Many changes to the code to allow internal pegs

Samo Penic

2016-07-13 90882f51387b945bc0f660d8b12200b2f48e80fa

 src/io.c

@@ -423,7 +423,7 @@
    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->clist->max_occupancy=16;
//    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);
@@ -861,7 +861,7 @@
   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, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
    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);
@@ -887,34 +887,6 @@
   }

       fprintf(fh,"</DataArray>\n");
	
   //here comes additional data as needed. Currently only spontaneous curvature
   fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%.17e ",vtx[i]->c);
   }
      //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,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
            }
         }
      }
      //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,"%.17e ",  vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
            }
         }
      }
    fprintf(fh,"</DataArray>\n");


   
   fprintf(fh,"</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++){
@@ -967,17 +939,24 @@
      }

   }

   for(i=0;i<vesicle->tlist->n;i++){
      fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
   }
    fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
    for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
    fprintf(fh,"%u ",i);
    }
   for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
      fprintf(fh,"%u ", j);
   }
    fprintf(fh,"\n");
    fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
     for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
     for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++){
        fprintf(fh,"3 ");
    }

   for(i=0;i<vesicle->tlist->n;i++){
      fprintf(fh,"5 ");
   }
    fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
    fclose(fh);
    return TS_SUCCESS;
@@ -1086,6 +1065,7 @@
        CFG_SIMPLE_INT("nmono", &tape->nmono),
   CFG_SIMPLE_INT("nfil",&tape->nfil),
   CFG_SIMPLE_INT("nfono",&tape->nfono),
   CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
   CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
   CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
   CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),