Full write of constant volume plugin

Samo Penic

2019-03-08 2afc2f4f1dd89518995f1b5a539aea932aecab65

 src/vertexmove.c

@@ -20,67 +20,45 @@
    ts_uint i;
    ts_bool retval; 
    ts_uint cellidx; 
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
    ts_double delta_energy, oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
    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;
   memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
    ts_vertex backupvtx[20]; // *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
    memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));

//random move in a sphere with radius stepsize:
   r=vesicle->stepsize*rn[0];
   phi=rn[1]*2*M_PI;
   costheta=2*rn[2]-1;
   sintheta=sqrt(1-pow(costheta,2));
   vtx->x=vtx->x+r*sintheta*cos(phi);
   vtx->y=vtx->y+r*sintheta*sin(phi);
   vtx->z=vtx->z+r*costheta;
    //random move in a sphere with radius stepsize:
    r=vesicle->stepsize*rn[0];
    phi=rn[1]*2*M_PI;
    costheta=2*rn[2]-1;
    sintheta=sqrt(1-pow(costheta,2));
    vtx->x=vtx->x+r*sintheta*cos(phi);
    vtx->y=vtx->y+r*sintheta*sin(phi);
    vtx->z=vtx->z+r*costheta;


// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
//#define SQ(x) x*x
if(vesicle->R_nucleus>0.0){
   if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
      return TS_FAIL;
   }
} else if(vesicle->R_nucleusX>0.0){
//   fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
//   if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
   if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
//   if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
      return TS_FAIL;
   }

}

   // plane confinement check whether the new position of vertex will be out of bounds
   if(vesicle->tape->plane_confinement_switch){
      if(vtx->z>vesicle->confinement_plane.z_max || vtx->z<vesicle->confinement_plane.z_min){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
      return TS_FAIL;
      }
   }
//#undef SQ

/* Entry point for plugin vm_hard_constraint() function */
   for(i=0; i<vesicle->plist->n;i++){
      retval = vesicle->plist->plugin[i]->function->vm_hard_constraint(vesicle,vtx,&backupvtx[0]);
   vesicle->plist->pointer=vesicle->plist->chain->vm_hard_constraint;
   while(vesicle->plist->pointer!=NULL){
      retval = vesicle->plist->pointer->plugin->function->vm_hard_constraint(vesicle,vtx, &backupvtx[0]);
      if(retval==TS_FAIL){
         vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
         return TS_FAIL;
      }
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_hard_constraint() */

 
//if all the tests are successful, then energy for vtx and neighbours is calculated
/* Backuping the neighbours */ 
   for(i=0;i<vtx->neigh_no;i++){
   memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
   }

   if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
      for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
/* Entry point for plugin vm_energy_before_prepare() */

   vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
   while(vesicle->plist->pointer!=NULL){
      vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }

    if(vesicle->tape->constareaswitch==2){
@@ -109,10 +87,16 @@
        delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
    }

   if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
      for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
        if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
   };

/* Entry point for plugin vm_energy_after_execute() */

   vesicle->plist->pointer=vesicle->plist->chain->vm_energy_after_execute;
   while(vesicle->plist->pointer!=NULL){
      delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }



    if(vesicle->tape->constareaswitch==2){
        /* check whether the darea is gt epsarea */
@@ -131,42 +115,6 @@

    }

   if(vesicle->tape->constvolswitch==2){
      /*check whether the dvol is gt than epsvol */
         //fprintf(stderr,"DVOL=%1.16e\n",dvol);
      if(fabs(vesicle->volume+dvol-V0)>epsvol){
         //restore old state.
          vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
              for(i=0;i<vtx->neigh_no;i++){
                 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");
                  return TS_FAIL;
      }

   } else
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
   if(vesicle->tape->constvolswitch == 1){
        retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
        if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
            vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
           for(i=0;i<vtx->neigh_no;i++){
              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");
            return TS_FAIL;
        }
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
//    fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
//    fprintf(stderr,"Denergy before=%e\n",delta_energy);
    
    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);

@@ -203,9 +151,29 @@
      }
   }


/* Entry point for plugin vm_before_montecarlo_constraint() function */
   vesicle->plist->pointer=vesicle->plist->chain->vm_before_montecarlo_constraint;
   while(vesicle->plist->pointer!=NULL){
      retval = vesicle->plist->pointer->plugin->function->vm_before_montecarlo_constraint(vesicle,vtx, &backupvtx[0]);
      if(retval==TS_FAIL){
         vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
         for(i=0;i<vtx->neigh_no;i++){
            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]); 
         return TS_FAIL;
      }
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_before_montecarlo_constraint() */





//   fprintf(stderr, "DE=%f\n",delta_energy);
    //MONTE CARLOOOOOOOO
//   if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
    if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48())
@@ -234,9 +202,9 @@
   }

//    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);
    }
//    if(vesicle->tape->constvolswitch == 1){
//        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
//    }
//    fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
@@ -256,18 +224,27 @@

    if(vesicle->tape->constvolswitch == 2){
   vesicle->volume+=dvol;
    } else
    if(vesicle->tape->constvolswitch == 1){
        constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
    }
    } 



    if(vesicle->tape->constareaswitch==2){
        vesicle->area+=darea;
    }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);


/* Entry point for plugin vm_before_montecarlo_constraint() function */
   vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
   while(vesicle->plist->pointer!=NULL){
      vesicle->plist->pointer->plugin->function->vm_new_state_accepted(vesicle,vtx, &backupvtx[0]);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_before_montecarlo_constraint() */





    return TS_SUCCESS;
}