/* vim: set ts=4 sts=4 sw=4 noet : */
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#include "general.h"
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#include<stdio.h>
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#include "io.h"
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#include "vertex.h"
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#include "bond.h"
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#include<string.h>
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#include<stdlib.h>
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#include <sys/types.h>
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#include <dirent.h>
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#include "initial_distribution.h"
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#include "poly.h"
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#include "cell.h"
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#include <getopt.h>
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#include <sys/stat.h>
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#include <sys/types.h>
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#include <dirent.h>
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#include <errno.h>
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#include <snapshot.h>
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/** DUMP STATE TO DISK DRIVE **/
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ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
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/* save current state with wrong pointers. Will fix that later */
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ts_uint i,j,k;
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FILE *fh=fopen(command_line_args.dump_fullfilename,"wb");
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/* dump vesicle */
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fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
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/* dump vertex list */
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fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
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/* dump bond list */
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fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
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/* dump triangle list */
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fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
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/* dump cell list */
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fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
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/* dump poly list */
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fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
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/* dump filament list */
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fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
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/* level 1 complete */
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/*dump vertices*/
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for(i=0;i<vesicle->vlist->n;i++){
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fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
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/* dump pointer offsets for:
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neigh
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bond
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tria
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cell is ignored
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*/
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for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
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fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
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}
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for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
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fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
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}
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for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
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fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
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}
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}
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/*dump bonds*/
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for(i=0;i<vesicle->blist->n;i++){
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fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
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/* dump pointer offsets for vtx1 and vtx2 */
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//off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
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fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
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//off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
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fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
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}
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/*dump triangles*/
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for(i=0;i<vesicle->tlist->n;i++){
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fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
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/* dump pointer offsets for vertex */
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fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
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fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
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fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
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/* dump pointer offsets for neigh */
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for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
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fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
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}
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}
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/*dump polymeres */
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for(i=0;i<vesicle->poly_list->n;i++){
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fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
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fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
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fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
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}
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/* dump poly vertex(monomer) list*/
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
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fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
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/* dump offset for neigh and bond */
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for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
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// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
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}
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for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
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//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
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fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
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}
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}
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// grafted vtx on vesicle data dump
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fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
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}
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/* dump poly bonds between monomers list*/
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
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fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
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/* dump vtx1 and vtx2 offsets */
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//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
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// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
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}
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}
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/*dump filamentes grandes svinjas */
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for(i=0;i<vesicle->filament_list->n;i++){
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fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
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fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
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fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
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}
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/* dump filamentes vertex(monomer) list*/
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
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fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
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/* dump offset for neigh and bond */
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for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
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// off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
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}
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for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
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//off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
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fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
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}
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}
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}
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/* dump poly bonds between monomers list*/
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
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fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
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/* dump vtx1 and vtx2 offsets */
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//off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
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// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
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fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
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}
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}
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/* pointer offsets for fixing the restored pointers */
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/* need pointers for
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vlist->vtx
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blist->bond
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tlist->tria
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clist->cell
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poly_list->poly
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and for each poly:
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poly_list->poly->vtx
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poly_list->poly->bond
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*/
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// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
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/* write tape information on vesicle */
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// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
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fwrite(&iteration, sizeof(ts_uint),1,fh);
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fclose(fh);
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return TS_SUCCESS;
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}
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/** RESTORE DUMP FROM DISK **/
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ts_vesicle *restore_state(ts_uint *iteration){
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ts_uint i,j,k;
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FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
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struct stat sb;
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if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
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//dump file does not exist.
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return NULL;
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}
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//check if it is regular file
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if((sb.st_mode & S_IFMT) != S_IFREG) {
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//dump file is not a regular file.
