCourseCompleted(ii) ) {
if ( !IntegratorInstance_integrateOneStep(ii) ) {
break;
}
IntegratorInstance_dumpPSensitivities(ii, p);
}
VariableIndex_free(p);
if ( SolverError_getNum(FATAL_ERROR_TYPE) ) {
printf("Integration not sucessful!\n");
SolverError_dumpAndClearErrors();
return(EXIT_FAILURE);
}
y = ODEModel_getVariableIndex(om, "MAPK_P");
printf("\nLet's look at a specific ODE variable:\n");
/* print sensitivities again, but now from stored results */
printf("### RESULTS for Sensitivity Analysis for one ODE variable\n");
printf("#time Variable Sensitivity Params...\n");
printf("#time ");
printf("%s ", ODEModel_getVariableName(om, y));
for ( j=0; j<ODEModel_getNsens(om); j++ ) {
p = ODEModel_getSensParamIndexByNum(om, j);
printf("%s ", ODEModel_getVariableName(om, p));
VariableIndex_free(p);
}
printf("\n");
results = IntegratorInstance_createResults(ii);
for ( i=0; i<CvodeResults_getNout(results); i++ ) {
printf("%g ", CvodeResults_getTime(results, i));
printf("%g ", CvodeResults_getValue(results, y, i));
for ( j=0; j<ODEModel_getNsens(om); j++ ) {
p = ODEModel_getSensParamIndexByNum(om, j);
printf("%g ", CvodeResults_getSensitivity(results, y, p, i));
VariableIndex_free(p);
}
printf("\n");
}
/* drawSensitivity(ii->data, "sensitivity", "ps", 0.9); */
p = ODEModel_getVariableIndex(om, "V1");
printf("\nWhat do sensitivities mean? Let's try out!\n\n");
printf("... add 1 to %s: %g + 1 = ",
ODEModel_getVariableName(om, p),
IntegratorInstance_getVariableValue(ii, p));
CvodeSettings_setSensitivity(set, 0);
IntegratorInstance_reset(ii);
IntegratorInstance_setVariableValue(ii, p,
IntegratorInstance_getVariableValue(ii,p)+1);
printf("%g\n", IntegratorInstance_getVariableValue(ii, p));
printf("... and integrate again:\n\n");
CvodeResults_free(results);
IntegratorInstance_integrate(ii);
results = IntegratorInstance_createResults(ii);
/* and print changed results */
printf("#time %s\n", ODEModel_getVariableName(om, y));
for ( i=0; i<CvodeResults_getNout(results); i++ ) {
printf("%g ", CvodeResults_getTime(results, i));
printf("%g\n", CvodeResults_getValue(results, y, i));
}
printf("\nSee the difference?\n");
printf("Look what happens when the sensitivity changes its sign\n");
printf("between times 180 and 210.\n\n");
VariableIndex_free(y);
VariableIndex_free(p);
/* now we have the results and can free the inputs */
IntegratorInstance_free(ii);
CvodeSettings_free(set);
CvodeResults_free(results);
ODEModel_free(om);
return (EXIT_SUCCESS);
}
int
main (int argc, char *argv[])
{
int i, j, k;
int neq, nsens;
odeModel_t *om;
odeSense_t *os;
cvodeSettings_t *set;
integratorInstance_t *ii;
variableIndex_t *p1, *p2, *p3, *vi;
double *weights;
/* Setting SBML ODE Solver integration parameters */
set = CvodeSettings_create();
CvodeSettings_setTime(set, 30, 10);
CvodeSettings_setErrors(set, 1e-15, 1e-10, 1e9);
CvodeSettings_setMethod(set, 0, 5);
/* CvodeSettings_setStoreResults(set, 0); */
CvodeSettings_setJacobian(set, 1); /* for testing only */
CvodeSettings_setCompileFunctions(set, 0); /* for testing only */
/* CvodeSettings_dump(set); */
CvodeSettings_setFIM(set); /* ACTIVATE FIM */
/* creating the odeModel */
om = ODEModel_createFromFile("MAPK.xml");
ii = IntegratorInstance_create(om, set);
