Debugging bondflip

Samo Penic

2013-12-09 d06a9476717d788c426e88b6365d7a863928b5c9

 src/bondflip.c

@@ -8,6 +8,7 @@
#include "energy.h"
#include "timestep.h"
#include "cell.h"
#include "bondflip.h"
//#include "io.h"
#include<stdio.h>

@@ -26,50 +27,28 @@
*/
    ts_vertex *it=bond->vtx1;
    ts_vertex *k=bond->vtx2;
    ts_uint nei,neip,neim;
    ts_uint i,j;
  //  ts_uint nei,neip,neim;
    ts_uint i;
    ts_double oldenergy, delta_energy;
 //   ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL;

    ts_vertex *kp,*km;

    if(it->neigh_no< 3) return TS_FAIL;
    if(k->neigh_no< 3) return TS_FAIL;
    if(k==NULL || it==NULL){
        fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
    }


    for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k 
        if(it->neigh[i]==k){
            nei=i;
            break;
        }
    }
    neip=nei+1;  // I don't like it.. Smells like I must have it in correct order
    neim=nei-1;
    if(neip>=it->neigh_no) neip=0;
    if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
there the neim is never <0 !!! */
  //  fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
    km=it->neigh[neim];  // We located km and kp
    kp=it->neigh[neip];

    if(km==NULL || kp==NULL){
        fatal("In bondflip, cannot determine km and kp!",999);
    }

  //  fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
#ifdef DEBUG
   if(bond->adjvtx[0]==NULL || bond->adjvtx[1]==NULL) fatal ("single_bondflip_timestep: Adjvertex for called bond is null. This should not happen!",999);
#endif
    ts_vertex *kp=bond->adjvtx[1],*km=bond->adjvtx[0];
//   ts_triangle *lm=NULL, *lp=NULL;

/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
 * km. If it is true, then don't flip! */
    for(i=0;i<km->neigh_no;i++){
        if(km->neigh[i] == kp) return TS_FAIL;
/*TODO: dec2013, i think this never happens!
      for(i=0;i<km->neigh->n;i++){
        if(km->neigh->vtx[i] == kp) return TS_FAIL;
    }
*/


 //   fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
/* if bond would be too long, return... */
    if(vertex_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
 //   fprintf(stderr,"Bond will not be too long.. Continue.\n");
    if(vtx_distance_sq(bond->adjvtx[0],bond->adjvtx[1]) > vesicle->dmax ) return TS_FAIL;
  //  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
@@ -83,33 +62,34 @@
//  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);
fprintf(stderr,"*** Naslov k=%ld\n",(long)k);
fprintf(stderr,"*** Naslov it=%ld\n",(long)it);
fprintf(stderr,"*** Naslov km=%ld\n",(long)km);
fprintf(stderr,"*** Naslov kp=%ld\n",(long)kp);

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

for(i=0;i<km->neigh_no;i++)
    fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
    fprintf(stderr,"km sosed=%ld\n",(long)km->neigh[i]);
for(i=0;i<kp->neigh_no;i++)
    fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);
    fprintf(stderr,"kp sosed=%ld\n",(long)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");
 //   fprintf(stderr,"I WAS HERE! Before bondflip!\n");
    ts_flip_bond(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]);
/* TODO: why this neighs are recalculated? Not necessary! */
  for(i=0;i<k->neigh->n;i++) energy_vertex(k->neigh->vtx[i]);
  for(i=0;i<kp->neigh->n;i++) energy_vertex(kp->neigh->vtx[i]);
  for(i=0;i<km->neigh->n;i++) energy_vertex(km->neigh->vtx[i]);
  for(i=0;i<it->neigh->n;i++) energy_vertex(it->neigh->vtx[i]);
  delta_energy+=k->xk* k->energy;
  delta_energy+=kp->xk* kp->energy;
  delta_energy+=km->xk* km->energy;
@@ -136,7 +116,7 @@
       //     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);
            ts_flip_bond(bond);
                

/*
@@ -170,16 +150,15 @@
}


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

ts_bool ts_flip_bond(ts_bond *bond){
fprintf(stderr,"Called!\n");
    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){
    ts_uint i; //lmidx, lpidx;
/*This is no longer necessary! if(k==NULL || it==NULL || km==NULL || kp==NULL){
    fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
}
}*/
// 1. step. We find lm and lp from k->tristar !
    for(i=0;i<it->tristar_no;i++){
/*    for(i=0;i<it->tristar_no;i++){
        for(j=0;j<k->tristar_no;j++){
            if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
                if((it->tristar[i]->vertex[0] == km || it->tristar[i]->vertex[1]
@@ -215,6 +194,14 @@
            } 
        }
    }
*/
//Upper block no longer neccessary.
ts_vertex *it=bond->vtx1;
ts_vertex *k=bond->vtx2;
ts_vertex *km=bond->adjvtx[0];
ts_vertex *kp=bond->adjvtx[1];
lm=bond->tria[0];
lp=bond->tria[1];
/*
// DEBUG TESTING!
fprintf(stderr,"*** Naslov k=%d\n",k);
@@ -230,28 +217,35 @@

