Bondflip doesnt segfaults anymore. Bondflip is disabled, debugging vertexmove

Samo Penic

2014-04-29 b2fa8c6b55c420c079f285224f8d56ed03939767

 src/vertexmove.c

@@ -9,19 +9,21 @@
#include "timestep.h"
#include "cell.h"
//#include "io.h"
#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
#include <string.h>
#include "constvol.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,oenergy,dvol=0.0;
    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0;
    ts_double costheta,sintheta,phi,r;
   //This will hold all the information of vtx and its neighbours
   ts_vertex backupvtx[20];
   ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
   memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));

   //Some stupid tests for debugging cell occupation!
@@ -67,11 +69,18 @@
      }
   }

    //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);
	
// 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[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,vtx);

    if(retval==TS_FAIL){
      vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
        return TS_FAIL;
@@ -83,11 +92,15 @@
   memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
   }

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

    delta_energy=0;

 
//    fprintf(stderr,"Success for now.\n");

    //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;
@@ -100,11 +113,23 @@
        delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
    }

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

   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]); 
            return TS_FAIL;
        }
    delta_energy+=delta_energy_cv;
    }
/* No poly-bond energy for now!
   if(vtx->grafted_poly!=NULL){
      delta_energy+=
@@ -126,6 +151,7 @@
#endif
    {
    //not accepted, reverting changes
  //  fprintf(stderr,"MC failed\n");
   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));
@@ -134,10 +160,14 @@
    //update the normals of triangles that share bead i.
   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);

    if(vesicle->tape->constvolswitch == 1){
        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
    }
    return TS_FAIL; 
    }
}
		
   //accepted	
 //   fprintf(stderr,"MC accepted\n");
//   oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
   if(vtx->cell!=vesicle->clist->cell[cellidx]){
      retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
@@ -145,6 +175,10 @@
      if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
      
   }

    if(vesicle->tape->constvolswitch == 1){
        constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
    }
//   if(oldcellidx);
    //END MONTE CARLOOOOOOO
    return TS_SUCCESS;
@@ -291,12 +325,18 @@
      }
   }

// 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;