From bd826de2f539f2e48c8c01d2d7f9f34c7e97104a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 13 May 2016 07:43:27 +0000
Subject: [PATCH] Fix in trisurf output, inhibiting print of successful reconstruction. Multiple fixes and improvements in python module. Added symlinking of tapes into the running directories and dumping tapes from snapshots into tape files.
---
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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