From 032273a4cf21e1a43038b60b8744021930c97a5b Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 21 Jun 2016 13:29:35 +0000
Subject: [PATCH] Testing and fixes
---
src/cell.c | 147 +++++++++++++++++++++++++++++++++---------------
1 files changed, 100 insertions(+), 47 deletions(-)
diff --git a/src/cell.c b/src/cell.c
index ae912fe..a1413eb 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -1,87 +1,134 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#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 *)calloc(1,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!
}
+ return clist;
+}
+
+ts_bool cell_free(ts_cell* cell){
+ if(cell->vertex!=NULL) free(cell->vertex);
+ 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 cellidx;
ts_uint ncx, ncy,ncz;
+ ts_cell_list *clist=vesicle->clist;
+ ncx=(ts_uint)((vtx->x-vesicle->cm[0])*clist->dcell+clist->shift);
+ ncy=(ts_uint)((vtx->y-vesicle->cm[1])*clist->dcell+clist->shift);
+ ncz=(ts_uint)((vtx->z-vesicle->cm[2])*clist->dcell+clist->shift);
- 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){
+ 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;
}
-
-ts_bool cell_add_vertex(ts_cell *cell, ts_vertex *vtx){
-
+inline ts_bool cell_add_vertex(ts_cell *cell, ts_vertex *vtx){
+ ts_uint i;
+ for(i=0;i<cell->nvertex;i++){
+ if(cell->vertex[i]==vtx){
+ //vertex is already in the cell!
+ //fprintf(stderr,"VTX in the cell!\n");
+ return TS_FAIL;
+ }
+ }
+ //fprintf(stderr,"VTX added to the cell!\n");
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->vertex=(ts_vertex **)realloc(cell->vertex,cell->nvertex*sizeof(ts_vertex *));
+ if(cell->vertex == NULL){
+ fatal("Reallocation of memory failed during insertion of vertex in cell_add_vertex",3);
}
cell->vertex[cell->nvertex-1]=vtx;
-
+ vtx->cell=cell;
return TS_SUCCESS;
}
-ts_bool cell_list_cell_ocupation_clear(ts_cell_list *clist){
+inline ts_bool cell_remove_vertex(ts_cell *cell, ts_vertex *vtx){
+ ts_uint i,j=0;
+ for(i=0;i<cell->nvertex;i++){
+ if(cell->vertex[i]!=vtx){
+ cell->vertex[j]=cell->vertex[i];
+ j++;
+ }
+ }
+ if(j==i){
+ fatal("Vertex was not in the cell!",3);
+ }
+ //fprintf(stderr, "Vertex deleted from the cell!\n");
+
+/* resize memory. potentionally time consuming */
+ cell->nvertex--;
+ cell->vertex=(ts_vertex **)realloc(cell->vertex,cell->nvertex*sizeof(ts_vertex *));
+ if(vtx->neigh == NULL && vtx->neigh_no!=0)
+ if(cell->vertex == NULL){
+ fatal("Reallocation of memory failed during removal of vertex in cell_remove_vertex",3);
+ }
+ return TS_SUCCESS;
+}
+
+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]->vertex != NULL){
+ free(clist->cell[i]->vertex);
+ clist->cell[i]->vertex=NULL;
}
- clist->cell[i].nvertex=0;
+ clist->cell[i]->nvertex=0;
}
return TS_SUCCESS;
}
-ts_bool cell_occupation_number_and_internal_proximity(ts_cell_list *clist, ts_uint cellidx, ts_vertex *vtx, ts_vertex *tvtx){
+
+ts_bool cell_occupation_number_and_internal_proximity(ts_cell_list *clist, ts_uint cellidx, ts_vertex *vtx){
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];
@@ -92,26 +139,32 @@
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]->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);
}
// Now we check whether we didn't come close to some other vertices in the same
// cell!
- if(cell_occupation>1){
+ if(cell_occupation>0){
for(l=0;l<cell_occupation;l++){
- if(clist->cell[neigh_cidx].vertex[l]!=vtx){
+
+ //carefull with this checks!
+ if(clist->cell[neigh_cidx]->vertex[l]!=vtx){
// fprintf(stderr,"calling dist on vertex %i\n",l);
- dist=vertex_distance_sq(clist->cell[neigh_cidx].vertex[l],tvtx);
- // fprintf(stderr,"dist was %f\n",dist);
- if(dist<1) return TS_FAIL;
+ dist=vtx_distance_sq(clist->cell[neigh_cidx]->vertex[l],vtx);
+
+// if(vtx->idx==1)
+// fprintf(stderr,"VTX(0) ima bliznji vertex z indeksom, %d, tipa %d \n", clist->cell[neigh_cidx]->vertex[l]->idx, clist->cell[neigh_cidx]->vertex[l]->id);
+// if(vtx->idx==0 && clist->cell[neigh_cidx]->vertex[l]->idx==0)
+// fprintf(stderr,"*** dist was %f\n",dist);
+
+ if(dist<=1.0 || (dist<=clist->dmin_interspecies && (clist->cell[neigh_cidx]->vertex[l]->id != vtx->id))) return TS_FAIL;
}
}
}
}
}
- }
-
+ }
return TS_SUCCESS;
}
--
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