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Fix vecst mod for nrn90 compat #1

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merged 3 commits into from
May 27, 2022
Merged

Fix vecst mod for nrn90 compat #1

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99ae597
Fix vecst mod for nrn90 compat
ferdonline May 16, 2022
f5a98fb
other mod file changes for successfull compilation
pramodk May 18, 2022
1dded18
Cleanup for merge.
olupton May 20, 2022
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7 changes: 6 additions & 1 deletion README
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ III mswin pc.

target simulation shown in jnsci18_6444F6B.jpg

Changelog
---------

20120112 cad.mod and gababS.mod updated to use derivimplicit and cnexp
in place of euler and cadecay.mod switched to derivimplicit as per
http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592
Expand All @@ -29,4 +32,6 @@ be called with the same number of arguments with which the function is
declared. A net_send() call had a flag parameter added to it to
satisfy this. The results of the auto-launch demo simulation are
unchanged.


20220520: Updated MOD files to contain valid C++ and be compatible with
the upcoming versions 8.2 and 9.0 of NEURON.
7 changes: 6 additions & 1 deletion matrix.mod
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Expand Up @@ -34,6 +34,12 @@ PARAMETER {
MATRIX_INSTALLED=0
}

VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
extern double hoc_call_func(Symbol*, int narg);
#endif
ENDVERBATIM

:* mat.outprod(x,y) // mat = outer product of vectors x and y
VERBATIM
static double outprod(void* vv) {
Expand Down Expand Up @@ -84,7 +90,6 @@ VERBATIM
static double spltp(void* vv) {
int ii, jj, nstpr, nstpo, nw, npr, npo, flag, cnt;
double *stpr, *stpo, *w, *pr, *po;
extern double hoc_call_func(Symbol*, int narg);

char func[4] = "ltp";
Symbol* s = hoc_lookup(func);
Expand Down
8 changes: 7 additions & 1 deletion pointer.inc
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Expand Up @@ -13,9 +13,15 @@ ASSIGNED {
p
}

VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
extern Object** hoc_objgetarg(int);
#endif
ENDVERBATIM

PROCEDURE setptr() {
VERBATIM
{ extern Object** hoc_objgetarg();
{
p = (double)(unsigned long)*hoc_objgetarg(1);
}
ENDVERBATIM
Expand Down
8 changes: 5 additions & 3 deletions ppsav.inc
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Expand Up @@ -32,12 +32,14 @@ ASSIGNED {
}

VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
extern double* vector_vec();
extern int vector_capacity();
extern void* vector_arg();
extern double* hoc_pgetarg();
extern Object** hoc_objgetarg();
extern Object** hoc_objgetarg(int);
extern char* hoc_object_name(Object*);
#endif
double *a1, *a2, *a3;
Object *tvec, *tmpvec;
char str[100];
Expand All @@ -46,7 +48,7 @@ ENDVERBATIM
PROCEDURE recval () {
VERBATIM
{ void* vv; int i, size; double* px;
if (savnum==0) { return; }
if (savnum==0) { return 0; }
vv = *((void**)(&space0));
if (! vv) { hoc_execerror("ERR: no time vector defined for PP::recval.\n",0); }

Expand Down Expand Up @@ -85,7 +87,7 @@ VERBATIM
{
void** vv;

if (! ifarg(1)) { savnum=0; return;
if (! ifarg(1)) { savnum=0; return 0;
}

if (ifarg(3)) { /* nice place to save time */
Expand Down
61 changes: 33 additions & 28 deletions vecst.mod
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Expand Up @@ -77,16 +77,18 @@ ASSIGNED { RES }
VERBATIM
#include <stdlib.h>
#include <math.h>
/* #include <values.h> /* contains MAXLONG */
#include <limits.h> /* contains MAXLONG */
#include <sys/time.h>

#ifndef NRN_VERSION_GTEQ_8_2_0
extern double* hoc_pgetarg();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double hoc_epsilon;
#endif
ENDVERBATIM

