Constant area plugin done -- fix

Samo Penic

2019-03-08 06f70cc6f065746cf79c9792228356e3f015f4ec

 src/vertexmove.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -8,72 +9,281 @@
#include "energy.h"
#include "timestep.h"
#include "cell.h"
//#include "io.h"
#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
#include <string.h>
#include "constvol.h"
#include "plugins.h"

ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
*rn){
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
    ts_uint i;
    ts_double dist;
    ts_bool retval; 
    ts_uint cellidx; 
    ts_double delta_energy,oenergy;
    ts_double delta_energy, oenergy, 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=(ts_vertex **)calloc(vtx->neigh_no+1,sizeof(ts_vertex *));
   ts_vertex backupvtx[20];
//   backupvtx[0]=(ts_vertex *)malloc(sizeof(ts_vertex));	
   memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
       //temporarly moving the vertex
   vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
       vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
       vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
       //check we if some length to neighbours are too much
    for(i=0;i<vtx->neigh_no;i++){
        dist=vtx_distance_sq(vtx,vtx->neigh[i]);
        if(dist<1.0 || dist>vesicle->dmax) {
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
//      free(backupvtx[0]);
//      free(backupvtx);
//   fprintf(stderr,"Fail 1, dist=%f, vesicle->dmax=%f\n", dist, vesicle->dmax);
      return TS_FAIL;
    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;


/* Entry point for plugin vm_hard_constraint() function */
   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;
      }
    }
    //self avoidance check with distant vertices
     cellidx=vertex_self_avoidance(vesicle, vtx);
    //check occupation number
     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,&backupvtx[0],vtx);
    if(retval==TS_FAIL){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
//      free(backupvtx[0]);
//      free(backupvtx);
//   fprintf(stderr,"Fail 2\n");
        return TS_FAIL;
    } 
   
 
    //if all the tests are successful, then energy for vtx and neighbours is calculated
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_hard_constraint() */

/* Backuping the neighbours */ 
   for(i=0;i<vtx->neigh_no;i++){
//   backupvtx[i+1]=(ts_vertex *)malloc(sizeof(ts_vertex));	
   memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
   }

/* 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;
   }
/* End of vm_energy_before_prepare() */

   //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;
    //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]);
    //energy and curvature
   oenergy=vtx->energy;
    energy_vertex(vtx);
    delta_energy=vtx->xk*(vtx->energy - (&backupvtx[0])->energy);
    delta_energy=vtx->xk*(vtx->energy - oenergy);
    //the same is done for neighbouring vertices
    for(i=0;i<vtx->neigh_no;i++){
        oenergy=vtx->neigh[i]->energy;
        energy_vertex(vtx->neigh[i]);
        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);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }


/* 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+=
         (pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
         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 */
   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(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48())
#endif
#ifdef TS_DOUBLE_FLOAT
        if(expf(-delta_energy)< (ts_float)drand48())
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
        if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
    {
/*************************************************** 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]);
         }
   }



/* 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; 
    }
}
/*************************************************** 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(backupvtx[0].cell,vtx);	
   }

/* 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;
}





ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
   ts_uint i;
   ts_bool retval; 
   ts_uint cellidx; 
//   ts_double delta_energy;
   ts_double costheta,sintheta,phi,r;
   ts_double dist;
   //This will hold all the information of vtx and its neighbours
   ts_vertex backupvtx;
//   ts_bond backupbond[2];
   memcpy((void *)&backupvtx,(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;


   //distance with neighbours check
   for(i=0;i<vtx->neigh_no;i++){
      dist=vtx_distance_sq(vtx,vtx->neigh[i]);
      if(dist<1.0 || dist>vesicle->dmax) {
         vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
         return TS_FAIL;
      }
   }

// Distance with grafted vesicle-vertex check:	
   if(vtx==poly->vlist->vtx[0]){
      dist=vtx_distance_sq(vtx,poly->grafted_vtx);
        if(dist<1.0 || dist>vesicle->dmax) {
      vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
      return TS_FAIL;
      }
   }


