Changes in plates movement

Samo Penic

2018-10-11 b4e2e6dbd5049ae279f0f74838cd21b625148c72

 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=0, min_z=0, cm_backup[3];
   FILE *fd1,*fd2=NULL,*fd3=NULL;
    char filename[10000];
   //struct stat st;
@@ -49,31 +50,51 @@
      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
   V0=vesicle->volume; 
    A0=vesicle->area;
   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);
   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;
   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;
            }
            if(max_z-min_z<=vesicle->tape->plane_d) {
               vesicle->confinement_plane.z_max=max_z;
               vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
            }  else {
               vesicle->confinement_plane.z_min=min_z;//-1e-5;
               vesicle->confinement_plane.z_max=max_z;//+1e-5;
            }
   }

  //  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;


/*    vesicle_volume(vesicle);
    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
      for(j=0;j<mcsweeps;j++){
@@ -86,18 +107,41 @@
    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
      vmsr/=(ts_double)mcsweeps;
      bfsr/=(ts_double)mcsweeps;
      for (k=0;k<3;k++) cm_backup[k]=vesicle->cm[k];

      centermass(vesicle);
      cell_occupation(vesicle);
      ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
            dump_state(vesicle,i);
      fd3=fopen(".status","w");
      if(fd3==NULL){
         fatal("Cannot open .status file for writing",1);

      // plane confinement
      if(vesicle->tape->plane_confinement_switch){
         if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min<=vesicle->tape->plane_d){
            ts_fprintf(stdout,"Force is off\n");
         } else {
            ts_fprintf(stdout,"Force is on\n");
			
            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;
            }
            if(max_z-min_z<=vesicle->tape->plane_d) {
               vesicle->confinement_plane.z_max+=(vesicle->cm[2]-cm_backup[2]);	
               vesicle->confinement_plane.z_min+=(vesicle->cm[2]-cm_backup[2]);
               //vesicle->confinement_plane.z_max=max_z;
               //vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
            }  else {
               vesicle->confinement_plane.z_min=min_z;//-1e-5;
               vesicle->confinement_plane.z_max=max_z;//+1e-5;
            }
         }
         ts_fprintf(stdout,"Planes (zmin, zmax)=(%e,%e)\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);	
      }
      fprintf(fd3,"%d",i);
      fclose(fd3);
      // end plane confinement

            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);
@@ -146,7 +190,14 @@
          fflush(fd);   
      //   sprintf(filename,"timestep-%05d.pov",i-inititer);
      //   write_pov_file(vesicle,filename);
      } //end if(inititer....)
      fd3=fopen(".status","w"); //write status file when everything is written to disk.
      if(fd3==NULL){
         fatal("Cannot open .status file for writing",1);
      }
      fprintf(fd3,"%d",i);
      fclose(fd3);
      ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
   }
   fclose(fd);
   if(fd2!=NULL) fclose(fd2);