static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
if (use_cachevec) {
_v = VEC_V(_ni[_iml]);
}else
#endif
{
_nd = _ml->_nodelist[_iml];
_v = NODEV(_nd);
}
ena = _ion_ena;
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
{ double _dina;
_dina = ina;
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
_ion_dinadv += (_dina - ina)/.001 ;
}
_g = (_g - _rhs)/.001;
_ion_ina += ina ;
#if CACHEVEC
if (use_cachevec) {
VEC_RHS(_ni[_iml]) -= _rhs;
}else
#endif
{
NODERHS(_nd) -= _rhs;
}
}}
static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type){
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
_ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
for (_iml = 0; _iml < _cntml; ++_iml) {
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
if (use_cachevec) {
_v = VEC_V(_ni[_iml]);
}else
#endif
{
_nd = _ml->_nodelist[_iml];
_v = NODEV(_nd);
}
ek = _ion_ek;
cai = _ion_cai;
_g = _nrn_current(_v + .001);
{ double _dik;
_dik = ik;
_rhs = _nrn_current(_v);
_ion_dikdv += (_dik - ik)/.001 ;
}
_g = (_g - _rhs)/.001;
_ion_ik += ik ;
#if CACHEVEC
if (use_cachevec) {
VEC_RHS(_ni[_iml]) -= _rhs;
}else
#endif
{
NODERHS(_nd) -= _rhs;
}
}}
void NonLinImpRep::didv() {
int i, j, ip;
Node* nd;
NrnThread* _nt = nrn_threads;
// d2v/dv2 terms
for (i=_nt->ncell; i < n_v_; ++i) {
nd = _nt->_v_node[i];
ip = _nt->_v_parent[i]->v_node_index;
double* a = cmplx_spGetElement(m_, v_index_[ip], v_index_[i]);
double* b = cmplx_spGetElement(m_, v_index_[i], v_index_[ip]);
*a += NODEA(nd);
*b += NODEB(nd);
*diag_[i] -= NODEB(nd);
*diag_[ip] -= NODEA(nd);
}
// jwC term
Memb_list* mlc = _nt->tml->ml;
int n = mlc->nodecount;
for (i=0; i < n; ++i) {
double* cd = mlc->data[i];
j = mlc->nodelist[i]->v_node_index;
diag_[v_index_[j]-1][1] += .001 * cd[0] * omega_;
}
// di/dv terms
// because there may be several point processes of the same type
// at the same location, we have to be careful to neither increment that
// nd->v multiple times nor count the rhs multiple times.
// So we can't take advantage of vectorized point processes.
// To avoid this we do each mechanism item separately.
// We assume there is no interaction between
// separate locations. Note that interactions such as gap junctions
// would not be handled in any case without computing a full jacobian.
// i.e. calling nrn_rhs varying every state one at a time (that would
// give the d2v/dv2 terms as well), but the expense is unwarranted.
for (NrnThreadMembList* tml = _nt->tml; tml; tml = tml->next) {
i = tml->index;
if (i == CAP) { continue; }
if (!memb_func[i].current) { continue; }
Memb_list* ml = tml->ml;
double* x1 = rv_; // use as temporary storage
double* x2 = jv_;
for (j = 0; j < ml->nodecount; ++j) { Node* nd = ml->nodelist[j];
// zero rhs
// save v
NODERHS(nd) = 0;
x1[j] = NODEV(nd);
// v+dv
NODEV(nd) += delta_;
current(i, ml, j);
// save rhs
// zero rhs
// restore v
x2[j] = NODERHS(nd);
NODERHS(nd) = 0;
NODEV(nd) = x1[j];
current(i, ml, j);
// conductance
// add to matrix
*diag_[v_index_[nd->v_node_index]-1] -= (x2[j] - NODERHS(nd))/delta_;
}
}
}
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;
}
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();
}