From bc4e1ee61725fdf7ec81a9583b7fa545f847e07b Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 30 Nov 2013 17:12:09 +0000
Subject: [PATCH] It works
---
src/vertex.c | 272 +++++++++++++++++++++++++++--------------------------
1 files changed, 138 insertions(+), 134 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index b5f8519..ffd5f7d 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -8,100 +8,76 @@
ts_vertex_list *init_vertex_list(ts_uint N){
ts_int i;
- ts_vertex *tlist;
- ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
-
+ ts_vertex_list *vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+
if(N==0){
- err("Initialized vertex list with zero elements. Pointer set to NULL");
- vlist->n=0;
- vlist->vtx=NULL;
+ vlist->n=0;
+ vlist->vtx=(ts_vertex **)calloc(1,sizeof(ts_vertex *)); /*Allocate one memory space for vlist anyway */
return vlist;
}
- vlist->vtx=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
- tlist=(ts_vertex *)malloc(N*sizeof(ts_vertex));
- if(vlist->vtx==NULL || tlist==NULL)
+ vlist->vtx=(ts_vertex **)calloc(N,sizeof(ts_vertex *));
+ if(vlist->vtx==NULL)
fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
for(i=0;i<N;i++) {
- vlist->vtx[i]=&tlist[i];
- vlist->vtx[i]->data=init_vertex_data();
+ vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
vlist->vtx[i]->idx=i;
- }
+ vlist->vtx[i]->neigh=init_vertex_list(0);
+ /* initialize Ylm for spherical hamonics DONE in sh.c */
+ }
vlist->n=N;
+ vlist->list_size=TS_VLIST_CHUNK; //TODO: can be buggy in some cases, when N>0 and we want to delete some vertices.
return vlist;
}
-ts_vertex_data *init_vertex_data(){
- ts_vertex_data *data;
- data=(ts_vertex_data *)calloc(1,sizeof(ts_vertex_data));
- if(data==NULL)
- fatal("Fatal error reserving memory space for ts_vertex! Memory full?", 100);
- return data;
+
+ts_bool vertex_list_add_vtx(ts_vertex_list *vlist, ts_vertex *vtx){
+
+#ifdef DEBUG
+ if(vtx==NULL)
+ err("VTX is null");
+ if(vlist==NULL) err("VLIST is null");
+
+ if(vtx==NULL || vlist==NULL)
+ return TS_FAIL;
+#endif
+ if(vlist->list_size < vlist->n+1){
+ vlist->vtx=(ts_vertex **)realloc(vlist->vtx, (vlist->list_size+TS_VLIST_CHUNK)*sizeof(ts_vertex*));
+ if(vlist->vtx==NULL){
+ fatal("Error in vertex_list_add. Could not reallocate memory space.",9999);
+ }
+ vlist->list_size+=TS_VLIST_CHUNK;
+ }
+// printf("Test %u (max %u)!\n", vlist->n, vlist->list_size);
+ vlist->vtx[vlist->n]=vtx;
+ vlist->n++;
+ return TS_SUCCESS;
}
-ts_bool vtx_add_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
- ts_uint i;
- /* no neighbour can be null! */
- if(vtx==NULL || nvtx==NULL) return TS_FAIL;
-
- /*if it is already a neighbour don't add it to the list */
- for(i=0; i<vtx->data->neigh_no;i++){
- if(vtx->data->neigh[i]==nvtx) return TS_FAIL;
- }
- ts_uint nn=++vtx->data->neigh_no;
- vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh, nn*sizeof(ts_vertex *));
- vtx->data->neigh[nn-1]=nvtx;
-/* This was a bug in creating DIPYRAMID (the neighbours were not in right
- * order).
