Started with arg parsing

Samo Penic

2014-03-06 083e03adeaf985c9da1ed31d259ced9bb54c207c

 src/io.c

@@ -1,11 +1,426 @@
#include<general.h>
#include "general.h"
#include<stdio.h>
#include "io.h"
#include "confuse.h"
#include <confuse.h>
#include "vertex.h"
#include "bond.h"
#include<string.h>
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
#include "initial_distribution.h"
#include "poly.h"

#include <getopt.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
#include <errno.h>
/** DUMP STATE TO DISK DRIVE **/

ts_bool dump_state(ts_vesicle *vesicle){

    /* save current state with wrong pointers. Will fix that later */
    ts_uint i,j,k;
    FILE *fh=fopen("dump.bin","wb");

    /* dump vesicle */
    fwrite(vesicle, sizeof(ts_vesicle),1,fh);
    /* dump vertex list */
    fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* dump bond list */
    fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
    /* dump triangle list */
    fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
    /* dump cell list */
    fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* dump poly list */
    fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

    /*dump vertices*/
    for(i=0;i<vesicle->vlist->n;i++){
        fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
        /* dump pointer offsets for:
                    neigh
                    bond
                    tria
                    cell is ignored
        */
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh); 
        }
    }

    /*dump bonds*/
    for(i=0;i<vesicle->blist->n;i++){
        fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* dump pointer offsets for vtx1 and vtx2 */
        //off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
        fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh); 
        //off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
        fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh); 
    }

    /*dump triangles*/
    for(i=0;i<vesicle->tlist->n;i++){
        fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* dump pointer offsets for vertex */
        fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh); 
        fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh); 
        fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh); 
        /* dump pointer offsets for neigh */
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh); 
        }
    }


    /*dump polymeres */
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
        fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
    } 
     
    /* dump poly vertex(monomer) list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            /* dump offset for neigh and bond */
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
               // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
                fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh); 
            }
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
                fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh); 
            }
        }
   // grafted vtx on vesicle data dump
      fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
    }
    /* dump poly bonds between monomers list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* dump vtx1 and vtx2 offsets */
            //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh); 
//            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh); 
        }
    }

/* pointer offsets for fixing the restored pointers */
/* need pointers for 
    vlist->vtx
    blist->bond
    tlist->tria
    clist->cell
    poly_list->poly
    and for each poly:
        poly_list->poly->vtx
        poly_list->poly->bond
*/

   fwrite(vesicle->clist, sizeof(ts_cell_list),1,  fh);

    fclose(fh);
    return TS_SUCCESS;
}


/** RESTORE DUMP FROM DISK **/
ts_vesicle *restore_state(){
    ts_uint i,j,k;
    FILE *fh=fopen("dump.bin","rb");
    ts_uint retval;
   ts_uint idx;

/* we restore all the data from the dump */
    /* restore vesicle */
    ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
    retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
//   fprintf(stderr,"was here! %e\n",vesicle->dmax);

    /* restore vertex list */
    vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
    retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* restore bond list */
    vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
    retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
    /* restore triangle list */
    vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
    retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
    /* restore cell list */
    vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
    retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* restore poly list */
    vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

/* prerequisity. Bonds must be malloced before vertexes are recreated */
  vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
    for(i=0;i<vesicle->blist->n;i++){
        vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
   }
/* prerequisity. Triangles must be malloced before vertexes are recreated */
  vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
    for(i=0;i<vesicle->tlist->n;i++){
        vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
}
/* prerequisity. Vertices must be malloced before vertexes are recreated */
    vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
 for(i=0;i<vesicle->vlist->n;i++){
        vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
 }
  /*restore vertices*/
    for(i=0;i<vesicle->vlist->n;i++){
        retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
        /*restore neigh, bond, tristar. Ignoring cell */
        vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            retval=fread(&idx,sizeof(ts_uint),1,fh);
            vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
        }
        vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            retval=fread(&idx,sizeof(ts_uint),1,fh);
/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
            vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];    
        }

        vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            retval=fread(&idx,sizeof(ts_uint),1,fh);
/* same comment as above */
            vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
        }

    }

    /*restore bonds*/
   // vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
    for(i=0;i<vesicle->blist->n;i++){
     //   vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
        retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* restore vtx1 and vtx2 */
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
    }

    /*restore triangles*/
//    vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
    for(i=0;i<vesicle->tlist->n;i++){
 //       vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
        retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* restore pointers for vertices */
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
        /* restore pointers for neigh */
    vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            retval=fread(&idx,sizeof(ts_uint),1,fh);
            vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
        }

    }
   
    /*restore cells */
/*TODO: do we need to recalculate cells here? */
/*    vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
    for(i=0;i<vesicle->clist->cellno;i++){
        vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
        retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
    }
*/
    /*restore polymeres */
    vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
        retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
        vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
        retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
        retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
   /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
        vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
    for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
   }
   for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
   }

