Code cleanup

Samo Penic

2019-03-09 9a1f16ae3affc4db83f2eb2623418ac5cff2af03

 src/vertexmove.c

@@ -9,188 +9,78 @@
#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_uint i;
    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, 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;
   memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
    ts_vertex backupvtx[20];
    memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));

   //Some stupid tests for debugging cell occupation!
/*        cellidx=vertex_self_avoidance(vesicle, vtx);
   if(vesicle->clist->cell[cellidx]==vtx->cell){
      fprintf(stderr,"Idx match!\n");
   } else {
      fprintf(stderr,"***** Idx don't match!\n");
      fatal("ENding.",1);
   }
*/

       //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);

//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;


//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[0],sizeof(ts_vertex));
          return TS_FAIL;
/* 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;
      }
    }

// Distance with grafted poly-vertex check:	
   if(vtx->grafted_poly!=NULL){
      dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
        if(dist<1.0 || dist>vesicle->dmax) {
      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() */

// 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;
   }

}
//#undef SQ
//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[0],sizeof(ts_vertex));
        return TS_FAIL;
    } 
   
 
//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;
   }
/* End of vm_energy_before_prepare() */

   //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);
   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);
   }

    if(vesicle->tape->constareaswitch==2){
      for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
    
    }

    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.
    for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
   oenergy=vtx->energy;
    energy_vertex(vtx);
    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);
    }

   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;
   };

    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;
      }
/* 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, backupvtx);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }
/* End of vm_energy_after_execute() */


    }

   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);
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -198,9 +88,30 @@
         pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
   }
*/


/* 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())
@@ -212,54 +123,50 @@
        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]);
   //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;
    } else
    if(vesicle->tape->constvolswitch == 1){
        constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
    }
/* 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() */

    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);
    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;