Removed some old non-essential files

Samo Penic

2020-04-13 a7fb2b94260897ec914f0bbf31698e166263036c

 src/io.c

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

/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
@@ -423,7 +424,8 @@
    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=8;
//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);
@@ -749,22 +751,6 @@
}


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;
@@ -825,6 +811,7 @@
   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;
@@ -843,7 +830,8 @@
   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;
@@ -851,7 +839,8 @@
   }

   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;
@@ -973,9 +962,26 @@
      }
    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,"</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);
   }
@@ -1152,6 +1158,7 @@
        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),
@@ -1163,6 +1170,8 @@
   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),
@@ -1173,8 +1182,8 @@
        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),
@@ -1183,12 +1192,23 @@
   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);
   }
@@ -1217,6 +1237,8 @@
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.