    } 

     
    /* restore poly vertex(monomer) list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
           	 
            /* restore neigh and bonds */
            vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
            }
            vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
            }

        }
   /* restore grafted vtx on vesicle and grafted_poly */
                retval=fread(&idx,sizeof(ts_uint),1,fh);
      vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
      vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];	
    }

    /* restore poly bonds between monomers list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
       //     vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
            retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* restore vtx1 and vtx2 */
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
        }
    }

// recreating space for cells // 
   vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
   retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh); 
   vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
   for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
           vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
           vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
       }

    if(retval); 
    fclose(fh);
    return vesicle;
}



ts_bool parse_args(int argc, char **argv){
 int c, retval;
 DIR *dir;
    path[0]=0;
while (1)
     {
       static struct option long_options[] =
         {
           {"force-from-tape", no_argument,       &force_from_tape, 1},
           {"tape",     no_argument,       0, 't'},
           {"output-file",  required_argument, 0, 'o'},
           {"directory",  required_argument, 0, 'd'},
           {"dump-file", required_argument,0, 'f'},
           {0, 0, 0, 0}
         };
       /* getopt_long stores the option index here. */
       int option_index = 0;

       c = getopt_long (argc, argv, "d:fot",
                        long_options, &option_index);

       /* Detect the end of the options. */
       if (c == -1)
         break;

       switch (c)
         {
         case 0:
           /* If this option set a flag, do nothing else now. */
           if (long_options[option_index].flag != 0)
             break;
           printf ("option %s", long_options[option_index].name);
           if (optarg)
             printf (" with arg %s", optarg);
           printf ("\n");
           break;

         case 't':
            //check if tape exists. If not, fail immediately.
           puts ("option -t\n");
           break;

         case 'o':
            //set filename of master output file
           printf ("option -o with value `%s'\n", optarg);
           break;

         case 'd':
            //check if directory exists. If not create one. If creation is
            //successful, set directory for output files.
            //printf ("option -d with value `%s'\n", optarg);
            dir = opendir(optarg);
            if (dir)
            {
                /* Directory exists. */
                closedir(dir);
            }
            else if (ENOENT == errno)
            {
                /* Directory does not exist. */
                retval=mkdir(optarg, 0700);
                if(retval){
                fatal("Could not create requested directory. Check if you have permissions",1);
                }
            }
            else
            {
                /* opendir() failed for some other reason. */
                fatal("Could not check if directory exists. Reason unknown",1);
            }
            ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
//            sprintf(path,"%s", optarg);
            strcpy(path, optarg);
           // ts_fprintf(stdout,"ok!\n"); 

           break;

        case 'f':
            //check if dump file specified exists. Defaults to dump.bin
            break;

         case '?':
           /* getopt_long already printed an error message. */

            ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
            fatal("Ooops, read help first",1);
           break;

         default:
           exit (1);
         }
     }

    return TS_SUCCESS;

}




ts_bool print_vertex_list(ts_vertex_list *vlist){
@@ -13,7 +428,7 @@
   printf("Number of vertices: %u\n",vlist->n);
   for(i=0;i<vlist->n;i++){
      printf("%u: %f %f %f\n",
vlist->vtx[i]->idx,vlist->vtx[i]->data->x, vlist->vtx[i]->data->y, vlist->vtx[i]->data->z);
vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
   }
   return TS_SUCCESS;
}
@@ -23,10 +438,10 @@
   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]->data->neigh_no);
      for(j=0;j<vtx[i]->data->neigh_no;j++){
         printf("(%f,%f,%f)",vtx[i]->data->neigh[j]->data->x,
vtx[i]->data->neigh[j]->data->y,vtx[i]->data->neigh[j]->data->z);
      printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
      for(j=0;j<vtx[i]->neigh_no;j++){
         printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
      }
      printf("\n");
   }
@@ -45,7 +460,7 @@
      return TS_FAIL;
   }
   for(i=0;i<vlist->n;i++)
      fprintf(fh," %E\t%E\t%E\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
      fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);

