Moved all global variables to separate file and defined extern keyword wher...

Samo Penic

2022-05-04 06afc729f9061c1cfa14c78728d61d518324c2f0

 src/io.c

@@ -1,6 +1,7 @@

/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include "globals.h"
#include<stdio.h>
#include "io.h"
#include "vertex.h"
@@ -424,7 +425,8 @@
    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=16;
//THIS IS HARDCODED IN CELL.C NOW
//   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);
@@ -750,22 +752,6 @@
}


ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
   FILE *fh;
   fh=fopen(filename, "w");
    if(fh==NULL){
        err("Cannot open file %s for writing");
        return TS_FAIL;
    }
    fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
    fprint_vertex_list(fh,vesicle->vlist);
    fprint_tristar(fh,vesicle);
    fprint_triangle_list(fh,vesicle);
    fprint_vertex_data(fh,vesicle->vlist);
    fprint_bonds(fh,vesicle);
   fclose(fh);	
   return TS_SUCCESS;
}

ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
   FILE *fh;
@@ -826,7 +812,7 @@
   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;
@@ -845,7 +831,8 @@
   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){
      if(vesicle->poly_list->n!=0){
      //if(vesicle->poly_list->poly[0]!=NULL){
      polyno=vesicle->poly_list->n;
      monono=vesicle->poly_list->poly[0]->vlist->n;
      poly=1;
@@ -853,7 +840,8 @@
   }

   if(vesicle->filament_list!=NULL){
      if(vesicle->filament_list->poly[0]!=NULL){
      if(vesicle->filament_list->n!=0){
      //if(vesicle->filament_list->poly[0]!=NULL){
      filno=vesicle->filament_list->n;
      fonono=vesicle->filament_list->poly[0]->vlist->n;
      fil=1;
@@ -948,6 +936,30 @@
         }
      }
    fprintf(fh,"</DataArray>\n");
   fprintf(fh,"<DataArray type=\"Float64\" Name=\"direct_interaction_force\" format=\"ascii\">");
   for(i=0;i<vlist->n;i++){
      fprintf(fh,"%.17e ",vtx[i]->direct_interaction_force);
   }
      //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]->direct_interaction_force);
            }
         }
      }
      //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]->direct_interaction_force);
            }
         }
      }
    fprintf(fh,"</DataArray>\n");

   //here comes additional data. Energy!
   fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
@@ -974,39 +986,27 @@
         }
      }
    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 +1217,23 @@
   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);
   }