From d43116b7d609fa9cabae4068d037c1af3a20dae8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 08 Aug 2019 17:42:46 +0000
Subject: [PATCH] An attempt to fix polymer error while recreating vesicle from vtu.
---
src/vertex.c | 306 +++++++++++++++++++++++++++++++++++++++++----------
1 files changed, 246 insertions(+), 60 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index 52a8f93..59a6419 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include<string.h>
@@ -6,9 +7,16 @@
#include "bond.h"
#include<stdio.h>
+ts_bool vertex_list_assign_id(ts_vertex_list *vlist, ts_uint id){
+ ts_uint i;
+ for(i=0;i<vlist->n;i++){
+ vlist->vtx[i]->id = id;
+ }
+ return TS_SUCCESS;
+}
+
ts_vertex_list *init_vertex_list(ts_uint N){
ts_int i;
- ts_vertex *tlist;
ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
if(N==0){
@@ -18,39 +26,27 @@
return vlist;
}
- vlist->vtx=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
- tlist=(ts_vertex *)malloc(N*sizeof(ts_vertex));
- if(vlist->vtx==NULL || tlist==NULL)
+ 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]=&tlist[i];
- vlist->vtx[i]->data=init_vertex_data();
+ 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_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);
- 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_uint i;
@@ -58,63 +54,112 @@
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->data->neigh_no;i++){
- if(vtx->data->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->data->neigh_no;
- vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh, nn*sizeof(ts_vertex *));
- vtx->data->neigh[nn-1]=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->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;
}
+
+/* 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;
+}
+
+
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->bond_no++;
+ vtx2->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;
+ vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->bond_no*sizeof(ts_bond *));
+ vtx2->bond=(ts_bond **)realloc(vtx2->bond, vtx2->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->bond[vtx2->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);
+ // retval=vtx_add_neighbour(vtx2,vtx1);
if(retval==TS_SUCCESS)
retval=vtx_add_bond(blist,vtx1,vtx2);
return retval;
}
-
-
-
-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);
- free(data);
+/*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;
}
-/*not usable. can be deleted */
+
ts_bool vtx_free(ts_vertex *vtx){
- vtx_data_free(vtx->data);
+ 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;
}
@@ -122,28 +167,169 @@
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]!=NULL) vtx_free(vlist->vtx[i]);
}
- free(*(vlist->vtx));
+ //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;
#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;
+}
+
+/** Calculates the triple product of vectors defined by vertices vtx1, vtx2 and vtx3, ($\mathrm{vtx}_1\cdot(\mathrm{vtx}_2\cross\mathrm{vtx}_3$):
+ * \begin{vmatrix}
+ * x_1 & y_1 & z_1 \\
+ * x_2-x_1 & y_2-y_1 & z_2-z_1\\
+ * x_3-x_1 & y_3-y_1 & z_3-z_1\\
+ * \end{vmatrix}
+ * where the vertices coordinates are denoted by corresponding vertex index number. Function is used to determine the orientation of area formed by triangle formed by the three given vertices.
+ *
+ * @param vtx1 is first vertex, according to which the orientation is calculated
+ * @param vtx2 is the second vertex
+ * @param vtx3 is the third vertex
+ * @returns directionality of the area of the triangle formed by vertices vtx1, vtx2 and vtx3. It is positive if vtx1, vtx2 and vtx3 are oriented counter-clockwise.
*/
+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;
+}
+
+
+/* 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
+ * elements in some order or not! */
+inline ts_bool vtx_remove_tristar(ts_vertex *vtx, ts_triangle *tristar){
+ ts_uint i,j=0;
+ for(i=0;i<vtx->tristar_no;i++){
+ if(vtx->tristar[i]!=tristar){
+ vtx->tristar[j]=vtx->tristar[i];
+ j++;
+ }
+ }
+ vtx->tristar_no--;
+ vtx->tristar=realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
+ if(vtx->neigh == NULL){
+ fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
+ }
+ 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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