Merge branch 'stretching-devel' into plane-new

Samo Penic

2019-02-08 4019ca8157136a68b6e43b31f166dc93acd81b4d

 src/io.c

@@ -826,7 +826,7 @@
   ts_bond_list *blist=vesicle->blist;
   ts_vertex **vtx=vlist->vtx;
    ts_uint i,j;
   ts_double senergy=0.0;
   //ts_double senergy=0.0;
       char filename[10000];
        char just_name[255];
   FILE *fh;
@@ -974,39 +974,27 @@
         }
      }
    fprintf(fh,"</DataArray>\n");

	
   fprintf(fh,"</PointData>\n<CellData>\n");

   if(vesicle->tape->stretchswitch==1){
      fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
         senergy=0.0;
         for(j=0;j<vtx[i]->tristar_no;j++){
            senergy+=vtx[i]->tristar[j]->energy;
         }
         fprintf(fh,"%.17e ",senergy);
      for(i=0;i<blist->n;i++){
         fprintf(fh, "0.0 ");
      }
         //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 ", 0.0);
               }
            }
         }
         //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 ", 0.0);
               }
            }
         }
      for(i=0;i<monono*polyno+filno*(fonono-1);i++){
         fprintf(fh,"0.0 ");
      }
      for(i=0;i<vesicle->tlist->n;i++){
         fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
      }
       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");


   fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
   }
@@ -1217,12 +1205,23 @@
   CFG_SIMPLE_FLOAT("c0",&tape->c0),
   CFG_SIMPLE_FLOAT("w",&tape->w),
   CFG_SIMPLE_FLOAT("F",&tape->F),
/* Variables related to plane confinement */
   CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
   CFG_FLOAT("plane_d", 15, CFGF_NONE),
   CFG_FLOAT("plane_F", 1000, CFGF_NONE),
/* Variables related to stretching */
   CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
   CFG_FLOAT("xkA0",0,CFGF_NONE),
        CFG_END()
    };
    cfg_t *cfg;    
    ts_uint retval;
    cfg = cfg_init(opts, 0);
    retval=cfg_parse_buf(cfg, buffer);
   tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
   tape->plane_d=cfg_getfloat(cfg,"plane_d");
   tape->plane_F=cfg_getfloat(cfg,"plane_F");

    if(retval==CFG_FILE_ERROR){
   fatal("No tape file.",100);
   }