ulm2 calculations in tsmeasure.c

Samo Penic

2016-05-25 fcfb89f8e0056e10631d3b09fca90bad7241db0e

 src/io.c

@@ -1,7 +1,7 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
#include "io.h"
#include <confuse.h>
#include "vertex.h"
#include "bond.h"
#include<string.h>
@@ -10,22 +10,23 @@
#include <dirent.h>
#include "initial_distribution.h"
#include "poly.h"

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

ts_bool dump_state(ts_vesicle *vesicle){
ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){

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

    /* dump vesicle */
    fwrite(vesicle, sizeof(ts_vesicle),1,fh);
    fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
    /* dump vertex list */
    fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
    /* dump bond list */
@@ -36,6 +37,8 @@
    fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
    /* dump poly list */
    fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* dump filament list */
    fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

    /*dump vertices*/
@@ -118,6 +121,43 @@
        }
    }


  /*dump filamentes grandes svinjas */
    for(i=0;i<vesicle->filament_list->n;i++){
        fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
        fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
    } 
     
    /* dump filamentes vertex(monomer) list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            /* dump offset for neigh and bond */
            for(k=0;k<vesicle->filament_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->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh); 
            }
            for(k=0;k<vesicle->filament_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->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh); 
            }
        }
    }
    /* dump poly bonds between monomers list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            fwrite(vesicle->filament_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->filament_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->filament_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
@@ -130,24 +170,40 @@
        poly_list->poly->bond
*/

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

//   fwrite(vesicle->clist, sizeof(ts_cell_list),1,  fh);
/* write tape information on vesicle */
//    fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
   fwrite(&iteration, sizeof(ts_uint),1,fh);
    fclose(fh);
    return TS_SUCCESS;
}


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

    struct stat sb;
    if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
        //dump file does not exist.
        return NULL;
    }

    //check if it is regular file
    if((sb.st_mode & S_IFMT) != S_IFREG) {
        //dump file is not a regular file.
        ts_fprintf(stderr,"Dump file is not a regular file!\n");
        return NULL;
    }

    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);
    retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
//   fprintf(stderr,"was here! %e\n",vesicle->dmax);

    /* restore vertex list */
@@ -165,6 +221,9 @@
    /* 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);
    /* restore filament list */
    vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

/* prerequisity. Bonds must be malloced before vertexes are recreated */
@@ -307,15 +366,67 @@
        }
    }

// 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!
       }
    /*restore filaments */
    vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
    for(i=0;i<vesicle->filament_list->n;i++){
        vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
        retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
        vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
        retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
        retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
   /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
        vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
    for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
   }
   for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
   }

    } 

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

        }
    }

    /* restore poly bonds between monomers list*/
    for(i=0;i<vesicle->filament_list->n;i++){
        for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
       //     vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
            retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* restore vtx1 and vtx2 */
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
        }
    }
    vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells // 
    vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
   vesicle->clist->max_occupancy=8;
//    vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
//    retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
   retval=fread(iteration,sizeof(ts_uint),1,fh);
    if(retval); 
    fclose(fh);
    return vesicle;
@@ -324,24 +435,35 @@


ts_bool parse_args(int argc, char **argv){
 int c, retval;
 DIR *dir;
    path[0]=0;
    int c, retval;
    struct stat sb;
    sprintf(command_line_args.path, "./"); //clear string;
    sprintf(command_line_args.output_fullfilename,"output.pvd");
    sprintf(command_line_args.dump_fullfilename,"dump.bin");
    sprintf(command_line_args.tape_fullfilename,"tape");
    sprintf(command_line_args.tape_templatefull,"./tape");
            FILE *file;
    
while (1)
     {
       static struct option long_options[] =
         {
           {"force-from-tape", no_argument,       &force_from_tape, 1},
           {"force-from-tape", no_argument,       &(command_line_args.force_from_tape), 1},
      {"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
           {"tape",     no_argument,       0, 't'},
      {"version", no_argument, 0, 'v'},
           {"output-file",  required_argument, 0, 'o'},
           {"directory",  required_argument, 0, 'd'},
           {"dump-file", required_argument,0, 'f'},
           {"dump-filename", required_argument,0, 'f'},
           {"tape-options",required_argument,0,'c'},
           {"tape-template", required_argument,0,0},
            {"restore-from-vtk",required_argument,0,0},
           {0, 0, 0, 0}
         };
       /* getopt_long stores the option index here. */
       int option_index = 0;

