From 459ff94855b2659de14ac2ac902b9658d28e19d5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@CAE-linux.(none)>
Date: Mon, 21 Apr 2014 11:11:37 +0000
Subject: [PATCH] Added complex spherical harmonics.
---
src/initial_distribution.c | 279 +++++++++++++++++++++++++++++++++++--------------------
1 files changed, 178 insertions(+), 101 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 4881e11..bff9f05 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -9,26 +9,103 @@
#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(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
+ 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);
- retval = init_sort_neighbours(vesicle->vlist);
- retval = init_vesicle_bonds(vesicle);
- retval = init_triangles(vesicle);
- retval = init_triangle_neighbours(vesicle);
- retval = init_common_vertex_triangle_neighbours(vesicle);
- retval = mean_curvature_and_energy(vesicle);
- ts_fprintf(stderr,"initial_distribution finished!\n");
+ 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;
+ ts_vertex *vtx;
+
+ vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
+ // Nucleus:
+ 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 vesicle;
+
+}
+
+
+
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
@@ -62,40 +139,40 @@
ts_double dx,dy; // end loop prereq
/* topmost vertex */
- vtx[1]->data->x=0.0;
- vtx[1]->data->y=0.0;
- vtx[1]->data->z=z0*(ts_double)nshell;
+ 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]->data->x=0.0;
- vtx[n0]->data->y=(ts_double)i*xl0;
- vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
- vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
- vtx[n0+2*i]->data->x=vtx[n0]->data->y*s2;
- vtx[n0+2*i]->data->y=vtx[n0]->data->y*c2;
- vtx[n0+3*i]->data->x=-vtx[n0+2*i]->data->x;
- vtx[n0+3*i]->data->y=vtx[n0+2*i]->data->y;
- vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
- vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
+ 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]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
- dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
- vtx[n0+4*i+j]->data->x=(ts_double)j*dx+vtx[n0+4*i]->data->x;
- vtx[n0+4*i+j]->data->y=(ts_double)j*dy+vtx[n0+4*i]->data->y;
+ 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]->data->x - vtx[n0+k*i]->data->x)/(ts_double) i;
- dy=(vtx[n0+(k+1)*i]->data->y - vtx[n0+k*i]->data->y)/(ts_double) i;
+ 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]->data->x= (ts_double)j*dx+vtx[n0+k*i]->data->x;
- vtx[n0+k*i+j]->data->y= (ts_double)j*dy+vtx[n0+k*i]->data->y;
+ 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;
}
}
}
@@ -103,15 +180,15 @@
for(i=1;i<=nshell;i++){
n0= 2+ 5*i*(i-1)/2;
for(j=0;j<=5*i-1;j++){
- vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
+ 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]->data->x=vtx[vlist->n - i +1]->data->x;
- vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
- vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
+ 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++){
@@ -150,29 +227,30 @@
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]->neigh[0]->idx+1]); //always add 1st
jjj=1;
jj=1;
- for(l=2;l<=vtx[i]->data->neigh_no;l++){
- for(j=2;j<=vtx[i]->data->neigh_no;j++){
- 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]);
+ 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_neighbour(tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
+ vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
jjj=jj;
jj=j;
break;
@@ -180,24 +258,19 @@
}
}
}
-
- 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;
}
@@ -209,8 +282,8 @@
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]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
- if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same
+ 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;
}
@@ -235,14 +308,15 @@
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]->data->neigh_no;j++){
- for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
+ 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]->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(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){
- triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
+ 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]);
}
}
}
@@ -253,11 +327,11 @@
for(i=0;i<tlist->n;i++){
k=0;
for(j=0;j<3;j++){
- if(tlist->tria[i]->data->vertex[j]!=NULL)
+ if(tlist->tria[i]->vertex[j]!=NULL)
k++;
}
if(k!=3){
- fatal("Some triangles has less than 3 vertices..",4);
+ fatal("Some triangles have less than 3 vertices..",4);
}
}
if(tlist->n!=2*(vesicle->vlist->n -2)){
@@ -277,14 +351,14 @@
ts_triangle **tria=tlist->tria -1;
nobo=0;
for(i=1;i<=tlist->n;i++){
- i1=tria[i]->data->vertex[0];
- i2=tria[i]->data->vertex[1];
- i3=tria[i]->data->vertex[2];
+ 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]->data->vertex[0];
- j2=tria[j]->data->vertex[1];
- j3=tria[j]->data->vertex[2];
+ 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++;
@@ -292,14 +366,14 @@
}
}
for(i=1;i<=tlist->n;i++){
- i1=tria[i]->data->vertex[0];
- i2=tria[i]->data->vertex[1];
- i3=tria[i]->data->vertex[2];
+ 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]->data->vertex[0];
- j2=tria[j]->data->vertex[1];
- j3=tria[j]->data->vertex[2];
+ 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++;
@@ -307,14 +381,14 @@
}
}
for(i=1;i<=tlist->n;i++){
- i1=tria[i]->data->vertex[0];
- i2=tria[i]->data->vertex[1];
- i3=tria[i]->data->vertex[2];
+ 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]->data->vertex[0];
- j2=tria[j]->data->vertex[1];
- j3=tria[j]->data->vertex[2];
+ 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++;
@@ -337,20 +411,23 @@
ts_triangle **tria=tlist->tria -1;
for(i=1;i<=vesicle->vlist->n;i++){
- for(j=1;j<=vtx[i]->data->neigh_no;j++){
- k1=vtx[i]->data->neigh[j-1];
+ for(j=1;j<=vtx[i]->neigh_no;j++){
+ k1=vtx[i]->neigh[j-1];
jp=j+1;
- if(j == vtx[i]->data->neigh_no) jp=1;
- k2=vtx[i]->data->neigh[jp-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]->data->vertex[0];
- k4=tria[k]->data->vertex[1];
- k5=tria[k]->data->vertex[2];
+ 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)){
- // 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]);
}
}
--
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