/* vim: set ts=4 sts=4 sw=4 noet : */
|
#include<stdlib.h>
|
#include<math.h>
|
#include<stdio.h>
|
#include "general.h"
|
#include "vertex.h"
|
#include "bond.h"
|
#include "vesicle.h"
|
#include "vertex.h"
|
#include "triangle.h"
|
#include "initial_distribution.h"
|
#include "energy.h"
|
#include "poly.h"
|
#include "io.h"
|
#include "sh.h"
|
#include "shcomplex.h"
|
|
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
|
ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
|
ts_bool retval;
|
ts_uint no_vertices=5*nshell*nshell+2;
|
ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
|
vesicle->nshell=nshell;
|
//retval = vtx_set_global_values(vesicle);
|
retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
|
retval = init_vertex_neighbours(vesicle->vlist);
|
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(stdout,"initial_distribution finished!\n");
|
if(retval);
|
return vesicle;
|
}
|
|
|
|
ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
|
ts_vesicle *vesicle;
|
|
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
|
vesicle->tape=tape;
|
set_vesicle_values_from_tape(vesicle);
|
return vesicle;
|
}
|
|
ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
|
// Nucleus:
|
ts_vertex *vtx;
|
ts_tape *tape=vesicle->tape;
|
vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
|
|
vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
|
|
//Initialize grafted polymers (brush):
|
vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
|
vesicle->spring_constant=tape->kspring;
|
poly_assign_spring_const(vesicle);
|
|
//Initialize filaments (polymers inside the vesicle):
|
vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
|
poly_assign_filament_xi(vesicle,tape);
|
|
ts_uint i,j;
|
for(i=0;i<vesicle->filament_list->n;i++){
|
for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
|
bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
|
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));
|
}
|
}
|
|
for(i=0;i<vesicle->filament_list->n;i++){
|
for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
|
vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
|
if(vtx->bond_no == 2){
|
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;
|
}
|
}
|
}
|
|
for(i=0;i<vesicle->filament_list->n;i++){
|
vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
|
}
|
|
// vesicle->spring_constant=tape->kspring;
|
// poly_assign_spring_const(vesicle);
|
|
|
vesicle->nshell=tape->nshell;
|
vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
|
vesicle->bending_rigidity=tape->xk0;
|
vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
|
ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
|
vesicle->stepsize=tape->stepsize;
|
vesicle->clist->ncmax[0]=tape->ncxmax;
|
vesicle->clist->ncmax[1]=tape->ncymax;
|
vesicle->clist->ncmax[2]=tape->nczmax;
|
vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
|
|
vesicle->pressure= tape->pressure;
|
vesicle->pswitch=tape->pswitch;
|
if(tape->shc>0){
|
vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
|
}
|
else {
|
vesicle->sphHarmonics=NULL;
|
}
|
return TS_SUCCESS;
|
|
}
|
|
|
|
|
|
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
|
/* Some often used relations */
|
const ts_double s1= sin(2.0*M_PI/5.0);
|
const ts_double s2= sin(4.0*M_PI/5.0);
|
const ts_double c1= cos(2.0*M_PI/5.0);
|
const ts_double c2= cos(4.0*M_PI/5.0);
|
|
/* Calculates projection lenght of an edge bond to pentagram plane */
|
const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
|
#ifdef TS_DOUBLE_DOUBLE
|
const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
|
#endif
|
#ifdef TS_DOUBLE_FLOAT
|
