Merging again because I was merging in detached state

Samo Penic

2016-12-06 c2c6364dc7d23f21dabd2179e775e93ba4eeb252

 src/cell.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include "general.h"
#include "vertex.h"
@@ -44,22 +45,21 @@
}


//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);
    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);

    if(ncx == 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 == 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 == 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)*clist->ncmax[2] + (ncx-1)*clist->ncmax[2]* 
@@ -68,17 +68,48 @@
}


//TODO: looks ok, but debug anyway in the future
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=(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;
}

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;
@@ -92,8 +123,8 @@
    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_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;
    ts_double dist;
@@ -115,19 +146,25 @@
                }
// 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++){

            //carefull with this checks!
                        if(clist->cell[neigh_cidx]->vertex[l]!=vtx){
                    //        fprintf(stderr,"calling dist on vertex %i\n",l);
                           dist=vtx_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;
}