void Cvode::do_ode(NrnThread* _nt){
// all the membrane mechanism ode's
CvodeThreadData& z = CTD(_nt->id);
CvMembList* cml;
Memb_func* mf;
for (cml = z.cv_memb_list_; cml; cml = cml->next) { // probably can start at 6 or hh
mf = memb_func + cml->index;
if (mf->ode_spec) {
Pfridot s = (Pfridot)mf->ode_spec;
Memb_list* ml = cml->ml;
if (mf->hoc_mech) {
int j, count;
count = ml->nodecount;
for (j = 0; j < count; ++j) {
Node* nd = ml->nodelist[j];
(*s)(nd, ml->prop[j]);
}
}else{
(*s)(_nt, ml, cml->index);
}
if (errno) {
if (nrn_errno_check(cml->index)) {
hoc_warning("errno set during ode evaluation", (char*)0);
}
}
}
}
long_difus_solve(1, _nt);
}
void Cvode::do_nonode(NrnThread* _nt) { // all the hacked integrators, etc, in SOLVE procedure
//almost a verbatim copy of nonvint in fadvance.c
if (!_nt) {
if (nrn_nthread > 1) {
nonode_cv = this;
nrn_multithread_job(nonode_thread);
return;
}
_nt = nrn_threads;
}
CvodeThreadData& z = CTD(_nt->id);
CvMembList* cml;
for (cml = z.cv_memb_list_; cml; cml = cml->next) {
Memb_func* mf = memb_func + cml->index;
if (mf->state) {
Memb_list* ml = cml->ml;
if (!mf->ode_spec){
Pfridot s = (Pfridot)mf->state;
(*s)(_nt, ml, cml->index);
#if 0
if (errno) {
if (nrn_errno_check(cml->index)) {
hoc_warning("errno set during calculation of states", (char*)0);
}
}
#endif
}else if (mf->singchan_) {
Pfridot s = (Pfridot)mf->singchan_;
(*s)(_nt, ml, cml->index);
}
}
}
}
void Cvode::solvemem(NrnThread* nt) {
// all the membrane mechanism matrices
CvodeThreadData& z = CTD(nt->id);
CvMembList* cml;
for (cml = z.cv_memb_list_; cml; cml = cml->next) { // probably can start at 6 or hh
Memb_func* mf = memb_func + cml->index;
if (mf->ode_matsol) {
Memb_list* ml = cml->ml;
Pfridot s = (Pfridot)mf->ode_matsol;
if (mf->hoc_mech) {
int j, count;
count = ml->nodecount;
for (j = 0; j < count; ++j) {
Node* nd = ml->nodelist[j];
(*s)(nd, ml->prop[j]);
}
}else{
(*s)(nt, ml, cml->index);
}
if (errno) {
if (nrn_errno_check(cml->index)) {
hoc_warning("errno set during ode jacobian solve", (char*)0);
}
}
}
}
long_difus_solve(2, nt);
}
void nonvint(NrnThread* _nt)
{
#if VECTORIZE
int i;
double w;
int measure = 0;
NrnThreadMembList* tml;
#if 1 || PARANEURON
/* nrnmpi_v_transfer if needed was done earlier */
if (nrnthread_v_transfer_) {(*nrnthread_v_transfer_)(_nt);}
#endif
if (_nt->id == 0 && nrn_mech_wtime_) { measure = 1; }
errno = 0;
for (tml = _nt->tml; tml; tml = tml->next) if (memb_func[tml->index].state) {
Pfri s = memb_func[tml->index].state;
if (measure) { w = nrnmpi_wtime(); }
(*s)(_nt, tml->ml, tml->index);
if (measure) { nrn_mech_wtime_[tml->index] += nrnmpi_wtime() - w; }
if (errno) {
if (nrn_errno_check(i)) {
hoc_warning("errno set during calculation of states", (char*)0);
}
}
}
long_difus_solve(0, _nt); /* if any longitudinal diffusion */
nrn_nonvint_block_fixed_step_solve(_nt->id);
#endif
}
void Cvode::lhs_memb(CvMembList* cmlist, NrnThread* _nt) {
CvMembList* cml;
for (cml = cmlist; cml; cml = cml->next) {
Memb_func* mf = memb_func + cml->index;
Memb_list* ml = cml->ml;
Pfridot s = (Pfridot)mf->jacob;
if (s) {
Pfridot s = (Pfridot)mf->jacob;
(*s)(_nt, ml, cml->index);
if (errno) {
if (nrn_errno_check(cml->index)) {
hoc_warning("errno set during calculation of di/dv", (char*)0);
}
}
}
}
activsynapse_lhs();
activclamp_lhs();
}
void Cvode::rhs_memb(CvMembList* cmlist, NrnThread* _nt) {
CvMembList* cml;
errno = 0;
for (cml = cmlist; cml; cml = cml->next) {
Memb_func* mf = memb_func + cml->index;
Pfridot s = (Pfridot)mf->current;
if (s) {
Memb_list* ml = cml->ml;
(*s)(_nt, ml, cml->index);
