From e016c401c98b6a33392b551b2c40fccded21efe3 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 23 Feb 2012 14:43:30 +0000
Subject: [PATCH] bond data removed
---
src/cell.c | 108 ++++++++++++++++++++++++++++++++----------------------
1 files changed, 64 insertions(+), 44 deletions(-)
diff --git a/src/cell.c b/src/cell.c
index ae912fe..1d66bc6 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -1,87 +1,107 @@
#include<stdlib.h>
#include "general.h"
#include "vertex.h"
-#include <stdio.h>
-ts_bool init_cell_list(ts_cell_list *clist, ts_double stepsize){
+
+ts_cell_list *init_cell_list(ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
ts_uint i;
- ts_uint nocells=clist->ncmax[0]*clist->ncmax[1]*clist->ncmax[2];
- clist->cell=malloc(nocells*sizeof(ts_cell));
+ ts_uint nocells=ncmax1*ncmax2*ncmax3;
+ ts_cell_list *clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ if(clist==NULL) fatal("Error while allocating memory for cell list!",100);
+
+ clist->ncmax[0]=ncmax1;
+ clist->ncmax[1]=ncmax2;
+ clist->ncmax[2]=ncmax3;
+ clist->cellno=nocells;
clist->dcell=1.0/(1.0 + stepsize);
clist->shift=(ts_double) clist->ncmax[0]/2;
- clist->cellno=nocells;
+
+ clist->cell=(ts_cell **)malloc(nocells*sizeof(ts_cell *));
+ if(clist->cell==NULL) fatal("Error while allocating memory for cell list! ncmax too large?",101);
+
for(i=0;i<nocells;i++){
- clist->cell[i].idx=i+1; // We enumerate cells! Probably never required!
- clist->cell[i].nvertex=0;
- clist->cell[i].vertex=NULL;
+ clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
+ if(clist->cell[i]==NULL) fatal("Error while allocating memory for cell list! ncmax too large?",102);
+ clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
+ clist->cell[i]->data=(ts_cell_data *)calloc(1,sizeof(ts_cell_data));
}
+ return clist;
+}
+
+ts_bool cell_free(ts_cell* cell){
+ if(cell->data!=NULL){
+ if(cell->data->vertex!=NULL) free(cell->data->vertex);
+ free(cell->data);
+ }
+ free(cell);
return TS_SUCCESS;
}
ts_bool cell_list_free(ts_cell_list *clist){
ts_uint i;
- ts_uint nocells=clist->ncmax[0]*clist->ncmax[1]*clist->ncmax[2];
-
+ if(clist==NULL) return TS_FAIL;
+ ts_uint nocells=clist->cellno;
for(i=0;i<nocells;i++)
- if(clist->cell->vertex != NULL) free(clist->cell->vertex);
+ if(clist->cell[i] != NULL) cell_free(clist->cell[i]);
free(clist->cell);
-
+ free(clist);
return TS_SUCCESS;
}
-inline ts_uint vertex_self_avoidance(ts_vesicle *vesicle, ts_vertex *vtx){
- ts_uint i,cellidx;
- ts_uint ncx, ncy,ncz;
- ncx=(ts_uint)((vtx->x-vesicle->cm[0])*vesicle->clist.dcell+vesicle->clist.shift);
- ncy=(ts_uint)((vtx->y-vesicle->cm[1])*vesicle->clist.dcell+vesicle->clist.shift);
- ncz=(ts_uint)((vtx->z-vesicle->cm[2])*vesicle->clist.dcell+vesicle->clist.shift);
-// fprintf(stderr,"(ncx,ncy,ncz)=(%i %i %i)\t",ncx,ncy,ncz);
-// fprintf(stderr,"(ncxmax,ncymax,nczmax)=(%i %i %i)\n",vesicle->clist.ncmax[0], vesicle->clist.ncmax[1], vesicle->clist.ncmax[2]);
- if(ncx == vesicle->clist.ncmax[0]-1 || ncx == 2){
+//TODO: not debugged at all!
