From 144784496550cccc927607be8edc487af7aa851f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 24 Mar 2014 08:53:44 +0000
Subject: [PATCH] Fix.
---
src/io.c | 728 +++++++++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 666 insertions(+), 62 deletions(-)
diff --git a/src/io.c b/src/io.c
index 4db7f56..17adda4 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,6 +11,547 @@
#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, ts_uint iteration){
+
+ /* save current state with wrong pointers. Will fix that later */
+ ts_uint i,j,k;
+ FILE *fh=fopen("dump.bin","wb");
+
+ /* dump vesicle */
+ fwrite(vesicle, sizeof(ts_vesicle),1,fh);
+ /* dump vertex list */
+ fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
+ /* dump bond list */
+ fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* dump triangle list */
+ fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* dump cell list */
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* dump poly list */
+ fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* dump filament list */
+ fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+ /*dump vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
+ fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
+ /* dump pointer offsets for:
+ neigh
+ bond
+ tria
+ cell is ignored
+ */
+ for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),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(&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 */
+ 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++){
+ fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),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*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ 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(&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(&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(&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);
+ }
+ }
+
+
+ /*dump filamentes grandes svinjas */
+ for(i=0;i<vesicle->filament_list->n;i++){
+ fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ }
+
+ /* dump filamentes vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->filament_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(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(k=0;k<vesicle->filament_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(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->filament_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(&vesicle->filament_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->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+
+
+/* pointer offsets for fixing the restored pointers */
+/* need pointers for
+ vlist->vtx
+ blist->bond
+ tlist->tria
+ clist->cell
+ poly_list->poly
+ and for each poly:
+ poly_list->poly->vtx
+ poly_list->poly->bond
+*/
+
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+
+ fwrite(&iteration, sizeof(ts_uint),1,fh);
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
+/** RESTORE DUMP FROM DISK **/
+ts_vesicle *restore_state(ts_uint *iteration){
+ ts_uint i,j,k;
+ FILE *fh=fopen("dump.bin","rb");
+
+ struct stat sb;
+ if (stat("dump.bin", &sb) == -1) {
+ //dump file does not exist.
+ return NULL;
+ }
+
+ //check if it is regular file
+ if((sb.st_mode & S_IFMT) != S_IFREG) {
+ //dump file is not a regular file.
+ ts_fprintf(stderr,"Dump file is not a regular file!\n");
+ return NULL;
+ }
+
+ ts_uint retval;
+ 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(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);
+ /* restore bond list */
+ vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
+ retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* restore triangle list */
+ vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
+ retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* restore cell list */
+ vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* restore poly list */
+ vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* restore filament list */
+ vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+/* 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++){
+ 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(&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(&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(&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 *)); // done before.
+ for(i=0;i<vesicle->blist->n;i++){
+ // 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(&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 *)); // done before
+ for(i=0;i<vesicle->tlist->n;i++){
+ // 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(&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(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
+ }
+
+ }
+
+ /*restore cells */
+/*TODO: do we need to recalculate cells here? */
+/* vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
+ for(i=0;i<vesicle->clist->cellno;i++){
+ vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
+ retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
+ }
+*/
+ /*restore polymeres */
+ vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
+ 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++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ 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(&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(&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++){
+ 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));
+ retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ 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];
+ }
+ }
+
+ /*restore filaments */
+ vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+
+ }
+
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
+ }
+
+ }
+ }
+
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ }
+
+// 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!
+ }
+
+ retval=fread(iteration,sizeof(ts_uint),1,fh);
+ if(retval);
+ fclose(fh);
+ return vesicle;
+}
+
+
+
+ts_bool parse_args(int argc, char **argv){
+ int c, retval;
+ struct stat sb;
+ sprintf(command_line_args.path, "./"); //clear string;
+ sprintf(command_line_args.output_fullfilename,"./output.pvd");
+ sprintf(command_line_args.dump_fullfilename,"./dump.bin");
+ sprintf(command_line_args.tape_fullfilename,"./tape");
+ FILE *file;
+
+while (1)
+ {
+ static struct option long_options[] =
+ {
+ {"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
+ {"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
+ {"tape", no_argument, 0, 't'},
+ {"output-file", required_argument, 0, 'o'},
+ {"directory", required_argument, 0, 'd'},
+ {"dump-filename", 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:f:o:t:",
+ 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.
