#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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#include "energy.h"
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#include "poly.h"
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#include "io.h"
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#include "sh.h"
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#include "shcomplex.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(stdout,"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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vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
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// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
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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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retval = init_normal_vectors(vesicle->tlist);
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retval = mean_curvature_and_energy(vesicle);
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ts_fprintf(stdout,"initial_distribution finished!\n");
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if(retval);
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return vesicle;
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}
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ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
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ts_vesicle *vesicle;
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vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
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vesicle->tape=tape;
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set_vesicle_values_from_tape(vesicle);
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return vesicle;
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}
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ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
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// Nucleus:
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ts_vertex *vtx;
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ts_tape *tape=vesicle->tape;
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vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
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vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
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//Initialize grafted polymers (brush):
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vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
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vesicle->spring_constant=tape->kspring;
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poly_assign_spring_const(vesicle);
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//Initialize filaments (polymers inside the vesicle):
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vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
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poly_assign_filament_xi(vesicle,tape);
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ts_uint i,j;
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
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bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
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vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
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}
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}
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for(i=0;i<vesicle->filament_list->n;i++){
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for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
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vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
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if(vtx->bond_no == 2){
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vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
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}
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}
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}
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for(i=0;i<vesicle->filament_list->n;i++){
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vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
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}
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// vesicle->spring_constant=tape->kspring;
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// poly_assign_spring_const(vesicle);
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vesicle->nshell=tape->nshell;
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vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
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vesicle->bending_rigidity=tape->xk0;
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vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
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ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
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vesicle->stepsize=tape->stepsize;
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vesicle->clist->ncmax[0]=tape->ncxmax;
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vesicle->clist->ncmax[1]=tape->ncymax;
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vesicle->clist->ncmax[2]=tape->nczmax;
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vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
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vesicle->pressure= tape->pressure;
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vesicle->pswitch=tape->pswitch;
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if(tape->shc>0){
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vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
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}
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else {
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vesicle->sphHarmonics=NULL;
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}
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return TS_SUCCESS;
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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]->x=0.0;
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vtx[1]->y=0.0;
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vtx[1]->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]->x=0.0;
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vtx[n0]->y=(ts_double)i*xl0;
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vtx[n0+i]->x=vtx[n0]->y*s1;
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vtx[n0+i]->y=vtx[n0]->y*c1;
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vtx[n0+2*i]->x=vtx[n0]->y*s2;
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vtx[n0+2*i]->y=vtx[n0]->y*c2;
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vtx[n0+3*i]->x=-vtx[n0+2*i]->x;
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vtx[n0+3*i]->y=vtx[n0+2*i]->y;
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vtx[n0+4*i]->x=-vtx[n0+i]->x;
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vtx[n0+4*i]->y=vtx[n0+i]->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]->x-vtx[n0+4*i]->x)/(ts_double)i;
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dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
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vtx[n0+4*i+j]->x=(ts_double)j*dx+vtx[n0+4*i]->x;
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vtx[n0+4*i+j]->y=(ts_double)j*dy+vtx[n0+4*i]->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]->x - vtx[n0+k*i]->x)/(ts_double) i;
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dy=(vtx[n0+(k+1)*i]->y - vtx[n0+k*i]->y)/(ts_double) i;
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for(j=1; j<=i-1;j++){
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vtx[n0+k*i+j]->x= (ts_double)j*dx+vtx[n0+k*i]->x;
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vtx[n0+k*i+j]->y= (ts_double)j*dy+vtx[n0+k*i]->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]->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]->x=vtx[vlist->n - i +1]->x;
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vtx[i]->y=vtx[vlist->n - i +1]->y;
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vtx[i]->z=-vtx[vlist->n - i +1]->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. Partially it is done, but it is complicated.
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ts_vertex_list *init_sort_neighbours(ts_bond_list *blist,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=vertex_list_copy(vlist);
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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_cneighbour(blist,tvtx[k], tvtx[vtx[i]->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]->neigh_no;l++){
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for(j=2;j<=vtx[i]->neigh_no;j++){
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dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
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direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
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// TODO: check if fabs can be used with all floating point types!!
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if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
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vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->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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/* We use the temporary vertex for our main vertices and we abandon main
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* vertices, because their neighbours are not correctly ordered */
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// tvtx=vlist->vtx;
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// vlist->vtx=tvtx;
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// tvlist->vtx=vtx;
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vtx_list_free(vlist);
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/* Let's make a check if the number of bonds is correct */
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if((blist->n)!=3*(tvlist->n-2)){
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ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->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 tvlist;
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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]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
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if(vtx[i]->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]->neigh_no;j++){
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for(jj=1;jj<=vtx[i]->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]->neigh[j-1],vtx[i]->neigh[jj-1]);
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direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
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// TODO: same as above
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if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
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triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->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]->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 have 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]->vertex[0];
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i2=tria[i]->vertex[1];
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i3=tria[i]->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]->vertex[0];
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j2=tria[j]->vertex[1];
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j3=tria[j]->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]->vertex[0];
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i2=tria[i]->vertex[1];
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i3=tria[i]->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]->vertex[0];
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j2=tria[j]->vertex[1];
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j3=tria[j]->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]->vertex[0];
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i2=tria[i]->vertex[1];
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i3=tria[i]->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]->vertex[0];
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j2=tria[j]->vertex[1];
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j3=tria[j]->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]->neigh_no;j++){
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k1=vtx[i]->neigh[j-1];
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jp=j+1;
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if(j == vtx[i]->neigh_no) jp=1;
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k2=vtx[i]->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]->vertex[0];
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k4=tria[k]->vertex[1];
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k5=tria[k]->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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//TODO: probably something wrong with neighbour distribution.
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// if(vtx[i]==k3 || vtx[i]==k4 || vtx[i]==k5){
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// if(i==6) ts_fprintf(stdout, "Vtx[%u] > Added to tristar!\n",i);
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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 */
|
ts_uint k;
|
ts_triangle **tria=tlist->tria -1; //for 0 indexing
|
for(k=1;k<=tlist->n;k++){
|
triangle_normal_vector(tria[k]);
|
}
|
return TS_SUCCESS;
|
}
|
