Merging again because I was merging in detached state

Samo Penic

2016-12-06 c2c6364dc7d23f21dabd2179e775e93ba4eeb252

 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);
@@ -820,7 +820,7 @@
   return TS_SUCCESS;
}

ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno, ts_cluster_list *cstlist){
   ts_vertex_list *vlist=vesicle->vlist;
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
@@ -862,7 +862,7 @@
   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)+vesicle->tlist->n);
    fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
    fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
      fprintf(fh,"%u ",vtx[i]->idx);
    }
@@ -887,7 +887,92 @@
   }

       fprintf(fh,"</DataArray>\n");
	
   if(cstlist!=NULL){
      fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
         if(vtx[i]->cluster!=NULL){
            fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
         } else {
            fprintf(fh,"-1 ");
         }
          }
      //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,"-1 ");
            }
         }
      }
      //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,"-1 ");
            }
         }
      }

      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");

   //here comes additional data. Energy!
   fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
   }
      //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]->energy* vesicle->poly_list->poly[i]->k);
            }
         }
      }
      //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]->energy*  vesicle->filament_list->poly[i]->k);
            }
         }
      }
    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");
@@ -1067,6 +1152,7 @@
        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),
@@ -1094,6 +1180,10 @@
        CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
        CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
   CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
   CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
   CFG_SIMPLE_FLOAT("c0",&tape->c0),
   CFG_SIMPLE_FLOAT("w",&tape->w),
   CFG_SIMPLE_FLOAT("F",&tape->F),
        CFG_END()
    };
    cfg_t *cfg;