From bba37cf9e0441224abc24f67d468a5bafbe8ab3c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 30 Nov 2013 10:25:41 +0000
Subject: [PATCH] step in rewritting
---
src/vertex.c | 124 ++++------------------------------------
src/general.h | 6 ++
src/vertex.h | 8 +-
3 files changed, 24 insertions(+), 114 deletions(-)
diff --git a/src/general.h b/src/general.h
index cc051f5..b1a7474 100644
--- a/src/general.h
+++ b/src/general.h
@@ -61,6 +61,11 @@
*/
#define TS_DOUBLE_DOUBLE
+/** @brief Constant defines the size by which vertex_list expands at once, so expansion is not needed each time new data arrives. Also
+ * vlist will be decreased by same steps.
+ */
+#define TS_VLIST_CHUNK 6
+
/** For the purpose of greater flexibility all data types used in the program
* shouldn't use standard C types, but should use types defined here.
* ts_int (uses int)
@@ -127,6 +132,7 @@
+
/** @brief Data structure of all data connected to a vertex
*
* ts_vertex holds the data for one single point (bead, vertex). To understand how to use it
diff --git a/src/vertex.c b/src/vertex.c
index f1ae60b..efe3cae 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;
}
@@ -23,18 +22,8 @@
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));
- }
- }
-*/
-
-
- }
+ /* initialize Ylm for spherical hamonics DONE in sh.c */
+ }
vlist->n=N;
return vlist;
}
@@ -52,7 +41,7 @@
}
vlist->list_size+=TS_VLIST_CHUNK;
}
- vlist->vtx[n]=vtx;
+ vlist->vtx[vlist->n]=vtx;
vlist->n++;
return TS_SUCCESS;
}
@@ -65,9 +54,10 @@
#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[n-1];
+ 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*));
@@ -80,63 +70,6 @@
}
}
return TS_FAIL;
-}
-
-
-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->n;i++){
- if(vtx->neigh->vtx[i]==nvtx) return TS_FAIL;
- }
- ts_uint nn=++vtx->neigh->n;
- vtx->neigh=(ts_vertex **)realloc(vtx->neigh, nn*sizeof(ts_vertex *));
- vtx->neigh[nn-1]=nvtx;
-
- 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;
}
@@ -158,12 +91,13 @@
return TS_SUCCESS;
}
-ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
+ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex_list *vlist, ts_vertex *vtx1, ts_vertex *vtx2){
ts_bool retval;
- retval=vtx_add_neighbour(vtx1,vtx2);
- // retval=vtx_add_neighbour(vtx2,vtx1);
+ retval=vertex_list_add_vtx(vtx1->neigh, vtx2);
+ retval=vertex_list_add_vtx(vtx2->neigh, vtx1);
if(retval==TS_SUCCESS)
- retval=vtx_add_bond(blist,vtx1,vtx2);
+ retval=vtx_add_bond(blist,vtx1,vtx2);
+
return retval;
}
@@ -247,35 +181,6 @@
}
-/* 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
@@ -305,7 +210,6 @@
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->tristar_no=0;
cvtx->bond_no=0;
cvtx->tristar=NULL;
diff --git a/src/vertex.h b/src/vertex.h
index 97775d2..2badec4 100644
--- a/src/vertex.h
+++ b/src/vertex.h
@@ -14,17 +14,17 @@
* @returns ts_bool value 1 on success, 0 otherwise
*/
ts_vertex_list *init_vertex_list(ts_uint N);
-ts_bool vtx_add_neighbour(ts_vertex *vtx, ts_vertex *nvtx);
-ts_bool vtx_add_cneighbour(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2);
+ts_bool vertex_list_add_vtx(ts_vertex_list *vlist, ts_vertex *vtx);
+ts_bool vertex_list_remove_vtx(ts_vertex_list *vlist, ts_vertex *vtx);
+ts_bool vtx_add_cneighbour(ts_bond_list *blist,ts_vertex_list *vlist, ts_vertex *vtx1,ts_vertex *vtx2);
ts_bool vtx_add_bond(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2);
-ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx);
+
ts_bool vtx_free(ts_vertex *vtx);
ts_bool vtx_list_free(ts_vertex_list *vlist);
inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2);
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);
--
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