changed the automake script

Samo Penic

2016-02-16 d0cafa2d67b4765450deb5781b08f4241d9c4d3a

 src/main.c

@@ -1,5 +1,6 @@
#include<stdio.h>
#include<math.h>
#include<stdlib.h>
#include "general.h"
#include "vertex.h"
#include "bond.h"
@@ -13,6 +14,7 @@
#include "poly.h"
#include "sh.h"
#include "shcomplex.h"
#include "dumpstate.h"

/** Entrance function to the program
  * @param argv is a number of parameters used in program call (including the program name
@@ -27,18 +29,26 @@
   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){

    if(command_line_args.dump_from_vtk[0]!=0){
      ts_fprintf(stdout,"************************************************\n");
      ts_fprintf(stdout,"***** Dumping vesicle from VTK points list *****\n");
      ts_fprintf(stdout,"************************************************\n\n");
        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("tape");
      tape=parsetape(command_line_args.tape_fullfilename);
      vesicle=create_vesicle_from_tape(tape);
   } else {

      ts_fprintf(stdout,"**********************************************************************\n");
      ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
      ts_fprintf(stdout,"**********************************************************************\n\n");
      tape=parsetape("tape");
      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");
@@ -51,9 +61,12 @@
      vesicle->pressure=tape->pressure;
      vesicle->dmax=tape->dmax*tape->dmax;
      poly_assign_filament_xi(vesicle,tape);
        tape_free(vesicle->tape);
        free(vesicle->tape);
        vesicle->tape=tape;
      vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;



        /* spherical harmonics */
        if(tape->shc>0){
           vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
@@ -69,10 +82,24 @@
         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;
      }

   /* 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){

      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);

      }
      }
   }

   run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
   write_master_xml_file("test.pvd");
   write_master_xml_file(command_line_args.output_fullfilename);
   write_dout_fcompat_file(vesicle,"dout");
   vesicle_free(vesicle);
   tape_free(tape);