Resolving the issues with restoring vesicles from vtu and fixing the volume...

Samo Penic

2018-06-27 6da644f98434d3eac8b4e19981754f6030a315a5

 src/vertexmove.c

@@ -21,7 +21,8 @@
    ts_double dist;
    ts_bool retval; 
    ts_uint cellidx; 
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
    ts_double temp_area=0.0; //for stretching
    ts_double costheta,sintheta,phi,r;
   //This will hold all the information of vtx and its neighbours
   ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
@@ -113,7 +114,16 @@
      for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
    
    }

   //stretching energy 1 of 3
   if(vesicle->tape->stretchswitch==1){
      temp_area=vesicle->area;
      dstretchenergy-=stretchenergy2(vesicle->area,vesicle->tlist->a0*vesicle->tlist->n);
      for(i=0;i<vtx->tristar_no;i++){
         temp_area-=vtx->tristar[i]->area;
      }
      //0.5*vesicle->tape->xkA0*pow((vesicle->area-vesicle->tlist->a0*vesicle->tlist->n),2)/(vesicle->tlist->a0*vesicle->tlist->n);
      //for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
   }
    delta_energy=0;
    
//    vesicle_volume(vesicle);
@@ -155,7 +165,7 @@

   if(vesicle->tape->constvolswitch==2){
      /*check whether the dvol is gt than epsvol */
         //fprintf(stderr,"DVOL=%1.16e\n",dvol);
         //fprintf(stderr,"DVOL=%1.16e, V0=%1.16e, vesicleVolume=%1.16e, |volume+dvol-V0|=%1.16e\n",dvol, V0, vesicle->volume, fabs(vesicle->volume+dvol-V0));
      if(fabs(vesicle->volume+dvol-V0)>epsvol){
         //restore old state.
          vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
@@ -163,11 +173,12 @@
                 vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
              }
                  for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]); 
                  //fprintf(stderr,"fajlam!\n");
               //   fprintf(stderr,"fajlam!\n");
                  return TS_FAIL;
      }

   } else
      //fprintf(stderr, "success\n");
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
   if(vesicle->tape->constvolswitch == 1){
@@ -189,6 +200,21 @@
    delta_energy+=delta_energy_cv;
//    fprintf(stderr,"Denergy after=%e\n",delta_energy);
    }
/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
   delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);

   //stretching energy 2 of 3
   if(vesicle->tape->stretchswitch==1){
      for(i=0;i<vtx->tristar_no;i++){
         temp_area+=vtx->tristar[i]->area; 
         }
      dstretchenergy+=stretchenergy2(temp_area,vesicle->tlist->a0*vesicle->tlist->n);
      dstretchenergy=0.5*vesicle->tape->xkA0*dstretchenergy;
		
   }

   delta_energy+=dstretchenergy;	
		
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -219,7 +245,13 @@
   
    //update the normals of triangles that share bead i.
   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);

/*   //stretching energy 3 of 3
   if(vesicle->tape->stretchswitch==1){
      for(i=0;i<vtx->tristar_no;i++){ 
         stretchenergy(vesicle,vtx->tristar[i]);
         }
   }
*/
//    fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
    if(vesicle->tape->constvolswitch == 1){
        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
@@ -250,6 +282,10 @@
    if(vesicle->tape->constareaswitch==2){
        vesicle->area+=darea;
    }
   //stretching energy 3 of 3
   if(vesicle->tape->stretchswitch==1){
      vesicle->area=temp_area;
   }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO
//    vesicle_volume(vesicle);