From 79fc9ce029be3e91d3249a654f84c7a1ce1ff9ee Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 07 Jun 2012 19:46:44 +0000
Subject: [PATCH] spherical harmonics coefficients co fixed and working. Zero based indexing was solved in such a manner, that we allocated more memory that is required by coefficients.
---
src/vertex.c | 245 ++++++++++++++++++++++++++++++++++++++----------
1 files changed, 193 insertions(+), 52 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index 60123ab..21ad48e 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -3,11 +3,12 @@
#include<string.h>
#include "general.h"
#include "vertex.h"
+#include "bond.h"
#include<stdio.h>
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 *)malloc(sizeof(ts_vertex_list));
if(N==0){
err("Initialized vertex list with zero elements. Pointer set to NULL");
@@ -16,97 +17,237 @@
return vlist;
}
- vlist->vtx=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
+ 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]=init_vertex(i);
+ 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->n=N;
return vlist;
}
-ts_vertex *init_vertex(ts_uint idx){
- ts_vertex *vtx;
- vtx=(ts_vertex *)malloc(sizeof(ts_vertex));
- if(vtx==NULL)
- fatal("Fatal error reserving memory space for ts_vertex! Memory full?", 100);
- vtx->idx=idx;
- return vtx;
-}
-
-/*
-ts_bool vtx_set_global_values(ts_vertex **vlist, ts_vesicle *vesicle){
- ts_double xk=vesicle->bending_rigidity;
- ts_uint i;
- for(i=0;i<vesicle->vlist.n;i++){
- vlist[i]->xk=xk;
- }
- return TS_SUCCESS;
-}
-*/
-
-
-
-ts_bool vtx_add_neighbour(ts_vertex **vtx, ts_vertex **nvtx){
+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;
+ 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]=nvtx;
-
+ 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)->neigh_no;i++){
- if((*nvtx)->neigh[i]==vtx) return TS_FAIL;
+/*
+ for(i=0; i<nvtx->data->neigh_no;i++){
+ if(nvtx->data->neigh[i]==vtx) return TS_FAIL;
}
- nn=(*nvtx)->neigh_no++;
- (*nvtx)->neigh=(ts_vertex ***)realloc((*nvtx)->neigh, nn*sizeof(ts_vertex **));
- (*nvtx)->neigh[nn]=vtx;
+ 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;
+}
-/* Ustvari bond in doloci dolzino */
+/* 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++){
+ if(vtx->neigh[i]!=nvtx){
+ vtx->neigh[j]=vtx->neigh[i];
+ j++;
+ }
+ }
+/* 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("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->neigh_no;i++){
+ if(nvtx->neigh[i]!=vtx){
+ nvtx->neigh[j]=nvtx->neigh[i];
+ j++;
+ }
+ }
+/* resize memory. potentionally time consuming. */
+ nvtx->neigh_no--;
+ nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
+ if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
+ fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
return TS_SUCCESS;
}
-ts_bool vtx_free(ts_vertex **vtx){
- if((*vtx)->neigh!=NULL) free((*vtx)->neigh);
- if((*vtx)->tristar!=NULL) free((*vtx)->tristar);
- if((*vtx)->bond!=NULL) free((*vtx)->bond);
- if((*vtx)->cell!=NULL) free((*vtx)->cell);
- free(*vtx);
+
+ts_bool vtx_add_bond(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2){
+ ts_bond *bond;
+ bond=bond_add(blist,vtx1,vtx2);
+ if(bond==NULL) return TS_FAIL;
+ vtx1->bond_no++;
+ // vtx2->data->bond_no++;
+
+ vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->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->ata->bond[vtx2->data->bond_no-1]=bond;
+ 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);
+ return retval;
+}
+
+/*TODO: write and optimize this urgently before use! */
+ts_bool vtx_remove_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex
+*vtx2){
+// ts_bool retval;
+/* remove the bond */
+//retval=vtx_remove_bond(blist,vtx1,vtx2);
+/* remove the vertices */
+ return TS_SUCCESS;
+}
+
+
+ts_bool vtx_free(ts_vertex *vtx){
+ if(vtx->neigh!=NULL) free(vtx->neigh);
+ if(vtx->tristar!=NULL) free(vtx->tristar);
+ if(vtx->bond!=NULL) free(vtx->bond);
+ free(vtx);
return TS_SUCCESS;
}
ts_bool vtx_list_free(ts_vertex_list *vlist){
int i;
for(i=0;i<vlist->n;i++){
- vtx_free(VTX(vlist,i));
+ if(vlist->vtx[i]!=NULL) vtx_free(vlist->vtx[i]);
}
+ //free(*(vlist->vtx));
+ free(vlist->vtx);
free(vlist);
return TS_SUCCESS;
}
-
-
-
-inline ts_double vtx_distance_sq(ts_vertex **vtx1, ts_vertex **vtx2){
+inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2){
ts_double dist;
#ifdef TS_DOUBLE_DOUBLE
- dist=pow((*vtx1)->x-(*vtx2)->x,2) + pow((*vtx1)->y-(*vtx2)->y,2) + pow((*vtx1)->z-(*vtx2)->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((*vtx1)->x-(*vtx2)->x,2) + powl((*vtx1)->y-(*vtx2)->y,2) + powl((*vtx1)->z-(*vtx2)->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((*vtx1)->x-(*vtx2)->x,2) + powf((*vtx1)->y-(*vtx2)->y,2) + powf((*vtx1)->z-(*vtx2)->z,2);
+ dist=powf(vtx1->x-vtx2->x,2) + powf(vtx1->y-vtx2->y,2) + powf(vtx1->z-vtx2->z,2);
#endif
return(dist);
}
+
+
+ts_bool vtx_set_global_values(ts_vesicle *vesicle){
+ ts_double xk=vesicle->bending_rigidity;
+ ts_uint i;
+ for(i=0;i<vesicle->vlist->n;i++){
+ 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->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->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->tristar[vtx->tristar_no-1]=tristarmem;
+ return TS_SUCCESS;
+}
+
+
+/* ****************************************************************** */
+/* ***** New vertex copy operations. Inherently they are slow. ***** */
+/* ****************************************************************** */
+
+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;
+ 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));
+ return TS_SUCCESS;
+}
+
+//TODO: needs to be done
+ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx){
+ return NULL;
+}
+
+
+
+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));
+ vlist=memcpy((void *)vlist, (void *)ovlist, sizeof(ts_vertex_list));
+ ts_vertex **vtx=(ts_vertex **)malloc(vlist->n*sizeof(ts_vertex *));
+ vlist->vtx=vtx;
+ 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]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
+ vlist->vtx[i]->idx=i;
+ vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
+ }
+
+ return vlist;
+}
--
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