printf("\nFirst try a few integrations without sensitivity\n");
IntegratorInstance_dumpNames(ii);
printf("\n");
for ( i=0; i<2; i++ )
{
printf("Run #%d:\n", i);
IntegratorInstance_integrate(ii);
/* IntegratorInstance_dumpData(ii); */
IntegratorInstance_printResults(ii, stderr);
IntegratorInstance_reset(ii);
printf("finished\n\n");
}
/* ACTIVATE SENSITIVITY ANALYSIS */
CvodeSettings_setSensitivity(set, 1);
/* 0: simultaneous 1: staggered, 2: staggered1
see CVODES user guide for details */
CvodeSettings_setSensMethod(set, 0);
/* reset integrator to new settings */
IntegratorInstance_reset(ii);
printf("Now Activate Sensitivity\n\n");
os = IntegratorInstance_getSensitivityModel(ii);
nsens = ODESense_getNsens(os);
printf("nsens = %i\n\n", nsens);
for ( i=0; i<nsens; i++ ) {
vi = ODESense_getSensParamIndexByNum(os, i);
printf("%s\n", ODEModel_getVariableName(om, vi) );
VariableIndex_free(vi);
}
printf("\n");
printf("sensitivities calculated for all constants\n");
p1 = ODESense_getSensParamIndexByNum(os, 1);
p2 = ODESense_getSensParamIndexByNum(os, 2);
p3 = ODESense_getSensParamIndexByNum(os, 3);
printf("sensitivities printed for constants %s, %s, %s\n\n",
ODEModel_getVariableName(om, p1),
ODEModel_getVariableName(om, p2),
ODEModel_getVariableName(om, p3));
/* create non-default weights for computation of FIM */
/* weights should be extracted from objective function! */
neq = ODEModel_getNeq(om);
ASSIGN_NEW_MEMORY_BLOCK(weights, neq, double, 0);
for ( i=0; i<neq; i++ )
weights[i] = 1.;
/* set weights (to non-default values) */
IntegratorInstance_setFIMweights(ii, weights, neq);
/* *** *** *** *** *** *** discrete data *** *** *** *** *** *** *** */
CvodeSettings_setDiscreteObservation(set);
printf("DISCRETE DATA\n\n");
i = 0;
while ( i < 2 )
{
printf("Run #%d:\n", i);
while( !IntegratorInstance_timeCourseCompleted(ii) )
{
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
if ( !IntegratorInstance_integrateOneStep(ii) )
break;
}
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
fprintf(stderr, "FIM =\n");
for ( j=0; j<nsens; j++ )
{
for ( k=0; k<nsens; k++ )
fprintf(stderr, "%g ", IntegratorInstance_getFIM(ii,j,k));
fprintf(stderr, "\n");
}
fprintf(stderr, "\n");
IntegratorInstance_reset(ii);
i++;
}
/* *** *** *** *** *** *** continuous data *** *** *** *** *** *** *** */
CvodeSettings_unsetDiscreteObservation(set);
printf("CONTINUOUS DATA\n\n");
i = 0;
while ( i < 2 )
{
printf("Run #%d:\n", i);
while( !IntegratorInstance_timeCourseCompleted(ii) )
{
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
if ( !IntegratorInstance_integrateOneStep(ii) )
break;
}
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
/* calculate FIM */
IntegratorInstance_CVODEQuad(ii);
fprintf(stderr, "FIM =\n");
for ( j=0; j<nsens; j++ )
{
for ( k=0; k<nsens; k++ )
fprintf(stderr, "%g ", IntegratorInstance_getFIM(ii,j,k));
fprintf(stderr, "\n");
}
fprintf(stderr, "\n");
IntegratorInstance_reset(ii);
i++;
}
fprintf(stderr, "finished\n");
/* VariableIndex_free(y); */
VariableIndex_free(p1);
VariableIndex_free(p2);
VariableIndex_free(p3);
free(weights);
/* now we have the results and can free the inputs */
IntegratorInstance_free(ii);
CvodeSettings_free(set);
ODEModel_free(om);
return (EXIT_SUCCESS);
}