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ts_fprintf(stderr,"Dump file is not a regular file!\n");
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return NULL;
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}
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ts_uint retval;
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ts_uint idx;
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/* we restore all the data from the dump */
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/* restore vesicle */
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ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
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retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
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// fprintf(stderr,"was here! %e\n",vesicle->dmax);
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/* restore vertex list */
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vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
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retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
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/* restore bond list */
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vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
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retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
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/* restore triangle list */
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vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
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retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
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/* restore cell list */
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vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
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retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
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/* restore poly list */
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vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
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retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
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/* restore filament list */
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vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
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retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
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/* level 1 complete */
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/* prerequisity. Bonds must be malloced before vertexes are recreated */
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vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
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for(i=0;i<vesicle->blist->n;i++){
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vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
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}
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/* prerequisity. Triangles must be malloced before vertexes are recreated */
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vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
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for(i=0;i<vesicle->tlist->n;i++){
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vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
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}
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/* prerequisity. Vertices must be malloced before vertexes are recreated */
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vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
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for(i=0;i<vesicle->vlist->n;i++){
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vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
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}
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/*restore vertices*/
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for(i=0;i<vesicle->vlist->n;i++){
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retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
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/*restore neigh, bond, tristar. Ignoring cell */
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vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
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for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
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}
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vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
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for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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/* 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 */
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vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
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}
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vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
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for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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/* same comment as above */
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vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
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}
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}
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/*restore bonds*/
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// vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
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for(i=0;i<vesicle->blist->n;i++){
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// vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
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retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
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/* restore vtx1 and vtx2 */
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
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}
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/*restore triangles*/
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// vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
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for(i=0;i<vesicle->tlist->n;i++){
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// vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
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retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
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/* restore pointers for vertices */
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
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/* restore pointers for neigh */
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vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
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for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
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}
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}
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/*restore cells */
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/*TODO: do we need to recalculate cells here? */
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/* vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
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for(i=0;i<vesicle->clist->cellno;i++){
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vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
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retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
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}
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*/
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/*restore polymeres */
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vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
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for(i=0;i<vesicle->poly_list->n;i++){
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vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
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retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
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vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
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retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
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vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
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retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
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/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
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vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
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vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
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vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
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}
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for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
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vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
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}
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}
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/* restore poly vertex(monomer) list*/
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
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retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
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/* restore neigh and bonds */
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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 *));
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for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
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}
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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 *));
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for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
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}
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}
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/* restore grafted vtx on vesicle and grafted_poly */
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
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vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
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}
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/* restore poly bonds between monomers list*/
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for(i=0;i<vesicle->poly_list->n;i++){
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for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
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// vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
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retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
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/* restore vtx1 and vtx2 */
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
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retval=fread(&idx,sizeof(ts_uint),1,fh);
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vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
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}
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}
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/*restore filaments */
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vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
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for(i=0;i<vesicle->filament_list->n;i++){
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vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
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retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
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vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
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retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
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vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
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retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
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/* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
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vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
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vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
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vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
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}
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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;
|
}
|
|
|
|
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");
|
sprintf(command_line_args.tape_templatefull,"./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'},
|
{"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:",
|
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"); */
|
//TODO: find a better way.
|
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 'c':
|
strcpy(command_line_args.tape_opts,optarg);
|
break;
|
case 't': //tape
|
strcpy(command_line_args.tape_fullfilename,optarg);
|
break;
|
|
case 'o': //set filename of master pvd output 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':
|
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);
|
}
|
}
|
|
//Here we set correct values for full filenames!
|
char *buffer=(char *)malloc(10000*sizeof(char));
|
//correct the path and add trailing /
|
if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
|
|
/* master pvd output file */
|
strcpy(buffer,command_line_args.path);
|
strcat(buffer,command_line_args.output_fullfilename);
|
if ((file = fopen(buffer, "w")) == NULL) {
|
fprintf(stderr,"Could not create output file %s!\n", buffer);
|
fatal("Please specify correct output file or check permissions of the file",1);
|
//there is a tape template. make a copy into desired directory
|
|
} else {
|
fclose(file);
|
strcpy(command_line_args.output_fullfilename,buffer);
|
}
|
|
/* tape file */
|
strcpy(buffer,command_line_args.path);
|
strcat(buffer,command_line_args.tape_fullfilename);
|
if (stat(buffer, &sb) == -1) {
|
|
//tape does not exist. does tape template exist?
|
if(stat(command_line_args.tape_templatefull, &sb)==-1){
|
ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
|
fatal("Please select correct tape or check permissions of the file",1);
|
} else {
|
//tape template found
|
fatal("Samo did not program template copy yet",1);
|
}
|
} else {
|
strcpy(command_line_args.tape_fullfilename,buffer);
|
}
|
|
|
/* dump file */
|
strcpy(buffer,command_line_args.path);
|
strcat(buffer,command_line_args.dump_fullfilename);
|
//check if dump file exist first.