const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
|
#endif
|
#ifdef TS_DOUBLE_LONGDOUBLE
|
const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
|
#endif
|
// 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 */
|
|
/*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!*/
|
ts_vertex **vtx=vlist->vtx -1 ;
|
|
|
ts_uint nshell=(ts_uint)( sqrt((ts_double)(vlist->n-2)/5));
|
// printf("nshell=%u\n",nshell);
|
ts_uint i,n0; // some for loop prereq
|
ts_int j,k;
|
ts_double dx,dy; // end loop prereq
|
|
/* topmost vertex */
|
vtx[1]->x=0.0;
|
vtx[1]->y=0.0;
|
vtx[1]->z=z0*(ts_double)nshell;
|
|
/* starting from to in circular order on pentagrams */
|
for(i=1;i<=nshell;i++){
|
n0=2+5*i*(i-1)/2; //-1 would be for the reason that C index starts from 0
|
vtx[n0]->x=0.0;
|
vtx[n0]->y=(ts_double)i*xl0;
|
vtx[n0+i]->x=vtx[n0]->y*s1;
|
vtx[n0+i]->y=vtx[n0]->y*c1;
|
vtx[n0+2*i]->x=vtx[n0]->y*s2;
|
vtx[n0+2*i]->y=vtx[n0]->y*c2;
|
vtx[n0+3*i]->x=-vtx[n0+2*i]->x;
|
vtx[n0+3*i]->y=vtx[n0+2*i]->y;
|
vtx[n0+4*i]->x=-vtx[n0+i]->x;
|
vtx[n0+4*i]->y=vtx[n0+i]->y;
|
}
|
|
/* vertexes on the faces of the dipyramid */
|
for(i=1;i<=nshell;i++){
|
n0=2+5*i*(i-1)/2; // -1 would be because of C!
|
for(j=1;j<=i-1;j++){
|
dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
|
dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
|
vtx[n0+4*i+j]->x=(ts_double)j*dx+vtx[n0+4*i]->x;
|
vtx[n0+4*i+j]->y=(ts_double)j*dy+vtx[n0+4*i]->y;
|
}
|
for(k=0;k<=3;k++){ // I would be worried about zero starting of for
|
dx=(vtx[n0+(k+1)*i]->x - vtx[n0+k*i]->x)/(ts_double) i;
|
dy=(vtx[n0+(k+1)*i]->y - vtx[n0+k*i]->y)/(ts_double) i;
|
for(j=1; j<=i-1;j++){
|
vtx[n0+k*i+j]->x= (ts_double)j*dx+vtx[n0+k*i]->x;
|
vtx[n0+k*i+j]->y= (ts_double)j*dy+vtx[n0+k*i]->y;
|
}
|
}
|
}
|
|
for(i=1;i<=nshell;i++){
|
n0= 2+ 5*i*(i-1)/2;
|
for(j=0;j<=5*i-1;j++){
|
vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
|
}
|
}
|
|
/* for botom part of dipyramide we calculate the positions of vertices */
|
for(i=2+5*nshell*(nshell+1)/2;i<=vlist->n;i++){
|
vtx[i]->x=vtx[vlist->n - i +1]->x;
|
vtx[i]->y=vtx[vlist->n - i +1]->y;
|
vtx[i]->z=-vtx[vlist->n - i +1]->z;
|
}
|
|
for(i=1;i<=vlist->n;i++){
|
for(j=1;j<=vlist->n;j++){
|
if(i!=j && vtx_distance_sq(vtx[i],vtx[j])<0.001){
|
printf("Vertices %u and %u are the same!\n",i,j);
|
}
|
}
|
}
|
return TS_SUCCESS;
|
}
|
|
|
|
ts_bool init_vertex_neighbours(ts_vertex_list *vlist){
|
ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
|
const ts_double eps=0.001; //TODO: find out if you can use EPS from math.h
|
ts_uint i,j;
|
ts_double dist2; // Square of distance of neighbours
|
/*this is not required if we zero all data in vertex structure at initialization */
|
/*if we force zeroing at initialization this for loop can safely be deleted */
|
//for(i=1;i<=vlist->n;i++){
|
// vtx[i].neigh_no=0;
|
//}
|
for(i=1;i<=vlist->n;i++){
|
for(j=1;j<=vlist->n;j++){
|
dist2=vtx_distance_sq(vtx[i],vtx[j]);
|
if( (dist2>eps) && (dist2<(A0*A0+eps))){
|
//if it is close enough, but not too much close (solves problem of comparing when i==j)
|
vtx_add_neighbour(vtx[i],vtx[j]);
|
}
|
}
|
// printf ("vertex %u ima %u sosedov!\n",i,vtx[i]->data->neigh_no);
|
}
|
|
return TS_SUCCESS;
|
}
|
|
// 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=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_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
|
jjj=1;
|
jj=1;
|
for(l=2;l<=vtx[i]->neigh_no;l++){
|
for(j=2;j<=vtx[i]->neigh_no;j++){
|
dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
|
direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
|
// TODO: check if fabs can be used with all floating point types!!
