void CVodesIntegrator::sensInit(double t0, FuncEval& func) {
m_np = func.nparams();
long int nv = func.neq();
doublereal* data;
int n, j;
N_Vector y;
y = N_VNew_Serial(nv);
m_yS = N_VCloneVectorArray_Serial(m_np, y);
for (n = 0; n < m_np; n++) {
data = NV_DATA_S(m_yS[n]);
for (j = 0; j < nv; j++) {
data[j] =0.0;
}
}
int flag;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
flag = CVodeSensMalloc(m_cvode_mem, m_np, CV_STAGGERED, m_yS);
if (flag != CV_SUCCESS) {
throw CVodesErr("Error in CVodeSensMalloc");
}
vector_fp atol(m_np, m_abstolsens);
double rtol = m_reltolsens;
flag = CVodeSetSensTolerances(m_cvode_mem, CV_SS, rtol, DATA_PTR(atol));
#elif defined(SUNDIALS_VERSION_24)
flag = CVodeSensInit(m_cvode_mem, m_np, CV_STAGGERED,
CVSensRhsFn (0), m_yS);
if (flag != CV_SUCCESS) {
throw CVodesErr("Error in CVodeSensMalloc");
}
vector_fp atol(m_np, m_abstolsens);
double rtol = m_reltolsens;
flag = CVodeSensSStolerances(m_cvode_mem, rtol, DATA_PTR(atol));
#endif
}
/* creates CVODES forward sensitivity solver structures
return 1 => success
return 0 => failure
*/
int
IntegratorInstance_createCVODESSolverStructures(integratorInstance_t *engine)
{
int i, j, flag, neq, ns;
realtype *ydata, *abstoldata, *ySdata, *senstoldata;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeSolver_t *solver = engine->solver;
cvodeSettings_t *opt = engine->opt;
/* realtype pbar[data->nsens+1]; */
/*int *plist; removed by AMF 8/11/05
realtype *pbar;
ASSIGN_NEW_MEMORY_BLOCK(plist, data->nsens+1, int, 0)
ASSIGN_NEW_MEMORY_BLOCK(pbar, data->nsens+1, realtype, 0)*/
/***** adding sensitivity specific structures ******/
/**
* construct sensitivity related structures
*/
/* free sensitivity from former runs (changed for non-default cases!) */
ODEModel_freeSensitivity(om);
/* if jacobian matrix has been constructed successfully,
construct sensitivity matrix dx/dp, sets om->sensitivity
to 1 if successful, 0 otherwise */
/*!!! this function will require additional input for
non-default case, via sensitivity input settings! !!!*/
if ( om->jacobian )
ODEModel_constructSensitivity(om);
else {
om->sensitivity = 0;
om->jacob_sens = NULL;
om->nsens = om->nconst;
ASSIGN_NEW_MEMORY_BLOCK(om->index_sens, om->nsens, int, 0);
/*!!! non-default case:
these values should be passed for other cases !!!*/
for ( i=0; i<om->nsens; i++ )
om->index_sens[i] = om->neq + om->nass + i;
}
engine->solver->nsens = data->nsens;
solver->yS = N_VNewVectorArray_Serial(data->nsens, data->neq);
if (check_flag((void *)solver->yS, "N_VNewVectorArray_Serial",
1, stderr))
return(0);
/*
* (re)initialize ySdata sensitivities
*/
/* absolute tolerance for sensitivity error control */
solver->senstol = N_VNew_Serial(data->nsens);
abstoldata = NV_DATA_S(solver->senstol);
for ( j=0; j<data->nsens; j++ ) {
abstoldata[j] = 1e-4;
ySdata = NV_DATA_S(solver->yS[j]);
for ( i=0; i<data->neq; i++ )
ySdata[i] = data->sensitivity[i][j];
}
/*
* set method
*/
if ( opt->SensMethod == 0 )
flag =CVodeSensMalloc(solver->cvode_mem,data->nsens,
CV_SIMULTANEOUS, solver->yS);
else if ( opt->SensMethod == 1 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED, solver->yS);
else if ( opt->SensMethod == 2 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED1, solver->yS);
if(check_flag(&flag, "CVodeSensMalloc", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
/* *** set parameter values or R.H.S function fS *****/
/* NOTES: */
/* !!! plist could later be used to specify requested parameters
for sens.analysis !!! */
/* was construction of Jacobian and
parametric matrix successfull ? */
if ( om->sensitivity && om->jacobian ) {
flag = CVodeSetSensRhs1Fn(solver->cvode_mem, fS);
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensFdata(solver->cvode_mem, data);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
data->p = NULL;
}
else {
ASSIGN_NEW_MEMORY_BLOCK(data->p, data->nsens, realtype, 0);
for ( i=0; i<data->nsens; i++ ) {
