Filament inside the vesicle added and debugged. Testing time...

mihaf

2014-03-21 bcf4557ddd61890f130247430267feac5b05c5b7

 src/bondflip.c

@@ -11,6 +11,7 @@
#include "bondflip.h"
//#include "io.h"
#include<stdio.h>
#include<string.h>

ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn){
/*c  Vertex and triangle (lm and lp) indexing for bond flip:
@@ -28,9 +29,9 @@
    ts_vertex *it=bond->vtx1;
    ts_vertex *k=bond->vtx2;
    ts_uint nei,neip,neim;
    ts_uint i; //j;
    ts_double oldenergy, delta_energy;
 //   ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL;
    ts_uint i,j;
    ts_double oldenergy, delta_energy, dvol=0.0;
    ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;

    ts_vertex *kp,*km;

@@ -73,112 +74,7 @@
 //   fprintf(stderr,"Bond will not be too long.. Continue.\n");

/* we make a bond flip. this is different than in original fortran */
// 0. step. Get memory prior the flip
  oldenergy=0;
  oldenergy+=k->xk* k->energy;
  oldenergy+=kp->xk* kp->energy;
  oldenergy+=km->xk* km->energy;
  oldenergy+=it->xk* it->energy;
//  for(i=0;i<k->neigh_no;i++) oldenergy+=k->neigh[i]->xk*k->neigh[i]->energy;
//  for(i=0;i<kp->neigh_no;i++) oldenergy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
//  for(i=0;i<km->neigh_no;i++) oldenergy+=km->neigh[i]->xk*km->neigh[i]->energy;
//  for(i=0;i<it->neigh_no;i++) oldenergy+=it->neigh[i]->xk*it->neigh[i]->energy;
/*
fprintf(stderr,"*** Naslov k=%d\n",k);
fprintf(stderr,"*** Naslov it=%d\n",it);
fprintf(stderr,"*** Naslov km=%d\n",km);
fprintf(stderr,"*** Naslov kp=%d\n",kp);

for(i=0;i<k->neigh_no;i++)
    fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
for(i=0;i<it->neigh_no;i++)
    fprintf(stderr,"it sosed=%d\n",it->neigh[i]);

for(i=0;i<km->neigh_no;i++)
    fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
for(i=0;i<kp->neigh_no;i++)
    fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);


*/
  //  fprintf(stderr,"I WAS HERE! Before bondflip!\n");
    ts_flip_bond(k,it,km,kp, bond);
   // fprintf(stderr,"I WAS HERE! Bondflip successful!\n");

/* Calculating the new energy */
  delta_energy=0;
  for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
  for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
  for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
  for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
  delta_energy+=k->xk* k->energy;
  delta_energy+=kp->xk* kp->energy;
  delta_energy+=km->xk* km->energy;
  delta_energy+=it->xk* it->energy;
//  for(i=0;i<k->neigh_no;i++) delta_energy+=k->neigh[i]->xk*k->neigh[i]->energy;
//  for(i=0;i<kp->neigh_no;i++) delta_energy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
//  for(i=0;i<km->neigh_no;i++) delta_energy+=km->neigh[i]->xk*km->neigh[i]->energy;
//  for(i=0;i<it->neigh_no;i++) delta_energy+=it->neigh[i]->xk*it->neigh[i]->energy;
  delta_energy-=oldenergy;
 // fprintf(stderr,"I WAS HERE! Got energy!\n");
/* MONTE CARLO */
    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
       //     fprintf(stderr,"Failed to move, due to MC\n");

//            ts_flip_bond(km,kp,it,k, bond);
            ts_flip_bond(kp,km,k,it, bond);
                

/*
fprintf(stderr,"*** Naslov k=%d\n",k);
fprintf(stderr,"*** Naslov it=%d\n",it);
fprintf(stderr,"*** Naslov km=%d\n",km);
fprintf(stderr,"*** Naslov kp=%d\n",kp);
for(i=0;i<k->neigh_no;i++)
    fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
for(i=0;i<it->neigh_no;i++)
    fprintf(stderr,"it sosed=%d\n",it->neigh[i]);


for(i=0;i<km->neigh_no;i++)
    fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
for(i=0;i<kp->neigh_no;i++)
    fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);
*/



        //    fprintf(stderr,"Reverted condition!\n");
            return TS_FAIL;
        }
    }
        //    fprintf(stderr,"Success\n");


