batch_run() /* avoid interpreter overhead */
{
double tstop, tstep, tnext;
char* filename;
char* comment;
tstopunset;
tstop = chkarg(1,0.,1e20);
tstep = chkarg(2, 0., 1e20);
if (ifarg(3)) {
filename = gargstr(3);
}else{
filename = 0;
}
if (ifarg(4)) {
comment = gargstr(4);
}else{
comment = "";
}
if (tree_changed) {
setup_topology();
}
#if VECTORIZE
if (v_structure_change) {
v_setup_vectors();
}
#endif
batch_open(filename, tstop, tstep, comment);
batch_out();
if (cvode_active_) {
while (t < tstop) {
cvode_fadvance(t+tstep);
batch_out();
}
}else{
tstep -= dt/4.;
tstop -= dt/4.;
tnext = t + tstep;
while (t < tstop) {
nrn_fixed_step();
if (t > tnext) {
batch_out();
tnext = t + tstep;
}
if (stoprun) { tstopunset; break; }
}
}
batch_close();
ret(1.);
}
int main(int argc, char** argv) {
MPI_Init(&argc, &argv);
int rank, size;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
assert_valid_configuration(size);
setup_topology(rank);
if (rank == 0) {
top_main(rank);
} else if (rank < size - 1) {
middle_main(rank);
} else {
bottom_main(rank);
}
MPI_Finalize();
return 0;
}
fcurrent()
{
int i;
if (tree_changed) {
setup_topology();
}
if (v_structure_change) {
v_setup_vectors();
}
if (diam_changed) {
recalc_diam();
}
dt2thread(-1.);
nrn_thread_table_check();
state_discon_allowed_ = 0;
nrn_multithread_job(setup_tree_matrix);
state_discon_allowed_ = 1;
ret(1.);
}
fadvance()
{
tstopunset;
#if CVODE
if (cvode_active_) {
cvode_fadvance(-1.);
tstopunset;
ret(1.);
return;
}
#endif
if (tree_changed) {
setup_topology();
}
if (v_structure_change) {
v_setup_vectors();
}
if (diam_changed) {
recalc_diam();
}
nrn_fixed_step();
tstopunset;
ret(1.);
}
method3_connection_coef() /* setup a and b */
{
int j;
double dx, diam, ra, coef;
hoc_Item* qsec;
Section* sec;
Node *nd;
Prop *p, *nrn_mechanism();
float r, s, t;
if (tree_changed) {
setup_topology();
}
/* for now assume diameter between node and parent is constant and located at the node */
/* r = 6 is standard method, 5 is third order, 4 is modified second order */
switch (_method3) {
case 1:
r = 6.;
break;
case 2:
r = 4.;
break;
case 3:
r = 5.;
break;
default:
hoc_execerror(" invalid spatial method", (char*)0);
}
s = 6. - r;
if (r == 5.) {
t = 1.;
}else{
t = 0.;
}
ForAllSections(sec)
dx = section_length(sec)/((double)(sec->nnode));
for (j = 0; j < sec->nnode; ++j) {
nd = sec->pnode[j];
p = nrn_mechanism(MORPHOLOGY, nd);
assert(p);
diam = p->param[0];
/* dv/(ra*dx) is nanoamps */
ra = nrn_ra(sec)*4.e-2/(PI * diam*diam);
/* coef*dx* mA/cm^2 should be nanoamps */
coef = PI *1e-2* diam;
nd->area = 100.;
sec->parentnode->area = 100.;
nd->toparent.coef0 = coef*r*dx/12.;
nd->fromparent.coef0 = coef*r*dx/12.;
nd->toparent.coefn = coef*s*dx/12.;
nd->fromparent.coefn = coef*s*dx/12.;
nd->toparent.coefjdot = t*ra*coef*dx*dx/12.;
nd->fromparent.coefjdot = t*ra*coef*dx*dx/12.;
nd->toparent.coefdg = t*coef*dx/12.;
nd->fromparent.coefdg = t*coef*dx/12.;
nd->toparent.coefj = 1./(ra*dx);
nd->fromparent.coefj = 1./(ra*dx);
nd->toparent.nd2 = 0;
nd->fromparent.nd2 = 0;
}
if (sec->nnode > 1) {
sec->pnode[0]->toparent.nd2 = sec->pnode[1];
if (sec->nnode > 2) {
sec->pnode[sec->nnode - 2]->fromparent.nd2 =
sec->pnode[sec->nnode - 3];
}else{
sec->pnode[sec->nnode - 2]->fromparent.nd2 =
sec->parentsec->pnode[sec->parentsec->nnode - 1];
}
}
}