/* data->p is only required if R.H.S. fS cannot be supplied */
/* plist[i] = i+1; */
data->p[i] = data->value[om->index_sens[i]];
/* pbar[i] = abs(data->p[i]); */ /*??? WHAT IS PBAR ???*/
}
flag = CVodeSetSensParams(solver->cvode_mem, data->p, NULL, NULL);
if (check_flag(&flag, "CVodeSetSensParams", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensRho(solver->cvode_mem, 0.0); /* what is it? */
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
/* ERROR HANDLING CODE if failes */
return 0;
}
}
/* CVodeSetSensTolerances(solver->cvode_mem, CV_SS, */
/* solver->reltol, &solver->senstol); */
/* difference FALSE/TRUE ? */
flag = CVodeSetSensErrCon(solver->cvode_mem, FALSE);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
return 1; /* OK */
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype t, tout;
N_Vector y;
int iout, flag;
realtype pbar[NS];
int is;
N_Vector *yS;
booleantype sensi, err_con;
int sensi_meth;
cvode_mem = NULL;
data = NULL;
y = NULL;
yS = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* User data structure */
data = (UserData) malloc(sizeof *data);
if (check_flag((void *)data, "malloc", 2)) return(1);
data->p[0] = RCONST(0.04);
data->p[1] = RCONST(1.0e4);
data->p[2] = RCONST(3.0e7);
/* Initial conditions */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
Ith(y,1) = Y1;
Ith(y,2) = Y2;
Ith(y,3) = Y3;
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if (check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
/* Allocate space for CVODES */
flag = CVodeMalloc(cvode_mem, f, T0, y, CV_WF, 0.0, NULL);
if (check_flag(&flag, "CVodeMalloc", 1)) return(1);
/* Use private function to compute error weights */
flag = CVodeSetEwtFn(cvode_mem, ewt, NULL);
if (check_flag(&flag, "CVodeSetEwtFn", 1)) return(1);
/* Attach user data */
flag = CVodeSetFdata(cvode_mem, data);
if (check_flag(&flag, "CVodeSetFdata", 1)) return(1);
/* Attach linear solver */
flag = CVDense(cvode_mem, NEQ);
if (check_flag(&flag, "CVDense", 1)) return(1);
flag = CVDenseSetJacFn(cvode_mem, Jac, data);
if (check_flag(&flag, "CVDenseSetJacFn", 1)) return(1);
printf("\n3-species chemical kinetics problem\n");
/* Sensitivity-related settings */
if (sensi) {
pbar[0] = data->p[0];
pbar[1] = data->p[1];
pbar[2] = data->p[2];
yS = N_VNewVectorArray_Serial(NS, NEQ);
if (check_flag((void *)yS, "N_VNewVectorArray_Serial", 0)) return(1);
for (is=0;is<NS;is++) N_VConst(ZERO, yS[is]);
flag = CVodeSensMalloc(cvode_mem, NS, sensi_meth, yS);
if(check_flag(&flag, "CVodeSensMalloc", 1)) return(1);
flag = CVodeSetSensRhs1Fn(cvode_mem, fS);
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1)) return(1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if (check_flag(&flag, "CVodeSetSensFdata", 1)) return(1);
flag = CVodeSetSensFdata(cvode_mem, data);
if (check_flag(&flag, "CVodeSetSensFdata", 1)) return(1);
flag = CVodeSetSensParams(cvode_mem, NULL, pbar, NULL);
if (check_flag(&flag, "CVodeSetSensParams", 1)) return(1);
printf("Sensitivity: YES ");
if(sensi_meth == CV_SIMULTANEOUS)
printf("( SIMULTANEOUS +");
else
if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +");
else printf("( STAGGERED1 +");
if(err_con) printf(" FULL ERROR CONTROL )");
else printf(" PARTIAL ERROR CONTROL )");
} else {
printf("Sensitivity: NO ");
}
/* In loop over output points, call CVode, print results, test for error */
printf("\n\n");
printf("===================================================");
printf("============================\n");
printf(" T Q H NST y1");
printf(" y2 y3 \n");
printf("===================================================");
printf("============================\n");
for (iout=1, tout=T1; iout <= NOUT; iout++, tout *= TMULT) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
if (check_flag(&flag, "CVode", 1)) break;
PrintOutput(cvode_mem, t, y);
if (sensi) {
flag = CVodeGetSens(cvode_mem, t, yS);
if (check_flag(&flag, "CVodeGetSens", 1)) break;
PrintOutputS(yS);
}
printf("-------------------------------------------------");
