void vfield(int *n, double *t, double *x, double *f,
double *rpar, int *ipar) {
FillCurrentExtInputValues(gIData, *t);
vfieldfunc(*n, (unsigned) gIData->paramDim, *t, x,
rpar, f, (unsigned) gIData->extraSpaceSize, gIData->gExtraSpace,
(unsigned) gIData->nExtInputs, gIData->gCurrentExtInputVals);
}
PyObject* JacobianP(double t, double *x, double *p) {
PyObject *OutObj = NULL;
PyObject *JacPOut = NULL;
double *jactual = NULL, **jtemp = NULL;
int i, n, m;
_init_numpy();
if( (gIData == NULL) || (gIData->isInitBasic == 0)
|| (gIData->hasJacP == 0) || (gIData->paramDim == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else if( (gIData->nExtInputs > 0) && (gIData->isInitExtInputs == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else {
OutObj = PyTuple_New(1);
assert(OutObj);
n = gIData->phaseDim;
m = gIData->paramDim;
jactual = (double *)PyMem_Malloc(n*m*sizeof(double));
assert(jactual);
jtemp = (double **)PyMem_Malloc(n*sizeof(double *));
assert(jtemp);
for( i = 0; i < n; i++ ) {
jtemp[i] = jactual + m * i;
}
if( gIData->nExtInputs > 0 ) {
FillCurrentExtInputValues( gIData, t );
}
/* Assume jacobianParam is returned in column-major format */
jacobianParam(gIData->phaseDim, gIData->paramDim, t, x, p, jtemp,
gIData->extraSpaceSize, gIData->gExtraSpace,
gIData->nExtInputs, gIData->gCurrentExtInputVals);
PyMem_Free(jtemp);
npy_intp dims[2] = {gIData->paramDim, gIData->phaseDim};
JacPOut = PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, jactual);
if(JacPOut) {
PyArray_UpdateFlags((PyArrayObject *)JacPOut, NPY_ARRAY_CARRAY | NPY_ARRAY_OWNDATA);
PyTuple_SetItem(OutObj, 0, PyArray_Transpose((PyArrayObject *)JacPOut, NULL));
return OutObj;
} else {
PyMem_Free(jactual);
Py_INCREF(Py_None);
return Py_None;
}
}
}
PyObject* MassMatrix(double t, double *x, double *p) {
PyObject *OutObj = NULL;
PyObject *MassOut = NULL;
double *mmactual = NULL, **mmtemp = NULL;
int i, j, n;
import_array();
if( (gIData == NULL) || (gIData->isInitBasic == 0) || (gIData->hasMass == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else if( (gIData->nExtInputs > 0) && (gIData->isInitExtInputs == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else {
OutObj = PyTuple_New(1);
assert(OutObj);
n = gIData->phaseDim;
mmactual = (double *)PyMem_Malloc(n*n*sizeof(double));
assert(mmactual);
mmtemp = (double **)PyMem_Malloc(n*sizeof(double *));
assert(mmtemp);
for( i = 0; i < n; i++ ) {
mmtemp[i] = mmactual + n * i;
}
if( gIData->nExtInputs > 0 ) {
FillCurrentExtInputValues( gIData, t );
}
/* Assume massMatrix is returned in column-major format */
massMatrix(gIData->phaseDim, gIData->paramDim, t, x, p, mmtemp,
gIData->extraSpaceSize, gIData->gExtraSpace,
gIData->nExtInputs, gIData->gCurrentExtInputVals);
PyMem_Free(mmtemp);
npy_intp dims[2] = {gIData->phaseDim, gIData->phaseDim};
MassOut = PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, mmactual);
if(MassOut) {
PyArray_UpdateFlags((PyArrayObject *)MassOut, NPY_ARRAY_CARRAY | NPY_ARRAY_OWNDATA);
PyTuple_SetItem(OutObj, 0, PyArray_Transpose((PyArrayObject *)MassOut, NULL));
return OutObj;
} else {
PyMem_Free(mmactual);
Py_INCREF(Py_None);
return Py_None;
}
}
}
/* Phase space dim n, pointer to mass array write location am,
int mass matrix lower bandwidth lmas,
double real-valued parameters rpar
int int-valued parameters ipar */
void vfieldmas(int *n, double *am, int *lmas, double *rpar, int *ipar, double *t, double *x) {
double **f = NULL;
setMassPtrs(gIData, am);
f = gIData->gMassPtrs;
FillCurrentExtInputValues(gIData, *t);
massMatrix(*n, (unsigned) gIData->paramDim, *t, x, rpar, f,
(unsigned) gIData->extraSpaceSize, gIData->gExtraSpace,
(unsigned) gIData->nExtInputs, gIData->gCurrentExtInputVals);
}
void vfieldjac(int *n, double *t, double *x, double *df, int *ldf,
double *rpar, int *ipar) {
double **f = NULL;
setJacPtrs(gIData, df);
f = gIData->gJacPtrs;
