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 | 934 +++++++++++++--------------------------------------------
1 files changed, 217 insertions(+), 717 deletions(-)
diff --git a/src/io.c b/src/io.c
index ead2de3..a2b50d9 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
#include "io.h"
@@ -15,421 +16,7 @@
#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(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=8;
-// 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;
-}
-
+#include <snapshot.h>
ts_bool parse_args(int argc, char **argv){
@@ -449,17 +36,19 @@
{"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'},
+ {"version", no_argument, 0, 'v'},
{"output-file", required_argument, 0, 'o'},
{"directory", required_argument, 0, 'd'},
{"dump-filename", required_argument,0, 'f'},
{"tape-options",required_argument,0,'c'},
{"tape-template", required_argument,0,0},
+ {"restore-from-vtk",required_argument,0,0},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
- c = getopt_long (argc, argv, "d:f:o:t:c:",
+ c = getopt_long (argc, argv, "d:f:o:t:c:v",
long_options, &option_index);
/* Detect the end of the options. */
@@ -480,7 +69,15 @@
if(strcmp(long_options[option_index].name,"tape-template")==0){
strcpy(command_line_args.tape_templatefull,optarg);
}
+ if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
+ strcpy(command_line_args.dump_from_vtk,optarg);
+ }
break;
+ case 'v':
+ fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+ fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
+ fprintf(stdout,"Released under terms of GPLv3\n");
+ exit(0);
case 'c':
strcpy(command_line_args.tape_opts,optarg);
@@ -519,8 +116,8 @@
case '?':
/* getopt_long already printed an error message. */
-
- ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
+ print_help(stdout);
+//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
fatal("Ooops, read help first",1);
break;
@@ -589,204 +186,37 @@
}
+ts_bool print_help(FILE *fd){
+ fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+ fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
+ fprintf(fd,"Released under terms of GPLv3\n\n");
-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);
- }
+ fprintf(fd, "Invoking trisurf-ng without any flags results in default operation. Program reads 'tape' file and 'dump.bin' binary representation of the vesicle from disk and continues the simulation where it was aborted (as specified in 'dump.bin').\n\n");
+ fprintf(fd,"If 'tape' has different values than binary dump, those are used (if possible -- some values in tape, such as nshell cannot be modified).\n\n\n");
+ fprintf(fd,"However, if dump.bin is not present, user is notified to specify --force-from-tape flag. The vesicle will be created from specifications in tape.\n\n\n");
+ fprintf(fd,"Flags:\n\n");
+ fprintf(fd,"--force-from-tape\t\t makes initial shape of the vesicle from tape. Ignores already existing binary dump and possible simulation results.\n");
+ fprintf(fd,"--restore-from-vtk\t\t VTK's file ending with '.vtu' are preferred way to make state snapshots for restoration. With this flag the restoration of the vesicle from vtk is possible. The simulation will continue if hidden '.status' file with last iteration done is present. Otherwise it will start simulation from timestep 0.\n");
+ fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
+ fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
+ fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
+ fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
+ fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
+ fprintf(fd,"Examples:\n\n");
+ fprintf(fd,"trisurf --force-from-tape\n");
+ fprintf(fd,"trisurf --reset-iteration-count\n");
+ fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
+ fprintf(fd,"\n\n");
+
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_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;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -820,19 +250,27 @@
}
}
- 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+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
- fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
+ fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
+ 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=\"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
@@ -841,20 +279,131 @@
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</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
+ fprintf(fh,"</DataArray>\n");
+ if(cstlist!=NULL){
+ fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ if(vtx[i]->cluster!=NULL){
+ fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
+ } else {
+ fprintf(fh,"-1 ");
+ }
+ }
+ //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,"-1 ");
+ }
+ }
+ }
+ //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,"-1 ");
+ }
+ }
+ }
+
+ fprintf(fh,"</DataArray>\n");
+
+
+ }
+
+ //here comes additional data as needed. Currently only spontaneous curvature
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ fprintf(fh,"%.17e ",vtx[i]->c);
+ }
+ //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 ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
+ }
+ }
+ }
+ //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 ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+
+ //here comes additional data. Energy!
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
+ }
+ //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 ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
+ }
+ }
+ }
+ //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 ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
+ }
+ }
+ }
+ 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<blist->n;i++){
+ fprintf(fh, "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,"</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);
}
//polymeres
if(poly){
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ fprintf(fh,"%.17e %.17e %.17e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
}
}
}
@@ -862,7 +411,7 @@
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,"%.17e %.17e %.17e\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 );
}
}
}
@@ -897,67 +446,29 @@
}
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
+ for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
+ fprintf(fh,"%u ", j);
+ }
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
+ for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++){
fprintf(fh,"3 ");
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"5 ");
+ }
fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
fclose(fh);
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;
@@ -993,6 +504,20 @@
ts_tape *parsetape(char *filename){
+ FILE *fd = fopen (filename, "r");
+ long length;
+ size_t size;
+ fseek (fd, 0, SEEK_END);
+ length = ftell (fd);
+ fseek (fd, 0, SEEK_SET);
+ size=fread (tapetxt, 1, length, fd);
+ fclose(fd);
+ if(size);
+ ts_tape *tape=parsetapebuffer(tapetxt);
+ return tape;
+}
+
+ts_tape *parsetapebuffer(char *buffer){
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
tape->multiprocessing=calloc(255,sizeof(char));
@@ -1002,7 +527,11 @@
CFG_SIMPLE_INT("nmono", &tape->nmono),
CFG_SIMPLE_INT("nfil",&tape->nfil),
CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
+ CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
+ CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
@@ -1010,6 +539,8 @@
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
+ CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
+ CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -1020,18 +551,33 @@
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_BOOL("quiet",(cfg_bool_t *)&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_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
+ CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
+ 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(cfg, filename);
+ 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);
}
@@ -1060,6 +606,8 @@
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
+ operator[0]=0;
+ operator[1]=0;
ts_uint i,j;
commands=(char *)malloc(10000*sizeof(char));
backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
@@ -1110,53 +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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