/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
    return TS_SUCCESS;
}


ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
ts_bond *bond){

    ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
    ts_uint i,j; //lmidx, lpidx;
if(k==NULL || it==NULL || km==NULL || kp==NULL){
    fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
}
// find lm, lp
// 1. step. We find lm and lp from k->tristar !
    for(i=0;i<it->tristar_no;i++){
        for(j=0;j<k->tristar_no;j++){
@@ -216,59 +112,150 @@
            } 
        }
    }
/*
// DEBUG TESTING!
fprintf(stderr,"*** Naslov k=%d\n",k);
fprintf(stderr,"*** Naslov it=%d\n",it);
fprintf(stderr,"*** Naslov km=%d\n",km);
fprintf(stderr,"*** Naslov kp=%d\n",kp);

for(i=0;i<k->neigh_no;i++)
    fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
for(i=0;i<it->neigh_no;i++)
    fprintf(stderr,"it sosed=%d\n",it->neigh[i]);


// END DEBUG TESTING!
*/
if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);


//fprintf(stderr,"1. step: lm, lm2, lp1 and lp found!\n");
/* backup old structure */
/* need to backup:
 * vertices k, kp, km, it
 * triangles lm, lp, lm2, lp1
 * bond
 */
ts_vertex *bck_vtx[4];
ts_triangle *bck_tria[4];
ts_bond *bck_bond;
ts_vertex *orig_vtx[]={k,it,kp,km};
ts_triangle *orig_tria[]={lm,lp,lm2,lp1};

/*
//DEBUG TESTING
fprintf(stderr,"--- Naslov lm=%d",lm);


fprintf(stderr,"   vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]);
fprintf(stderr,"--- Naslov lp=%d",lp);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]);
fprintf(stderr,"--- Naslov lm2=%d",lm2);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]);
fprintf(stderr,"--- Naslov lp1=%d",lp1);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]);

for(i=0;i<lm->neigh_no;i++)
    fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
for(i=0;i<lp->neigh_no;i++)
    fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
// END DEBUG TESTING
//fprintf(stderr,"Backuping!!!\n");
   bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
for(i=0;i<4;i++){
/*   fprintf(stderr,"vtx neigh[%d]=",i);
   for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
   fprintf(stderr,"\n");
*/
/*
// DEBUG TESTING!
   bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
   bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
   memcpy((void *)bck_vtx[i],(void *)orig_vtx[i],sizeof(ts_vertex));
   memcpy((void *)bck_tria[i],(void *)orig_tria[i],sizeof(ts_triangle));
   /* level 2 pointers */

for(i=0;i<3;i++){
   bck_vtx[i]->neigh=(ts_vertex **)malloc(orig_vtx[i]->neigh_no*sizeof(ts_vertex *));
   bck_vtx[i]->tristar=(ts_triangle **)malloc(orig_vtx[i]->tristar_no*sizeof(ts_triangle *));
   bck_vtx[i]->bond=(ts_bond **)malloc(orig_vtx[i]->bond_no*sizeof(ts_bond *));
   bck_tria[i]->neigh=(ts_triangle **)malloc(orig_tria[i]->neigh_no*sizeof(ts_triangle *));

    if(lp1->neigh[i]==lp) fprintf(stderr,"Nasel sem par lp1->lp\n");
    if(lp->neigh[i]==lp1) fprintf(stderr,"Nasel sem par lp->lp1\n");
    if(lm2->neigh[i]==lm) fprintf(stderr,"Nasel sem par lm2->lm\n");
    if(lm->neigh[i]==lm2) fprintf(stderr,"Nasel sem par lm->lm2\n");
   memcpy((void *)bck_vtx[i]->neigh,(void *)orig_vtx[i]->neigh,orig_vtx[i]->neigh_no*sizeof(ts_vertex *));
   memcpy((void *)bck_vtx[i]->tristar,(void *)orig_vtx[i]->tristar,orig_vtx[i]->tristar_no*sizeof(ts_triangle *));
   memcpy((void *)bck_vtx[i]->bond,(void *)orig_vtx[i]->bond,orig_vtx[i]->bond_no*sizeof(ts_bond *));
	
   memcpy((void *)bck_tria[i]->neigh,(void *)orig_tria[i]->neigh,orig_tria[i]->neigh_no*sizeof(ts_triangle *));	
}
// END DEBUG TESTING!
*/
   memcpy(bck_bond,bond,sizeof(ts_bond));
//fprintf(stderr,"Backup complete!!!\n");
/* end backup vertex */