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

       /* Detect the end of the options. */
@@ -354,54 +476,57 @@
           /* 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);
/*           printf ("option %s", long_options[option_index].name);
           if (optarg)
             printf (" with arg %s", optarg);
           printf ("\n");
             printf (" with arg %s", optarg); 
           printf ("\n"); */
            //TODO: find a better way.
            if(strcmp(long_options[option_index].name,"tape-template")==0){
                strcpy(command_line_args.tape_templatefull,optarg);
            }
            if(strcmp(long_options[option_index].name,"restore-from-vtk")==0){
                strcpy(command_line_args.dump_from_vtk,optarg);
            }
           break;
    case 'v':
      fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
           fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
           fprintf(stdout,"Released under terms of GPLv3\n");
      exit(0);

         case 'c':
              strcpy(command_line_args.tape_opts,optarg);
            break;
         case 't': //tape
                strcpy(command_line_args.tape_fullfilename,optarg);
           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 'o':  //set filename of master pvd output file
            strcpy(command_line_args.output_fullfilename, optarg);
            break;

         case 'd':
            //check if directory exists. If not create one. If creation is
            //successful, set directory for output files.
            //printf ("option -d with value `%s'\n", optarg);
            dir = opendir(optarg);
            if (dir)
            {
                /* Directory exists. */
                closedir(dir);
            }
            else if (ENOENT == errno)
            {
                /* Directory does not exist. */
            if (stat(optarg, &sb) == -1) {
                //directory does not exist
                retval=mkdir(optarg, 0700);
                if(retval){
                fatal("Could not create requested directory. Check if you have permissions",1);
                    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);
            //check if is a proper directory
            else if((sb.st_mode & S_IFMT) != S_IFDIR) {
                //it is not a directory. fatal error.
                ts_fprintf(stderr,"%s is not a directory!\n",optarg);
                fatal("Cannot continue",1);
            }
            ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
//            sprintf(path,"%s", optarg);
            strcpy(path, optarg);
           // ts_fprintf(stdout,"ok!\n"); 

            strcpy(command_line_args.path, optarg);
           break;

        case 'f':
            //check if dump file specified exists. Defaults to dump.bin
            strcpy(command_line_args.dump_fullfilename, optarg);
            break;

         case '?':
@@ -416,10 +541,64 @@
         }
     }

//Here we set correct values for full filenames!
    char *buffer=(char *)malloc(10000*sizeof(char));
    //correct the path and add trailing /
    if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
   
/* master pvd output file */ 
    strcpy(buffer,command_line_args.path);
    strcat(buffer,command_line_args.output_fullfilename);
    if ((file = fopen(buffer, "w")) == NULL) {
                fprintf(stderr,"Could not create output file %s!\n", buffer);
                fatal("Please specify correct output file or check permissions of the file",1);
                //there is a tape template. make a copy into desired directory
                
            } else {
                fclose(file);
                strcpy(command_line_args.output_fullfilename,buffer);
            }

/* tape file */
    strcpy(buffer,command_line_args.path);
    strcat(buffer,command_line_args.tape_fullfilename);
    if (stat(buffer, &sb) == -1) {

                //tape does not exist. does tape template exist?
                if(stat(command_line_args.tape_templatefull, &sb)==-1){ 
                    ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
                    fatal("Please select correct tape or check permissions of the file",1);
                } else {
                    //tape template found
                    fatal("Samo did not program template copy yet",1); 
                }
            } else {
                strcpy(command_line_args.tape_fullfilename,buffer);
            }


/* dump file */
            strcpy(buffer,command_line_args.path);
            strcat(buffer,command_line_args.dump_fullfilename);
            //check if dump file exist first.
            if (stat(buffer, &sb) == -1) {
                //no dump file. check if we can create one.
                if ((file = fopen(buffer, "w")) == NULL) {
                    fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
                    fatal("Please specify correct dump file or check permissions of the file",1);
                } else {
                    fclose(file);
                    //good, file is writeable. delete it for now.
                    remove(buffer);
                }
            }
            strcpy(command_line_args.dump_fullfilename, buffer);


    free(buffer);
    return TS_SUCCESS;

