void CVodesIntegrator::sensInit(double t0, FuncEval& func)
{
m_np = func.nparams();
size_t nv = func.neq();
m_sens_ok = false;
doublereal* data;
N_Vector y;
y = N_VNew_Serial(static_cast<sd_size_t>(nv));
m_yS = N_VCloneVectorArray_Serial(static_cast<sd_size_t>(m_np), y);
for (size_t n = 0; n < m_np; n++) {
data = NV_DATA_S(m_yS[n]);
for (size_t j = 0; j < nv; j++) {
data[j] =0.0;
}
}
int flag = CVodeSensInit(m_cvode_mem, static_cast<sd_size_t>(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, atol.data());
}
void CVodesIntegrator::sensInit(double t0, FuncEval& func)
{
m_np = func.nparams();
m_sens_ok = false;
N_Vector y = N_VNew_Serial(static_cast<sd_size_t>(func.neq()));
m_yS = N_VCloneVectorArray_Serial(static_cast<sd_size_t>(m_np), y);
for (size_t n = 0; n < m_np; n++) {
N_VConst(0.0, m_yS[n]);
}
N_VDestroy_Serial(y);
int flag = CVodeSensInit(m_cvode_mem, static_cast<sd_size_t>(m_np),
CV_STAGGERED, CVSensRhsFn(0), m_yS);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::sensInit", "Error in CVodeSensInit");
}
vector_fp atol(m_np);
for (size_t n = 0; n < m_np; n++) {
// This scaling factor is tuned so that reaction and species enthalpy
// sensitivities can be computed simultaneously with the same abstol.
atol[n] = m_abstolsens / func.m_paramScales[n];
}
flag = CVodeSensSStolerances(m_cvode_mem, m_reltolsens, atol.data());
}
void CVodeInt::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
if (m_y) {
N_VFree(nv(m_y)); // free solution vector if already allocated
}
m_y = reinterpret_cast<void*>(N_VNew(m_neq, 0)); // allocate solution vector
// check abs tolerance array size
if (m_itol == 1 && m_nabs < m_neq)
throw CVodeErr("not enough absolute tolerance values specified.");
func.getInitialConditions(m_t0, m_neq, N_VDATA(nv(m_y)));
// set options
m_iopt[MXSTEP] = m_maxsteps;
m_iopt[MAXORD] = m_maxord;
m_ropt[HMAX] = m_hmax;
if (m_cvode_mem) CVodeFree(m_cvode_mem);
// pass a pointer to func in m_data
m_data = (void*)&func;
if (m_itol) {
m_cvode_mem = CVodeMalloc(m_neq, cvode_rhs, m_t0, nv(m_y), m_method,
m_iter, m_itol, &m_reltol,
nv(m_abstol), m_data, NULL, TRUE, m_iopt,
DATA_PTR(m_ropt), NULL);
}
else {
m_cvode_mem = CVodeMalloc(m_neq, cvode_rhs, m_t0, nv(m_y), m_method,
m_iter, m_itol, &m_reltol,
&m_abstols, m_data, NULL, TRUE, m_iopt,
DATA_PTR(m_ropt), NULL);
}
if (!m_cvode_mem) throw CVodeErr("CVodeMalloc failed.");
if (m_type == DENSE + NOJAC) {
CVDense(m_cvode_mem, NULL, NULL);
}
else if (m_type == DENSE + JAC) {
CVDense(m_cvode_mem, cvode_jac, NULL);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, NONE, MODIFIED_GS, 0, 0.0,
NULL, NULL, NULL);
}
else {
throw CVodeErr("unsupported option");
}
}
/**
* Function called by cvodes to evaluate ydot given y. The CVODE integrator
* allows passing in a void* pointer to access external data. This pointer
* is cast to a pointer to a instance of class FuncEval. The equations to be
* integrated should be specified by deriving a class from FuncEval that
* evaluates the desired equations.
