From 80ebbe388f3e945e62f47b0141c660ee6f05c8fc Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 17 Oct 2019 17:06:50 +0000
Subject: [PATCH] have some kind of memory allocation error :(
---
src/io.c | 777 +++--------------------------------------------------------
1 files changed, 42 insertions(+), 735 deletions(-)
diff --git a/src/io.c b/src/io.c
index 83bb26d..a2b50d9 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,4 +1,3 @@
-
/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
@@ -18,421 +17,6 @@
#include <dirent.h>
#include <errno.h>
#include <snapshot.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(command_line_args.dump_fullfilename,"wb");
-
- /* dump vesicle */
- fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),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);
-/* write tape information on vesicle */
-// fwrite(vesicle->tape,sizeof(ts_tape),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(command_line_args.dump_fullfilename,"rb");
-
- struct stat sb;
- if (stat(command_line_args.dump_fullfilename, &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)-sizeof(ts_double),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];
- }
- }
- vesicle->tape=parsetape(command_line_args.tape_fullfilename);
-// recreating space for cells //
- vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
- vesicle->clist->max_occupancy=16;
-// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
-// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
- retval=fread(iteration,sizeof(ts_uint),1,fh);
- if(retval);
- fclose(fh);
- return vesicle;
-}
-
ts_bool parse_args(int argc, char **argv){
@@ -627,206 +211,12 @@
return TS_SUCCESS;
}
-
-
-ts_bool print_vertex_list(ts_vertex_list *vlist){
- ts_uint i;
- printf("Number of vertices: %u\n",vlist->n);
- for(i=0;i<vlist->n;i++){
- printf("%u: %f %f %f\n",
-vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
- }
- return TS_SUCCESS;
-}
-
-ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
- ts_uint i,j;
- ts_vertex **vtx=vlist->vtx;
- printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
- for(i=0;i<vlist->n;i++){
- printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
- for(j=0;j<vtx[i]->neigh_no;j++){
- printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
-vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
- }
- printf("\n");
- }
-
-return TS_SUCCESS;
-}
-
-ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
- ts_vertex **vtx=vlist->vtx;
- ts_uint i;
- FILE *fh;
-
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
-
- fclose(fh);
-return TS_SUCCESS;
-}
-
-
-ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
- ts_uint i,j;
- for(i=0;i<vlist->n;i++){
- fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
- vlist->vtx[i]->y, vlist->vtx[i]->z,
- vlist->vtx[i]->neigh_no);
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
- //-vlist->vtx+1));
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
- ts_uint i,j;
- for(i=0;i<vesicle->vlist->n;i++){
- fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
- for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
- ts_triangle_list *tlist=vesicle->tlist;
- ts_uint i,j;
- for(i=0;i<tlist->n;i++){
- fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
- for(j=0;j<tlist->tria[i]->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
- }
- fprintf(fh,"\n");
- for(j=0;j<3;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
- }
- fprintf(fh,"\n");
- fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
-tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
- fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_vertex_data(FILE *fh,ts_vertex_list *vlist){
- ts_uint i,j;
- for(i=0;i<vlist->n;i++){
- 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]->bond_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
- }
- fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->bond_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
- ts_uint i;
- for(i=0;i<vesicle->blist->n;i++){
- fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
-//-vesicle->vlist->vtx+1),
- (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
- //-vesicle->vlist.vtx+1));
- }
- return TS_SUCCESS;
-}
-
-
-ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
- FILE *fh;
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
- fprint_vertex_list(fh,vesicle->vlist);
- fprint_tristar(fh,vesicle);
- fprint_triangle_list(fh,vesicle);
- fprint_vertex_data(fh,vesicle->vlist);
- fprint_bonds(fh,vesicle);
- fclose(fh);
- return TS_SUCCESS;
-}
-
-ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
- FILE *fh;
- char line[255];
- fh=fopen(filename, "r");
- if(fh==NULL){
- err("Cannot open file for reading... Nonexistant file?");
- return TS_FAIL;
- }
- ts_uint retval=1;
- while(retval!=EOF){
- retval=fscanf(fh,"%s",line);
-
- fprintf(stderr,"%s",line);
- }
- fclose(fh);
- return TS_SUCCESS;
-}
-
-ts_bool write_master_xml_file(ts_char *filename){
- FILE *fh;
- ts_char *i,*j;
- ts_uint tstep;
- ts_char *number;
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
-
- fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
- DIR *dir = opendir(command_line_args.path);
- if(dir){
- struct dirent *ent;
- tstep=0;
- while((ent = readdir(dir)) != NULL)
- {
- i=rindex(ent->d_name,'.');
- if(i==NULL) continue;
- if(strcmp(i+1,"vtu")==0){
- j=rindex(ent->d_name,'_');
- if(j==NULL) continue;
- number=strndup(j+1,j-i);
- fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
- tstep++;
- free(number);
- }
- }
- }
- free(dir);
