#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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#include "poly.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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/** 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("dump.bin","wb");
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/* dump vesicle */
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fwrite(vesicle, sizeof(ts_vesicle),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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/* 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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/* 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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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("dump.bin","rb");
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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),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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/* 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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// recreating space for cells //
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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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vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
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for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
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vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
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vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
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}
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retval=fread(iteration,sizeof(ts_uint),1,fh);
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if(retval);
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fclose(fh);
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return vesicle;
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}
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ts_bool parse_args(int argc, char **argv){
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int c, retval;
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DIR *dir;
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path[0]=0;
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while (1)
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{
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static struct option long_options[] =
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{
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{"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
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{"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
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{"tape", no_argument, 0, 't'},
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{"output-file", required_argument, 0, 'o'},
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{"directory", required_argument, 0, 'd'},
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{"dump-file", required_argument,0, 'f'},
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{0, 0, 0, 0}
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};
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/* getopt_long stores the option index here. */
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int option_index = 0;
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c = getopt_long (argc, argv, "d:fot",
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long_options, &option_index);
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/* Detect the end of the options. */
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if (c == -1)
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break;
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switch (c)
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{
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case 0:
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/* If this option set a flag, do nothing else now. */
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if (long_options[option_index].flag != 0)
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break;
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printf ("option %s", long_options[option_index].name);
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if (optarg)
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printf (" with arg %s", optarg);
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printf ("\n");
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break;
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case 't':
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//check if tape exists. If not, fail immediately.
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puts ("option -t\n");
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break;
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case 'o':
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//set filename of master output file
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printf ("option -o with value `%s'\n", optarg);
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break;
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case 'd':
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//check if directory exists. If not create one. If creation is
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//successful, set directory for output files.
|
//printf ("option -d with value `%s'\n", optarg);
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dir = opendir(optarg);
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if (dir)
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{
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/* Directory exists. */
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closedir(dir);
|
}
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else if (ENOENT == errno)
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{
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/* Directory does not exist. */
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retval=mkdir(optarg, 0700);
|
if(retval){
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fatal("Could not create requested directory. Check if you have permissions",1);
|
}
|
}
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else
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{
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/* opendir() failed for some other reason. */
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fatal("Could not check if directory exists. Reason unknown",1);
|
}
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ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
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// sprintf(path,"%s", optarg);
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strcpy(path, optarg);
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// ts_fprintf(stdout,"ok!\n");
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break;
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case 'f':
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//check if dump file specified exists. Defaults to dump.bin
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break;
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case '?':
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/* getopt_long already printed an error message. */
|
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ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
|
fatal("Ooops, read help first",1);
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break;
|
|
default:
|
exit (1);
|
}
|
}
|
|
return TS_SUCCESS;
|
|
}
|
|
|
|
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ts_bool print_vertex_list(ts_vertex_list *vlist){
|
ts_uint i;
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printf("Number of vertices: %u\n",vlist->n);
|
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);
|
}
|
return TS_SUCCESS;
|
}
|
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ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
|
ts_uint i,j;
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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,
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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(".");
|
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[255];
|
FILE *fh;
|
|
sprintf(filename,"timestep_%.6u.vtu",timestepno);
|
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;
|
ts_bool poly=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;
|
}
|
}
|
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
|
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
|
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);
|
}
|
}
|
}
|
|
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 );
|
}
|
}
|
}
|
|
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);
|
}
|
|
}
|
|
|
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
|
for (i=2;i<(blist->n+monono*polyno)*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;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_tape *parsetape(char *filename){
|
// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
|
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
|
tape->multiprocessing=calloc(255,sizeof(char));
|
/* long int brezveze0=1;
|
long int brezveze1=1;
|
long int brezveze2=1;
|
ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
|
long int iter=1000, init=1000, mcsw=1000;
|
*/
|
|
cfg_opt_t opts[] = {
|
CFG_SIMPLE_INT("nshell", &tape->nshell),
|
CFG_SIMPLE_INT("npoly", &tape->npoly),
|
CFG_SIMPLE_INT("nmono", &tape->nmono),
|
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
|
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
|
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
|
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
|
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
|
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_END()
|
};
|
cfg_t *cfg;
|
ts_uint retval;
|
cfg = cfg_init(opts, 0);
|
retval=cfg_parse(cfg, filename);
|
if(retval==CFG_FILE_ERROR){
|
fatal("No tape file.",100);
|
}
|
else if(retval==CFG_PARSE_ERROR){
|
fatal("Invalid tape!",100);
|
}
|
|
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 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;
|
}
|
