From b01cc1ac677dc712c27337be8ee4f11ea336f31b Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@andromeda>
Date: Sun, 05 Dec 2010 13:02:22 +0000
Subject: [PATCH] Fixed some nasty bugs. Still, I suspect the vertex neighbours are not correctly oriented or something, since tristar triangles are not successfully set. (tristar_no is not always the same as neigh_no!)
---
src/cell.c | 2
src/main.c | 6 ++-
src/vertex.c | 22 +++++++----
src/initial_distribution.h | 2
src/bond.c | 9 +++-
src/energy.c | 2 +
src/initial_distribution.c | 46 +++++++++++------------
src/vertex.h | 2
8 files changed, 52 insertions(+), 39 deletions(-)
diff --git a/src/bond.c b/src/bond.c
index 289079a..1478720 100644
--- a/src/bond.c
+++ b/src/bond.c
@@ -10,10 +10,15 @@
}
ts_bond *bond_add(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
-
+ ts_uint i;
/* no vertices must be null! */
if(vtx1==NULL || vtx2==NULL) return NULL;
- /* TODO: Verify if the bond already exists... Don't do multiple bonds */
+ /* Verify if the bond already exists... Don't do multiple bonds */
+ for(i=0;i<blist->n;i++){
+ if((blist->bond[i]->data->vtx1==vtx1 || blist->bond[i]->data->vtx1==vtx2)
+ &&(blist->bond[i]->data->vtx2==vtx1 || blist->bond[i]->data->vtx2==vtx2))
+ return blist->bond[i];
+ }
blist->n++;
blist->bond=(ts_bond **)realloc(blist->bond,blist->n*sizeof(ts_bond *));
if(blist->bond==NULL) fatal("Cannot reallocate memory for additional **ts_bond.",100);
diff --git a/src/cell.c b/src/cell.c
index b3d90e4..26ce2d6 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -77,7 +77,7 @@
cell->data->nvertex++;
cell->data->vertex=(ts_vertex **)realloc(cell->data->vertex,cell->data->nvertex*sizeof(ts_vertex *));
if(vtx->data->neigh == NULL){
- fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
+ fatal("Reallocation of memory failed during insertion of vertex in cell_add_vertex",3);
}
cell->data->vertex[cell->data->nvertex-1]=vtx;
return TS_SUCCESS;
diff --git a/src/energy.c b/src/energy.c
index 540686b..e30295b 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -13,6 +13,7 @@
for(i=0;i<vlist->n;i++){
energy_vertex(vtx[i]);
+
}
return TS_SUCCESS;
@@ -38,6 +39,7 @@
j=data->neigh[jj-1];
jp=data->neigh[jjp-1];
jm=data->neigh[jjm-1];
+// printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj);
jt=data->tristar[jj-1];
x1=vtx_distance_sq(vtx,jp); //shouldn't be zero!
x2=vtx_distance_sq(j,jp); // shouldn't be zero!
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 4881e11..6a13a23 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -20,8 +20,8 @@
retval = vtx_set_global_values(vesicle);
retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
retval = init_vertex_neighbours(vesicle->vlist);
- retval = init_sort_neighbours(vesicle->vlist);
- retval = init_vesicle_bonds(vesicle);
+ vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
+ // retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
retval = init_triangles(vesicle);
retval = init_triangle_neighbours(vesicle);
retval = init_common_vertex_triangle_neighbours(vesicle);
@@ -150,21 +150,21 @@
return TS_SUCCESS;
}
-// TODO: with new datastructure can be rewritten.
-ts_bool init_sort_neighbours(ts_vertex_list *vlist){
+// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
+ts_vertex_list *init_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){
ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
ts_uint i,l,j,jj,jjj,k=0;
ts_double eps=0.001; // Take a look if EPS from math.h can be used
/*lets initialize memory for temporary vertex_list. Should we write a function instead */
- ts_vertex_list *tvlist=init_vertex_list(vlist->n);
+ ts_vertex_list *tvlist=vertex_list_copy(vlist);
ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */
ts_double dist2; // Square of distance of neighbours
ts_double direct; // Something, dont know what, but could be normal of some kind
for(i=1;i<=vlist->n;i++){
k++; // WHY i IS NOT GOOD??
- vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
+ vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
jjj=1;
jj=1;
for(l=2;l<=vtx[i]->data->neigh_no;l++){
@@ -172,7 +172,7 @@
dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
- vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
+ vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
jjj=jj;
jj=j;
break;
@@ -180,24 +180,19 @@
}
}
}
-
- for(i=1;i<=vlist->n;i++){
- for(j=1;j<=vtx[i]->data->neigh_no;j++){
- if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1!
-// fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no);
- fatal("Number of neighbours not the same in init_sort_neighbours.",4);
- }
- //we must correct the pointers in original to point to their
- //neighbours according to indexes. Must be sure not to do it any
- //other way! Also, we need to repair the collection of bonds...
- vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1];
- }
+/* We use the temporary vertex for our main vertices and we abandon main
+ * vertices, because their neighbours are not correctly ordered */
+ // tvtx=vlist->vtx;
+ // vlist->vtx=tvtx;
+ // tvlist->vtx=vtx;
+ vtx_list_free(vlist);
+/* Let's make a check if the number of bonds is correct */
+ if((blist->n)!=3*(tvlist->n-2)){
+ ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
+ fatal("Number of bonds is not 3*(no_vertex-2).",4);
}
- // Must free memory for temporary vertex array to avoid memory leak! HERE! NOW!
