Merge branch 'bondflip'

Samo Penic

2012-07-10 737e1c8236e7e9b72cf08c5d173e0a307c38600c

Merge branch 'bondflip'

 src/Makefile.am

@@ -1,6 +1,6 @@
trisurfdir=../
trisurf_PROGRAMS = trisurf
trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c main.c
trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c
#trisurf_LDFLAGS = -lm -lconfuse
shdiscoverdir=../
shdiscover_PROGRAMS= shdiscover

 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>

@@ -27,7 +28,7 @@
    ts_vertex *it=bond->vtx1;
    ts_vertex *k=bond->vtx2;
    ts_uint nei,neip,neim;
    ts_uint i,j;
    ts_uint i; //j;
    ts_double oldenergy, delta_energy;
 //   ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL;

@@ -39,7 +40,7 @@
        fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
    }


    nei=0;
    for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k 
        if(it->neigh[i]==k){
            nei=i;
@@ -68,7 +69,7 @@
    }
 //   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;
    if(vtx_distance_sq(km,kp) > 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 */
@@ -83,26 +84,26 @@
//  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");
//    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! Bondflip successful!\n");

/* Calculating the new energy */
  delta_energy=0;
@@ -174,7 +175,7 @@
ts_bond *bond){

    ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
    ts_uint i,j, lmidx, lpidx;
    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);
}
@@ -232,26 +233,24 @@
*/
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
*/
/*
@@ -276,14 +275,17 @@
//   * 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);
            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);
            vtx_insert_neighbour(km,kp,k);
            vtx_insert_neighbour(kp,km,it);
//            vertex_add_neighbour(km,kp); //pazi na vrstni red.
//            vertex_add_neighbour(kp,km);
//fprintf(stderr,"3. step: vertex neighbours corrected\n");
@@ -300,7 +302,7 @@
// 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 +320,8 @@
// 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");

/*

 src/bondflip.h

@@ -1,4 +1,4 @@
#ifdef _H_BONDFLIP
#ifndef _H_BONDFLIP
#define _H_BONDFLIP

ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn);

 src/main.c

@@ -30,11 +30,12 @@
retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]);
if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n");

retval=vtx_add_cneighbour(blist,vlist->vtx[0],vlist->vtx[1]);
retval=vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");

retval=vtx_remove_neighbour(vlist->vtx[0],vlist->vtx[1]);
fprintf(stderr,"Was here");
retval=vtx_remove_neighbour(vlist->vtx[1],vlist->vtx[0]);
vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
fprintf(stderr,"Was here too!\n");

vlist->vtx[0]->x=1.0;
vlist->vtx[0]->x=1.1;

 src/timestep.c

@@ -5,6 +5,7 @@
#include "general.h"
#include "timestep.h"
#include "vertexmove.h"
#include "bondflip.h"

ts_bool single_timestep(ts_vesicle *vesicle){
    ts_bool retval;
@@ -23,7 +24,7 @@
        rnvec[2]=drand48();
        //find a bond and return a pointer to a bond...
        //call single_bondflip_timestep...
//        retval=single_bondflip_timestep(vesicle,&vesicle->blist.bond[i],rnvec);
        retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[i],rnvec);
        
    } 
    if(retval);

 src/triangle.c

@@ -147,11 +147,13 @@
        //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
    }
    tria->neigh_no--;
//    fprintf(stderr,"*** tria_number=%d\n",tria->neigh_no);
    tria->neigh=(ts_triangle **)realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *));
    if(tria->neigh == NULL){
        fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);
    }
/* we repeat the procedure for neighbour */
    j=0;
    for(i=0;i<ntria->neigh_no;i++){
        if(ntria->neigh[i]!=tria){
            ntria->neigh[j]=ntria->neigh[i];
@@ -163,6 +165,7 @@
        //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
    }
    ntria->neigh_no--;
//    fprintf(stderr,"*** ntria_number=%d\n",ntria->neigh_no);
    ntria->neigh=(ts_triangle **)realloc(ntria->neigh,ntria->neigh_no*sizeof(ts_triangle *));
    if(ntria->neigh == NULL){
        fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);

 src/triangle.h

@@ -6,5 +6,5 @@
ts_bool triangle_add_neighbour(ts_triangle *tria, ts_triangle *ntria);
ts_bool triangle_normal_vector(ts_triangle *tria);
ts_bool triangle_list_free(ts_triangle_list *tlist);

ts_bool triangle_remove_neighbour(ts_triangle *tria, ts_triangle *ntria);
#endif

 src/vertex.c

@@ -74,20 +74,23 @@
/* remove it from the list while shifting remaining neighbours up */
    ts_uint i,j=0;
    for(i=0;i<vtx->neigh_no;i++){
//        fprintf(stderr,"neigh_addr=%ld\n", (long)vtx->neigh[i]);
        if(vtx->neigh[i]!=nvtx){
            vtx->neigh[j]=vtx->neigh[i];
            j++;
        }
    }
//    fprintf(stderr,"remove_neighbour: vtx1_addr=%ld, vtx2_addr=%ld\n",(long)vtx,(long)nvtx);
/* resize memory. potentionally time consuming */
    vtx->neigh_no--;
    vtx->neigh=(ts_vertex **)realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
    if(vtx->neigh == NULL && vtx->neigh_no!=0)
        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);

