From 82a8abcddd62838bfcd06b6081042caf4d385a88 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 21:37:13 +0000
Subject: [PATCH] Seems that the bugs are fixed. Pegs are self avoidant now
---
src/initial_distribution.c | 78 +++++++++++++++++++++++++++++++++------
1 files changed, 66 insertions(+), 12 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 7601f13..71a2c4f 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include<stdio.h>
@@ -11,6 +12,8 @@
#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);
@@ -37,26 +40,77 @@
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->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist);
+ 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->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
+ vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
+ vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
+ 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);
+// 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->clist->max_occupancy=16; /* hard coded max occupancy? */
vesicle->pressure= tape->pressure;
vesicle->pswitch=tape->pswitch;
-
- return vesicle;
+ if(tape->shc>0){
+ vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
+ }
+ else {
+ vesicle->sphHarmonics=NULL;
+ }
+ return TS_SUCCESS;
}
@@ -72,15 +126,15 @@
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));
+ const ts_double xl0=DEF_A0/(2.0*sin(M_PI/5.0));
#ifdef TS_DOUBLE_DOUBLE
- const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
+ const ts_double z0=sqrt(pow(DEF_A0,2)-pow(xl0,2));
#endif
#ifdef TS_DOUBLE_FLOAT
- const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
+ const ts_double z0=sqrtf(powf(DEF_A0,2)-powf(xl0,2));
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
+ const ts_double z0=sqrtl(powl(DEF_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 */
@@ -172,7 +226,7 @@
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( (dist2>eps) && (dist2<(DEF_A0*DEF_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]);
}
@@ -205,7 +259,7 @@
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) ){
+ if( (fabs(dist2-DEF_A0*DEF_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;
@@ -271,7 +325,7 @@
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){
+ if(fabs(dist-DEF_A0*DEF_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]);
}
}
--
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