void Cvode::maxstate(bool b, NrnThread* nt) {
if (!maxstate_) { return; }
if (!nt) {
if (nrn_nthread > 1) {
maxstate_cv = this;
maxstate_b = b;
nrn_multithread_job(maxstate_thread);
return;
}
nt = nrn_threads;
}
CvodeThreadData& z = ctd_[nt->id];
int i;
double x;
double* y = n_vector_data(y_, nt->id);
double* m = n_vector_data(maxstate_, nt->id);
for (i=0; i < z.nvsize_; ++i) {
x = Math::abs(y[i]);
if (m[i] < x) {
m[i] = x;
}
}
if (b) {
y = n_vector_data(acorvec(), nt->id);
m = n_vector_data(maxacor_, nt->id);
for (i=0; i < z.nvsize_; ++i) {
x = Math::abs(y[i]);
if (m[i] < x) {
m[i] = x;
}
}
}
}
void Cvode::error_weights(double* pd) {
int i, id;
for (id=0; id < nctd_; ++id) {
CvodeThreadData& z = ctd_[id];
double* s = n_vector_data(ewtvec(), id);
for (i=0; i < z.nvsize_; ++i) {
pd[i + z.nvoffset_] = s[i];
}
}
}
void Cvode::states(double* pd) {
int i, id;
for (id=0; id < nctd_; ++id) {
CvodeThreadData& z = ctd_[id];
double* s = n_vector_data(y_, id);
for (i=0; i < z.nvsize_; ++i) {
pd[i + z.nvoffset_] = s[i];
}
}
}
void Cvode::acor(double* pd) {
int i, id;
NrnThread* nt;
for (id=0; id < nctd_; ++id) {
CvodeThreadData& z = ctd_[id];
double* s = n_vector_data(acorvec(), id);
for (i=0; i < z.nvsize_; ++i) {
pd[i + z.nvoffset_] = s[i];
}
}
}
void Cvode::maxacor(double* pd) {
int i;
NrnThread* nt;
if (maxacor_) {
FOR_THREADS(nt) {
double* m = n_vector_data(maxacor_, nt->id);
int n = ctd_[nt->id].nvsize_;
int o = ctd_[nt->id].nvoffset_;
for (i=0; i < n; ++i) {
pd[i+o] = m[i];
}
}
}
}
void Cvode::daspk_init_eqn(){
// DASPK equation order is exactly the same order as the
// fixed step method for current balance (including
// extracellular nodes) and linear mechanism. Remaining ode
// equations are same order as for Cvode. Thus, daspk differs from
// cvode order primarily in that cap and no-cap nodes are not
// distinguished.
// note that only one thread is allowed for sparse right now.
NrnThread* _nt = nrn_threads;
CvodeThreadData&z = ctd_[0];
double vtol;
//printf("Cvode::daspk_init_eqn\n");
int i, j, in, ie, k, neq_v;
// how many equations are there?
Memb_func* mf;
CvMembList* cml;
//start with all the equations for the fixed step method.
if (use_sparse13 == 0 || diam_changed != 0) {
recalc_diam();
}
z.neq_v_ = spGetSize(_nt->_sp13mat, 0);
z.nvsize_ = z.neq_v_;
// now add the membrane mechanism ode's to the count
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
Pfridot s = (Pfridot)memb_func[cml->index].ode_count;
if (s) {
z.nvsize_ += cml->ml->nodecount * (*s)(cml->index);
}
}
neq_ = z.nvsize_;
//printf("Cvode::daspk_init_eqn: neq_v_=%d neq_=%d\n", neq_v_, neq_);
if (z.pv_) {
delete [] z.pv_;
delete [] z.pvdot_;
}
z.pv_ = new double*[z.nvsize_];
z.pvdot_ = new double*[z.nvsize_];
atolvec_alloc(neq_);
double* atv = n_vector_data(atolnvec_, 0);
for (i=0; i < neq_; ++i) {
atv[i] = ncv_->atol();
}
vtol = 1.;
if (!vsym) {
vsym = hoc_table_lookup("v", hoc_built_in_symlist);
}
if (vsym->extra) {
double x;
x = vsym->extra->tolerance;
if (x != 0 && x < vtol) {
vtol = x;
}
}
// deal with voltage and extracellular and linear circuit nodes
// for daspk the order is the same
assert(use_sparse13);
if (use_sparse13) {
for (in = 0; in < _nt->end; ++in) {
Node* nd; Extnode* nde;
nd = _nt->_v_node[in];
nde = nd->extnode;
i = nd->eqn_index_ - 1; // the sparse matrix index starts at 1
z.pv_[i] = &NODEV(nd);
z.pvdot_[i] = nd->_rhs;
if (nde) {
for (ie=0; ie < nlayer; ++ie) {
k = i + ie + 1;
z.pv_[k] = nde->v + ie;
z.pvdot_[k] = nde->_rhs[ie];
}
}
}
linmod_dkmap(z.pv_, z.pvdot_);
for (i=0; i < z.neq_v_; ++i) {
atv[i] *= vtol;
}
}
// map the membrane mechanism ode state and dstate pointers
int ieq = z.neq_v_;
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
int n;
mf = memb_func + cml->index;
Pfridot sc = (Pfridot)mf->ode_count;
if (sc && ( (n = (*sc)(cml->index)) > 0)) {
Memb_list* ml = cml->ml;
Pfridot s = (Pfridot)mf->ode_map;