- */
- /* pa se sosedu dodamo vertex */
- /*if it is already a neighbour don't add it to the list */
-/*
- for(i=0; i<nvtx->data->neigh_no;i++){
- if(nvtx->data->neigh[i]==vtx) return TS_FAIL;
- }
- nn=++nvtx->data->neigh_no;
- nvtx->data->neigh=(ts_vertex **)realloc(nvtx->data->neigh, nn*sizeof(ts_vertex *));
- nvtx->data->neigh[nn-1]=vtx;
-*/
-
- return TS_SUCCESS;
-}
-
-/* TODO: optimize this. test this. */
-ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
-/* find a neighbour */
-/* remove it from the list while shifting remaining neighbours up */
- ts_uint i,j=0;
- for(i=0;i<vtx->data->neigh_no;i++){
- if(vtx->data->neigh[i]!=nvtx){
- vtx->data->neigh[j]=vtx->data->neigh[i];
- j++;
- }
- }
-/* resize memory. potentionally time consuming */
- vtx->data->neigh_no--;
- vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh,vtx->data->neigh_no*sizeof(ts_vertex *));
- if(vtx->data->neigh == NULL && vtx->data->neigh_no!=0)
- fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
-
-/* repeat for the neighbour */
-/* find a neighbour */
-/* remove it from the list while shifting remaining neighbours up */
- for(i=0;i<nvtx->data->neigh_no;i++){
- if(nvtx->data->neigh[i]!=vtx){
- nvtx->data->neigh[j]=nvtx->data->neigh[i];
- j++;
- }
- }
-/* resize memory. potentionally time consuming. */
- nvtx->data->neigh_no--;
- nvtx->data->neigh=(ts_vertex **)realloc(nvtx->data->neigh,nvtx->data->neigh_no*sizeof(ts_vertex *));
- if(nvtx->data->neigh == NULL && nvtx->data->neigh_no!=0)
- fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
-
- return TS_SUCCESS;
+/* Idea is to delete vertex by removing it from list. The emply place is then filled in by the last
+vertex in the list. List can then be resized by one -- unless resize is required when max list size -
+real list size > predefined value */
+ts_bool vertex_list_remove_vtx(ts_vertex_list *vlist, ts_vertex *vtx){
+#ifdef DEBUG
+ if(vtx==NULL || vlist==NULL) return TS_FAIL;
+#endif
+ ts_uint i;
+ for(i=0; i<vlist->n;i++){
+ if(vlist->vtx[i]==vtx){
+ vlist->vtx[i]=vlist->vtx[vlist->n-1];
+ vlist->n--;
+ if(vlist->list_size-vlist->n > TS_VLIST_CHUNK){
+ vlist->vtx=(ts_vertex **)realloc(vlist->vtx, (vlist->list_size-TS_VLIST_CHUNK)*sizeof(ts_vertex*));
+ if(vlist->vtx==NULL){
+ fatal("Error in vertex_list_add. Could not reallocate memory space.",9999);
+ }
+ vlist->list_size-=TS_VLIST_CHUNK;
+ }
+ return TS_SUCCESS;
+ }
+ }
+ return TS_FAIL;
}
@@ -110,21 +86,41 @@
ts_bond *bond;
bond=bond_add(blist,vtx1,vtx2);
if(bond==NULL) return TS_FAIL;
- vtx1->data->bond_no++;
+ vtx1->bond_no++;
+ vtx2->bond_no++;
// vtx2->data->bond_no++;
- vtx1->data->bond=(ts_bond **)realloc(vtx1->data->bond, vtx1->data->bond_no*sizeof(ts_bond *));
+ 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->data->bond[vtx1->data->bond_no-1]=bond;
- // vtx2->data->bond[vtx2->data->bond_no-1]=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;
+}
+
+// Add neighbour just in one direction (add vtx2 as a neigh of vtx1 and not another way around!
+ts_bool vtx_add_neighbour(ts_vertex *vtx1, ts_vertex *vtx2){
+ ts_uint i;
+ if(vtx1==NULL || vtx2==NULL) return TS_FAIL;
+ for(i=0;i<vtx1->neigh->n;i++){
+ if (vtx1->neigh->vtx[i]==vtx2){
+ return TS_FAIL;
+ }
+ }
+ vertex_list_add_vtx(vtx1->neigh, vtx2);
+ return TS_SUCCESS;
}
ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
ts_bool retval;
- retval=vtx_add_neighbour(vtx1,vtx2);
- if(retval==TS_SUCCESS)
- retval=vtx_add_bond(blist,vtx1,vtx2);
+ retval=vtx_add_neighbour(vtx1, vtx2);
+// retval=vertex_list_add_vtx(vtx1->neigh, vtx2);
+// retval=vertex_list_add_vtx(vtx2->neigh, vtx1);
+ if(retval==TS_SUCCESS){
+ // fprintf(stderr,"Bond added\n");
+ retval=vtx_add_bond(blist,vtx1,vtx2);
+ }
return retval;
}
@@ -139,20 +135,13 @@
}
-
-ts_bool vtx_data_free(ts_vertex_data *data){
- if(data->neigh!=NULL) free(data->neigh);
- if(data->tristar!=NULL) free(data->tristar);
- if(data->bond!=NULL) free(data->bond);
-//Cells are freed separately.