+ if (stat(optarg, &sb) == -1) {
+ ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
+ fatal("Please select correct tape",1);
+ } else {
+ strcpy(command_line_args.tape_fullfilename,optarg);
+ }
+ break;
+
+ case 'o':
+ //set filename of master output file
+ if ((file = fopen(optarg, "w")) == NULL) {
+ fprintf(stderr,"Could not create output file!\n");
+ fatal("Please specify correct output file",1);
+
+ } else {
+ fclose(file);
+ }
+ strcpy(command_line_args.output_fullfilename, 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);
+ if (stat(optarg, &sb) == -1) {
+ //directory does not exist
+ retval=mkdir(optarg, 0700);
+ if(retval){
+ fatal("Could not create requested directory. Check if you have permissions",1);
+ }
+ }
+ //check if is a proper directory
+ else if((sb.st_mode & S_IFMT) != S_IFDIR) {
+ //it is not a directory. fatal error.
+ ts_fprintf(stderr,"%s is not a directory!\n",optarg);
+ fatal("Cannot continue",1);
+ }
+ strcpy(command_line_args.path, optarg);
+ break;
+
+ case 'f':
+ //check if dump file specified exists. Defaults to dump.bin
+ if ((file = fopen(optarg, "w")) == NULL) {
+ fprintf(stderr,"Could not create dump file!\n");
+ fatal("Please specify correct dump file",1);
+
+ } else {
+ fclose(file);
+ }
+ strcpy(command_line_args.dump_fullfilename, optarg);
+ 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;
+
+}
+
+
+
+
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
printf("Number of vertices: %u\n",vlist->n);
@@ -108,11 +649,11 @@
fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ for(j=0;j<vlist->vtx[i]->bond_no;j++){
fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
}
fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ for(j=0;j<vlist->vtx[i]->bond_no;j++){
fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
@@ -220,8 +761,8 @@
/* Here comes header of the file */
//find number of extra vtxs and bonds of polymeres
- ts_uint monono=0, polyno=0;
- ts_bool poly=0;
+ ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
+ ts_bool poly=0, fil=0;
if(vesicle->poly_list!=NULL){
if(vesicle->poly_list->poly[0]!=NULL){
polyno=vesicle->poly_list->n;
@@ -229,17 +770,37 @@
poly=1;
}
}
+
+ if(vesicle->filament_list!=NULL){
+ if(vesicle->filament_list->poly[0]!=NULL){
+ filno=vesicle->filament_list->n;
+ fonono=vesicle->filament_list->poly[0]->vlist->n;
+ fil=1;
+ }
+ }
+
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
//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);
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
+ fprintf(fh,"%u ", poly_idx);
}
}
}
@@ -256,6 +817,14 @@
}
}
}
+ //filaments
+ if(fil){
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
+ }
fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
for(i=0;i<blist->n;i++){
@@ -263,24 +832,38 @@
}
//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);
}
}
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
+// fprintf(stderr,"was here\n");
+
+ }
+ }
+
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno;i++){
+ for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
fprintf(fh,"3 ");
}
@@ -335,79 +918,100 @@
-ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // THIS IS DUE TO CONFUSE BUG!