|
if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
|
vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
|
jjj=jj;
|
jj=j;
|
break;
|
}
|
}
|
}
|
}
|
/* 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);
|
}
|
|
return tvlist;
|
}
|
|
|
ts_bool init_vesicle_bonds(ts_vesicle *vesicle){
|
ts_vertex_list *vlist=vesicle->vlist;
|
ts_bond_list *blist=vesicle->blist;
|
ts_vertex **vtx=vesicle->vlist->vtx - 1; // Because of 0 indexing
|
/* lets make correct clockwise ordering of in nearest neighbour list */
|
ts_uint i,j,k;
|
for(i=1;i<=vlist->n;i++){
|
for(j=i+1;j<=vlist->n;j++){
|
for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
|
if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
|
bond_add(blist,vtx[i],vtx[j]);
|
break;
|
}
|
}
|
}
|
}
|
/* Let's make a check if the number of bonds is correct */
|
if((blist->n)!=3*(vlist->n-2)){
|
ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(vlist->n-2));
|
fatal("Number of bonds is not 3*(no_vertex-2).",4);
|
}
|
return TS_SUCCESS;
|
}
|
|
|
|
ts_bool init_triangles(ts_vesicle *vesicle){
|
ts_uint i,j,jj,k;
|
ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
|
ts_triangle_list *tlist=vesicle->tlist;
|
ts_double dist, direct;
|
ts_double eps=0.001; // can we use EPS from math.h?
|
k=0;
|
for(i=1;i<=vesicle->vlist->n;i++){
|
for(j=1;j<=vtx[i]->neigh_no;j++){
|
for(jj=1;jj<=vtx[i]->neigh_no;jj++){
|
// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
|
// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
|
dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
|
direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
|
// TODO: same as above
|
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){
|
triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
|
}
|
}
|
}
|
}
|
/* We check if all triangles have 3 vertices and if the number of triangles
|
* matches the theoretical value.
|
*/
|
for(i=0;i<tlist->n;i++){
|
k=0;
|
for(j=0;j<3;j++){
|
if(tlist->tria[i]->vertex[j]!=NULL)
|
k++;
|
}
|
if(k!=3){
|
fatal("Some triangles have less than 3 vertices..",4);
|
}
|
}
|
if(tlist->n!=2*(vesicle->vlist->n -2)){
|
ts_fprintf(stderr,"The number of triangles is %u but should be %u!\n",tlist->n,2*(vesicle->vlist->n -2));
|
fatal("The number of triangles doesn't match 2*(no_vertex -2).",4);
|
}
|
return TS_SUCCESS;
|
}
|
|
|
|
ts_bool init_triangle_neighbours(ts_vesicle *vesicle){
|
ts_uint i,j,nobo;
|
ts_vertex *i1,*i2,*i3,*j1,*j2,*j3;
|
// ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
|
ts_triangle_list *tlist=vesicle->tlist;
|