        fatal("(1) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
//fprintf(stderr,"first alloc");
/* repeat for the neighbour */
/* find a neighbour */
/* remove it from the list while shifting remaining neighbours up */
    j=0;
    for(i=0;i<nvtx->neigh_no;i++){
        if(nvtx->neigh[i]!=vtx){
            nvtx->neigh[j]=nvtx->neigh[i];
@@ -95,10 +98,12 @@
        }
    }
/* resize memory. potentionally time consuming. */
//    fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
    nvtx->neigh_no--;
    nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
            nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
//    fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
    if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
        fatal("(2) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);

    return TS_SUCCESS;
}
@@ -110,11 +115,14 @@
    bond=bond_add(blist,vtx1,vtx2);
    if(bond==NULL) return TS_FAIL;
    vtx1->bond_no++;
    vtx2->bond_no++;
   // vtx2->data->bond_no++;

    vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->bond_no*sizeof(ts_bond *)); 
    vtx2->bond=(ts_bond **)realloc(vtx2->bond, vtx2->bond_no*sizeof(ts_bond *)); 
   // vtx2->data->bond=(ts_bond **)realloc(vtx2->data->bond, vtx2->data->bond_no*sizeof(ts_bond *)); 
    vtx1->bond[vtx1->bond_no-1]=bond;
    vtx2->bond[vtx2->bond_no-1]=bond;
   // vtx2->ata->bond[vtx2->data->bond_no-1]=bond;
    return TS_SUCCESS;
}
@@ -122,6 +130,7 @@
ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
    ts_bool retval;
    retval=vtx_add_neighbour(vtx1,vtx2);
  //  retval=vtx_add_neighbour(vtx2,vtx1);
    if(retval==TS_SUCCESS)
    retval=vtx_add_bond(blist,vtx1,vtx2); 
    return retval;
@@ -207,6 +216,57 @@
}


/* Insert neighbour is a function that is required in bondflip. It inserts a
 * neighbour exactly in the right place. */
inline ts_bool vtx_insert_neighbour(ts_vertex *vtx, ts_vertex *nvtx, ts_vertex *vtxm){
//nvtx is a vertex that is to be inserted after vtxm!
        ts_uint i,j,midx;
        vtx->neigh_no++;
        if(vtxm==NULL ||  nvtx==NULL || vtx==NULL)
                fatal("vertex_insert_neighbour: one of pointers has been zero.. Cannot proceed.",3);
        //We need to reallocate space! The pointer *neight must be zero if not having neighbours jey (if neigh_no was 0 at thime of calling
        vtx->neigh=realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
        if(vtx->neigh == NULL){
            fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_insert_neighbour",3);
        }
        midx=0;
        for(i=0;i<vtx->neigh_no-1;i++) if(vtx->neigh[i]==vtxm) {midx=i; break;}
     //   fprintf(stderr,"midx=%d, vseh=%d\n",midx,vtx->neigh_no-2);
        if(midx==vtx->neigh_no-2) {
            vtx->neigh[vtx->neigh_no-1]=nvtx;
        } else {
            for(j=vtx->neigh_no-2;j>midx;j--) {
                vtx->neigh[j+1]=vtx->neigh[j];
//                vtx->bond_length[j+1]=vtx->bond_length[j];
//                vtx->bond_length_dual[j+1]=vtx->bond_length_dual[j];
            }
            vtx->neigh[midx+1]=nvtx;
        }
    return TS_SUCCESS;
}


/* vtx remove tristar is required in  bondflip. */
/* TODO: Check whether it is important to keep the numbering of tristar
 * elements in some order or not! */
inline ts_bool vtx_remove_tristar(ts_vertex *vtx, ts_triangle *tristar){
    ts_uint i,j=0;
    for(i=0;i<vtx->tristar_no;i++){
        if(vtx->tristar[i]!=tristar){
            vtx->tristar[j]=vtx->tristar[i];
            j++;
        }
    }
    vtx->tristar_no--;
    vtx->tristar=realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
    if(vtx->neigh == NULL){
            fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
        }
    return TS_SUCCESS;
}



/* ****************************************************************** */
/* ***** New vertex copy operations. Inherently they are slow.  ***** */
/* ****************************************************************** */

 src/vertex.h

@@ -24,7 +24,8 @@
ts_bool vtx_set_global_values(ts_vesicle *vesicle);
inline ts_double vtx_direct(ts_vertex *vtx1, ts_vertex *vtx2, ts_vertex *vtx3);
inline ts_bool vertex_add_tristar(ts_vertex *vtx, ts_triangle *tristarmem);

inline ts_bool vtx_insert_neighbour(ts_vertex *vtx, ts_vertex *nvtx, ts_vertex *vtxm);
inline ts_bool vtx_remove_tristar(ts_vertex *vtx, ts_triangle *tristar);
ts_bool vtx_copy(ts_vertex *cvtx,ts_vertex *ovtx);
ts_bool vtx_duplicate(ts_vertex *cvtx, ts_vertex *ovtx);
ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx);