From af3bad5b0ffbe0f19b0f85519c85a385326dec03 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@amalthea>
Date: Sat, 19 Mar 2011 21:10:19 +0000
Subject: [PATCH] Spherical harmonics should be ok. Note, that there are some difference from proposed theoretical scheme. Is Miha's theory wrong?
---
src/vertex.c | 222 ++++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 187 insertions(+), 35 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index b83f609..b5f8519 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -3,11 +3,13 @@
#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 *tlist;
+ 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");
@@ -16,33 +18,26 @@
return vlist;
}
- vlist->vtx=(ts_vertex *)malloc(N*sizeof(ts_vertex));
- if(vlist->vtx==NULL)
+ vlist->vtx=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
+ tlist=(ts_vertex *)malloc(N*sizeof(ts_vertex));
+ 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<N;i++) vlist->vtx[i].data=init_vertex_data();
+ for(i=0;i<N;i++) {
+ vlist->vtx[i]=&tlist[i];
+ vlist->vtx[i]->data=init_vertex_data();
+ vlist->vtx[i]->idx=i;
+ }
vlist->n=N;
return vlist;
}
ts_vertex_data *init_vertex_data(){
ts_vertex_data *data;
- data=(ts_vertex_data *)malloc(sizeof(ts_vertex_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 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){
@@ -54,35 +49,108 @@
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++;
+ ts_uint nn=++vtx->data->neigh_no;
vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh, nn*sizeof(ts_vertex *));
- vtx->data->neigh[nn]=nvtx;
-
+ 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++;
+ nn=++nvtx->data->neigh_no;
nvtx->data->neigh=(ts_vertex **)realloc(nvtx->data->neigh, nn*sizeof(ts_vertex *));
- nvtx->data->neigh[nn]=vtx;
-
-
-/* Ustvari bond in doloci dolzino */
+ 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;
+}
+
+
+
+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->data->bond_no++;
+ // vtx2->data->bond_no++;
+
+ vtx1->data->bond=(ts_bond **)realloc(vtx1->data->bond, vtx1->data->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;
+ 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_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);
- if(data->cell!=NULL) free(data->cell);
+//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);
free(vtx);
@@ -92,27 +160,111 @@
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);
free(vlist);
return TS_SUCCESS;
}
-
-
-/* rewrite for additional structure in chain */
-/*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;
+ ts_vertex_data *vd1=vtx1->data, *vd2=vtx2->data;
#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(vd1->x-vd2->x,2) + pow(vd1->y-vd2->y,2) + pow(vd1->z-vd2->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(vd1->x-vd2->x,2) + powl(vd1->y-vd2->y,2) + powl(vd1->z-vd2->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(vd1->x-vd2->x,2) + powf(vd1->y-vd2->y,2) + powf(vd1->z-vd2->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]->data->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);
+ 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){
+ fatal("Reallocation of memory while adding tristar failed.",3);
+ }
+ vtx->data->tristar[vtx->data->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->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;
+ 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;
+}
+
+//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 *));
+ 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;
+}
--
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