From dac2e5020dc34c236b741ff5c4591244e73f56f2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@andromeda>
Date: Tue, 28 Dec 2010 23:48:08 +0000
Subject: [PATCH] Rewrite of frame is complete.

---
 src/vertex.c |  278 ++++++++++++++++++++++++++++++++++++++++++++-----------
 1 files changed, 222 insertions(+), 56 deletions(-)

diff --git a/src/vertex.c b/src/vertex.c
index 54ae9b7..b5f8519 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -3,102 +3,268 @@
 #include<string.h>
 #include "general.h"
 #include "vertex.h"
+#include "bond.h"
 #include<stdio.h>
 
-/* Argument je struktura vlist in stevilo vertexov, ki jih zelimo dati v
- * vlist je lahko NULL, N mora biti vecje od 0. Ce vlist obstaja, potem resizamo
- * vlist na stevilo N.
- */
-ts_vertex **init_vertex_list(ts_uint N){	
+ts_vertex_list *init_vertex_list(ts_uint N){	
 	ts_int i;
-    ts_vertex **vlist;
+    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");
-		vlist=NULL;
-		return NULL;
+        vlist->n=0;
+		vlist->vtx=NULL;
+		return vlist;
 	}
-		vlist=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
-        if(vlist==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[i]=init_vertex(i); 
-        }
+	
+    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]=&tlist[i];
+        vlist->vtx[i]->data=init_vertex_data();
+        vlist->vtx[i]->idx=i;
+    }
+    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)
+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);
-    vtx->idx=idx;
-    return vtx;
+    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){
+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->data->neigh_no;i++){
+        if(vtx->data->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->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)->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->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_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->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;
 }
 
 
-inline ts_double vertex_distance_sq(ts_vertex **vtx1, ts_vertex **vtx2){
+
+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);
+    free(vtx);
+    return TS_SUCCESS;
+}
+
+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);
+    }
+    free(*(vlist->vtx));
+    free(vlist->vtx);
+    free(vlist);
+    return TS_SUCCESS;
+}
+
+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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