if (errno) {
if (nrn_errno_check(cml->index)) {
hoc_warning("errno set during calculation of currents", (char*)0);
}
}
}
}
activsynapse_rhs();
activstim_rhs();
activclamp_rhs();
}
method3_setup_tree_matrix() /* construct diagonal elements */
{
int i;
if (diam_changed) {
recalc_diam();
}
#if _CRAY
#pragma _CRI ivdep
#endif
for (i = 0; i < v_node_count; ++i) {
Node* nd = v_node[i];
NODED(nd) = 0.;
NODERHS(nd) = 0.;
nd->thisnode.GC = 0.;
nd->thisnode.EC = 0.;
}
for (i=0; i < n_memb_func; ++i) if (memb_func[i].current && memb_list[i].nodecount) {
if (memb_func[i].vectorized) {
memb_func[i].current(
memb_list[i].nodecount,
memb_list[i].nodelist,
memb_list[i].data,
memb_list[i].pdata
);
}else{
int j, count;
Pfrd s = memb_func[i].current;
Memb_list* m = memb_list + i;
count = m->nodecount;
if (memb_func[i].is_point) {
for (j = 0; j < count; ++j) {
Node* nd = m->nodelist[j];
NODERHS(nd) -= (*s)(m->data[j], m->pdata[j],
&NODED(nd),nd->v);
};
}else{
for (j = 0; j < count; ++j) {
Node* nd = m->nodelist[j];
nd->thisnode.EC -= (*s)(m->data[j], m->pdata[j],
&nd->thisnode.GC,nd->v);
};
}
}
if (errno) {
if (nrn_errno_check(i)) {
hoc_warning("errno set during calculation of currents", (char*)0);
}
}
}
#if 0 && _CRAY
#pragma _CRI ivdep
#endif
for (i=rootnodecount; i < v_node_count; ++i) {
Node* nd2;
Node* nd = v_node[i];
Node* pnd = v_parent[nd->v_node_index];
double dg, de, dgp, dep, fac;
#if 0
if (i == rootnodecount) {
printf("v0 %g vn %g jstim %g jleft %g jright %g\n",
nd->v, pnd->v, nd->fromparent.current, nd->toparent.current,
nd[1].fromparent.current);
}
#endif
/* dg and de must be second order when used */
if ((nd2 = nd->toparent.nd2) != (Node*)0) {
dgp = -(3*(pnd->thisnode.GC - pnd->thisnode.Cdt)
- 4*(nd->thisnode.GC - nd->thisnode.Cdt)
+(nd2->thisnode.GC - nd2->thisnode.Cdt))/2
;
dep = -(3*(pnd->thisnode.EC - pnd->thisnode.Cdt * pnd->v)
- 4*(nd->thisnode.EC - nd->thisnode.Cdt * nd->v)
+(nd2->thisnode.EC - nd2->thisnode.Cdt * nd2->v))/2
;
}else{
dgp = 0.;
dep = 0.;
}
if ((nd2 = pnd->fromparent.nd2) != (Node*)0) {
dg = -(3*(nd->thisnode.GC - nd->thisnode.Cdt)
- 4*(pnd->thisnode.GC - pnd->thisnode.Cdt)
+(nd2->thisnode.GC - nd2->thisnode.Cdt))/2
;
de = -(3*(nd->thisnode.EC - nd->thisnode.Cdt * nd->v)
- 4*(pnd->thisnode.EC - pnd->thisnode.Cdt * pnd->v)
+(nd2->thisnode.EC - nd2->thisnode.Cdt * nd2->v))/2
;
}else{
dg = 0.;
de = 0.;
}
fac = 1. + nd->toparent.coefjdot * nd->thisnode.GC;
nd->toparent.djdv0 = (
nd->toparent.coefj
+ nd->toparent.coef0 * nd->thisnode.GC
+ nd->toparent.coefdg * dg
)/fac;
NODED(nd) += nd->toparent.djdv0;
nd->toparent.current = (
- nd->toparent.coef0 * nd->thisnode.EC
- nd->toparent.coefn * pnd->thisnode.EC
+ nd->toparent.coefjdot *
nd->thisnode.Cdt * nd->toparent.current
- nd->toparent.coefdg * de
)/fac;
NODERHS(nd) -= nd->toparent.current;
NODEB(nd) = (
- nd->toparent.coefj
+ nd->toparent.coefn * pnd->thisnode.GC
)/fac;
/* this can break cray vectors */
fac = 1. + nd->fromparent.coefjdot * pnd->thisnode.GC;
nd->fromparent.djdv0 = (
nd->fromparent.coefj
+ nd->fromparent.coef0 * pnd->thisnode.GC
+ nd->fromparent.coefdg * dgp
)/fac;
pNODED(nd) += nd->fromparent.djdv0;
nd->fromparent.current = (
- nd->fromparent.coef0 * pnd->thisnode.EC
- nd->fromparent.coefn * nd->thisnode.EC
+ nd->fromparent.coefjdot *
nd->thisnode.Cdt * nd->fromparent.current
- nd->fromparent.coefdg * dep
)/fac;
pNODERHS(nd) -= nd->fromparent.current;
NODEA(nd) = (
- nd->fromparent.coefj
+ nd->fromparent.coefn * nd->thisnode.GC
)/fac;
}
activstim();
activsynapse();
#if SEJNOWSKI
activconnect();
#endif
activclamp();
}