- fprintf(fh,"</Collection>\n</VTKFile>\n");
- fclose(fh);
- return TS_SUCCESS;
-}
-
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno, ts_cluster_list *cstlist){
ts_vertex_list *vlist=vesicle->vlist;
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
- ts_double senergy=0.0;
+ //ts_double senergy=0.0;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -864,17 +254,23 @@
xml_trisurf_data(fh,vesicle);
fprintf(fh, " <UnstructuredGrid>\n");
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
- fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
+ fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"binary\">");
+ int *int_vector=(int *)malloc(vlist->n+monono*polyno+fonono*filno*sizeof(ts_uint));
+ int offset=0;
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%u ",vtx[i]->idx);
+ // fprintf(fh,"%u ",vtx[i]->idx);
+ int_vector[i+offset]=vtx[i]->idx;
}
//polymeres
if(poly){
poly_idx=vlist->n;
+ offset=offset+i;
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"%u ", poly_idx);
+ //fprintf(fh,"%u ", poly_idx);
+ int_vector[j+offset]=poly_idx;
}
+ offset=offset+j;
}
}
//filaments
@@ -883,10 +279,15 @@
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);
+ //fprintf(fh,"%u ", poly_idx);
+ int_vector[j+offset]=poly_idx;
}
+ offset=offset+j;
}
}
+ char *printout=ts_compress_intlist(int_vector,vlist->n+monono*polyno+fonono*filno*sizeof(ts_uint));
+ fprintf(fh,"%s",printout);
+ free(printout);
fprintf(fh,"</DataArray>\n");
if(cstlist!=NULL){
@@ -974,39 +375,27 @@
}
}
fprintf(fh,"</DataArray>\n");
+
+
+ fprintf(fh,"</PointData>\n<CellData>\n");
+
if(vesicle->tape->stretchswitch==1){
fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
- senergy=0.0;
- for(j=0;j<vtx[i]->tristar_no;j++){
- senergy+=vtx[i]->tristar[j]->energy;
- }
- fprintf(fh,"%.17e ",senergy);
+ for(i=0;i<blist->n;i++){
+ fprintf(fh, "0.0 ");
}
- //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++,poly_idx++){
- fprintf(fh,"%.17e ", 0.0);
- }
- }
- }
- //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,"%.17e ", 0.0);
- }
- }
- }
+ for(i=0;i<monono*polyno+filno*(fonono-1);i++){
+ fprintf(fh,"0.0 ");
+ }
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
+ }
fprintf(fh,"</DataArray>\n");
}
-
- fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
+
+
+ fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
@@ -1080,51 +469,6 @@
return TS_SUCCESS;
}
-
-ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
- ts_vertex_list *vlist=vesicle->vlist;
- ts_bond_list *blist=vesicle->blist;
- ts_vertex **vtx=vlist->vtx;
- ts_uint i;
- FILE *fh;
-
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- /* Here comes header of the file */
-// fprintf(stderr,"NSHELL=%u\n",nshell);
- fprintf(fh, "# vtk DataFile Version 2.0\n");
- /* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
- fprintf(fh, "%s\n", text);
- fprintf(fh,"ASCII\n");
- fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
- fprintf(fh,"POINTS %u double\n", vlist->n);
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
- }
-
- fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
- for(i=0;i<blist->n;i++){
- fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
- }
- fprintf(fh,"CELL_TYPES %u\n",blist->n);
- for(i=0;i<blist->n;i++)
- fprintf(fh,"3\n");
-
- fprintf(fh,"POINT_DATA %u\n", vlist->n);
- fprintf(fh,"SCALARS scalars long 1\n");
- fprintf(fh,"LOOKUP_TABLE default\n");
-
- for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i]->idx);
-
- fclose(fh);
- return TS_SUCCESS;
-}
-
-
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
FILE *fh;
@@ -1217,12 +561,23 @@
CFG_SIMPLE_FLOAT("c0",&tape->c0),
CFG_SIMPLE_FLOAT("w",&tape->w),
CFG_SIMPLE_FLOAT("F",&tape->F),
+/* Variables related to plane confinement */
+ CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
+ CFG_FLOAT("plane_d", 15, CFGF_NONE),
+ CFG_FLOAT("plane_F", 1000, CFGF_NONE),
+/* Variables related to stretching */
+// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
+// CFG_FLOAT("xkA0",0,CFGF_NONE),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
retval=cfg_parse_buf(cfg, buffer);
+ tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
+ tape->plane_d=cfg_getfloat(cfg,"plane_d");
+ tape->plane_F=cfg_getfloat(cfg,"plane_F");
+
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
@@ -1303,53 +658,5 @@
break;
}
- return TS_SUCCESS;
-}
-
-
-
-ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
- FILE *fh;
- ts_uint i, nvtx,nedges,ntria;
- ts_uint vtxi1,vtxi2;
- float x,y,z;
- ts_vertex_list *vlist;
- fh=fopen(fname, "r");
- if(fh==NULL){
- err("Cannot open file for reading... Nonexistant file?");
- return TS_FAIL;
- }
- ts_uint retval;
- retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
- vesicle->vlist=init_vertex_list(nvtx);
- vlist=vesicle->vlist;
- for(i=0;i<nvtx;i++){
- // fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
- retval=fscanf(fh,"%F %F %F",&x,&y,&z);
- vlist->vtx[i]->x=x;
- vlist->vtx[i]->y=y;
- vlist->vtx[i]->z=z;
- }
- for(i=0;i<nedges;i++){
- retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
- bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
- }
- //TODO: neighbours from bonds,
- //TODO: triangles from neigbours
-
-// Don't need to read triangles. Already have enough data
- /*
- for(i=0;i<ntria;i++){
- retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
- vtxi1=vesicle->blist->vertex1->idx;
- vtxi2=vesicle->blist->vertex1->idx;
-
- }
- */
- if(retval);
- fclose(fh);
-
-
-
return TS_SUCCESS;
}
--
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