ts_triangle **tria=tlist->tria -1;
|
nobo=0;
|
for(i=1;i<=tlist->n;i++){
|
i1=tria[i]->vertex[0];
|
i2=tria[i]->vertex[1];
|
i3=tria[i]->vertex[2];
|
for(j=1;j<=tlist->n;j++){
|
if(j==i) continue;
|
j1=tria[j]->vertex[0];
|
j2=tria[j]->vertex[1];
|
j3=tria[j]->vertex[2];
|
if((i1==j1 && i3==j2) || (i1==j2 && i3==j3) || (i1==j3 && i3==j1)){
|
triangle_add_neighbour(tria[i],tria[j]);
|
nobo++;
|
}
|
}
|
}
|
for(i=1;i<=tlist->n;i++){
|
i1=tria[i]->vertex[0];
|
i2=tria[i]->vertex[1];
|
i3=tria[i]->vertex[2];
|
for(j=1;j<=tlist->n;j++){
|
if(j==i) continue;
|
j1=tria[j]->vertex[0];
|
j2=tria[j]->vertex[1];
|
j3=tria[j]->vertex[2];
|
if((i1==j1 && i2==j3) || (i1==j3 && i2==j2) || (i1==j2 && i2==j1)){
|
triangle_add_neighbour(tria[i],tria[j]);
|
nobo++;
|
}
|
}
|
}
|
for(i=1;i<=tlist->n;i++){
|
i1=tria[i]->vertex[0];
|
i2=tria[i]->vertex[1];
|
i3=tria[i]->vertex[2];
|
for(j=1;j<=tlist->n;j++){
|
if(j==i) continue;
|
j1=tria[j]->vertex[0];
|
j2=tria[j]->vertex[1];
|
j3=tria[j]->vertex[2];
|
if((i2==j1 && i3==j3) || (i2==j3 && i3==j2) || (i2==j2 && i3==j1)){
|
triangle_add_neighbour(tria[i],tria[j]);
|
nobo++;
|
}
|
}
|
}
|
if(nobo != vesicle->blist->n*2) {
|
ts_fprintf(stderr,"Number of triangles= %u, number of bonds= %u\n",nobo/2, vesicle->blist->n);
|
fatal("Number of triangle neighbour pairs differs from double the number of bonds!",4);
|
}
|
return TS_SUCCESS;
|
}
|
|
|
ts_bool init_common_vertex_triangle_neighbours(ts_vesicle *vesicle){
|
ts_uint i,j,jp,k;
|
ts_vertex *k1,*k2,*k3,*k4,*k5;
|
ts_vertex **vtx=vesicle->vlist->vtx -1; // difference between 0 indexing and 1 indexing
|
ts_triangle_list *tlist=vesicle->tlist;
|
ts_triangle **tria=tlist->tria -1;
|
|
for(i=1;i<=vesicle->vlist->n;i++){
|
for(j=1;j<=vtx[i]->neigh_no;j++){
|
k1=vtx[i]->neigh[j-1];
|
jp=j+1;
|
if(j == vtx[i]->neigh_no) jp=1;
|
k2=vtx[i]->neigh[jp-1];
|
for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
|
k3=tria[k]->vertex[0];
|
k4=tria[k]->vertex[1];
|
k5=tria[k]->vertex[2];
|
// ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
|
if((vtx[i]==k3 && k1==k4 && k2==k5) ||
|
(vtx[i]==k4 && k1==k5 && k2==k3) ||
|
(vtx[i]==k5 && k1==k3 && k2==k4)){
|
|
//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]);
|
}
|
}
|
}
|
/* ts_fprintf(stderr,"TRISTAR for %u (%u):",i-1,vtx[i].tristar_no);
|
for(j=0;j<vtx[i].tristar_no;j++){
|
ts_fprintf(stderr," %u,",vtx[i].tristar[j]->idx);
|
}
|
ts_fprintf(stderr,"\n"); */
|
}
|
return TS_SUCCESS;
|
}
|
|
|
ts_bool init_normal_vectors(ts_triangle_list *tlist){
|
/* 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;
|
}
|
