#include<stdlib.h>
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#include<math.h>
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#include<stdio.h>
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#include "general.h"
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#include "vertex.h"
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#include "bond.h"
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#include "vesicle.h"
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#include "vertex.h"
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#include "triangle.h"
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#include "initial_distribution.h"
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ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
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ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
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ts_bool retval;
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ts_uint no_vertices=5*nshell*nshell+2;
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ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
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vesicle->nshell=nshell;
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retval = vtx_set_global_values(vesicle);
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retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
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retval = init_vertex_neighbours(vesicle->vlist);
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retval = init_sort_neighbours(vesicle->vlist);
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retval = init_vesicle_bonds(vesicle);
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retval = init_triangles(vesicle);
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retval = init_triangle_neighbours(vesicle);
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retval = init_common_vertex_triangle_neighbours(vesicle);
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ts_fprintf(stderr,"initial_distribution finished!\n");
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return vesicle;
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}
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ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
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/* Some often used relations */
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const ts_double s1= sin(2.0*M_PI/5.0);
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const ts_double s2= sin(4.0*M_PI/5.0);
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const ts_double c1= cos(2.0*M_PI/5.0);
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const ts_double c2= cos(4.0*M_PI/5.0);
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/* Calculates projection lenght of an edge bond to pentagram plane */
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const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
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#ifdef TS_DOUBLE_DOUBLE
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const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
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#endif
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#ifdef TS_DOUBLE_FLOAT
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const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
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#endif
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#ifdef TS_DOUBLE_LONGDOUBLE
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const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
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#endif
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// const z0=sqrt(A0*A0 -xl0*xl0); /* I could use pow function but if pow is used make a check on the float type. If float then powf, if long double use powl */
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/*placeholder for the pointer to vertex datastructure list... DIRTY: actual pointer points towards invalid address, one position before actual beginning of the list... This is to solve the difference between 1 based indexing in original program in fortran and 0 based indexing in C. All algorithms remain unchanged because of this!*/
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ts_vertex **vtx=vlist->vtx -1 ;
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ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
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// printf("nshell=%u\n",nshell);
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ts_uint i,n0; // some for loop prereq
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ts_int j,k;
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ts_double dx,dy; // end loop prereq
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/* topmost vertex */
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vtx[1]->data->x=0.0;
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vtx[1]->data->y=0.0;
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vtx[1]->data->z=z0*(ts_double)nshell;
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/* starting from to in circular order on pentagrams */
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for(i=1;i<=nshell;i++){
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n0=2+5*i*(i-1)/2; //-1 would be for the reason that C index starts from 0
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vtx[n0]->data->x=0.0;
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vtx[n0]->data->y=(ts_double)i*xl0;
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vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
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vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
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vtx[n0+2*i]->data->x=vtx[n0]->data->y*s2;
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vtx[n0+2*i]->data->y=vtx[n0]->data->y*c2;
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vtx[n0+3*i]->data->x=-vtx[n0+2*i]->data->x;
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vtx[n0+3*i]->data->y=vtx[n0+2*i]->data->y;
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vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
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vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
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}
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/* vertexes on the faces of the dipyramid */
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for(i=1;i<=nshell;i++){
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n0=2+5*i*(i-1)/2; // -1 would be because of C!
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for(j=1;j<=i-1;j++){
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dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
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dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
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vtx[n0+4*i+j]->data->x=(ts_double)j*dx+vtx[n0+4*i]->data->x;
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vtx[n0+4*i+j]->data->y=(ts_double)j*dy+vtx[n0+4*i]->data->y;
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}
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for(k=0;k<=3;k++){ // I would be worried about zero starting of for
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dx=(vtx[n0+(k+1)*i]->data->x - vtx[n0+k*i]->data->x)/(ts_double) i;
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dy=(vtx[n0+(k+1)*i]->data->y - vtx[n0+k*i]->data->y)/(ts_double) i;
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for(j=1; j<=i-1;j++){
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vtx[n0+k*i+j]->data->x= (ts_double)j*dx+vtx[n0+k*i]->data->x;
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vtx[n0+k*i+j]->data->y= (ts_double)j*dy+vtx[n0+k*i]->data->y;
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}
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}
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}
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for(i=1;i<=nshell;i++){
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n0= 2+ 5*i*(i-1)/2;
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for(j=0;j<=5*i-1;j++){
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vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
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}
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}
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/* for botom part of dipyramide we calculate the positions of vertices */
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for(i=2+5*nshell*(nshell+1)/2;i<=vlist->n;i++){
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vtx[i]->data->x=vtx[vlist->n - i +1]->data->x;
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vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
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vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
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}
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for(i=1;i<=vlist->n;i++){
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for(j=1;j<=vlist->n;j++){
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if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
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printf("Vertices %u and %u are the same!\n",i,j);
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}
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}
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}
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return TS_SUCCESS;
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}
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ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
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ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
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const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
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ts_uint i,j;
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ts_double dist2; // Square of distance of neighbours
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/*this is not required if we zero all data in vertex structure at initialization */
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/*if we force zeroing at initialization this for loop can safely be deleted */
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//for(i=1;i<=vlist->n;i++){
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// vtx[i].neigh_no=0;
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//}
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for(i=1;i<=vlist->n;i++){
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for(j=1;j<=vlist->n;j++){
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dist2=vtx_distance_sq(vtx[i],vtx[j]);
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if( (dist2>eps) && (dist2<(A0*A0+eps))){
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//if it is close enough, but not too much close (solves problem of comparing when i==j)
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vtx_add_neighbour(vtx[i],vtx[j]);
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}
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}
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// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
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}
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return TS_SUCCESS;
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}
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// TODO: with new datastructure can be rewritten.
