From 304510886da7e3969efd6d506e68652b533c0975 Mon Sep 17 00:00:00 2001
From: Miha <mihaf@hapi.(none)>
Date: Fri, 21 Feb 2014 12:22:07 +0000
Subject: [PATCH] Removed harmonic potential between poly-monomers for now. Added min and max distance between neighboring poly-vertices.
---
src/tape | 2 +-
src/energy.c | 4 +++-
src/vertexmove.c | 47 ++++++++++++++++++++++++++++++++++-------------
3 files changed, 38 insertions(+), 15 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 1e37e08..440f319 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -21,7 +21,9 @@
inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){
- bond->energy=poly->k*pow(bond->bond_length-1,2);
+//TODO: This value to be changed and implemented in data structure:
+ ts_double d_relaxed=1.0;
+ bond->energy=poly->k*pow(bond->bond_length-d_relaxed,2);
return TS_SUCCESS;
};
diff --git a/src/tape b/src/tape
index 10db609..9a44ef3 100644
--- a/src/tape
+++ b/src/tape
@@ -2,7 +2,7 @@
# nshell is a number of divisions of dipyramid
nshell=17
# dmax is the max. bond length
-dmax=1.4
+dmax=1.7
# bending rigidity of the membrane
xk0=25.0
# max step size
diff --git a/src/vertexmove.c b/src/vertexmove.c
index f78fd61..86b8533 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -57,6 +57,16 @@
return TS_FAIL;
}
}
+
+// Distance with grafted poly-vertex check:
+ if(vtx->grafted_poly!=NULL){
+ dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
@@ -87,15 +97,13 @@
energy_vertex(vtx->neigh[i]);
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
-
+/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
-
-
}
-
+*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
@@ -139,11 +147,12 @@
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;
//This will hold all the information of vtx and its neighbours
ts_vertex backupvtx;
- ts_bond backupbond[2];
+// ts_bond backupbond[2];
memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
//random move in a sphere with radius stepsize:
@@ -157,13 +166,23 @@
//distance with neighbours check
-// for(i=0;i<vtx->neigh_no;i++){
-// dist=vtx_distance_sq(vtx,vtx->neigh[i]);
-// if(dist<1.0 || dist>vesicle->dmax) {
-// vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
-// return TS_FAIL;
-// }
-// }
+ for(i=0;i<vtx->neigh_no;i++){
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// Distance with grafted vesicle-vertex check:
+ if(vtx==poly->vlist->vtx[0]){
+ dist=vtx_distance_sq(vtx,poly->grafted_vtx);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
@@ -177,6 +196,7 @@
//if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Energy ignored for now!
delta_energy=0;
for(i=0;i<vtx->bond_no;i++){
memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
@@ -214,6 +234,7 @@
return TS_FAIL;
}
}
+*/
// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
if(vtx->cell!=vesicle->clist->cell[cellidx]){
--
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