:* v1.slope(num) does a linear regression to find the slope, assuming num=timestep of vector
Expand Down Expand Up @@ -335,7 +337,7 @@ static double fewind(void* vv) {
for (j=0;j<num;j++) {
for (i=0;i<ni;i++) x[i]=vvo[j][scr[i]];
for (i=0;i<ni;i++) vvo[j][i]=x[i];
vv=vector_arg(j+2); vector_resize(vv, ni);
vv=vector_arg(j+2); vector_resize((IvocVect*)vv, ni);
}
return ni;
}
Expand Down Expand Up @@ -364,8 +366,8 @@ static double findx(void* vv) {
for (i=0;i<num;i++) {
bv[i]=vector_arg_px(num+i+1, &bvo[i]); /* dest vectors */
vv=vector_arg(num+i+1);
if (vector_buffer_size(vv)<ni) {
printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size(vv));
if (vector_buffer_size((IvocVect*)vv)<ni) {
printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size((IvocVect*)vv));
hoc_execerror("Destination vector with insufficient size: ", 0); }
}
if (ni>scrsz) {
Expand All @@ -379,7 +381,7 @@ static double findx(void* vv) {
}
for (j=0,i=0;j<num;j++) { // j goes through vectors
vv=vector_arg(j+num+1);
vector_resize(vv, ni);
vector_resize((IvocVect*)vv, ni);
for (i=0;i<ni;i++) bvo[j][i]=avo[j][scr[i]];
}
return ni;
Expand Down Expand Up @@ -468,7 +470,7 @@ static double slct(void* vv) {
int i, j, k, m, n, ni, nk, na, nv[10], num, fl;
double *ind, *key, *arg, *vvo[10];
ni = vector_instance_px(vv, &ind); // vv is ind
for (i=0;ifarg(i);i++); i--; // drop back by one to get numarg()
for (i=0;ifarg(i);i++) {} i--; // drop back by one to get numarg()
if (i>12) hoc_execerror("ERR: vecst::slct can only handle 10 vectors", 0);
num = i-2; /* number of vectors to be picked apart */
for (i=0;i<num;i++) {
Expand Down Expand Up @@ -510,7 +512,7 @@ static double slct(void* vv) {
}
if (fl) ind[k++]=j; // all equal
}
vector_resize(vv, k);
vector_resize((IvocVect*)vv, k);
return k;
}
ENDVERBATIM
Expand All @@ -521,7 +523,7 @@ VERBATIM
static double iwr(void* vv) {
int i, j, nx;
double *x;
FILE* f, *hoc_obj_file_arg();
FILE* f;
f = hoc_obj_file_arg(1);
nx = vector_instance_px(vv, &x);
if (nx>scrsz) {
Expand All @@ -542,7 +544,7 @@ VERBATIM
static double ird(void* vv) {
int i, j, nx, n;
double *x;
FILE* f, *hoc_obj_file_arg();
FILE* f;
f = hoc_obj_file_arg(1);
nx = vector_instance_px(vv, &x);
fread(&n,sizeof(int),1,f); // size
Expand All @@ -552,9 +554,9 @@ static double ird(void* vv) {
scr=(int *)ecalloc(scrsz, sizeof(int));
}
if (n!=nx) {
nx=vector_buffer_size(vv);
nx=vector_buffer_size((IvocVect*)vv);
if (n<=nx) {
vector_resize(vv, n); nx=n;
vector_resize((IvocVect*)vv, n); nx=n;
} else {
printf("%d > %d :: ",n,nx);
hoc_execerror("Vector max capacity too small for ird ", 0);
Expand All @@ -573,15 +575,15 @@ static double insct(void* vv) {
int i, j, k, nx, nv1, nv2, maxsz;
double *x, *v1, *v2;
nx = vector_instance_px(vv, &x);
maxsz=vector_buffer_size(vv);
vector_resize(vv, maxsz);
maxsz=vector_buffer_size((IvocVect*)vv);
vector_resize((IvocVect*)vv, maxsz);
nv1 = vector_arg_px(1, &v1);
nv2 = vector_arg_px(2, &v2);
for (i=0,k=0;i<nv1;i++) for (j=0;j<nv2;j++) if (v1[i]==v2[j]) {
if (k<maxsz) { x[k++]=v1[i]; } else {k++;}} /* v1[i] found in both vectors */
if (k>maxsz) {
printf("\tinsct WARNING: ran out of room: %d<%d\n",maxsz,k);
} else { vector_resize(vv, k); }
} else { vector_resize((IvocVect*)vv, k); }
return (double)k;
}
ENDVERBATIM
Expand All @@ -593,8 +595,8 @@ static double cull(void* vv) {
int i, j, k, nx, nv1, nv2, maxsz, flag;
double *x, *v1, *v2;
nx = vector_instance_px(vv, &x);
maxsz=vector_buffer_size(vv);
vector_resize(vv, maxsz);
maxsz=vector_buffer_size((IvocVect*)vv);
vector_resize((IvocVect*)vv, maxsz);
nv1 = vector_arg_px(1, &v1);
nv2 = vector_arg_px(2, &v2);
for (i=0,k=0;i<nv1;i++) {
Expand All @@ -604,7 +606,7 @@ static double cull(void* vv) {
}
if (k>maxsz) {
printf("\tcull WARNING: ran out of room: %d<%d\n",maxsz,k);
} else { vector_resize(vv, k); }
} else { vector_resize((IvocVect*)vv, k); }
return (double)k;
}
ENDVERBATIM
Expand All @@ -617,14 +619,14 @@ static double redundout(void* vv) {
double *x, *v1, val;
if (ifarg(2)) indflag=1; else indflag=0;
nx = vector_instance_px(vv, &x);
maxsz=vector_buffer_size(vv);
vector_resize(vv, maxsz);
maxsz=vector_buffer_size((IvocVect*)vv);
vector_resize((IvocVect*)vv, maxsz);
nv1 = vector_arg_px(1, &v1);
val=v1[0]; x[0]=(indflag?0:val);
for (j=1,i=1;i<nv1&&j<maxsz;i++) if (v1[i]!=val) { val=v1[i]; x[j++]=(indflag?i:val); }
if (j==maxsz) {
printf("\tredundout WARNING: ran out of room: %d<needed\n",maxsz);
} else { vector_resize(vv, j); }
} else { vector_resize((IvocVect*)vv, j); }
return (double)j;
}
ENDVERBATIM
Expand All @@ -646,6 +648,7 @@ static double cvlv(void* vv) {
if (k>0 && k<nsrc-1) x[i]+=filt[j]*src[k];
}
}
return 0.;
}
ENDVERBATIM