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ts_bool init_sort_neighbours(ts_vertex_list *vlist){
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ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
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ts_uint i,l,j,jj,jjj,k=0;
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ts_double eps=0.001; // Take a look if EPS from math.h can be used
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/*lets initialize memory for temporary vertex_list. Should we write a function instead */
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ts_vertex_list *tvlist=init_vertex_list(vlist->n);
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ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */
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ts_double dist2; // Square of distance of neighbours
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ts_double direct; // Something, dont know what, but could be normal of some kind
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for(i=1;i<=vlist->n;i++){
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k++; // WHY i IS NOT GOOD??
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vtx_add_neighbour(tvtx[k], tvtx[vtx[i]->data->neigh[0]->idx+1]); //always add 1st
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jjj=1;
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jj=1;
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for(l=2;l<=vtx[i]->data->neigh_no;l++){
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for(j=2;j<=vtx[i]->data->neigh_no;j++){
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dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
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direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
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if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
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vtx_add_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
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jjj=jj;
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jj=j;
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break;
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}
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}
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}
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}
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for(i=1;i<=vlist->n;i++){
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for(j=1;j<=vtx[i]->data->neigh_no;j++){
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if(vtx[i]->data->neigh_no!=tvtx[i]->data->neigh_no){ //doesn't work with nshell=1!
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// fprintf(stderr,"data1=%u data2=%u\n",vtx[i]->data->neigh_no,tvtx[i]->data->neigh_no);
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fatal("Number of neighbours not the same in init_sort_neighbours.",4);
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}
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//we must correct the pointers in original to point to their
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//neighbours according to indexes. Must be sure not to do it any
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//other way! Also, we need to repair the collection of bonds...
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vtx[i]->data->neigh[j-1]=vtx[tvtx[i]->data->neigh[j-1]->idx+1];
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}
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}
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// Must free memory for temporary vertex array to avoid memory leak! HERE! NOW!
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// free_vertex(tvlist.vertex,tvlist.n);
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vtx_list_free(tvlist);
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return TS_SUCCESS;
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}
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ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
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ts_vertex_list *vlist=vesicle->vlist;
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ts_bond_list *blist=vesicle->blist;
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ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
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/* lets make correct clockwise ordering of in nearest neighbour list */
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ts_uint i,j,k;
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for(i=1;i<=vlist->n;i++){
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for(j=i+1;j<=vlist->n;j++){
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for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
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if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same
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bond_add(blist,vtx[i],vtx[j]);
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break;
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}
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}
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}
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}
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/* Let's make a check if the number of bonds is correct */
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if((blist->n)!=3*(vlist->n-2)){
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ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
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fatal("Number of bonds is not 3*(no_vertex-2).",4);
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}
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return TS_SUCCESS;
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}
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ts_bool init_triangles(ts_vesicle *vesicle){
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ts_uint i,j,jj,k;
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ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
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ts_triangle_list *tlist=vesicle->tlist;
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ts_double dist, direct;
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ts_double eps=0.001; // can we use EPS from math.h?
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k=0;
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for(i=1;i<=vesicle->vlist->n;i++){
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for(j=1;j<=vtx[i]->data->neigh_no;j++){
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for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
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// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
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// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
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dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
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direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
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if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->data->neigh[j-1]->idx+1 > i && vtx[i]->data->neigh[jj-1]->idx+1 >i){
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triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
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}
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}
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}
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}
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/* We check if all triangles have 3 vertices and if the number of triangles
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* matches the theoretical value.
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*/
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for(i=0;i<tlist->n;i++){
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k=0;
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for(j=0;j<3;j++){
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if(tlist->tria[i]->data->vertex[j]!=NULL)
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k++;
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}
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if(k!=3){
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fatal("Some triangles has less than 3 vertices..",4);
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}
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}
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if(tlist->n!=2*(vesicle->vlist->n -2)){
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ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
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fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
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}
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return TS_SUCCESS;
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}
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ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
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ts_uint i,j,nobo;
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ts_vertex *i1,*i2,*i3,*j1,*j2,*j3;
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// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
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ts_triangle_list *tlist=vesicle->tlist;
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ts_triangle **tria=tlist->tria -1;
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nobo=0;
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for(i=1;i<=tlist->n;i++){
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i1=tria[i]->data->vertex[0];
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i2=tria[i]->data->vertex[1];
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i3=tria[i]->data->vertex[2];
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for(j=1;j<=tlist->n;j++){
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if(j==i) continue;
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j1=tria[j]->data->vertex[0];
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j2=tria[j]->data->vertex[1];
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j3=tria[j]->data->vertex[2];
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if((i1==j1 && i3==j2) || (i1==j2 && i3==j3) || (i1==j3 && i3==j1)){
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triangle_add_neighbour(tria[i],tria[j]);
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nobo++;
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}
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}
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}
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for(i=1;i<=tlist->n;i++){
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i1=tria[i]->data->vertex[0];
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i2=tria[i]->data->vertex[1];
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i3=tria[i]->data->vertex[2];
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for(j=1;j<=tlist->n;j++){
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if(j==i) continue;
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j1=tria[j]->data->vertex[0];
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j2=tria[j]->data->vertex[1];
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j3=tria[j]->data->vertex[2];
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if((i1==j1 && i2==j3) || (i1==j3 && i2==j2) || (i1==j2 && i2==j1)){
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triangle_add_neighbour(tria[i],tria[j]);
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nobo++;
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}
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}
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}
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for(i=1;i<=tlist->n;i++){
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i1=tria[i]->data->vertex[0];
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i2=tria[i]->data->vertex[1];
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i3=tria[i]->data->vertex[2];
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for(j=1;j<=tlist->n;j++){
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if(j==i) continue;
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j1=tria[j]->data->vertex[0];
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j2=tria[j]->data->vertex[1];
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j3=tria[j]->data->vertex[2];
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if((i2==j1 && i3==j3) || (i2==j3 && i3==j2) || (i2==j2 && i3==j1)){
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triangle_add_neighbour(tria[i],tria[j]);
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nobo++;
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}
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}
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}
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if(nobo != vesicle->blist->n*2) {
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ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
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fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
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}
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return TS_SUCCESS;
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}
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ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
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ts_uint i,j,jp,k;
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ts_vertex *k1,*k2,*k3,*k4,*k5;
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ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
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ts_triangle_list *tlist=vesicle->tlist;
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ts_triangle **tria=tlist->tria -1;
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for(i=1;i<=vesicle->vlist->n;i++){
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for(j=1;j<=vtx[i]->data->neigh_no;j++){
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k1=vtx[i]->data->neigh[j-1];
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jp=j+1;
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if(j == vtx[i]->data->neigh_no) jp=1;
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k2=vtx[i]->data->neigh[jp-1];
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for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
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k3=tria[k]->data->vertex[0];
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k4=tria[k]->data->vertex[1];
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k5=tria[k]->data->vertex[2];
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// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
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if((vtx[i]==k3 && k1==k4 && k2==k5) ||
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(vtx[i]==k4 && k1==k5 && k2==k3) ||
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(vtx[i]==k5 && k1==k3 && k2==k4)){
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// ts_fprintf(stderr, "Added to tristar! ");
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vertex_add_tristar(vtx[i],tria[k]);
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}
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}
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}
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/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
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for(j=0;j<vtx[i].tristar_no;j++){
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ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
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}
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ts_fprintf(stderr,"\n"); */
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}
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return TS_SUCCESS;
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}
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ts_bool init_normal_vectors(ts_triangle_list *tlist){
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/* Normals point INSIDE vesicle */
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ts_uint k;
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ts_triangle **tria=tlist->tria -1; //for 0 indexing
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for(k=1;k<=tlist->n;k++){
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triangle_normal_vector(tria[k]);
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}
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return TS_SUCCESS;
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}
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