}




@@ -520,11 +699,11 @@
        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]->neigh_no;j++){
        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]->neigh_no;j++){
        for(j=0;j<vlist->vtx[i]->bond_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
        }
            fprintf(fh,"\n");
@@ -591,7 +770,7 @@
        }

   fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
   DIR *dir = opendir(".");
   DIR *dir = opendir(command_line_args.path);
   if(dir){
      struct dirent *ent;
        tstep=0;
@@ -620,10 +799,13 @@
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
    ts_uint i,j;
       char filename[255];
       char filename[10000];
        char just_name[255];
   FILE *fh;
        strcpy(filename,command_line_args.path);
       sprintf(just_name,"timestep_%.6u.vtu",timestepno);
        strcat(filename,just_name);

       sprintf(filename,"timestep_%.6u.vtu",timestepno);
   fh=fopen(filename, "w");
   if(fh==NULL){
      err("Cannot open file %s for writing");
@@ -632,8 +814,8 @@
   /* 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;
   ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
   ts_bool poly=0, fil=0;
   if(vesicle->poly_list!=NULL){
      if(vesicle->poly_list->poly[0]!=NULL){
      polyno=vesicle->poly_list->n;
@@ -641,8 +823,19 @@
      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);

   if(vesicle->filament_list!=NULL){
      if(vesicle->filament_list->poly[0]!=NULL){
      filno=vesicle->filament_list->n;
      fonono=vesicle->filament_list->poly[0]->vlist->n;
      fil=1;
      }
   }

   fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
   xml_trisurf_data(fh,vesicle);
   fprintf(fh, " <UnstructuredGrid>\n");
    fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
    fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
      fprintf(fh,"%u ",vtx[i]->idx);
@@ -656,16 +849,34 @@
         }
      }
   }
   //filaments
   if(fil){
      poly_idx=vlist->n+monono*polyno;
      for(i=0;i<vesicle->filament_list->n;i++){
         for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
   //   fprintf(stderr,"was here\n");
            fprintf(fh,"%u ", poly_idx);
         }
      }
   }

    fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
      fprintf(fh,"%.17e %.17e %.17e\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,"%.17e %.17e %.17e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
         }
      }
   }
   //filaments
   if(fil){
      for(i=0;i<vesicle->filament_list->n;i++){
         for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
            fprintf(fh,"%.17e %.17e %.17e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
         }
      }
   }
@@ -688,14 +899,26 @@

   }
   
   //filaments
   if(fil){
      poly_idx=vlist->n+monono*polyno;
      for(i=0;i<vesicle->filament_list->n;i++){
         for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
            fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
//      fprintf(stderr,"was here\n");
			
         }
      }

   }

    fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
    for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
    for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
    fprintf(fh,"%u ",i);
    }
    fprintf(fh,"\n");
    fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
     for (i=0;i<blist->n+monono*polyno;i++){
     for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
        fprintf(fh,"3 ");
    }

@@ -750,76 +973,175 @@



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;
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
   FILE *fh;
   ts_uint i;
	
   fh=fopen(filename, "w");
   if(fh==NULL){
      err("Cannot open file %s for writing");
      return TS_FAIL;
   }

   for(i=0;i<vesicle->tlist->n;i++){
	
   fprintf(fh,"\ttriangle {");
   fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n", 
   vesicle->tlist->tria[i]->vertex[0]->x,
   vesicle->tlist->tria[i]->vertex[0]->y,
   vesicle->tlist->tria[i]->vertex[0]->z,

   vesicle->tlist->tria[i]->vertex[1]->x,
   vesicle->tlist->tria[i]->vertex[1]->y,
   vesicle->tlist->tria[i]->vertex[1]->z,

   vesicle->tlist->tria[i]->vertex[2]->x,
   vesicle->tlist->tria[i]->vertex[2]->y,
   vesicle->tlist->tria[i]->vertex[2]->z
   );
   }
		
   fclose(fh);
   return TS_SUCCESS;
}


ts_tape *parsetape(char *filename){
   FILE *fd = fopen (filename, "r");
   long length;
   size_t size;
   fseek (fd, 0, SEEK_END);
     length = ftell (fd);
   fseek (fd, 0, SEEK_SET);
   size=fread (tapetxt, 1, length, fd);
   fclose(fd);
   if(size);
   ts_tape *tape=parsetapebuffer(tapetxt);
   return tape;
}

