Added direct force plugin and fixes in stretching energy

Samo Penic

2019-03-09 2c4278db6ead5c27e30a3000097ed898c968534e

 src/vertexmove.c

@@ -20,7 +20,7 @@
    ts_uint i;
    ts_bool retval; 
    ts_uint cellidx; 
    ts_double delta_energy, oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
    ts_double delta_energy, oenergy;
    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;
@@ -60,22 +60,9 @@
      vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_energy_before_prepare() */

    if(vesicle->tape->constareaswitch==2){
      for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
    
    }
   //stretching energy 1 of 3
   if(vesicle->tape->stretchswitch==1){
      for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
   }
    delta_energy=0;


//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);

    //update the normals of triangles that share bead i.
//update the normals of triangles that share bead i.
    for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
   oenergy=vtx->energy;
    energy_vertex(vtx);
@@ -87,47 +74,16 @@
        delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
    }


/* 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);
      delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx, backupvtx);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_energy_after_execute() */



    if(vesicle->tape->constareaswitch==2){
        /* check whether the darea is gt epsarea */
      for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
        if(fabs(vesicle->area+darea-A0)>epsarea){
           //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;
      }


    }

/* 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++){ 
         stretchenergy(vesicle, vtx->tristar[i]);
         dstretchenergy+=vtx->tristar[i]->energy;
         }
   }

   delta_energy+=dstretchenergy;	
		
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -135,21 +91,6 @@
         pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
   }
*/

// plane confinement energy due to compressing force
   if(vesicle->tape->plane_confinement_switch){
      if(vesicle->confinement_plane.force_switch){
         //substract old energy
         if(abs(vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_max)>1e-10) {
            delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-backupvtx[0].z,2);
            delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-vtx->z,2);
         }
         if(abs(-vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_min)>1e-10) {
            delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-backupvtx[0].z,2);
            delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-vtx->z,2);
         }
      }
   }


/* Entry point for plugin vm_before_montecarlo_constraint() function */
@@ -185,53 +126,34 @@
        if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
    {
    //not accepted, reverting changes
  //  fprintf(stderr,"MC failed\n");
/*************************************************** MC step rejected **************************************************************/
   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));
   }
   
    //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]);
         }
   }
   //update the normals of triangles that share bead i.
   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(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);
//    }
//    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);

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


    return TS_FAIL; 
    }
}
   //accepted	
 //   fprintf(stderr,"MC accepted\n");
//   oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
/*************************************************** MC step accepted **************************************************************/
   cellidx=vertex_self_avoidance(vesicle, vtx);
   if(vtx->cell!=vesicle->clist->cell[cellidx]){
      retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
//      if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
      if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
		
      if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);	
   }

    if(vesicle->tape->constvolswitch == 2){
   vesicle->volume+=dvol;
    } 



    if(vesicle->tape->constareaswitch==2){
        vesicle->area+=darea;
    }


/* Entry point for plugin vm_before_montecarlo_constraint() function */
   vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
@@ -241,14 +163,13 @@
   }
/* End of vm_before_montecarlo_constraint() */





    return TS_SUCCESS;
}





ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
   ts_uint i;
   ts_bool retval;