printf("------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy_Serial(y); /* Free y vector */
if (sensi) {
N_VDestroyVectorArray_Serial(yS, NS); /* Free yS vector */
}
free(data); /* Free user data */
CVodeFree(cvode_mem); /* Free CVODES memory */
return(0);
}
int main(int argc, char *argv[])
{
void *cvode_mem;
UserData data;
realtype abstol, reltol, t, tout;
N_Vector y;
int iout, flag;
realtype *pbar;
int is, *plist;
N_Vector *uS;
booleantype sensi, err_con;
int sensi_meth;
pbar = NULL;
plist = NULL;
uS = NULL;
y = NULL;
data = NULL;
cvode_mem = NULL;
/* Process arguments */
ProcessArgs(argc, argv, &sensi, &sensi_meth, &err_con);
/* Problem parameters */
data = AllocUserData();
if(check_flag((void *)data, "AllocUserData", 2)) return(1);
InitUserData(data);
/* Initial states */
y = N_VNew_Serial(NEQ);
if(check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
SetInitialProfiles(y, data->dx, data->dz);
/* Tolerances */
abstol=ATOL;
reltol=RTOL;
/* Create CVODES object */
cvode_mem = CVodeCreate(CV_BDF, CV_NEWTON);
if(check_flag((void *)cvode_mem, "CVodeCreate", 0)) return(1);
flag = CVodeSetFdata(cvode_mem, data);
if(check_flag(&flag, "CVodeSetFdata", 1)) return(1);
flag = CVodeSetMaxNumSteps(cvode_mem, 2000);
if(check_flag(&flag, "CVodeSetMaxNumSteps", 1)) return(1);
/* Allocate CVODES memory */
flag = CVodeMalloc(cvode_mem, f, T0, y, CV_SS, reltol, &abstol);
if(check_flag(&flag, "CVodeMalloc", 1)) return(1);
/* Attach CVSPGMR linear solver */
flag = CVSpgmr(cvode_mem, PREC_LEFT, 0);
if(check_flag(&flag, "CVSpgmr", 1)) return(1);
flag = CVSpilsSetPreconditioner(cvode_mem, Precond, PSolve, data);
if(check_flag(&flag, "CVSpilsSetPreconditioner", 1)) return(1);
printf("\n2-species diurnal advection-diffusion problem\n");
/* Forward sensitivity analysis */
if(sensi) {
plist = (int *) malloc(NS * sizeof(int));
if(check_flag((void *)plist, "malloc", 2)) return(1);
for(is=0; is<NS; is++) plist[is] = is;
pbar = (realtype *) malloc(NS * sizeof(realtype));
if(check_flag((void *)pbar, "malloc", 2)) return(1);
for(is=0; is<NS; is++) pbar[is] = data->p[plist[is]];
uS = N_VCloneVectorArray_Serial(NS, y);
if(check_flag((void *)uS, "N_VCloneVectorArray_Serial", 0)) return(1);
for(is=0;is<NS;is++)
N_VConst(ZERO,uS[is]);
flag = CVodeSensMalloc(cvode_mem, NS, sensi_meth, uS);
if(check_flag(&flag, "CVodeSensMalloc", 1)) return(1);
flag = CVodeSetSensErrCon(cvode_mem, err_con);
if(check_flag(&flag, "CVodeSetSensErrCon", 1)) return(1);
flag = CVodeSetSensRho(cvode_mem, ZERO);
if(check_flag(&flag, "CVodeSetSensRho", 1)) return(1);
flag = CVodeSetSensParams(cvode_mem, data->p, pbar, plist);
if(check_flag(&flag, "CVodeSetSensParams", 1)) return(1);
printf("Sensitivity: YES ");
if(sensi_meth == CV_SIMULTANEOUS)
printf("( SIMULTANEOUS +");
else
if(sensi_meth == CV_STAGGERED) printf("( STAGGERED +");
else printf("( STAGGERED1 +");
if(err_con) printf(" FULL ERROR CONTROL )");
else printf(" PARTIAL ERROR CONTROL )");
} else {
printf("Sensitivity: NO ");
}
/* In loop over output points, call CVode, print results, test for error */
printf("\n\n");
printf("========================================================================\n");
printf(" T Q H NST Bottom left Top right \n");
printf("========================================================================\n");
for (iout=1, tout = TWOHR; iout <= NOUT; iout++, tout += TWOHR) {
flag = CVode(cvode_mem, tout, y, &t, CV_NORMAL);
if(check_flag(&flag, "CVode", 1)) break;
PrintOutput(cvode_mem, t, y);
if (sensi) {
flag = CVodeGetSens(cvode_mem, t, uS);
if(check_flag(&flag, "CVodeGetSens", 1)) break;
PrintOutputS(uS);
}
printf("------------------------------------------------------------------------\n");
}
/* Print final statistics */
PrintFinalStats(cvode_mem, sensi);
/* Free memory */
N_VDestroy_Serial(y);
if (sensi) {
N_VDestroyVectorArray_Serial(uS, NS);
free(pbar);
free(plist);
}
FreeUserData(data);
CVodeFree(&cvode_mem);
return(0);
}