* @ingroup odeGroup
*/
static int cvodes_rhs(realtype t, N_Vector y, N_Vector ydot, void* f_data)
{
try {
FuncEval* f = (FuncEval*) f_data;
f->eval(t, NV_DATA_S(y), NV_DATA_S(ydot), f->m_sens_params.data());
} catch (CanteraError& err) {
std::cerr << err.what() << std::endl;
return 1; // possibly recoverable error
} catch (std::exception& err) {
std::cerr << "cvodes_rhs: unhandled exception:" << std::endl;
std::cerr << err.what() << std::endl;
return -1; // unrecoverable error
} catch (...) {
std::cerr << "cvodes_rhs: unhandled exception of uknown type" << std::endl;
return -1; // unrecoverable error
}
return 0; // successful evaluation
}
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
}
/**
* Function called by cvodes to evaluate ydot given y. The CVODE
* integrator allows passing in a void* pointer to access
* external data. This pointer is cast to a pointer to a instance
* of class FuncEval. The equations to be integrated should be
* specified by deriving a class from FuncEval that evaluates the
* desired equations.
* @ingroup odeGroup
*/
static int cvodes_rhs(realtype t, N_Vector y, N_Vector ydot,
void* f_data)
{
try {
double* ydata = NV_DATA_S(y);
double* ydotdata = NV_DATA_S(ydot);
FuncData* d = (FuncData*)f_data;
FuncEval* f = d->m_func;
if (d->m_pars.size() == 0) {
f->eval(t, ydata, ydotdata, NULL);
} else {
f->eval(t, ydata, ydotdata, d->m_pars.data());
}
} catch (CanteraError& err) {
std::cerr << err.what() << std::endl;
return 1; // possibly recoverable error
} catch (...) {
std::cerr << "cvodes_rhs: unhandled exception" << std::endl;
return -1; // unrecoverable error
}
return 0; // successful evaluation
}
void CVodesIntegrator::reinitialize(double t0, FuncEval& func)
{
m_t0 = t0;
m_time = t0;
func.getState(NV_DATA_S(m_y));
int result = CVodeReInit(m_cvode_mem, m_t0, m_y);
if (result != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::reinitialize",
"CVodeReInit failed. result = {}", result);
}
applyOptions();
}
void CVodesIntegrator::reinitialize(double t0, FuncEval& func)
{
m_t0 = t0;
m_time = t0;
func.getInitialConditions(m_t0, static_cast<sd_size_t>(m_neq),
NV_DATA_S(m_y));
int result;
result = CVodeReInit(m_cvode_mem, m_t0, m_y);
if (result != CV_SUCCESS) {
throw CVodesErr("CVodeReInit failed. result = "+int2str(result));
}
applyOptions();
}
void CVodeInt::reinitialize(double t0, FuncEval& func)
{
m_t0 = t0;
func.getInitialConditions(m_t0, m_neq, N_VDATA(nv(m_y)));
// set options
m_iopt[MXSTEP] = m_maxsteps;
m_iopt[MAXORD] = m_maxord;
m_ropt[HMAX] = m_hmax;
//if (m_cvode_mem) CVodeFree(m_cvode_mem);
// pass a pointer to func in m_data
m_data = (void*)&func;
int result;
if (m_itol) {
result = CVReInit(m_cvode_mem, cvode_rhs, m_t0, nv(m_y), m_method,
m_iter, m_itol, &m_reltol,
nv(m_abstol), m_data, NULL, TRUE, m_iopt,
DATA_PTR(m_ropt), NULL);
}
else {
result = CVReInit(m_cvode_mem, cvode_rhs, m_t0, nv(m_y), m_method,
m_iter, m_itol, &m_reltol,
&m_abstols, m_data, NULL, TRUE, m_iopt,
DATA_PTR(m_ropt), NULL);
}
if (result != 0) throw CVodeErr("CVReInit failed.");
if (m_type == DENSE + NOJAC) {
CVDense(m_cvode_mem, NULL, NULL);
}
else if (m_type == DENSE + JAC) {
CVDense(m_cvode_mem, cvode_jac, NULL);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, NONE, MODIFIED_GS, 0, 0.0,
NULL, NULL, NULL);
}
else {
throw CVodeErr("unsupported option");
}
}
void CVodesIntegrator::reinitialize(double t0, FuncEval& func)
{
m_t0 = t0;
//try {
func.getInitialConditions(m_t0, m_neq, NV_DATA_S(nv(m_y)));
//}
//catch (CanteraError) {
//showErrors();
//error("Teminating execution");
//}
int result, flag;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
if (m_itol == CV_SV) {
result = CVodeReInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y),
m_itol, m_reltol,
nv(m_abstol));
}
else {
result = CVodeReInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y),
m_itol, m_reltol,
&m_abstols);
}
if (result != CV_SUCCESS) {
throw CVodesErr("CVodeReInit failed. result = "+int2str(result));
}
#elif defined(SUNDIALS_VERSION_24)
result = CVodeReInit(m_cvode_mem, m_t0, nv(m_y));
if (result != CV_SUCCESS) {
throw CVodesErr("CVodeReInit failed. result = "+int2str(result));
}
#endif
if (m_type == DENSE + NOJAC) {
long int N = m_neq;
CVDense(m_cvode_mem, N);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == BAND + NOJAC) {
long int N = m_neq;
long int nu = m_mupper;
long int nl = m_mlower;
CVBand(m_cvode_mem, N, nu, nl);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, PREC_NONE, 0);
}
else {
throw CVodesErr("unsupported option");
}
// set options
if (m_maxord > 0)
flag = CVodeSetMaxOrd(m_cvode_mem, m_maxord);
if (m_maxsteps > 0)
flag = CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
if (m_hmax > 0)
flag = CVodeSetMaxStep(m_cvode_mem, m_hmax);
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
if (m_y) {
N_VDestroy_Serial(nv(m_y)); // free solution vector if already allocated
}
m_y = reinterpret_cast<void*>(N_VNew_Serial(m_neq)); // allocate solution vector
for (int i=0; i<m_neq; i++) {
NV_Ith_S(nv(m_y), i) = 0.0;
}
// check abs tolerance array size
if (m_itol == CV_SV && m_nabs < m_neq)
throw CVodesErr("not enough absolute tolerance values specified.");
func.getInitialConditions(m_t0, m_neq, NV_DATA_S(nv(m_y)));
if (m_cvode_mem) CVodeFree(&m_cvode_mem);
/*
* Specify the method and the iteration type:
* Cantera Defaults:
* CV_BDF - Use BDF methods
* CV_NEWTON - use newton's method
*/
m_cvode_mem = CVodeCreate(m_method, m_iter);
if (!m_cvode_mem) throw CVodesErr("CVodeCreate failed.");
int flag = 0;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
if (m_itol == CV_SV) {
// vector atol
flag = CVodeMalloc(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol,
m_reltol, nv(m_abstol));
}
else {
// scalar atol
flag = CVodeMalloc(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol,
m_reltol, &m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
}
else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeMalloc input argument.");
}
else
throw CVodesErr("CVodeMalloc failed.");
}
#elif defined(SUNDIALS_VERSION_24)
flag = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y));
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, nv(m_abstol));
} else {
flag = CVodeSStolerances(m_cvode_mem, m_reltol, m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
#else
printf("unknown sundials verson\n");
exit(-1);
#endif
if (m_type == DENSE + NOJAC) {
long int N = m_neq;
CVDense(m_cvode_mem, N);
}
else if (m_type == DIAG) {
CVDiag(m_cvode_mem);
}
else if (m_type == GMRES) {
CVSpgmr(m_cvode_mem, PREC_NONE, 0);
}
else if (m_type == BAND + NOJAC) {
long int N = m_neq;
long int nu = m_mupper;
long int nl = m_mlower;
CVBand(m_cvode_mem, N, nu, nl);
}
else {
throw CVodesErr("unsupported option");
}
// pass a pointer to func in m_data
m_fdata = new FuncData(&func, func.nparams());
//m_data = (void*)&func;
#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23)
flag = CVodeSetFdata(m_cvode_mem, (void*)m_fdata);
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetFdata failed.");
}
#elif defined(SUNDIALS_VERSION_24)
flag = CVodeSetUserData(m_cvode_mem, (void*)m_fdata);
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetUserData failed.");
}
#endif
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, DATA_PTR(m_fdata->m_pars),
NULL, NULL);
}
// set options
if (m_maxord > 0)
flag = CVodeSetMaxOrd(m_cvode_mem, m_maxord);
if (m_maxsteps > 0)
flag = CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps);
if (m_hmax > 0)
flag = CVodeSetMaxStep(m_cvode_mem, m_hmax);
