From e5858ff1dcf5cecfcfe81602f52d255de9d508f4 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 21 Jun 2016 10:49:57 +0000
Subject: [PATCH] Change in location of setting spontaneous curvature. Now it is done in initial_distribution.c, in function set_vesicle_values_from_tape. Also, energy assigning function is done and sweeping of the whole vesicle aswell.
---
src/initial_distribution.c | 50 +++++++++++++++++++++++++++++++++++++-------------
1 files changed, 37 insertions(+), 13 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 35d533d..0f04e5f 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>
@@ -39,13 +40,21 @@
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);
- vesicle->tape=tape;
- // Nucleus:
- vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
+ 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):
@@ -86,7 +95,7 @@
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;
@@ -101,7 +110,22 @@
else {
vesicle->sphHarmonics=NULL;
}
- return vesicle;
+
+ int rndvtx;
+ if(tape->number_of_vertices_with_c0>0){
+ ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
+ for(i=0;i<tape->number_of_vertices_with_c0;i++){
+ rndvtx=rand() % vesicle->vlist->n;
+ vesicle->vlist->vtx[rndvtx]->c=tape->c0;
+ }
+ mean_curvature_and_energy(vesicle);
+ if(fabs(tape->w)>1e-16){ //if nonzero energy
+ ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
+ sweep_attraction_bond_energy(vesicle);
+ }
+ }
+
+ return TS_SUCCESS;
}
@@ -117,15 +141,15 @@
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 */
@@ -217,7 +241,7 @@
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]);
}
@@ -250,7 +274,7 @@
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;
@@ -316,7 +340,7 @@
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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