Added possibility of internal pegs. It can break the system however

Samo Penic

2016-07-11 e984829db39b2778e4f66c34524329ad09749c45

 src/main.c

@@ -1,5 +1,7 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdio.h>
#include<math.h>
#include<stdlib.h>
#include "general.h"
#include "vertex.h"
#include "bond.h"
@@ -11,7 +13,12 @@
#include "frame.h"
#include "timestep.h"
#include "poly.h"
#include "sh.h"
#include "shcomplex.h"
#include "dumpstate.h"
#include "restore.h"

#include <fcntl.h>
/** Entrance function to the program
  * @param argv is a number of parameters used in program call (including the program name
  * @param argc is a pointer to strings (character arrays) which holds the arguments
@@ -19,74 +26,111 @@
*/

int main(int argv, char *argc[]){
ts_uint inititer,mcsweeps, iterations;
ts_vesicle *vesicle, *vesicle1;
/* THIS SHOULD GO INTO UNIT TEST
ts_bool retval;
    ts_vertex_list *vlist=init_vertex_list(5);
ts_vertex_list *vlist1;
ts_bond_list *blist=init_bond_list();
ts_triangle_list *tlist=init_triangle_list();
ts_cell_list *clist=init_cell_list(3,3,3,0.3);
   ts_vesicle *vesicle;
   ts_tape *tape;
   ts_uint start_iteration=0;
   force_from_tape=0;
   /* Area and volume for constant area and constant volume are initialized to be zero */
   A0=0;
   V0=0;
   /* create lock file */
   createPidFile("ts_trisurf",".lock",0);
   parse_args(argv,argc); // sets global variable command_line_args (defined in io.h)
   ts_fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
   ts_fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
   ts_fprintf(stdout,"Released under terms of GPLv3\n");
   ts_fprintf(stdout,"Starting program...\n\n");
//   vesicle = parseDump("timestep_000000.vtu");
//      run_simulation(vesicle, vesicle->tape->mcsweeps, vesicle->tape->inititer, vesicle->tape->iterations, 1);

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");
    if(command_line_args.dump_from_vtk[0]!=0){
      ts_fprintf(stdout,"************************************************\n");
      ts_fprintf(stdout,"**** Restoring vesicle from VTK points list ****\n");
      ts_fprintf(stdout,"************************************************\n\n");
      vesicle = parseDump(command_line_args.dump_from_vtk);
      tape = vesicle->tape;
      int arguments_no;
      FILE *fd=fopen(".status","r");
      if(fd!=NULL){
         arguments_no=fscanf(fd,"%u", &start_iteration);
         if(arguments_no==0){
            ts_fprintf(stdout,"No information of start iteration in .status file\n");
            }
         fclose(fd);
         start_iteration++; 
      }
      else
         ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n");
/* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */
//        tape=parsetape(command_line_args.tape_fullfilename);
  //      vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape);
    }
   else 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(command_line_args.tape_fullfilename);
      vesicle=create_vesicle_from_tape(tape);
   } else {

retval=vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");
fprintf(stderr,"Was here");
retval=vtx_remove_neighbour(vlist->vtx[1],vlist->vtx[0]);
vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
fprintf(stderr,"Was here too!\n");

vlist->vtx[0]->x=1.0;
vlist->vtx[0]->x=1.1;
vlist1=vertex_list_copy(vlist);
bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);

triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);

printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
cell_add_vertex(clist->cell[0], vlist->vtx[0]);
printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->vertex[0]->x);
cell_list_cell_occupation_clear(clist);
printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
cell_add_vertex(clist->cell[0], vlist->vtx[0]);
      ts_fprintf(stdout,"**********************************************************************\n");
      ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
      ts_fprintf(stdout,"**********************************************************************\n\n");
      tape=parsetape(command_line_args.tape_fullfilename);
      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->pswitch =tape->pswitch;
      vesicle->pressure=tape->pressure;
      vesicle->dmax=tape->dmax*tape->dmax;
      poly_assign_filament_xi(vesicle,tape);
        free(vesicle->tape);
        vesicle->tape=tape;
      vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;


triangle_list_free(tlist);
bond_list_free(blist);
vtx_list_free(vlist);
cell_list_free(clist);

vtx_list_free(vlist1);
printf("Tests complete.\n");
*/
vesicle1=parsetape(&mcsweeps, &inititer, &iterations);
        /* spherical harmonics */
        if(tape->shc>0){
           vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
        }
        else {
            vesicle->sphHarmonics=NULL;
        }

/*Testing */
//vesicle->poly_list=init_poly_list(1400,20,vesicle->vlist);
      if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
      else start_iteration++;

//poly_list_free(vesicle->poly_list);
/*End testing*/
      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;
      }

//write_vertex_xml_file(vesicle,0);
//vesicle_free(vesicle);
dump_state(vesicle1);
vesicle=restore_state();
//write_vertex_xml_file(vesicle,1);
//write_master_xml_file("test.pvd");
//vesicle_free(vesicle1);
//vesicle_free(vesicle);
vesicle_free(vesicle1);
fprintf(stderr,"Starting simulation...");
run_simulation(vesicle, mcsweeps, inititer, iterations);
   /* if requested in tape, we can have smaller number of polymeres attached to membrane than the number of polymeres in dump file */
      if(vesicle->tape->npoly != vesicle->poly_list->n){

write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);
      ts_fprintf(stdout,"(INFO) the number of polymeres attached to membrane in tape is different than a number of polymeres in dump file!\n");
      if(vesicle->tape->npoly > vesicle->poly_list->n){
         ts_fprintf(stdout,"(INFO) It is possible to decrease the number of polymeres on the membrane, but it is not allowed to increase its number. The maximal allowed number in tape is %d The execution of program will terminate!\n",vesicle->poly_list->n);
         fatal("Terminating due to increase of number of polymeres",1);
      } else {
         remove_random_polymeres(vesicle->poly_list, vesicle->poly_list->n - vesicle->tape->npoly);
         ts_fprintf(stdout,"(INFO)\n(INFO) The new number of polymeres from tape is %d.\n\n",vesicle->poly_list->n);

return 0; //program finished perfectly ok. We return 0.
      }
      }
   }
         //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);

   run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
   write_master_xml_file(command_line_args.output_fullfilename);
   write_dout_fcompat_file(vesicle,"dout");
   vesicle_free(vesicle);
   tape_free(tape);
   return 0; //program finished perfectly ok. We return 0.
}