/* Save old energy */
  oldenergy=0;
  oldenergy+=k->xk* k->energy;
  oldenergy+=kp->xk* kp->energy;
  oldenergy+=km->xk* km->energy;
  oldenergy+=it->xk* it->energy;
  //Neigbours of k, it, km, kp don't change its energy.

   if(vesicle->pswitch == 1){dvol = -lm->volume - lp->volume;}

/* fix data structure for flipped bond */
    ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);


/* Calculating the new energy */
  delta_energy=0;
  delta_energy+=k->xk* k->energy;
  delta_energy+=kp->xk* kp->energy;
  delta_energy+=km->xk* km->energy;
  delta_energy+=it->xk* it->energy;
  //Neigbours of k, it, km, kp don't change its energy.

  delta_energy-=oldenergy;
   if(vesicle->pswitch == 1){
      dvol = dvol + lm->volume + lp->volume;
      delta_energy-= vesicle->pressure*dvol;
   }

/* MONTE CARLO */
    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
       //restore all backups
//      fprintf(stderr,"Restoring!!!\n");

      for(i=0;i<4;i++){
//         fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
         free(orig_vtx[i]->neigh);
         free(orig_vtx[i]->tristar);
         free(orig_vtx[i]->bond);
         free(orig_tria[i]->neigh);
         memcpy((void *)orig_vtx[i],(void *)bck_vtx[i],sizeof(ts_vertex));
         memcpy((void *)orig_tria[i],(void *)bck_tria[i],sizeof(ts_triangle));
//         fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
         /* level 2 pointers are redirected*/
      }
      memcpy(bond,bck_bond,sizeof(ts_bond));

      for(i=0;i<4;i++){
         free(bck_vtx[i]);
         free(bck_tria[i]);
/*         fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
         for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
         fprintf(stderr,"\n"); */
      }

      free(bck_bond);
//      fprintf(stderr,"Restoration complete!!!\n");

      return TS_FAIL;
        }
    }
     /* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
  //          fprintf(stderr,"SUCCESS!!!\n");

   // delete all backups
   for(i=0;i<4;i++){
   free(bck_vtx[i]->neigh);
   free(bck_vtx[i]->bond);
   free(bck_vtx[i]->tristar);
   free(bck_vtx[i]);
    free(bck_tria[i]->neigh);
        free(bck_tria[i]);
/*   fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
   for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
   fprintf(stderr,"\n");
*/	
   }
   free(bck_bond);

    return TS_SUCCESS;
}


ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1){

    ts_uint i; //lmidx, lpidx;
if(k==NULL || it==NULL || km==NULL || kp==NULL){
    fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
}
// 2. step. We change the triangle vertices... (actual bond flip)
    for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
    for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
@@ -277,11 +264,14 @@
//   * normals are recalculated here
    triangle_normal_vector(lp);
    triangle_normal_vector(lm);
//fprintf(stderr,"2a. step: triangle normals recalculated\n");
// 3. step. Correct neighbours in vertex_list


            vtx_remove_neighbour(k,it);
            vtx_remove_neighbour(it,k);
//            vtx_remove_neighbour(it,k);
//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
    
            //Tukaj pa nastopi tezava... Kam dodati soseda?
            vtx_insert_neighbour(km,kp,k);
            vtx_insert_neighbour(kp,km,it);
@@ -301,7 +291,7 @@
// 5. step. Correct neighbouring triangles 
   
    triangle_remove_neighbour(lp,lp1);
   // fprintf(stderr,".\n");
  //  fprintf(stderr,".\n");
    triangle_remove_neighbour(lp1,lp);
  //  fprintf(stderr,".\n");
    triangle_remove_neighbour(lm,lm2);
@@ -322,34 +312,10 @@
            vtx_remove_tristar(it,lm);
            vtx_remove_tristar(k,lp);
//fprintf(stderr,"6. step: tristar corrected\n");

/*
//DEBUG TESTING
fprintf(stderr,"--- Naslov lm=%d",lm);


fprintf(stderr,"   vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]);
fprintf(stderr,"--- Naslov lp=%d",lp);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]);
fprintf(stderr,"--- Naslov lm2=%d",lm2);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]);
fprintf(stderr,"--- Naslov lp1=%d",lp1);
fprintf(stderr,"   vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]);

for(i=0;i<lm->neigh_no;i++)
    fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
for(i=0;i<lp->neigh_no;i++)
    fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
// END DEBUG TESTING
*/
  energy_vertex(k);
  energy_vertex(kp);
  energy_vertex(km);
  energy_vertex(it);


// END modifications to data structure!


    return TS_SUCCESS;
}