#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<string.h>
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#include <sys/types.h>
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#include <dirent.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", vlist->vertex[i].idx,vlist->vertex[i].x, vlist->vertex[i].y, vlist->vertex[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->vertex;
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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_no);
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for(j=0;j<vtx[i].neigh_no;j++){
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printf("(%f,%f,%f)",vtx[i].neigh[j]->x, vtx[i].neigh[j]->y,vtx[i].neigh[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->vertex;
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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->vertex[i].x,
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vlist->vertex[i].y, vlist->vertex[i].z, vlist->vertex[i].neigh_no);
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for(j=0;j<vlist->vertex[i].neigh_no;j++){
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fprintf(fh,"\t%u",(ts_uint)(vlist->vertex[i].neigh[j]-vlist->vertex+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.vertex[i].tristar_no);
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for(j=0;j<vesicle->vlist.vertex[i].tristar_no;j++){
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fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist.vertex[i].tristar[j]-vesicle->tlist.triangle+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->triangle[i].neigh_no);
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for(j=0;j<tlist->triangle[i].neigh_no;j++){
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fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].neigh[j]-tlist->triangle+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->triangle[i].vertex[j]-vesicle->vlist.vertex+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->triangle[i].xnorm,
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tlist->triangle[i].ynorm,tlist->triangle[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->vertex[i].xk,vlist->vertex[i].c,vlist->vertex[i].energy,
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vlist->vertex[i].energy_h, vlist->vertex[i].curvature, 0);
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for(j=0;j<vlist->vertex[i].neigh_no;j++){
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fprintf(fh," %.17E", vlist->vertex[i].bond_length_dual[j]);
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}
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fprintf(fh,"\n");
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for(j=0;j<vlist->vertex[i].neigh_no;j++){
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fprintf(fh," %.17E", vlist->vertex[i].bond_length[j]);
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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-vesicle->vlist.vertex+1),(ts_uint)(vesicle->blist.bond[i].vtx2-vesicle->vlist.vertex+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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ts_uint i,j;
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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;
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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",atol(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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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->vertex;
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ts_uint i,j;
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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 ",vlist->vertex[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->vertex;
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ts_uint i,j;
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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_bool parsetape(ts_vesicle *vesicle,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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ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
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*iterations=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",iterations),
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CFG_SIMPLE_BOOL("quiet",&quiet),
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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_new");
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if(retval==CFG_FILE_ERROR){
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fatal("No tape_new 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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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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// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
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return TS_SUCCESS;
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}
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