#include "general.h"
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#include<stdio.h>
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#include "io.h"
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#include <confuse.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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ts_bool print_vertex_list(ts_vertex_list *vlist){
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ts_uint i;
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printf("Number of vertices: %u\n",vlist->n);
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for(i=0;i<vlist->n;i++){
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printf("%u: %f %f %f\n",
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vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
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}
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return TS_SUCCESS;
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}
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ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
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ts_uint i,j;
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ts_vertex **vtx=vlist->vtx;
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printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
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for(i=0;i<vlist->n;i++){
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printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh->n);
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for(j=0;j<vtx[i]->neigh->n;j++){
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printf("(%f,%f,%f)",vtx[i]->neigh->vtx[j]->x,
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vtx[i]->neigh->vtx[j]->y,vtx[i]->neigh->vtx[j]->z);
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}
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printf("\n");
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}
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return TS_SUCCESS;
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}
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ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
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ts_vertex **vtx=vlist->vtx;
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ts_uint i;
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FILE *fh;
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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for(i=0;i<vlist->n;i++)
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fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
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ts_uint i,j;
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for(i=0;i<vlist->n;i++){
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fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
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vlist->vtx[i]->y, vlist->vtx[i]->z,
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vlist->vtx[i]->neigh->n);
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for(j=0;j<vlist->vtx[i]->neigh->n;j++){
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fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh->vtx[j]->idx));
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//-vlist->vtx+1));
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}
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fprintf(fh,"\n");
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}
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return TS_SUCCESS;
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}
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ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
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ts_uint i,j;
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for(i=0;i<vesicle->vlist->n;i++){
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fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
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for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
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fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
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}
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fprintf(fh,"\n");
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}
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return TS_SUCCESS;
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}
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ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
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ts_triangle_list *tlist=vesicle->tlist;
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ts_uint i,j;
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for(i=0;i<tlist->n;i++){
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fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
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for(j=0;j<tlist->tria[i]->neigh_no;j++){
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fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
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}
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fprintf(fh,"\n");
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for(j=0;j<3;j++){
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fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
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}
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fprintf(fh,"\n");
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fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
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tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
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fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
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}
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return TS_SUCCESS;
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}
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ts_bool fprint_vertex_data(FILE *fh,ts_vertex_list *vlist){
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ts_uint i,j;
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for(i=0;i<vlist->n;i++){
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fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
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vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
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vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
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for(j=0;j<vlist->vtx[i]->neigh->n;j++){
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fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
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}
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fprintf(fh,"\n");
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for(j=0;j<vlist->vtx[i]->neigh->n;j++){
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fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
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}
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fprintf(fh,"\n");
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}
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return TS_SUCCESS;
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}
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ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
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ts_uint i;
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for(i=0;i<vesicle->blist->n;i++){
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fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
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//-vesicle->vlist->vtx+1),
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(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
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//-vesicle->vlist.vtx+1));
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}
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return TS_SUCCESS;
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}
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ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
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FILE *fh;
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
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fprint_vertex_list(fh,vesicle->vlist);
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fprint_tristar(fh,vesicle);
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fprint_triangle_list(fh,vesicle);
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fprint_vertex_data(fh,vesicle->vlist);
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fprint_bonds(fh,vesicle);
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
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FILE *fh;
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char line[255];
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fh=fopen(filename, "r");
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if(fh==NULL){
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err("Cannot open file for reading... Nonexistant file?");
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return TS_FAIL;
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}
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ts_uint retval=1;
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while(retval!=EOF){
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retval=fscanf(fh,"%s",line);
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fprintf(stderr,"%s",line);
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}
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_bool write_master_xml_file(ts_char *filename){
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FILE *fh;
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ts_char *i,*j;
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ts_uint tstep;
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ts_char *number;
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
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DIR *dir = opendir(".");
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if(dir){
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struct dirent *ent;
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tstep=0;
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while((ent = readdir(dir)) != NULL)
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{
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i=rindex(ent->d_name,'.');
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if(i==NULL) continue;
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if(strcmp(i+1,"vtu")==0){
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j=rindex(ent->d_name,'_');
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if(j==NULL) continue;
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number=strndup(j+1,j-i);
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fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
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tstep++;
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free(number);
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}
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}
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}
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free(dir);
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fprintf(fh,"</Collection>\n</VTKFile>\n");
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
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ts_vertex_list *vlist=vesicle->vlist;
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ts_bond_list *blist=vesicle->blist;
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ts_vertex **vtx=vlist->vtx;
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ts_uint i;
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char filename[255];
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FILE *fh;
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sprintf(filename,"timestep_%.6u.vtu",timestepno);
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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/* Here comes header of the file */
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fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
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fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
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fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
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for(i=0;i<vlist->n;i++){
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fprintf(fh,"%u ",vtx[i]->idx);
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}
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fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
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for(i=0;i<vlist->n;i++){
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fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
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}
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fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
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for(i=0;i<blist->n;i++){
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fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
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}
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fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
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for (i=2;i<blist->n*2+1;i+=2){
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fprintf(fh,"%u ",i);
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}
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fprintf(fh,"\n");
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fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
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for (i=0;i<blist->n;i++){
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fprintf(fh,"3 ");
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}
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fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
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ts_vertex_list *vlist=vesicle->vlist;
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ts_bond_list *blist=vesicle->blist;
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ts_vertex **vtx=vlist->vtx;
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ts_uint i;
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FILE *fh;
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fh=fopen(filename, "w");
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if(fh==NULL){
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err("Cannot open file %s for writing");
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return TS_FAIL;
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}
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/* Here comes header of the file */
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// fprintf(stderr,"NSHELL=%u\n",nshell);
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fprintf(fh, "# vtk DataFile Version 2.0\n");
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/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
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fprintf(fh, "%s\n", text);
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fprintf(fh,"ASCII\n");
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fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
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fprintf(fh,"POINTS %u double\n", vlist->n);
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for(i=0;i<vlist->n;i++){
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fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
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}
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fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
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for(i=0;i<blist->n;i++){
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fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
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}
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fprintf(fh,"CELL_TYPES %u\n",blist->n);
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for(i=0;i<blist->n;i++)
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fprintf(fh,"3\n");
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fprintf(fh,"POINT_DATA %u\n", vlist->n);
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fprintf(fh,"SCALARS scalars long 1\n");
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fprintf(fh,"LOOKUP_TABLE default\n");
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for(i=0;i<vlist->n;i++)
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fprintf(fh,"%u\n",vtx[i]->idx);
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fclose(fh);
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return TS_SUCCESS;
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}
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ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
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long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
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char *buf=malloc(255*sizeof(char));
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long int brezveze0=1;
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long int brezveze1=1;
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long int brezveze2=1;
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ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
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long int iter=1000, init=1000, mcsw=1000;
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cfg_opt_t opts[] = {
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CFG_SIMPLE_INT("nshell", &nshell),
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CFG_SIMPLE_FLOAT("dmax", &dmax),
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CFG_SIMPLE_FLOAT("xk0",&xk0),
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CFG_SIMPLE_FLOAT("stepsize",&stepsize),
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CFG_SIMPLE_INT("nxmax", &ncxmax),
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CFG_SIMPLE_INT("nymax", &ncymax),
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CFG_SIMPLE_INT("nzmax", &nczmax),
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CFG_SIMPLE_INT("iterations",&iter),
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CFG_SIMPLE_INT("mcsweeps",&mcsw),
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CFG_SIMPLE_INT("inititer", &init),
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CFG_SIMPLE_BOOL("quiet",&quiet),
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CFG_SIMPLE_STR("multiprocessing",buf),
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CFG_SIMPLE_INT("smp_cores",&brezveze0),
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CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
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CFG_SIMPLE_INT("distributed_processes",&brezveze2),
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CFG_END()
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};
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cfg_t *cfg;
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ts_uint retval;
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cfg = cfg_init(opts, 0);
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retval=cfg_parse(cfg, "tape");
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if(retval==CFG_FILE_ERROR){
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fatal("No tape file.",100);
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}
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else if(retval==CFG_PARSE_ERROR){
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fatal("Invalid tape!",100);
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}
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ts_vesicle *vesicle;
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*iterations=iter;
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*inititer=init;
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*mcsweeps=mcsw;
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vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
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vesicle->nshell=nshell;
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vesicle->dmax=dmax*dmax;
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vesicle->bending_rigidity=xk0;
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vesicle->stepsize=stepsize;
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vesicle->clist->ncmax[0]=ncxmax;
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vesicle->clist->ncmax[1]=ncymax;
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vesicle->clist->ncmax[2]=nczmax;
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vesicle->clist->max_occupancy=8;
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cfg_free(cfg);
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free(buf);
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// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
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return vesicle;
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}
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ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
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FILE *fh;
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ts_uint i, nvtx,nedges,ntria;
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ts_uint vtxi1,vtxi2;
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float x,y,z;
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ts_vertex_list *vlist;
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fh=fopen(fname, "r");
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if(fh==NULL){
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err("Cannot open file for reading... Nonexistant file?");
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return TS_FAIL;
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}
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ts_uint retval;
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retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
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vesicle->vlist=init_vertex_list(nvtx);
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vlist=vesicle->vlist;
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for(i=0;i<nvtx;i++){
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// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
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retval=fscanf(fh,"%F %F %F",&x,&y,&z);
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vlist->vtx[i]->x=x;
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vlist->vtx[i]->y=y;
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vlist->vtx[i]->z=z;
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}
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for(i=0;i<nedges;i++){
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retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
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bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
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}
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//TODO: neighbours from bonds,
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//TODO: triangles from neigbours
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// Don't need to read triangles. Already have enough data
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/*
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for(i=0;i<ntria;i++){
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retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
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vtxi1=vesicle->blist->vertex1->idx;
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vtxi2=vesicle->blist->vertex1->idx;
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}
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*/
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if(retval);
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fclose(fh);
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return TS_SUCCESS;
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}
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