From 30ee9c409ed7c743c693f1e068c1d7393949207a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 14 Jun 2012 09:24:31 +0000
Subject: [PATCH] Started with bondflip. There is still an error in calling vtx_remove_neighbour with vertices that are actually not neighbours.
---
src/Makefile.am | 2
src/bondflip.h | 2
src/timestep.c | 3 +
src/vertex.c | 57 ++++++++++++++++++++++++++++
src/bondflip.c | 21 +++++-----
src/triangle.h | 2
src/vertex.h | 3 +
7 files changed, 75 insertions(+), 15 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index f9bc3e2..a6e0171 100644
--- a/src/Makefile.am
+++ b/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
diff --git a/src/bondflip.c b/src/bondflip.c
index e56cc4e..b444975 100644
--- a/src/bondflip.c
+++ b/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 */
@@ -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);
}
@@ -279,11 +280,11 @@
// 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");
@@ -318,8 +319,8 @@
// 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");
/*
diff --git a/src/bondflip.h b/src/bondflip.h
index 6713c31..8d7ee37 100644
--- a/src/bondflip.h
+++ b/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);
diff --git a/src/timestep.c b/src/timestep.c
index 1e1ffff..83e6f9b 100644
--- a/src/timestep.c
+++ b/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);
diff --git a/src/triangle.h b/src/triangle.h
index a3d8184..a1a0fd0 100644
--- a/src/triangle.h
+++ b/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
diff --git a/src/vertex.c b/src/vertex.c
index 21ad48e..466c064 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -79,6 +79,9 @@
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 *));
@@ -110,11 +113,14 @@
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;
}
@@ -207,6 +213,57 @@
}
+/* 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. ***** */
/* ****************************************************************** */
diff --git a/src/vertex.h b/src/vertex.h
index 98efff5..97775d2 100644
--- a/src/vertex.h
+++ b/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);
--
Gitblit v1.9.3