   fclose(fh);
return TS_SUCCESS;
@@ -55,11 +470,11 @@
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]->data->x,
         vlist->vtx[i]->data->y, vlist->vtx[i]->data->z,
            vlist->vtx[i]->data->neigh_no);
      for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->data->neigh[j]->idx));
      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");
@@ -70,9 +485,9 @@
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]->data->tristar_no);
      for(j=0;j<vesicle->vlist->vtx[i]->data->tristar_no;j++){
         fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->data->tristar[j]->idx));//-vesicle->tlist->tria+1));
      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");
   }
@@ -83,17 +498,17 @@
        ts_triangle_list *tlist=vesicle->tlist;
      ts_uint i,j;
   for(i=0;i<tlist->n;i++){
        fprintf(fh,"\t%u",tlist->tria[i]->data->neigh_no);
       for(j=0;j<tlist->tria[i]->data->neigh_no;j++){
          fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->data->neigh[j]->idx));//-tlist->tria+1)); 
        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]->data->vertex[j]->idx));//-vesicle->vlist->vtx+1)); 
          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]->data->xnorm,
tlist->tria[i]->data->ynorm,tlist->tria[i]->data->znorm);
      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;
@@ -103,14 +518,14 @@
    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]->data->xk,vlist->vtx[i]->data->c,vlist->vtx[i]->data->energy,
        vlist->vtx[i]->data->energy_h, vlist->vtx[i]->data->curvature, 0);
        for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length_dual);
        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]->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
        }
            fprintf(fh,"\n");
        for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length);
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
        }
            fprintf(fh,"\n");
    }
@@ -120,9 +535,9 @@
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]->data->vtx1->idx),
        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]->data->vtx2->idx));
        (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
    //-vesicle->vlist.vtx+1));
    }
    return TS_SUCCESS;
@@ -194,6 +609,7 @@
            }  
      }
   }
    free(dir);
   fprintf(fh,"</Collection>\n</VTKFile>\n");
   fclose(fh);
   return TS_SUCCESS;
@@ -203,7 +619,7 @@
   ts_vertex_list *vlist=vesicle->vlist;
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
    ts_uint i;
    ts_uint i,j;
       char filename[255];
   FILE *fh;

@@ -214,29 +630,72 @@
      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, blist->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]->data->x,vtx[i]->data->y, vtx[i]->data->z);
      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]->data->vtx1->idx,blist->bond[i]->data->vtx2->idx);
         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*2+1;i+=2){
    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;i++){
     for (i=0;i<blist->n+monono*polyno;i++){
        fprintf(fh,"3 ");
    }

@@ -267,12 +726,12 @@
   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]->data->x,vtx[i]->data->y, vtx[i]->data->z);
      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]->data->vtx1->idx,blist->bond[i]->data->vtx2->idx);
         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++)
@@ -283,7 +742,7 @@
   fprintf(fh,"LOOKUP_TABLE default\n");

   for(i=0;i<vlist->n;i++)
      fprintf(fh,"%u\n",vtx[i]->data->idx);
      fprintf(fh,"%u\n",vtx[i]->idx);

   fclose(fh);
   return TS_SUCCESS;
@@ -291,20 +750,35 @@



ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60;  // THIS IS DUE TO CONFUSE BUG!
    ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
    *iterations=1000;
ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
    long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20;  // THIS IS DUE TO CONFUSE BUG!
    char *buf=malloc(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;
   long int iter=1000, init=1000, mcsw=1000;


    cfg_opt_t opts[] = {
        CFG_SIMPLE_INT("nshell", &nshell),
        CFG_SIMPLE_INT("npoly", &npoly),
        CFG_SIMPLE_INT("nmono", &nmono),
        CFG_SIMPLE_FLOAT("dmax", &dmax),
        CFG_SIMPLE_FLOAT("xk0",&xk0),
        CFG_SIMPLE_FLOAT("k_spring",&kspring),
        CFG_SIMPLE_FLOAT("stepsize",&stepsize),
        CFG_SIMPLE_INT("nxmax", &ncxmax),
        CFG_SIMPLE_INT("nymax", &ncymax),
        CFG_SIMPLE_INT("nzmax", &nczmax),
        CFG_SIMPLE_INT("iterations",iterations),
        CFG_SIMPLE_INT("iterations",&iter),
   CFG_SIMPLE_INT("mcsweeps",&mcsw),
   CFG_SIMPLE_INT("inititer", &init),
        CFG_SIMPLE_BOOL("quiet",&quiet),
        CFG_SIMPLE_STR("multiprocessing",buf),
        CFG_SIMPLE_INT("smp_cores",&brezveze0),
        CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
        CFG_SIMPLE_INT("distributed_processes",&brezveze2),
        CFG_END()
    };
    cfg_t *cfg;    
@@ -317,6 +791,16 @@
    else if(retval==CFG_PARSE_ERROR){
   fatal("Invalid tape!",100);
   }
   ts_vesicle *vesicle;
       *iterations=iter;
   *inititer=init;
   *mcsweeps=mcsw;
   vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
   vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
   vesicle->spring_constant=kspring;
   poly_assign_spring_const(vesicle);
	

    vesicle->nshell=nshell;
    vesicle->dmax=dmax*dmax;
    vesicle->bending_rigidity=xk0;
@@ -325,8 +809,60 @@
    vesicle->clist->ncmax[1]=ncymax;
    vesicle->clist->ncmax[2]=nczmax;
    vesicle->clist->max_occupancy=8;
    cfg_free(cfg);
//    fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
    return TS_SUCCESS;

    cfg_free(cfg);
   free(buf);
  //  fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);

			

    return vesicle;

}


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;
}