// END DEBUG TESTING!
*/
//find bonds between k and kp (adj[1] vtx)
//find bonds between it and km (adj[0] vtx)
for(i=0;i<it->tristar_no;i++){
   if((it->tristar[i]->vertex[0]==km || it->tristar[i]->vertex[1]==km || it->tristar[i]->vertex[2]==km) && (it->tristar[i]->vertex[0]==it || it->tristar[i]->vertex[1]==it || it->tristar[i]->vertex[2]==it)){
      lm2=it->tristar[i];
   }
   else if ((it->tristar[i]->vertex[0]==kp || it->tristar[i]->vertex[1]==kp || it->tristar[i]->vertex[2]==kp) && (it->tristar[i]->vertex[0]==k || it->tristar[i]->vertex[1]==k || it->tristar[i]->vertex[2]==k)){
      lp1=it->tristar[i];
   }
}
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");

/*
//DEBUG TESTING
fprintf(stderr,"--- Naslov lm=%d",lm);
fprintf(stderr,"1. step: lm, lm2, lp1 and lp found!\n");
fprintf(stderr,"--- Naslov lm=%ld",(long)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]);
fprintf(stderr,"   vtxs(%ld, %ld, %ld)\n",(long)lm->vertex[0],(long)lm->vertex[1], (long)lm->vertex[2]);
fprintf(stderr,"--- Naslov lp=%ld",(long)lp);
fprintf(stderr,"   vtxs(%ld, %ld, %ld)\n",(long)lp->vertex[0],(long)lp->vertex[1], (long)lp->vertex[2]);
fprintf(stderr,"--- Naslov lm2=%ld",(long)lm2);
fprintf(stderr,"   vtxs(%ld, %ld, %ld)\n",(long)lm2->vertex[0],(long)lm2->vertex[1], (long)lm2->vertex[2]);
fprintf(stderr,"--- Naslov lp1=%ld",(long)lp1);
fprintf(stderr,"   vtxs(%ld, %ld, %ld)\n",(long)lp1->vertex[0],(long)lp1->vertex[1], (long)lp1->vertex[2]);

for(i=0;i<lm->neigh_no;i++)
    fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
    fprintf(stderr,"lm sosed=%ld\n",(long)lm->neigh[i]);
for(i=0;i<lp->neigh_no;i++)
    fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
    fprintf(stderr,"lp sosed=%ld\n",(long)lp->neigh[i]);
// END DEBUG TESTING
*/
/*
@@ -276,16 +270,22 @@
//   * 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


            vertex_remove_neighbour(k,it);
            vertex_remove_neighbour(it,k);
            vertex_list_remove_vtx(k->neigh, it);
            vertex_list_remove_vtx(it->neigh, k);
   //vtx_remove_neighbour(k,it);
//            vtx_remove_neighbour(it,k);
//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
    
            //Tukaj pa nastopi tezava... Kam dodati soseda?
            vertex_insert_neighbour(km,kp,k);
            vertex_insert_neighbour(kp,km,it);
//            vertex_add_neighbour(km,kp); //pazi na vrstni red.
//            vertex_add_neighbour(kp,km);
		
//            vtx_insert_neighbour(km,kp,k);
//            vtx_insert_neighbour(kp,km,it);
            vtx_add_neighbour(km,kp); //pazi na vrstni red.
            vtx_add_neighbour(kp,km);
//fprintf(stderr,"3. step: vertex neighbours corrected\n");

// 3a. step. If any changes to ts_vertex, do it here!
@@ -300,7 +300,7 @@
// 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);
@@ -318,8 +318,8 @@
// 6. step. Correct tristar for vertices km, kp, k and it
            vertex_add_tristar(km,lp);  // Preveri vrstni red!
            vertex_add_tristar(kp,lm);
            vertex_remove_tristar(it,lm);
            vertex_remove_tristar(k,lp);
            vtx_remove_tristar(it,lm);
            vtx_remove_tristar(k,lp);
//fprintf(stderr,"6. step: tristar corrected\n");

/*
@@ -346,6 +346,9 @@
  energy_vertex(km);
  energy_vertex(it);

//Extra steps for new bond data structure
bond->adjvtx[0]=k;
bond->adjvtx[1]=it;

// END modifications to data structure!