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
m_time = t0;
if (m_y) {
N_VDestroy_Serial(m_y); // free solution vector if already allocated
}
m_y = N_VNew_Serial(static_cast<sd_size_t>(m_neq)); // allocate solution vector
for (size_t i = 0; i < m_neq; i++) {
NV_Ith_S(m_y, i) = 0.0;
}
// check abs tolerance array size
if (m_itol == CV_SV && m_nabs < m_neq) {
throw CVodesErr("not enough absolute tolerance values specified.");
}
func.getInitialConditions(m_t0, m_neq, NV_DATA_S(m_y));
if (m_cvode_mem) {
CVodeFree(&m_cvode_mem);
}
/*
* Specify the method and the iteration type:
* Cantera Defaults:
* CV_BDF - Use BDF methods
* CV_NEWTON - use Newton's method
*/
m_cvode_mem = CVodeCreate(m_method, m_iter);
if (!m_cvode_mem) {
throw CVodesErr("CVodeCreate failed.");
}
int flag = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, m_y);
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
CVodeSetErrHandlerFn(m_cvode_mem, &cvodes_err, this);
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, m_abstol);
} else {
flag = CVodeSStolerances(m_cvode_mem, m_reltol, m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CVodesErr("Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CVodesErr("Illegal value for CVodeInit input argument.");
} else {
throw CVodesErr("CVodeInit failed.");
}
}
// pass a pointer to func in m_data
m_fdata.reset(new FuncData(&func, func.nparams()));
flag = CVodeSetUserData(m_cvode_mem, m_fdata.get());
if (flag != CV_SUCCESS) {
throw CVodesErr("CVodeSetUserData failed.");
}
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, m_fdata->m_pars.data(),
NULL, NULL);
}
applyOptions();
}
void CVodesIntegrator::initialize(double t0, FuncEval& func)
{
m_neq = func.neq();
m_t0 = t0;
m_time = t0;
if (m_y) {
N_VDestroy_Serial(m_y); // free solution vector if already allocated
}
m_y = N_VNew_Serial(static_cast<sd_size_t>(m_neq)); // allocate solution vector
N_VConst(0.0, m_y);
// check abs tolerance array size
if (m_itol == CV_SV && m_nabs < m_neq) {
throw CanteraError("CVodesIntegrator::initialize",
"not enough absolute tolerance values specified.");
}
func.getState(NV_DATA_S(m_y));
if (m_cvode_mem) {
CVodeFree(&m_cvode_mem);
}
//! Specify the method and the iteration type. Cantera Defaults:
//! CV_BDF - Use BDF methods
//! CV_NEWTON - use Newton's method
m_cvode_mem = CVodeCreate(m_method, m_iter);
if (!m_cvode_mem) {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeCreate failed.");
}
int flag = CVodeInit(m_cvode_mem, cvodes_rhs, m_t0, m_y);
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CanteraError("CVodesIntegrator::initialize",
"Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CanteraError("CVodesIntegrator::initialize",
"Illegal value for CVodeInit input argument.");
} else {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeInit failed.");
}
}
CVodeSetErrHandlerFn(m_cvode_mem, &cvodes_err, this);
if (m_itol == CV_SV) {
flag = CVodeSVtolerances(m_cvode_mem, m_reltol, m_abstol);
} else {
flag = CVodeSStolerances(m_cvode_mem, m_reltol, m_abstols);
}
if (flag != CV_SUCCESS) {
if (flag == CV_MEM_FAIL) {
throw CanteraError("CVodesIntegrator::initialize",
"Memory allocation failed.");
} else if (flag == CV_ILL_INPUT) {
throw CanteraError("CVodesIntegrator::initialize",
"Illegal value for CVodeInit input argument.");
} else {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeInit failed.");
}
}
flag = CVodeSetUserData(m_cvode_mem, &func);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeSetUserData failed.");
}
if (func.nparams() > 0) {
sensInit(t0, func);
flag = CVodeSetSensParams(m_cvode_mem, func.m_sens_params.data(),
func.m_paramScales.data(), NULL);
if (flag != CV_SUCCESS) {
throw CanteraError("CVodesIntegrator::initialize",
"CVodeSetSensParams failed.");
}
}
applyOptions();
}