Added nucleus. Better initial configuration of filaments.

mihaf

2014-03-25 fe24d29b3c8684f08dccd01f5785aa48b7137322

 src/main.c

@@ -3,8 +3,14 @@
#include "general.h"
#include "vertex.h"
#include "bond.h"
//#include "io.h"
//#include "initial_timestep.h"
#include "triangle.h"
#include "cell.h"
#include "vesicle.h"
#include "io.h"
#include "initial_distribution.h"
#include "frame.h"
#include "timestep.h"
#include "poly.h"

/** Entrance function to the program
  * @param argv is a number of parameters used in program call (including the program name
@@ -13,23 +19,50 @@
*/

int main(int argv, char *argc[]){
ts_bool retval;
ts_vertex_list *vlist=init_vertex_list(5);
ts_bond_list *blist=init_bond_list();
   ts_vesicle *vesicle;
   ts_tape *tape;
   ts_uint start_iteration=0;
   force_from_tape=0;
   parse_args(argv,argc); // sets global variable command_line_args (defined in io.h)
   ts_fprintf(stdout,"Starting program...\n\n");
   if(command_line_args.force_from_tape){
      ts_fprintf(stdout,"************************************************\n");
      ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n");
      ts_fprintf(stdout,"************************************************\n\n");
      tape=parsetape("tape");
      vesicle=create_vesicle_from_tape(tape);
   } else {

retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]);
if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n");
      ts_fprintf(stdout,"**********************************************************************\n");
      ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
      ts_fprintf(stdout,"**********************************************************************\n\n");
      tape=parsetape("tape");
      vesicle=restore_state(&start_iteration);
        if(vesicle==NULL){
            ts_fprintf(stderr, "Dump file does not exist or is not a regular file! Did you mean to invoke trisurf with --force-from-tape option?\n\n");
            return 1;
        }
      // nove vrednosti iz tapea...
      vesicle->bending_rigidity=tape->xk0;
      vtx_set_global_values(vesicle);
      vesicle->pressure=tape->pressure;
      vesicle->dmax=tape->dmax*tape->dmax;
      poly_assign_filament_xi(vesicle,tape);
      vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;

retval=vtx_add_cneighbour(blist,vlist->vtx[0],vlist->vtx[1]);
if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");
      if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
      else start_iteration++;

vlist->vtx[0]->data->x=1.0;
vlist->vtx[0]->data->x=1.1;
      if(start_iteration>=tape->iterations){
         ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n");
         return 0;
      }
   }

bond_add(blist, vlist->vtx[1],vlist->vtx[0]);

bond_list_free(blist);
vtx_list_free(vlist);
printf("Done.\n");
return 0; //program finished perfectly ok. We return 0.
   run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
   write_master_xml_file("test.pvd");
   write_dout_fcompat_file(vesicle,"dout");
   vesicle_free(vesicle);
   tape_free(tape);
   return 0; //program finished perfectly ok. We return 0.
}