-// free_vertex(tvlist.vertex,tvlist.n);
- vtx_list_free(tvlist);
- return TS_SUCCESS;
+ return tvlist;
}
@@ -350,7 +345,10 @@
if((vtx[i]==k3 && k1==k4 && k2==k5) ||
(vtx[i]==k4 && k1==k5 && k2==k3) ||
(vtx[i]==k5 && k1==k3 && k2==k4)){
- // ts_fprintf(stderr, "Added to tristar! ");
+
+//TODO: probably something wrong with neighbour distribution.
+// if(vtx[i]==k3 || vtx[i]==k4 || vtx[i]==k5){
+ if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
vertex_add_tristar(vtx[i],tria[k]);
}
}
diff --git a/src/initial_distribution.h b/src/initial_distribution.h
index 04fdfe1..7b3e2ba 100644
--- a/src/initial_distribution.h
+++ b/src/initial_distribution.h
@@ -27,7 +27,7 @@
//ts_bool init_vertex_neighbours(ts_vertex_list *vlist);
/** interior sites and their neighbours in circ. order + the triangles they are holding together */
-ts_bool init_sort_neighbours(ts_vertex_list *vlist);
+ts_vertex_list *init_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist);
ts_bool init_vesicle_bonds(ts_vesicle *vesicle);
ts_bool init_triangles(ts_vesicle *vesicle);
ts_bool init_triangle_neighbours(ts_vesicle *vesicle);
diff --git a/src/main.c b/src/main.c
index a66e81b..d0ee34d 100644
--- a/src/main.c
+++ b/src/main.c
@@ -18,6 +18,7 @@
int main(int argv, char *argc[]){
ts_bool retval;
ts_vertex_list *vlist=init_vertex_list(5);
+ts_vertex_list *vlist1;
ts_bond_list *blist=init_bond_list();
ts_triangle_list *tlist=init_triangle_list();
ts_cell_list *clist=init_cell_list(3,3,3,0.3);
@@ -34,7 +35,7 @@
vlist->vtx[0]->data->x=1.0;
vlist->vtx[0]->data->x=1.1;
-
+vlist1=vertex_list_copy(vlist);
bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
@@ -53,8 +54,9 @@
bond_list_free(blist);
vtx_list_free(vlist);
cell_list_free(clist);
-printf("Tests complete.\n");
+vtx_list_free(vlist1);
+printf("Tests complete.\n");
vesicle=initial_distribution_dipyramid(7,10,10,10,0.3);
write_vertex_xml_file(vesicle,0);
write_master_xml_file("test.pvd");
diff --git a/src/vertex.c b/src/vertex.c
index dfb0155..92c5032 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -156,7 +156,7 @@
ts_bool vtx_list_free(ts_vertex_list *vlist){
int i;
for(i=0;i<vlist->n;i++){
- vtx_data_free(vlist->vtx[i]->data);
+ if(vlist->vtx[i]->data!=NULL) vtx_data_free(vlist->vtx[i]->data);
}
free(*(vlist->vtx));
free(vlist->vtx);
@@ -219,8 +219,7 @@
/* ***** New vertex copy operations. Inherently they are slow. ***** */
/* ****************************************************************** */
-ts_vertex *vtx_copy(ts_vertex *ovtx){
- ts_vertex *cvtx=(ts_vertex *)malloc(sizeof(ts_vertex));
+ts_bool vtx_copy(ts_vertex *cvtx, ts_vertex *ovtx){
memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
cvtx->data=(ts_vertex_data *)malloc(sizeof(ts_vertex_data));
memcpy((void *)cvtx->data,(void *)ovtx->data,sizeof(ts_vertex_data));
@@ -230,8 +229,8 @@
cvtx->data->bond_no=0;
cvtx->data->tristar=NULL;
cvtx->data->bond=NULL;
- cvtx->data->cell=NULL;
- return cvtx;
+ cvtx->data->cell=NULL;
+ return TS_SUCCESS;
}
//TODO: needs to be done
ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx){
@@ -241,10 +240,17 @@
ts_vertex_list *vertex_list_copy(ts_vertex_list *ovlist){
ts_uint i;
ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
- memcpy((void *)vlist, (void *)ovlist, sizeof(ts_vertex_list));
+ vlist=memcpy((void *)vlist, (void *)ovlist, sizeof(ts_vertex_list));
ts_vertex **vtx=(ts_vertex **)malloc(vlist->n*sizeof(ts_vertex *));
- for(i=0;i<vlist->n;i++){
- vtx[i]=vtx_copy(ovlist->vtx[i]);
+ ts_vertex *tlist=(ts_vertex *)calloc(vlist->n,sizeof(ts_vertex));
+ vlist->vtx=vtx;
+ if(vlist->vtx==NULL || tlist==NULL)
+ fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
+ for(i=0;i<vlist->n;i++) {
+ vlist->vtx[i]=&tlist[i];
+ vlist->vtx[i]->idx=i;
+ vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
}
+
return vlist;
}
diff --git a/src/vertex.h b/src/vertex.h
index 0b353aa..0c61c85 100644
--- a/src/vertex.h
+++ b/src/vertex.h
@@ -27,7 +27,7 @@
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);
-ts_vertex *vtx_copy(ts_vertex *ovtx);
+ts_bool vtx_copy(ts_vertex *cvtx,ts_vertex *ovtx);
ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx);
ts_vertex_list *vertex_list_copy(ts_vertex_list *ovlist);
--
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