|
if (stat(buffer, &sb) == -1) {
|
//no dump file. check if we can create one.
|
if ((file = fopen(buffer, "w")) == NULL) {
|
fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
|
fatal("Please specify correct dump file or check permissions of the file",1);
|
} else {
|
fclose(file);
|
//good, file is writeable. delete it for now.
|
remove(buffer);
|
}
|
}
|
strcpy(command_line_args.dump_fullfilename, buffer);
|
|
|
free(buffer);
|
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_vertex_list *vlist=vesicle->vlist;
|
ts_bond_list *blist=vesicle->blist;
|
ts_vertex **vtx=vlist->vtx;
|
ts_uint i,j;
|
char filename[10000];
|
char just_name[255];
|
FILE *fh;
|
strcpy(filename,command_line_args.path);
|
sprintf(just_name,"timestep_%.6u.vtu",timestepno);
|
strcat(filename,just_name);
|
|
fh=fopen(filename, "w");
|
if(fh==NULL){
|
err("Cannot open file %s for writing");
|
return TS_FAIL;
|
}
|
/* Here comes header of the file */
|
|
//find number of extra vtxs and bonds of polymeres
|
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;
|
monono=vesicle->poly_list->poly[0]->vlist->n;
|
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");
|
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));
|
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++,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);
|
}
|
}
|
}
|
|
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
|
for(i=0;i<vlist->n;i++){
|
fprintf(fh,"%e %e %e\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 );
|
}
|
}
|
}
|
//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++){
|
fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->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]->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+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+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+(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+fonono*filno;i++){
|
fprintf(fh,"3 ");
|
}
|
|
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;
|
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){
|
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));
|
|
cfg_opt_t opts[] = {
|
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("dmin_interspecies", &tape->dmin_interspecies),
|
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
|
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
|
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
|
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
|
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
|
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_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
|
CFG_END()
|
};
|
cfg_t *cfg;
|
ts_uint retval;
|
cfg = cfg_init(opts, 0);
|
retval=cfg_parse_buf(cfg, buffer);
|
if(retval==CFG_FILE_ERROR){
|
fatal("No tape file.",100);
|
}
|
else if(retval==CFG_PARSE_ERROR){
|
fatal("Invalid tape!",100);
|
}
|
|
/* here we override all values read from tape with values from commandline*/
|
getcmdline_tape(cfg,command_line_args.tape_opts);
|
cfg_free(cfg);
|
|
|
/* 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;
|
}
|
|
|
|
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
|
|
char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
|
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.
|
strcpy(commands,opts);
|
for(i=0; ;i++, commands=NULL){
|
//breaks comma separated list of commands into specific commands.
|
command=strtok_r(commands,",",&saveptr);
|
if(command==NULL) break;
|
// fprintf(stdout,"Command %d: %s\n",i,command);
|
//extracts name of command and value of command into operator[2] array.
|
for(j=0; j<2;j++,command=NULL){
|
operator[j]=strtok_r(command,"=",&saveopptr);
|
if(operator[j]==NULL) break;
|
// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
|
}
|
//1. check: must have 2 operators.
|
if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
|
|
// cfg_setstr(cfg,operator[0],operator[1]);
|
cmdline_to_tape(cfg,operator[0],operator[1]);
|
//2. check: must be named properly.
|
//3. check: must be of right format (integer, double, string, ...)
|
|
}
|
free(backup);
|
return TS_SUCCESS;
|
}
|
|
|
ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val){
|
|
cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
|
if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
|
switch (cfg_opt->type){
|
case CFGT_INT:
|
cfg_setint(cfg,key,atol(val));
|
break;
|
case CFGT_FLOAT:
|
cfg_setfloat(cfg,key,atof(val));
|
break;
|
/* case CFGT_BOOL:
|
cfg_setbool(cfg,operator[0],operator[1]);
|
break; */
|
case CFGT_STR:
|
cfg_setstr(cfg,key,val);
|
break;
|
default:
|
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;
|
}
|
