Started with bondflip. There is still an error in calling vtx_remove_neighbour with vertices that are actually not neighbours.
| | |
| | | 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 |
| | |
| | | #include "energy.h" |
| | | #include "timestep.h" |
| | | #include "cell.h" |
| | | #include "bondflip.h" |
| | | //#include "io.h" |
| | | #include<stdio.h> |
| | | |
| | |
| | | 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; |
| | | |
| | |
| | | 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; |
| | |
| | | } |
| | | // 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 */ |
| | |
| | | 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); |
| | | } |
| | |
| | | // 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); |
| | | //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"); |
| | |
| | | // 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"); |
| | | |
| | | /* |
| | |
| | | #ifdef _H_BONDFLIP |
| | | #ifndef _H_BONDFLIP |
| | | #define _H_BONDFLIP |
| | | |
| | | ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn); |
| | |
| | | #include "general.h" |
| | | #include "timestep.h" |
| | | #include "vertexmove.h" |
| | | #include "bondflip.h" |
| | | |
| | | ts_bool single_timestep(ts_vesicle *vesicle){ |
| | | ts_bool retval; |
| | |
| | | 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); |
| | |
| | | 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 |
| | |
| | | j++; |
| | | } |
| | | } |
| | | if(j==0) { |
| | | fatal("vtx_remove_neighbour: Error, vertices are not neighbours", 100); |
| | | } |
| | | /* resize memory. potentionally time consuming */ |
| | | vtx->neigh_no--; |
| | | vtx->neigh=(ts_vertex **)realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *)); |
| | |
| | | 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; |
| | | } |
| | |
| | | } |
| | | |
| | | |
| | | /* 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. ***** */ |
| | | /* ****************************************************************** */ |
| | |
| | | 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); |