From b30f45332934a27d267bac995eb6a94cc7cf5d9d Mon Sep 17 00:00:00 2001
From: mihaf <miha.fosnaric@gmail.com>
Date: Wed, 19 Mar 2014 14:10:05 +0000
Subject: [PATCH] continuing...
---
src/io.c | 1 +
src/tape | 3 ++-
src/vertexmove.c | 43 ++++++++++++++++++++++++++-----------------
src/io.h | 1 +
4 files changed, 30 insertions(+), 18 deletions(-)
diff --git a/src/io.c b/src/io.c
index 9e23560..a47bd9a 100644
--- a/src/io.c
+++ b/src/io.c
@@ -844,6 +844,7 @@
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
+ CFG_SIMPLE_FLOAT("xi",&tape->xi),
CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
CFG_SIMPLE_INT("nymax", &tape->ncymax),
diff --git a/src/io.h b/src/io.h
index 71390bc..bfc6173 100644
--- a/src/io.h
+++ b/src/io.h
@@ -28,6 +28,7 @@
ts_double dmax;
ts_double stepsize;
ts_double kspring;
+ ts_double xi;
ts_double pressure;
long int iterations;
long int inititer;
diff --git a/src/tape b/src/tape
index ac316ef..751b9e6 100644
--- a/src/tape
+++ b/src/tape
@@ -27,7 +27,8 @@
nfil=1
# nfono is a number of monomers in each filament
nfono=300
-# Spring constant between monomers of the filament
+# Persistence lenght of the filaments (in units l_min)
+xi=10
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 04325ef..da8e70f 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -262,12 +262,14 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
-// ts_double delta_energy;
+ ts_double delta_energy;
ts_double costheta,sintheta,phi,r;
ts_double dist[2];
//This will hold all the information of vtx and its neighbours
- ts_vertex backupvtx;
+ ts_vertex backupvtx,backupneigh[2];
ts_bond backupbond[2];
+
+ //backup vertex:
memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
//random move in a sphere with radius stepsize:
@@ -305,26 +307,30 @@
memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
vtx->bond[i]->bond_length=sqrt(dist[i]);
bond_vector(vtx->bond[i]);
-
+ }
+
+ //backup neighboring vertices:
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
}
//if all the tests are successful, then energy for vtx and neighbours is calculated
-// delta_energy=0;
-/* for(i=0;i<vtx->neigh_no;i++){
-// memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
- xp = vtx->neigh[i]
- vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
- bond_energy(vtx->bond[i],poly);
- delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
+ delta_energy=0;
+
+ 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;
+ delta_energy += vtx->energy - backupvtx.energy;
}
- if(vtx==poly->vlist->vtx[0]){
- delta_energy+=
- (pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
- pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
-
+ for(i=0;i<vtx->neigh_no;i++){
+ if(vtx->neigh[i]->bond_no == 2){
+ vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
+ delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
+ }
}
+ // poly->k is filament persistence length (in units l_min)
+ delta_energy *= poly->k;
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
@@ -339,15 +345,18 @@
{
//not accepted, reverting changes
vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
+ }
for(i=0;i<vtx->bond_no;i++){
- vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
}
return TS_FAIL;
}
}
-*/
+
// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
if(vtx->cell!=vesicle->clist->cell[cellidx]){
retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
--
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