if (mf->hoc_mech) {
for (j=0; j < ml->nodecount; ++j) {
(*s)(ieq, z.pv_ + ieq, z.pvdot_ + ieq, ml->prop[j], atv + ieq);
ieq += n;
}
}else{
for (j=0; j < ml->nodecount; ++j) {
(*s)(ieq, z.pv_ + ieq, z.pvdot_ + ieq, ml->data[j], ml->pdata[j], atv + ieq, cml->index);
ieq += n;
}
}
}
}
structure_change_ = false;
}
void Cvode::init_eqn(){
double vtol;
NrnThread* _nt;
CvMembList* cml;
Memb_list* ml;
Memb_func* mf;
int i, j, zneq, zneq_v, zneq_cap_v;
//printf("Cvode::init_eqn\n");
if (nthsizes_) {
delete [] nthsizes_;
nthsizes_ = 0;
}
neq_ = 0;
for (int id = 0; id < nctd_; ++id) {
CvodeThreadData& z = ctd_[id];
z.cmlcap_ = nil;
z.cmlext_ = nil;
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
if (cml->index == CAP) {
z.cmlcap_ = cml;
}
if (cml->index == EXTRACELL) {
z.cmlext_ = cml;
}
}
}
if (use_daspk_) {
daspk_init_eqn();
return;
}
FOR_THREADS(_nt) {
// for lvardt, this body done only once and for ctd_[0]
CvodeThreadData& z = ctd_[_nt->id];
// how many ode's are there? First ones are non-zero capacitance
// nodes with non-zero capacitance
zneq_cap_v = z.cmlcap_ ? z.cmlcap_->ml->nodecount : 0;
zneq = zneq_cap_v;
// now add the membrane mechanism ode's to the count
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
Pfridot s = (Pfridot)memb_func[cml->index].ode_count;
if (s) {
zneq += cml->ml->nodecount * (*s)(cml->index);
}
}
//printf("%d Cvode::init_eqn neq_v=%d zneq_=%d\n", nrnmpi_myid, neq_v, zneq_);
if (z.pv_) {
delete [] z.pv_;
delete [] z.pvdot_;
z.pv_ = 0;
z.pvdot_ = 0;
}
if (zneq) {
z.pv_ = new double*[zneq];
z.pvdot_ = new double*[zneq];
}
z.nvoffset_ = neq_;
z.nvsize_ = zneq;
neq_ += zneq;
if (nth_) { break; } //lvardt
}
#if PARANEURON
if (use_partrans_) {
global_neq_ = nrnmpi_int_sum_reduce(neq_, mpicomm_);
//printf("%d global_neq_=%d neq=%d\n", nrnmpi_myid, global_neq_, neq_);
}
#endif
atolvec_alloc(neq_);
for (int id = 0; id < nctd_; ++id) {
CvodeThreadData& z = ctd_[id];
double* atv = n_vector_data(atolnvec_, id);
zneq_cap_v = z.cmlcap_ ? z.cmlcap_->ml->nodecount : 0;
zneq = z.nvsize_;
zneq_v = zneq_cap_v;
for (i=0; i < zneq; ++i) {
atv[i] = ncv_->atol();
}
vtol = 1.;
if (!vsym) {
vsym = hoc_table_lookup("v", hoc_built_in_symlist);
}
if (vsym->extra) {
double x;
x = vsym->extra->tolerance;
if (x != 0 && x < vtol) {
vtol = x;
}
}
for (i=0; i < zneq_cap_v; ++i) {
atv[i] *= vtol;
}
// deal with voltage nodes
// only cap nodes for cvode
for (i=0; i < z.v_node_count_; ++i) {
//sentinal values for determining no_cap
NODERHS(z.v_node_[i]) = 1.;
}
for (i=0; i < zneq_cap_v; ++i) {
ml = z.cmlcap_->ml;
z.pv_[i] = &NODEV(ml->nodelist[i]);
z.pvdot_[i] = &(NODERHS(ml->nodelist[i]));
*z.pvdot_[i] = 0.; // only ones = 1 are no_cap
}
// the remainder are no_cap nodes
if (z.no_cap_node_) {
delete [] z.no_cap_node_;
delete [] z.no_cap_child_;
}
z.no_cap_node_ = new Node*[z.v_node_count_ - zneq_cap_v];
z.no_cap_child_ = new Node*[z.v_node_count_ - zneq_cap_v];
z.no_cap_count_ = 0;
j = 0;
for (i=0; i < z.v_node_count_; ++i) {
if (NODERHS(z.v_node_[i]) > .5) {
z.no_cap_node_[z.no_cap_count_++] = z.v_node_[i];
}
if (z.v_parent_[i] && NODERHS(z.v_parent_[i]) > .5) {
z.no_cap_child_[j++] = z.v_node_[i];
}
}
z.no_cap_child_count_ = j;
// use the sentinal values in NODERHS to construct a new no cap membrane list
new_no_cap_memb(z, _nt);
// map the membrane mechanism ode state and dstate pointers
int ieq = zneq_v;
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
int n;
ml = cml->ml;
mf = memb_func + cml->index;
Pfridot sc = (Pfridot)mf->ode_count;
if (sc && ( (n = (*sc)(cml->index)) > 0)) {
Pfridot s = (Pfridot)mf->ode_map;
if (mf->hoc_mech) {
for (j=0; j < ml->nodecount; ++j) {
(*s)(ieq, z.pv_ + ieq, z.pvdot_ + ieq, ml->prop[j], atv + ieq);
ieq += n;
}
}else{
for (j=0; j < ml->nodecount; ++j) {
(*s)(ieq, z.pv_ + ieq, z.pvdot_ + ieq, ml->data[j], ml->pdata[j], atv + ieq, cml->index);
ieq += n;
}
}
}
}
}
structure_change_ = false;
}