   //self avoidance check with distant vertices
   cellidx=vertex_self_avoidance(vesicle, vtx);
   //check occupation number
   retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
	
   if(retval==TS_FAIL){
      vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
        return TS_FAIL;
   } 


   //if all the tests are successful, then energy for vtx and neighbours is calculated
/* Energy ignored for now!
   delta_energy=0;
   for(i=0;i<vtx->bond_no;i++){
      memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));

      vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
      bond_energy(vtx->bond[i],poly);
      delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
   }

   if(vtx==poly->vlist->vtx[0]){
      delta_energy+=
         (pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
         pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
		
   }


   if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48() )
#endif
@@ -83,33 +293,144 @@
#ifdef TS_DOUBLE_LONGDOUBLE
        if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
    {
    //not accepted, reverting changes
   vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
//   free(backupvtx[0]);
   for(i=0;i<vtx->neigh_no;i++){
   vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
//   free(backupvtx[i+1]);
       {
   //not accepted, reverting changes
   vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
   for(i=0;i<vtx->bond_no;i++){
   vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
   }
//   free(backupvtx);
//   fprintf(stderr,"Reverted\n");
	
    //update the normals of triangles that share bead i.
   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);

    return TS_FAIL; 
    }
}
   }
   }
*/
		
//   oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
   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.cell,vtx);	
   }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO

    //TODO: change cell occupation if necessary!
//   fprintf(stderr,"Success!!\n");
//   free(backupvtx[0]);
//   for(i=0;i<vtx->neigh_no;i++){
//   free(backupvtx[i+1]);
//   }
//   free(backupvtx);
//   fprintf(stderr,"Accepted\n");
    return TS_SUCCESS;
}




ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
   ts_uint i;
   ts_bool retval; 
   ts_uint cellidx; 
   ts_double delta_energy;
   ts_double costheta,sintheta,phi,r;
   ts_double dist[2];
   //This will hold all the information of vtx and its neighbours
   ts_vertex backupvtx,backupneigh[2];
   ts_bond backupbond[2];

   //backup vertex:		
   memcpy((void *)&backupvtx,(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;


   //distance with neighbours check
   for(i=0;i<vtx->bond_no;i++){
      dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
      if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
         vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
         return TS_FAIL;
      }
   }

// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
   if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
      vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
      return TS_FAIL;
   }


   //self avoidance check with distant vertices
   cellidx=vertex_self_avoidance(vesicle, vtx);
   //check occupation number
   retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
   if(retval==TS_FAIL){
      vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
        return TS_FAIL;
   } 

   //backup bonds
   for(i=0;i<vtx->bond_no;i++){
      memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
      vtx->bond[i]->bond_length=sqrt(dist[i]);
      bond_vector(vtx->bond[i]);
   }

   //backup neighboring vertices:
   for(i=0;i<vtx->neigh_no;i++){
      memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
   }
	
   //if all the tests are successful, then energy for vtx and neighbours is calculated
   delta_energy=0;
	
   if(vtx->bond_no == 2){
      vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
      delta_energy += vtx->energy - backupvtx.energy;
   }

   for(i=0;i<vtx->neigh_no;i++){
      if(vtx->neigh[i]->bond_no == 2){
         vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
         delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
      }
   }

   // poly->k is filament persistence length (in units l_min)
   delta_energy *= poly->k;

   if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
        if(exp(-delta_energy)< drand48() )
#endif
#ifdef TS_DOUBLE_FLOAT
        if(expf(-delta_energy)< (ts_float)drand48())
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
        if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
       {
   //not accepted, reverting changes
   vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
   for(i=0;i<vtx->neigh_no;i++){
      memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
   }
   for(i=0;i<vtx->bond_no;i++){
      vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
   }

    return TS_FAIL; 
   }
   }
	
	
//   oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
   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.cell,vtx);	
   }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO
    return TS_SUCCESS;
}