Constant area plugin done -- fix

Samo Penic

2019-03-08 06f70cc6f065746cf79c9792228356e3f015f4ec

 src/timestep.c

@@ -24,6 +24,7 @@
   ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
   ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
   ts_ulong epochtime;
   ts_double max_z,min_z;
   FILE *fd1,*fd2=NULL,*fd3=NULL;
    char filename[10000];
   //struct stat st;
@@ -49,35 +50,63 @@
      fd2=fopen(filename,"w");
   else
      fd2=fopen(filename,"a");
      if(fd2==NULL){
         fatal("Cannot open ulm2.csv file for writing",1);
      }
      if(start_iteration==0) //file does not exist
         fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");	

   if(fd2==NULL){
      fatal("Cannot open ulm2.csv file for writing",1);
   }
   if(start_iteration==0) //file does not exist
      fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");	
   }

/* RANDOM SEED SET BY CURRENT TIME */
   epochtime=get_epoch();         
   srand48(epochtime);

   centermass(vesicle);
   cell_occupation(vesicle);
   vesicle_volume(vesicle); //needed for constant volume at this moment
    vesicle_area(vesicle); //needed for constant area at this moment
   vesicle_area(vesicle); //needed for constant area at this moment
   if(V0<0.000001) 
      V0=vesicle->volume; 
   ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
   if(A0<0.000001)
      A0=vesicle->area;
      ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
   ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
   epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
    epsarea=A0/(ts_double)vesicle->tlist->n;
  //  fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
   epsarea=A0/(ts_double)vesicle->tlist->n;

   if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
   for(i=start_iteration;i<inititer+iterations;i++){
      vmsr=0.0;
      bfsr=0.0;

   //plane confinement
   if(vesicle->tape->plane_confinement_switch){
      min_z=1e10;
      max_z=-1e10;
      for(k=0;k<vesicle->vlist->n;k++){
         if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
         if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
      }
      vesicle->confinement_plane.force_switch=0;
      if(max_z>=vesicle->tape->plane_d/2.0){
         ts_fprintf(stdout, "Max vertex out of bounds (z>=%e). Plane set to max_z = %e.\n",vesicle->tape->plane_d/2.0,max_z);
         vesicle->confinement_plane.z_max = max_z;
         vesicle->confinement_plane.force_switch=1;
      } else {
         vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
      }
      if(min_z<=-vesicle->tape->plane_d/2.0){
         ts_fprintf(stdout, "Min vertex out of bounds (z<=%e). Plane set to min_z = %e.\n",-vesicle->tape->plane_d/2.0,min_z);
         vesicle->confinement_plane.z_min = min_z;
         vesicle->confinement_plane.force_switch=1;
      } else {
         vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
      }
      ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
      if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
   }

   //end plane confinement

/*    vesicle_volume(vesicle);
    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
      for(j=0;j<mcsweeps;j++){
@@ -94,7 +123,7 @@
      cell_occupation(vesicle);
            dump_state(vesicle,i);
      if(i>=inititer){
         write_vertex_xml_file(vesicle,i-inititer);
         write_vertex_xml_file(vesicle,i-inititer,NULL);
         write_master_xml_file(command_line_args.output_fullfilename);
         epochtime=get_epoch();         
         gyration_eigen(vesicle, &l1, &l2, &l3);