From 083e03adeaf985c9da1ed31d259ced9bb54c207c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 06 Mar 2014 14:18:21 +0000
Subject: [PATCH] Started with arg parsing
---
src/io.c | 349 ++++++++++++++++++++++++++++++++++++---------------------
1 files changed, 221 insertions(+), 128 deletions(-)
diff --git a/src/io.c b/src/io.c
index 8ebfb97..aeda240 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,19 +11,21 @@
#include "initial_distribution.h"
#include "poly.h"
-
-
+#include <getopt.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <errno.h>
/** DUMP STATE TO DISK DRIVE **/
ts_bool dump_state(ts_vesicle *vesicle){
/* save current state with wrong pointers. Will fix that later */
ts_uint i,j,k;
- ts_ulong off;
FILE *fh=fopen("dump.bin","wb");
/* dump vesicle */
- fwrite(vesicle, sizeof(vesicle),1,fh);
+ fwrite(vesicle, sizeof(ts_vesicle),1,fh);
/* dump vertex list */
fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
/* dump bond list */
@@ -46,64 +48,45 @@
cell is ignored
*/
for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
- off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
}
for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
- off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
}
for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
}
-// off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
-// fwrite(&off,sizeof(ts_ulong),1,fh);
-
}
/*dump bonds*/
for(i=0;i<vesicle->blist->n;i++){
fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
/* dump pointer offsets for vtx1 and vtx2 */
- off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
- off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ //off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
+ fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
+ //off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
+ fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
}
/*dump triangles*/
for(i=0;i<vesicle->tlist->n;i++){
fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
/* dump pointer offsets for vertex */
- off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
- off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
- off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
/* dump pointer offsets for neigh */
for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
- off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
}
}
-
- /*dump cells and its contents is not dumped but recalculated on restore*/
-
-/* for(i=0;i<vesicle->clist->cellno;i++){
- fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
- for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
- off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
- }
- }
-*/
/*dump polymeres */
for(i=0;i<vesicle->poly_list->n;i++){
fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
}
/* dump poly vertex(monomer) list*/
@@ -112,24 +95,26 @@
fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
/* dump offset for neigh and bond */
for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
- off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
}
for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
- off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
+ fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
}
}
+ // grafted vtx on vesicle data dump
+ fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
}
/* dump poly bonds between monomers list*/
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
/* dump vtx1 and vtx2 offsets */
- off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
- off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
- fwrite(&off,sizeof(ts_ulong),1,fh);
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
+// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
}
}
@@ -145,15 +130,8 @@
poly_list->poly->bond
*/
- fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
- fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
- fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
- fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
- fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
- for(i=0;i<vesicle->poly_list->n;i++){
- fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
- fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
- }
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+
fclose(fh);
return TS_SUCCESS;
}
@@ -164,12 +142,14 @@
ts_uint i,j,k;
FILE *fh=fopen("dump.bin","rb");
ts_uint retval;
- ts_ulong off;
+ ts_uint idx;
/* we restore all the data from the dump */
/* restore vesicle */
ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
- retval=fread(vesicle, sizeof(vesicle),1,fh);
+ retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
+// fprintf(stderr,"was here! %e\n",vesicle->dmax);
+
/* restore vertex list */
vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
@@ -187,59 +167,75 @@
retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
- /*restore vertices*/
+/* prerequisity. Bonds must be malloced before vertexes are recreated */
+ vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
+ for(i=0;i<vesicle->blist->n;i++){
+ vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+/* prerequisity. Triangles must be malloced before vertexes are recreated */
+ vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
+ for(i=0;i<vesicle->tlist->n;i++){
+ vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
+}
+/* prerequisity. Vertices must be malloced before vertexes are recreated */
vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
- for(i=0;i<vesicle->vlist->n;i++){
+ for(i=0;i<vesicle->vlist->n;i++){
vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ /*restore vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
/*restore neigh, bond, tristar. Ignoring cell */
vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
}
vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
+ vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
}
vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+/* same comment as above */
+ vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
}
}
/*restore bonds*/
- vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
+ // vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
for(i=0;i<vesicle->blist->n;i++){
- vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
+ // vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
/* restore vtx1 and vtx2 */
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
}
/*restore triangles*/
- vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
+// vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
for(i=0;i<vesicle->tlist->n;i++){
- vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
+ // vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
/* restore pointers for vertices */
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
/* restore pointers for neigh */
+ vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
}
}
@@ -257,79 +253,173 @@
for(i=0;i<vesicle->poly_list->n;i++){
vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+
}
+
/* restore poly vertex(monomer) list*/
for(i=0;i<vesicle->poly_list->n;i++){
- vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
-
+
/* restore neigh and bonds */
vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
}
vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
}
}
+ /* restore grafted vtx on vesicle and grafted_poly */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
+ vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
}
+
/* restore poly bonds between monomers list*/
for(i=0;i<vesicle->poly_list->n;i++){
- vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
- vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
/* restore vtx1 and vtx2 */
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
- retval=fread(&off,sizeof(ts_ulong),1,fh);
- vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
}
}
-
- /* recalculate pointers using saved information on pointer addresses */
- /* following pointers need to be recalculated:
- all vtx->neigh
- all vtx->tristar
- all vtx->bond
- vtx->cell
- vtx->grafted_poly
- bond->vtx1
- bond->vtx2
- tria->vertex[*]
- tria->neigh
- cell->vertex
- poly->grafted_vtx
- poly->vlist->vtx->neigh
- poly->vlist->vtx->bond
- poly->vlist->vtx->cell
- */
-
- /* read pointers from disk */
-/* fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
- fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
- fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
- fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
- fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
- for(i=0;i<vesicle->poly_list->n;i++){
- fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
- fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
- }
-*/
-
+// recreating space for cells //
+ vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
+ vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
+ for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
+ vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
+ vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
+ }
if(retval);
fclose(fh);
return vesicle;
}
+
+
+
+ts_bool parse_args(int argc, char **argv){
+ int c, retval;
+ DIR *dir;
+ path[0]=0;
+while (1)
+ {
+ static struct option long_options[] =
+ {
+ {"force-from-tape", no_argument, &force_from_tape, 1},
+ {"tape", no_argument, 0, 't'},
+ {"output-file", required_argument, 0, 'o'},
+ {"directory", required_argument, 0, 'd'},
+ {"dump-file", required_argument,0, 'f'},
+ {0, 0, 0, 0}
+ };
+ /* getopt_long stores the option index here. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:fot",
+ long_options, &option_index);
+
+ /* Detect the end of the options. */
+ if (c == -1)
+ break;
+
+ switch (c)
+ {
+ case 0:
+ /* If this option set a flag, do nothing else now. */
+ if (long_options[option_index].flag != 0)
+ break;
+ printf ("option %s", long_options[option_index].name);
+ if (optarg)
+ printf (" with arg %s", optarg);
+ printf ("\n");
+ break;
+
+ case 't':
+ //check if tape exists. If not, fail immediately.
+ puts ("option -t\n");
+ break;
+
+ case 'o':
+ //set filename of master output file
+ printf ("option -o with value `%s'\n", optarg);
+ break;
+
+ case 'd':
+ //check if directory exists. If not create one. If creation is
+ //successful, set directory for output files.
+ //printf ("option -d with value `%s'\n", optarg);
+ dir = opendir(optarg);
+ if (dir)
+ {
+ /* Directory exists. */
+ closedir(dir);
+ }
+ else if (ENOENT == errno)
+ {
+ /* Directory does not exist. */
+ retval=mkdir(optarg, 0700);
+ if(retval){
+ fatal("Could not create requested directory. Check if you have permissions",1);
+ }
+ }
+ else
+ {
+ /* opendir() failed for some other reason. */
+ fatal("Could not check if directory exists. Reason unknown",1);
+ }
+ ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
+// sprintf(path,"%s", optarg);
+ strcpy(path, optarg);
+ // ts_fprintf(stdout,"ok!\n");
+
+ break;
+
+ case 'f':
+ //check if dump file specified exists. Defaults to dump.bin
+ break;
+
+ case '?':
+ /* getopt_long already printed an error message. */
+
+ ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
+ fatal("Ooops, read help first",1);
+ break;
+
+ default:
+ exit (1);
+ }
+ }
+
+ return TS_SUCCESS;
+
+}
+
@@ -542,7 +632,7 @@
/* Here comes header of the file */
//find number of extra vtxs and bonds of polymeres
- ts_uint monono=0, polyno=0;
+ ts_uint monono=0, polyno=0, poly_idx=0;
ts_bool poly=0;
if(vesicle->poly_list!=NULL){
if(vesicle->poly_list->poly[0]!=NULL){
@@ -559,9 +649,10 @@
}
//polymeres
if(poly){
+ poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%u ", poly_idx);
}
}
}
@@ -585,12 +676,14 @@
}
//polymeres
if(poly){
+ poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
- fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
+// fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
}
//grafted bonds
- fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
}
}
--
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