ts_tape *parsetapebuffer(char *buffer){
    ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
    tape->multiprocessing=calloc(255,sizeof(char));

    cfg_opt_t opts[] = {
        CFG_SIMPLE_INT("nshell", &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",&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_SIMPLE_INT("nshell", &tape->nshell),
        CFG_SIMPLE_INT("npoly", &tape->npoly),
        CFG_SIMPLE_INT("nmono", &tape->nmono),
   CFG_SIMPLE_INT("nfil",&tape->nfil),
   CFG_SIMPLE_INT("nfono",&tape->nfono),
   CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
   CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
   CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
        CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
   CFG_SIMPLE_INT("pswitch",&tape->pswitch),
   CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
   CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
   CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
   CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
   CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
   CFG_SIMPLE_FLOAT("xi",&tape->xi),
        CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
        CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
        CFG_SIMPLE_INT("nymax", &tape->ncymax),
        CFG_SIMPLE_INT("nzmax", &tape->nczmax),
        CFG_SIMPLE_INT("iterations",&tape->iterations),
   CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
   CFG_SIMPLE_INT("inititer", &tape->inititer),
        CFG_SIMPLE_BOOL("quiet",&tape->quiet),
        CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
        CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
        CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
        CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
   CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
        CFG_END()
    };
    cfg_t *cfg;    
    ts_uint retval;
    cfg = cfg_init(opts, 0);
    retval=cfg_parse(cfg, "tape");
    retval=cfg_parse_buf(cfg, buffer);
    if(retval==CFG_FILE_ERROR){
   fatal("No tape file.",100);
   }
    else if(retval==CFG_PARSE_ERROR){
   fatal("Invalid tape!",100);
   }
   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;
    vesicle->stepsize=stepsize;
    vesicle->clist->ncmax[0]=ncxmax;
    vesicle->clist->ncmax[1]=ncymax;
    vesicle->clist->ncmax[2]=nczmax;
    vesicle->clist->max_occupancy=8;

    /* here we override all values read from tape with values from commandline*/
    getcmdline_tape(cfg,command_line_args.tape_opts);
    cfg_free(cfg);
   free(buf);
  //  fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);

			

    return vesicle;

   /* global variables are set automatically */
   quiet=tape->quiet;
   return tape;
}

ts_bool tape_free(ts_tape *tape){
   free(tape->multiprocessing);
   free(tape);
   return TS_SUCCESS;
}



ts_bool getcmdline_tape(cfg_t *cfg, char *opts){

   char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
   ts_uint i,j;
   commands=(char *)malloc(10000*sizeof(char));
    backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
   strcpy(commands,opts);
   for(i=0; ;i++, commands=NULL){
      //breaks comma separated list of commands into specific commands.
      command=strtok_r(commands,",",&saveptr);	
      if(command==NULL) break;
//      fprintf(stdout,"Command %d: %s\n",i,command);	
      //extracts name of command and value of command into operator[2] array.
      for(j=0; j<2;j++,command=NULL){
         operator[j]=strtok_r(command,"=",&saveopptr);
         if(operator[j]==NULL) break;
//         fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);		
      }
      //1. check: must have 2 operators.
      if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);

    //    cfg_setstr(cfg,operator[0],operator[1]);
        cmdline_to_tape(cfg,operator[0],operator[1]);
      //2. check: must be named properly.
      //3. check: must be of right format (integer, double, string, ...)
        
   }
   free(backup);
    return TS_SUCCESS;
}


ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val){

    cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
    if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL; 
    switch (cfg_opt->type){
        case CFGT_INT:
            cfg_setint(cfg,key,atol(val));
            break;
        case CFGT_FLOAT:
            cfg_setfloat(cfg,key,atof(val));
            break;
/*        case CFGT_BOOL:
            cfg_setbool(cfg,operator[0],operator[1]);
            break; */
        case CFGT_STR:
            cfg_setstr(cfg,key,val);
            break;
        default:
            break;

    }
    return TS_SUCCESS;
}



ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
   FILE *fh;