+inline ts_uint vertex_self_avoidance(ts_vesicle *vesicle, ts_vertex *vtx){
+ ts_uint cellidx;
+ ts_uint ncx, ncy,ncz;
+ ts_cell_list *clist=vesicle->clist;
+ ncx=(ts_uint)((vtx->data->x-vesicle->cm[0])*clist->dcell+clist->shift);
+ ncy=(ts_uint)((vtx->data->y-vesicle->cm[1])*clist->dcell+clist->shift);
+ ncz=(ts_uint)((vtx->data->z-vesicle->cm[2])*clist->dcell+clist->shift);
+
+ if(ncx == clist->ncmax[0]-1 || ncx == 2){
fatal("Vesicle is positioned outside the cell covered area. Coordinate x is the problem.",1500);
}
- if(ncy == vesicle->clist.ncmax[1]-1 || ncy == 2){
+ if(ncy == clist->ncmax[1]-1 || ncy == 2){
fatal("Vesicle is positioned outside the cell covered area. Coordinate y is the problem.",1500);
}
- if(ncz == vesicle->clist.ncmax[2]-1 || ncz == 2){
+ if(ncz == clist->ncmax[2]-1 || ncz == 2){
fatal("Vesicle is positioned outside the cell covered area. Coordinate z is the problem.",1500);
}
- cellidx=ncz+(ncy-1)*vesicle->clist.ncmax[2] +
-(ncx-1)*vesicle->clist.ncmax[2]* vesicle->clist.ncmax[1] - 1; // -1 is because of 0 based indexing
- return cellidx;
+ cellidx=ncz+(ncy-1)*clist->ncmax[2] + (ncx-1)*clist->ncmax[2]*
+ clist->ncmax[1] - 1; // -1 is because of 0 based indexing
+ return cellidx;
}
-
+//TODO: looks ok, but debug anyway in the future
ts_bool cell_add_vertex(ts_cell *cell, ts_vertex *vtx){
-
- cell->nvertex++;
- cell->vertex=realloc(cell->vertex,cell->nvertex*sizeof(ts_vertex *));
- if(vtx->neigh == NULL){
- fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
+ cell->data->nvertex++;
+ cell->data->vertex=(ts_vertex **)realloc(cell->data->vertex,cell->data->nvertex*sizeof(ts_vertex *));
+ if(cell->data->vertex == NULL){
+ fatal("Reallocation of memory failed during insertion of vertex in cell_add_vertex",3);
}
- cell->vertex[cell->nvertex-1]=vtx;
-
+ cell->data->vertex[cell->data->nvertex-1]=vtx;
return TS_SUCCESS;
}
-ts_bool cell_list_cell_ocupation_clear(ts_cell_list *clist){
+
+ts_bool cell_list_cell_occupation_clear(ts_cell_list *clist){
ts_uint i;
for(i=0;i<clist->cellno;i++){
- if(clist->cell[i].vertex != NULL){
- free(clist->cell[i].vertex);
- clist->cell[i].vertex=NULL;
+ if(clist->cell[i]->data->vertex != NULL){
+ free(clist->cell[i]->data->vertex);
+ clist->cell[i]->data->vertex=NULL;
}
- clist->cell[i].nvertex=0;
+ clist->cell[i]->data->nvertex=0;
}
return TS_SUCCESS;
}
+// TODO: compiles ok, but it is completely untested and undebugged. It was debugged before rewrite, but this was long time ago.
ts_bool cell_occupation_number_and_internal_proximity(ts_cell_list *clist, ts_uint cellidx, ts_vertex *vtx, ts_vertex *tvtx){
ts_uint ncx,ncy,ncz,remainder,cell_occupation;
- ts_uint i,j,k,l,neigh_cidx,mcell;
+ ts_uint i,j,k,l,neigh_cidx;
ts_double dist;
- ncx=(cellidx+1)/(clist->ncmax[2]*clist->ncmax[1])+1;
+ ncx=(cellidx+1)/(clist->ncmax[2]*clist->ncmax[1])+1; //+1 because of zero indexing.
remainder=(cellidx+1)%(clist->ncmax[2]*clist->ncmax[1]);
ncy=remainder/clist->ncmax[2]+1;
ncz=remainder%clist->ncmax[2];
@@ -92,7 +112,7 @@
for(k=ncz-1;k<=ncz+1;k++){
neigh_cidx=k+(j-1)*clist->ncmax[2]+(i-1)*clist->ncmax[2]*clist->ncmax[1] -1;
// fprintf(stderr,"neigh_cell_index=%i\n",neigh_cidx);
- cell_occupation=clist->cell[neigh_cidx].nvertex;
+ cell_occupation=clist->cell[neigh_cidx]->data->nvertex;
// fprintf(stderr, "cell_occupation=%i\n",cell_occupation);
if(cell_occupation>clist->max_occupancy){
fatal("Neighbouring cell occupation more than set max_occupancy value.",2000);
@@ -101,9 +121,9 @@
// cell!
if(cell_occupation>1){
for(l=0;l<cell_occupation;l++){
- if(clist->cell[neigh_cidx].vertex[l]!=vtx){
+ if(clist->cell[neigh_cidx]->data->vertex[l]!=vtx){
// fprintf(stderr,"calling dist on vertex %i\n",l);
- dist=vertex_distance_sq(clist->cell[neigh_cidx].vertex[l],tvtx);
+ dist=vtx_distance_sq(clist->cell[neigh_cidx]->data->vertex[l],tvtx);
// fprintf(stderr,"dist was %f\n",dist);
if(dist<1) return TS_FAIL;
}
--
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