Fixing the vesicle 123 and neighbours just for a test

Samo Penic

2019-04-23 13f45e61241e43d709df10228b946ed9870e8ebb

 src/io.c

@@ -1,3 +1,4 @@

/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
@@ -423,7 +424,7 @@
    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);
@@ -612,11 +613,17 @@
   fprintf(fd,"Flags:\n\n");
   fprintf(fd,"--force-from-tape\t\t makes initial shape of the vesicle from tape. Ignores already existing binary dump and possible simulation results.\n");
   fprintf(fd,"--restore-from-vtk\t\t VTK's file ending with '.vtu' are preferred way to make state snapshots for restoration. With this flag the restoration of the vesicle from vtk is possible. The simulation will continue if hidden '.status' file with last iteration done is present. Otherwise it will start simulation from timestep 0.\n");
   fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump or tape).\n");
   fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
   fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
   fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
   fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
   fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n");
   fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
   fprintf(fd,"Examples:\n\n");
   fprintf(fd,"trisurf --force-from-tape\n");
   fprintf(fd,"trisurf --reset-iteration-count\n");
   fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
   fprintf(fd,"\n\n");

   return TS_SUCCESS;
}

@@ -814,11 +821,12 @@
   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;
    ts_uint i,j;
   //ts_double senergy=0.0;
       char filename[10000];
        char just_name[255];
   FILE *fh;
@@ -855,8 +863,8 @@
   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\">");
    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=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
      for(i=0;i<vlist->n;i++){
      fprintf(fh,"%u ",vtx[i]->idx);
    }
@@ -880,7 +888,113 @@
      }
   }

    fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
       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");

   if(vesicle->tape->stretchswitch==1){
      fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
      for(i=0;i<blist->n;i++){
         fprintf(fh, "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,"</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);
   }
@@ -931,17 +1045,24 @@
      }

   }

   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;
@@ -1050,6 +1171,7 @@
        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),
@@ -1061,6 +1183,8 @@
   CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
   CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
   CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
   CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
   CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),	
   CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
   CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
   CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -1071,18 +1195,33 @@
        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_BOOL("quiet",(cfg_bool_t *)&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_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),
/* 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);
   }
@@ -1111,6 +1250,8 @@
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){

   char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
   operator[0]=0;
   operator[1]=0;
   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.