Added spherical harmonics routine.I've got a feeling that some harmonics ar...

Samo Penic

2011-03-19 88f45143117f3ae973be6e3ea5dac8063a7b8ece

 src/initial_distribution.c

@@ -20,11 +20,12 @@
    retval = vtx_set_global_values(vesicle);
    retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
    retval = init_vertex_neighbours(vesicle->vlist);
    retval = init_sort_neighbours(vesicle->vlist);
    retval = init_vesicle_bonds(vesicle);
    vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
   // retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
    retval = init_triangles(vesicle);
    retval = init_triangle_neighbours(vesicle);
    retval = init_common_vertex_triangle_neighbours(vesicle);
    retval = init_normal_vectors(vesicle->tlist);
    retval = mean_curvature_and_energy(vesicle);
 ts_fprintf(stderr,"initial_distribution finished!\n");
   return vesicle;
@@ -150,21 +151,21 @@
   return TS_SUCCESS;
}

// TODO: with new datastructure can be rewritten.
ts_bool init_sort_neighbours(ts_vertex_list *vlist){
// TODO: with new datastructure can be rewritten. Partially it is done, but it is complicated.
ts_vertex_list *init_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){
   ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
   ts_uint i,l,j,jj,jjj,k=0;   
    ts_double eps=0.001; // Take a look if EPS from math.h can be used

/*lets initialize memory for temporary vertex_list. Should we write a function instead */
    ts_vertex_list *tvlist=init_vertex_list(vlist->n);
    ts_vertex_list *tvlist=vertex_list_copy(vlist);
    ts_vertex **tvtx=tvlist->vtx -1;  /* again to compensate for 0-indexing */

   ts_double dist2; // Square of distance of neighbours
    ts_double direct; // Something, dont know what, but could be normal of some kind
   for(i=1;i<=vlist->n;i++){
      k++; // WHY i IS NOT GOOD??
          vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
          vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
          jjj=1;
          jj=1;
          for(l=2;l<=vtx[i]->data->neigh_no;l++){
@@ -172,7 +173,7 @@
                  dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
                  direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
                  if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
                    vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
                    vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
                    jjj=jj;
                    jj=j;
                    break;
@@ -180,24 +181,19 @@
             }
          }   
   }

    for(i=1;i<=vlist->n;i++){
        for(j=1;j<=vtx[i]->data->neigh_no;j++){
            if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1!
//                fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no);
                fatal("Number of neighbours not the same in init_sort_neighbours.",4);
            }
            //we must correct the pointers in original to point to their
            //neighbours according to indexes. Must be sure not to do it any
            //other way! Also, we need to repair the collection of bonds...
            vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1];
        }
/* We use the temporary vertex for our main vertices and we abandon main
 * vertices, because their neighbours are not correctly ordered */
   // tvtx=vlist->vtx;
   // vlist->vtx=tvtx;
   // tvlist->vtx=vtx;
    vtx_list_free(vlist);
/* Let's make a check if the number of bonds is correct */
    if((blist->n)!=3*(tvlist->n-2)){
        ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
        fatal("Number of bonds is not 3*(no_vertex-2).",4);
    }

   // Must free memory for temporary vertex array to avoid memory leak! HERE! NOW!
//    free_vertex(tvlist.vertex,tvlist.n);
    vtx_list_free(tvlist);
   return TS_SUCCESS;
   return tvlist;
}


@@ -350,7 +346,10 @@
                if((vtx[i]==k3 && k1==k4 && k2==k5) ||
                (vtx[i]==k4 && k1==k5 && k2==k3) ||
                (vtx[i]==k5 && k1==k3 && k2==k4)){
          //          ts_fprintf(stderr, "Added to tristar! ");

//TODO: probably something wrong with neighbour distribution.
//                if(vtx[i]==k3 || vtx[i]==k4 || vtx[i]==k5){
    //                    if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
                    vertex_add_tristar(vtx[i],tria[k]);
                }
            }