- // if(data->cell!=NULL) free(data->cell);
- free(data);
- return TS_SUCCESS;
-}
-
-/*not usable. can be deleted */
ts_bool vtx_free(ts_vertex *vtx){
- vtx_data_free(vtx->data);
+ if(vtx->neigh!=NULL) {
+ if (vtx->neigh->vtx!=NULL) free(vtx->neigh->vtx);
+ free(vtx->neigh);
+ }
+ if(vtx->tristar!=NULL) free(vtx->tristar);
+ if(vtx->bond!=NULL) free(vtx->bond);
free(vtx);
return TS_SUCCESS;
}
@@ -160,9 +149,9 @@
ts_bool vtx_list_free(ts_vertex_list *vlist){
int i;
for(i=0;i<vlist->n;i++){
- if(vlist->vtx[i]->data!=NULL) vtx_data_free(vlist->vtx[i]->data);
+ if(vlist->vtx[i]!=NULL) vtx_free(vlist->vtx[i]);
}
- free(*(vlist->vtx));
+ //free(*(vlist->vtx));
free(vlist->vtx);
free(vlist);
return TS_SUCCESS;
@@ -170,15 +159,14 @@
inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2){
ts_double dist;
- ts_vertex_data *vd1=vtx1->data, *vd2=vtx2->data;
#ifdef TS_DOUBLE_DOUBLE
- dist=pow(vd1->x-vd2->x,2) + pow(vd1->y-vd2->y,2) + pow(vd1->z-vd2->z,2);
+ dist=pow(vtx1->x-vtx2->x,2) + pow(vtx1->y-vtx2->y,2) + pow(vtx1->z-vtx2->z,2);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- dist=powl(vd1->x-vd2->x,2) + powl(vd1->y-vd2->y,2) + powl(vd1->z-vd2->z,2);
+ dist=powl(vtx1->x-vtx2->x,2) + powl(vtx1->y-vtx2->y,2) + powl(vtx1->z-vtx2->z,2);
#endif
#ifdef TS_DOUBLE_FLOAT
- dist=powf(vd1->x-vd2->x,2) + powf(vd1->y-vd2->y,2) + powf(vd1->z-vd2->z,2);
+ dist=powf(vtx1->x-vtx2->x,2) + powf(vtx1->y-vtx2->y,2) + powf(vtx1->z-vtx2->z,2);
#endif
return(dist);
}
@@ -189,34 +177,56 @@
ts_double xk=vesicle->bending_rigidity;
ts_uint i;
for(i=0;i<vesicle->vlist->n;i++){
- vesicle->vlist->vtx[i]->data->xk=xk;
+ vesicle->vlist->vtx[i]->xk=xk;
}
return TS_SUCCESS;
}
inline ts_double vtx_direct(ts_vertex *vtx1, ts_vertex *vtx2, ts_vertex *vtx3){
- ts_double dX2=vtx2->data->x-vtx1->data->x;
- ts_double dY2=vtx2->data->y-vtx1->data->y;
- ts_double dZ2=vtx2->data->z-vtx1->data->z;
- ts_double dX3=vtx3->data->x-vtx1->data->x;
- ts_double dY3=vtx3->data->y-vtx1->data->y;
- ts_double dZ3=vtx3->data->z-vtx1->data->z;
- ts_double direct=vtx1->data->x*(dY2*dZ3 -dZ2*dY3)+
- vtx1->data->y*(dZ2*dX3-dX2*dZ3)+
- vtx1->data->z*(dX2*dY3-dY2*dX3);
+ ts_double dX2=vtx2->x-vtx1->x;
+ ts_double dY2=vtx2->y-vtx1->y;
+ ts_double dZ2=vtx2->z-vtx1->z;
+ ts_double dX3=vtx3->x-vtx1->x;
+ ts_double dY3=vtx3->y-vtx1->y;
+ ts_double dZ3=vtx3->z-vtx1->z;
+ ts_double direct=vtx1->x*(dY2*dZ3 -dZ2*dY3)+
+ vtx1->y*(dZ2*dX3-dX2*dZ3)+
+ vtx1->z*(dX2*dY3-dY2*dX3);
return(direct);
}
inline ts_bool vertex_add_tristar(ts_vertex *vtx, ts_triangle *tristarmem){
- vtx->data->tristar_no++;
- vtx->data->tristar=(ts_triangle **)realloc(vtx->data->tristar,vtx->data->tristar_no*sizeof(ts_triangle *));
- if(vtx->data->tristar==NULL){
+ vtx->tristar_no++;
+ vtx->tristar=(ts_triangle **)realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
+ if(vtx->tristar==NULL){
fatal("Reallocation of memory while adding tristar failed.",3);
}
- vtx->data->tristar[vtx->data->tristar_no-1]=tristarmem;
+ vtx->tristar[vtx->tristar_no-1]=tristarmem;
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;
+}
+
/* ****************************************************************** */
@@ -225,22 +235,17 @@
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));
- cvtx->data->neigh=NULL;
- cvtx->data->neigh_no=0;
- cvtx->data->tristar_no=0;
- cvtx->data->bond_no=0;
- cvtx->data->tristar=NULL;
- cvtx->data->bond=NULL;
- cvtx->data->cell=NULL;
+ cvtx->neigh=init_vertex_list(0);
+ cvtx->tristar_no=0;
+ cvtx->bond_no=0;
+ cvtx->tristar=NULL;
+ cvtx->bond=NULL;
+ cvtx->cell=NULL;
return TS_SUCCESS;
}
ts_bool vtx_duplicate(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));
return TS_SUCCESS;
}
@@ -256,12 +261,11 @@
ts_vertex_list *vlist=(ts_vertex_list *)malloc(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 *));
- ts_vertex *tlist=(ts_vertex *)calloc(vlist->n,sizeof(ts_vertex));
vlist->vtx=vtx;
- if(vlist->vtx==NULL || tlist==NULL)
+ if(vlist->vtx==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]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
vlist->vtx[i]->idx=i;
vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
}
--
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