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Fixes for new data structures #4

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Apr 30, 2023
Merged

Fixes for new data structures #4

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53 changes: 30 additions & 23 deletions Na12 Analysis/mechanisms/branching.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,13 @@ VERBATIM
#ifndef _NrnThread
#define _NrnThread NrnThread
#endif
#ifdef NRN_MECHANISM_DATA_IS_SOA
#define get_nnode(sec) _nrn_mechanism_get_nnode(sec)
#define get_node(sec, node_index) _nrn_mechanism_get_node(sec, node_index)
#else
#define get_nnode(sec) sec->nnode
#define get_node(sec, node_index) sec->pnode[node_index]
#endif
ENDVERBATIM
PROCEDURE init_files(){
VERBATIM {
Expand All @@ -30,13 +37,13 @@ Section* sec;
Node* nd;
sec = chk_access();
if (_lx < 0. || _lx > 1.) {
//printf("_lx is %f and _lx*(double)(sec->nnode-1) is %f\n",_lx,_lx*(double)(sec->nnode-1));
//printf("_lx is %f and _lx*(double)(get_nnode(sec)-1) is %f\n",_lx,_lx*(double)(get_nnode(sec)-1));
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
return NODEA(nd);
}
Expand All @@ -51,13 +58,13 @@ Section* sec;
Node* nd;
sec = chk_access();
if (_lx < 0. || _lx > 1.) {
//printf("_lx is %f and _lx*(double)(sec->nnode-1) is %f\n",_lx,_lx*(double)(sec->nnode-1));
//printf("_lx is %f and _lx*(double)(get_nnode(sec)-1) is %f\n",_lx,_lx*(double)(get_nnode(sec)-1));
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec) - 1)));
}
return NODEB(nd);
}
Expand All @@ -75,9 +82,9 @@ Section* sec;
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
//printf("index is %d,NODEA(nd) is %f _la is %f\n",nd->v_node_index,NODEA(nd),_la);
NODEA(nd) = _la;
Expand All @@ -96,9 +103,9 @@ Section* sec;
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
//printf("index is %d,NODEB(nd) is %f _lb is %f\n",nd->v_node_index,NODEB(nd),_lb);
NODEB(nd) = _lb;
Expand All @@ -124,19 +131,19 @@ fclose(fm);
}
ENDVERBATIM
}
PROCEDURE MyAdb() {
VERBATIM {
int ii;
#if defined(t)
_NrnThread* _nt = nrn_threads;
#endif
for(ii=0;ii<_nt->end;ii++){

printf("%d,%1.15f %1.15f %1.15f %1.15f\n",ii, _nt->_actual_a[ii],_nt->_actual_d[ii],_nt->_actual_b[ii],_nt->_actual_rhs[ii]);
}
}
ENDVERBATIM
}
:PROCEDURE MyAdb() {
:VERBATIM {
: int ii;
:#if defined(t)
: _NrnThread* _nt = nrn_threads;
:#endif
:for(ii=0;ii<_nt->end;ii++){
:
:printf("%d,%1.15f %1.15f %1.15f %1.15f\n",ii, _nt->_actual_a[ii],_nt->_actual_d[ii],_nt->_actual_b[ii],_nt->_actual_rhs[ii]);
:}
:}
:ENDVERBATIM
:}

PROCEDURE PrintRHS_D() {
VERBATIM {
Expand Down
1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,3 +20,4 @@ For additional information, please contact [email protected] or henry.kyoung@uc

## Changelog
2023-02-28: updated for C++ compatibility (NEURON 9+)
2023-04-20: updated for SoA data compatibility (NEURON 9+)
59 changes: 34 additions & 25 deletions Ri Increase/mechanisms/branching.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,16 @@ ENDCOMMENT
NEURON { SUFFIX nothing }

VERBATIM

#ifndef _NrnThread
#define _NrnThread NrnThread
#endif
#ifdef NRN_MECHANISM_DATA_IS_SOA
#define get_nnode(sec) _nrn_mechanism_get_nnode(sec)
#define get_node(sec, node_index) _nrn_mechanism_get_node(sec, node_index)
#else
#define get_nnode(sec) sec->nnode
#define get_node(sec, node_index) sec->pnode[node_index]
#endif
ENDVERBATIM
PROCEDURE init_files(){
VERBATIM {
Expand All @@ -28,13 +37,13 @@ Section* sec;
Node* nd;
sec = chk_access();
if (_lx < 0. || _lx > 1.) {
//printf("_lx is %f and _lx*(double)(sec->nnode-1) is %f\n",_lx,_lx*(double)(sec->nnode-1));
//printf("_lx is %f and _lx*(double)(get_nnode(sec)-1) is %f\n",_lx,_lx*(double)(get_nnode(sec)-1));
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
return NODEA(nd);
}
Expand All @@ -49,13 +58,13 @@ Section* sec;
Node* nd;
sec = chk_access();
if (_lx < 0. || _lx > 1.) {
//printf("_lx is %f and _lx*(double)(sec->nnode-1) is %f\n",_lx,_lx*(double)(sec->nnode-1));
//printf("_lx is %f and _lx*(double)(get_nnode(sec)-1) is %f\n",_lx,_lx*(double)(get_nnode(sec)-1));
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec) - 1)));
}
return NODEB(nd);
}
Expand All @@ -73,9 +82,9 @@ Section* sec;
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
//printf("index is %d,NODEA(nd) is %f _la is %f\n",nd->v_node_index,NODEA(nd),_la);
NODEA(nd) = _la;
Expand All @@ -94,9 +103,9 @@ Section* sec;
hoc_execerror("out of range, must be 0 < x <= 1", (char*)0);
}
if (_lx == 1.) {
nd = sec->pnode[sec->nnode-1];
nd = get_node(sec, get_nnode(sec) - 1);
}else{
nd = sec->pnode[(int) (_lx*(double)(sec->nnode-1))];
nd = get_node(sec, (int) (_lx*(double)(get_nnode(sec)-1)));
}
//printf("index is %d,NODEB(nd) is %f _lb is %f\n",nd->v_node_index,NODEB(nd),_lb);
NODEB(nd) = _lb;
Expand All @@ -122,19 +131,19 @@ fclose(fm);
}
ENDVERBATIM
}
PROCEDURE MyAdb() {
VERBATIM {
int ii;
#if defined(t)
_NrnThread* _nt = nrn_threads;
#endif
for(ii=0;ii<_nt->end;ii++){

printf("%d,%1.15f %1.15f %1.15f %1.15f\n",ii, _nt->_actual_a[ii],_nt->_actual_d[ii],_nt->_actual_b[ii],_nt->_actual_rhs[ii]);
}
}
ENDVERBATIM
}
:PROCEDURE MyAdb() {
:VERBATIM {
: int ii;
:#if defined(t)
: _NrnThread* _nt = nrn_threads;
:#endif
:for(ii=0;ii<_nt->end;ii++){
:
:printf("%d,%1.15f %1.15f %1.15f %1.15f\n",ii, _nt->_actual_a[ii],_nt->_actual_d[ii],_nt->_actual_b[ii],_nt->_actual_rhs[ii]);
:}
:}
:ENDVERBATIM
:}

PROCEDURE PrintRHS_D() {
VERBATIM {
Expand Down Expand Up @@ -235,4 +244,4 @@ fprintf(fm,"%d %1.15f %1.15f %1.15f %1.15f\n", ii, NODEB(nd), NODEA(nd), NODED(n
fclose (fm);
}
ENDVERBATIM
}
}