FillCurrentExtInputValues(gIData, *t);
jacobian(*n, (unsigned) gIData->paramDim, *t, x, rpar, f,
(unsigned) gIData->extraSpaceSize, gIData->gExtraSpace,
(unsigned) gIData->nExtInputs, gIData->gCurrentExtInputVals);
}
PyObject* AuxFunc(double t, double *x, double *p) {
PyObject *OutObj = NULL;
PyObject *AuxOut = NULL;
double *ftemp = NULL;
int i;
import_array();
if( (gIData == NULL) || (gIData->isInitBasic == 0) || (gIData->nAuxVars == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else if( (gIData->nExtInputs > 0) && (gIData->isInitExtInputs == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else {
OutObj = PyTuple_New(1);
assert(OutObj);
ftemp = (double *)PyMem_Malloc((gIData->nAuxVars)*sizeof(double));
assert(ftemp);
if( gIData->nExtInputs > 0 ) {
FillCurrentExtInputValues( gIData, t );
}
auxvars(gIData->phaseDim, gIData->phaseDim, t, x, p, ftemp,
gIData->extraSpaceSize, gIData->gExtraSpace,
gIData->nExtInputs, gIData->gCurrentExtInputVals);
npy_intp dims[1] = {gIData->nAuxVars};
AuxOut = PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, ftemp);
if(AuxOut) {
PyArray_UpdateFlags((PyArrayObject *)AuxOut, NPY_ARRAY_CARRAY | NPY_ARRAY_OWNDATA);
PyTuple_SetItem(OutObj, 0, AuxOut);
return OutObj;
}
else {
PyMem_Free(ftemp);
Py_INCREF(Py_None);
return Py_None;
}
return OutObj;
}
}
/* Performs calculation of auxilliary variables after integration, event finding
are complete. This is the only place where memory is allocated outside of
an "Init" function. */
void AuxVarCalc( IData *GS ) {
int i;
assert(GS);
if( (GS->nAuxVars > 0) && (GS->pointsIdx > 0 ) ) {
/* Allocate space for aux variable calculations if this is the first
time we have done aux calculations */
if( GS->gAuxPoints == NULL ) {
GS->gAuxPoints = (double **)PyMem_Malloc(GS->pointsIdx*sizeof(double *));
assert(GS->gAuxPoints);
for( i = 0; i < GS->pointsIdx; i++ ) {
GS->gAuxPoints[i] = (double *)PyMem_Malloc(GS->nAuxVars*sizeof(double));
assert(GS->gAuxPoints[i]);
}
}
/* Otherwise, realloc space for the additional pointers, PyMem_Malloc
space for the new aux points */
else {
double **temp = NULL;
temp = (double **)PyMem_Realloc(GS->gAuxPoints,GS->pointsIdx*sizeof(double *));
assert(temp);
GS->gAuxPoints = temp;
for( i = GS->auxIdx; i < GS->pointsIdx; i++ ) {
GS->gAuxPoints[i] = (double *)PyMem_Malloc(GS->nAuxVars*sizeof(double));
assert(GS->gAuxPoints[i]);
}
}
/* Perform calculation on each integrated point */
for( i = GS->auxIdx; i < GS->pointsIdx; i++ ) {
if( GS->nExtInputs > 0 ) {
FillCurrentExtInputValues(GS, GS->gTimeV[i]);
}
auxvars((unsigned) GS->phaseDim, (unsigned) GS->paramDim, GS->gTimeV[i],
GS->gPoints[i], GS->gParams, GS->gAuxPoints[i],
(unsigned) GS->extraSpaceSize, GS->gExtraSpace,
(unsigned) GS->nExtInputs, GS->gCurrentExtInputVals);
}
GS->auxIdx = GS->pointsIdx;
}
}
PyObject* Vfield(double t, double *x, double *p) {
PyObject *OutObj = NULL;
PyObject *PointsOut = NULL;
double *ftemp = NULL;
_init_numpy();
if( (gIData == NULL) || (gIData->isInitBasic == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else if( (gIData->nExtInputs > 0) && (gIData->isInitExtInputs == 0) ) {
Py_INCREF(Py_None);
return Py_None;
}
else {
OutObj = PyTuple_New(1);
assert(OutObj);
ftemp = (double *)PyMem_Malloc((gIData->phaseDim)*sizeof(double));
assert(ftemp);
if( gIData->nExtInputs > 0 ) {
FillCurrentExtInputValues( gIData, t );
}
vfieldfunc(gIData->phaseDim, gIData->paramDim, t, x, p, ftemp,
gIData->extraSpaceSize, gIData->gExtraSpace,
gIData->nExtInputs, gIData->gCurrentExtInputVals);
npy_intp dims[1] = {gIData->phaseDim};
PointsOut = PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, ftemp);
if(!PointsOut) {
PyMem_Free(ftemp);
Py_INCREF(Py_None);
return Py_None;
}
PyArray_UpdateFlags((PyArrayObject *)PointsOut, NPY_ARRAY_CARRAY | NPY_ARRAY_OWNDATA);
PyTuple_SetItem(OutObj, 0, PointsOut);
return OutObj;
}
}
