From 8ed8fdb663089e2bc53fd537611a6b45a09cc502 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 30 Nov 2013 16:54:34 +0000
Subject: [PATCH] Seems to solve everything until bondflip
---
src/vertex.c | 193 +++++++++++++++++++-----------------------------
1 files changed, 77 insertions(+), 116 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index 38647aa..871fe29 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -8,12 +8,11 @@
ts_vertex_list *init_vertex_list(ts_uint N){
ts_int i;
- 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;
}
@@ -23,89 +22,62 @@
for(i=0;i<N;i++) {
vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
vlist->vtx[i]->idx=i;
-
- /* initialize Ylm for spherical hamonics DONE in sh.c */
-/* for(i=0;i<l;i++){
- vlist->vtx[i]->Ylm[i]=(ts_double **)calloc(2*i+1,sizeof(ts_double *));
- for(j=0;j<(2*i+1);j++){
- clist->vtx[i]->Ylm[i][j]=(ts_double *)calloc(sizeof(ts_double));
- }
- }
-*/
-
-
- }
+ 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_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->neigh_no;i++){
- if(vtx->neigh[i]==nvtx) return TS_FAIL;
- }
- ts_uint nn=++vtx->neigh_no;
- vtx->neigh=(ts_vertex **)realloc(vtx->neigh, nn*sizeof(ts_vertex *));
- vtx->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;
+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;
}
-/* 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->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("(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];
- j++;
- }
- }
-/* 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 *));
-// fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
- if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
- fatal("(2) 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;
}
@@ -127,12 +99,28 @@
return TS_SUCCESS;
}
+
+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);
- // retval=vtx_add_neighbour(vtx2,vtx1);
- 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;
}
@@ -148,7 +136,10 @@
ts_bool vtx_free(ts_vertex *vtx){
- if(vtx->neigh!=NULL) free(vtx->neigh);
+ 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);
@@ -216,35 +207,6 @@
}
-/* 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
@@ -273,8 +235,7 @@
ts_bool vtx_copy(ts_vertex *cvtx, ts_vertex *ovtx){
memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
- cvtx->neigh=NULL;
- cvtx->neigh_no=0;
+ cvtx->neigh=init_vertex_list(0);
cvtx->tristar_no=0;
cvtx->bond_no=0;
cvtx->tristar=NULL;
--
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