Added stretching variables

Samo Penic

2018-12-11 6c274defd904dedd6cb89c002f5eeced6c079d47

 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;
@@ -72,19 +73,40 @@
   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;

   //plane confinement part 1

   if(vesicle->tape->plane_confinement_switch){
      vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
      vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
      ts_fprintf(stderr,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
   }
	
  //  fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
   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++){