Expand All @@ -665,6 +668,7 @@ static double intrp(void* vv) {
for (i=la+1; i<lb; i++) x[i]= a + (b-a)/(lb-la)*(i-la);
a=b; la=lb;
}
return 0.;
}
ENDVERBATIM

Expand Down Expand Up @@ -704,7 +708,7 @@ static double nind(void* vv) {
}
for (k=last+1;k<nx;k++,m++) { x[m]=vvo[j][k]; }
for (i=0;i<c;i++) vvo[j][i]=x[i];
vv=vector_arg(j+2); vector_resize(vv, c);
vv=vector_arg(j+2); vector_resize((IvocVect*)vv, c);
}
return c;
}
Expand All @@ -717,7 +721,7 @@ static double keyind(void* vv) {
int i, j, k, ni, nk, nv[10], num;
double *ind, *key, *vvo[10];
ni = vector_instance_px(vv, &ind); // vv is ind
for (i=0;ifarg(i);i++); i--; // drop back by one to get numarg()
for (i=0;ifarg(i);i++) {} i--; // drop back by one to get numarg()
if (i>10) hoc_execerror("ERR: keyind can only handle 9 vectors", 0);
num = i-1; /* number of vectors to be picked apart */
for (i=0;i<num;i++) {
Expand All @@ -739,7 +743,7 @@ static double keyind(void* vv) {
}
if (i==nk) ind[k++]=j; // all equal
}
vector_resize(vv, k);
vector_resize((IvocVect*)vv, k);
return k;
}
ENDVERBATIM
Expand Down Expand Up @@ -895,6 +899,7 @@ static double bpeval(void* vv) {
} else {
for (i=0;i<n;i++) vo[i]=outp[i]*(1.-1.*outp[i])*del[i];
}
return 0.;
}
ENDVERBATIM

Expand Down Expand Up @@ -968,8 +973,8 @@ static double xing(void* vv) {
nsrc = vector_arg_px(1, &src);
ntvec = vector_arg_px(2, &tvec);
th = *getarg(3);
maxsz=vector_buffer_size(vv);
vector_resize(vv, maxsz);
maxsz=vector_buffer_size((IvocVect*)vv);
vector_resize((IvocVect*)vv, maxsz);
if (nsrc!=ntvec) hoc_execerror("v.xing: vectors not all same size", 0);
for (i=0,f=0,j=0; i<nsrc; i++) {
if (src[i]>th) { /* ? passing thresh */
Expand All @@ -987,7 +992,7 @@ static double xing(void* vv) {
if (f==1) { f=0; } /* just passed going down */
}
}
vector_resize(vv, j);
vector_resize((IvocVect*)vv, j);
return (double)i;
}
ENDVERBATIM
Expand Down Expand Up @@ -1180,9 +1185,9 @@ static double smgs(void* vv) {

points = (int)((high-low)/step+hoc_epsilon);
if (nsum!=points) {
maxsz=vector_buffer_size(vv);
maxsz=vector_buffer_size((IvocVect*)vv);
if (points<=maxsz) {
vector_resize(vv, nsum); nsum=points;
vector_resize((IvocVect*)vv, nsum); nsum=points;
} else {
printf("%d > %d :: ",points,maxsz);
hoc_execerror("Vector max capacity too small in smgs ", 0);
Expand Down