- char *buf=malloc(255*sizeof(char));
- long int brezveze0=1;
+ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
+ FILE *fh;
+ ts_uint i;
+
+ fh=fopen(filename, "w");
+ if(fh==NULL){
+ err("Cannot open file %s for writing");
+ return TS_FAIL;
+ }
+
+ for(i=0;i<vesicle->tlist->n;i++){
+
+ fprintf(fh,"\ttriangle {");
+ fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
+ vesicle->tlist->tria[i]->vertex[0]->x,
+ vesicle->tlist->tria[i]->vertex[0]->y,
+ vesicle->tlist->tria[i]->vertex[0]->z,
+
+ vesicle->tlist->tria[i]->vertex[1]->x,
+ vesicle->tlist->tria[i]->vertex[1]->y,
+ vesicle->tlist->tria[i]->vertex[1]->z,
+
+ vesicle->tlist->tria[i]->vertex[2]->x,
+ vesicle->tlist->tria[i]->vertex[2]->y,
+ vesicle->tlist->tria[i]->vertex[2]->z
+ );
+ }
+
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
+ts_tape *parsetape(char *filename){
+ // long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
+ ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
+ tape->multiprocessing=calloc(255,sizeof(char));
+ /* long int brezveze0=1;
long int brezveze1=1;
long int brezveze2=1;
ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
long int iter=1000, init=1000, mcsw=1000;
-
+*/
cfg_opt_t opts[] = {
- CFG_SIMPLE_INT("nshell", &nshell),
- CFG_SIMPLE_INT("npoly", &npoly),
- CFG_SIMPLE_INT("nmono", &nmono),
- CFG_SIMPLE_FLOAT("dmax", &dmax),
- CFG_SIMPLE_FLOAT("xk0",&xk0),
- CFG_SIMPLE_FLOAT("pressure",&pressure),
- CFG_SIMPLE_FLOAT("k_spring",&kspring),
- CFG_SIMPLE_FLOAT("stepsize",&stepsize),
- CFG_SIMPLE_INT("nxmax", &ncxmax),
- CFG_SIMPLE_INT("nymax", &ncymax),
- CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",&iter),
- CFG_SIMPLE_INT("mcsweeps",&mcsw),
- CFG_SIMPLE_INT("inititer", &init),
- CFG_SIMPLE_BOOL("quiet",&quiet),
- CFG_SIMPLE_STR("multiprocessing",buf),
- CFG_SIMPLE_INT("smp_cores",&brezveze0),
- CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
- CFG_SIMPLE_INT("distributed_processes",&brezveze2),
+ CFG_SIMPLE_INT("nshell", &tape->nshell),
+ CFG_SIMPLE_INT("npoly", &tape->npoly),
+ CFG_SIMPLE_INT("nmono", &tape->nmono),
+ CFG_SIMPLE_INT("nfil",&tape->nfil),
+ CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
+ CFG_SIMPLE_INT("pswitch",&tape->pswitch),
+ CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
+ CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
+ CFG_SIMPLE_FLOAT("xi",&tape->xi),
+ CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
+ CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
+ CFG_SIMPLE_INT("nymax", &tape->ncymax),
+ CFG_SIMPLE_INT("nzmax", &tape->nczmax),
+ CFG_SIMPLE_INT("iterations",&tape->iterations),
+ CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
+ CFG_SIMPLE_INT("inititer", &tape->inititer),
+ CFG_SIMPLE_BOOL("quiet",&tape->quiet),
+ CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
+ CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape");
+ retval=cfg_parse(cfg, filename);
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
- ts_vesicle *vesicle;
- *iterations=iter;
- *inititer=init;
- *mcsweeps=mcsw;
- vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
- vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
- vesicle->spring_constant=kspring;
- poly_assign_spring_const(vesicle);
-
-
- vesicle->nshell=nshell;
- vesicle->dmax=dmax*dmax;
- vesicle->bending_rigidity=xk0;
- vtx_set_global_values(vesicle); //copies xk0 to every vertex
-
-
- vesicle->stepsize=stepsize;
- vesicle->clist->ncmax[0]=ncxmax;
- vesicle->clist->ncmax[1]=ncymax;
- vesicle->clist->ncmax[2]=nczmax;
- vesicle->clist->max_occupancy=8;
- vesicle->pressure=pressure/vesicle->bending_rigidity; //all energy contributions need to be divided by bending_rigidity!
cfg_free(cfg);
- free(buf);
- // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
-
- return vesicle;
+ /* global variables are set automatically */
+ quiet=tape->quiet;
+ return tape;
+}
+ts_bool tape_free(ts_tape *tape){
+ free(tape->multiprocessing);
+ free(tape);
+ return TS_SUCCESS;
}
--
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