From 9166cbcd0e28d61a69646911af35bb7895ff9203 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 28 Apr 2014 11:16:45 +0000
Subject: [PATCH] Did major change in vesicle datastructure. Added tape information into vesicle. This means the dump files will be broken each time tape structure changes. Beware.

---
 src/vertexmove.c |   75 ++++++++++++++++++++++++-------------
 1 files changed, 49 insertions(+), 26 deletions(-)

diff --git a/src/vertexmove.c b/src/vertexmove.c
index 04325ef..7b099e4 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,6 +9,7 @@
 #include "timestep.h"
 #include "cell.h"
 //#include "io.h"
+#include "io.h"
 #include<stdio.h>
 #include "vertexmove.h"
 #include <string.h>
@@ -67,11 +68,18 @@
 		}
 	}
 
-    //self avoidance check with distant vertices
-     cellidx=vertex_self_avoidance(vesicle, vtx);
-    //check occupation number
-     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
-	
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+	if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+		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
+	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+
     if(retval==TS_FAIL){
 		vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
         return TS_FAIL;
@@ -83,7 +91,7 @@
 	memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
 	}
 
-	if(vesicle->pswitch == 1){
+	if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch == 1){
 		for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
 	};
 
@@ -100,9 +108,9 @@
         delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
     }
 
-	if(vesicle->pswitch == 1){
+	if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch == 1){
 		for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
-		delta_energy-=vesicle->pressure*dvol;
+        if(vesicle->pswitch == 1) delta_energy-=vesicle->pressure*dvol;
 	};
 
 /* No poly-bond energy for now!
@@ -262,12 +270,14 @@
 	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:
@@ -289,12 +299,18 @@
 		}
 	}
 
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+	if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+		vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+		return TS_FAIL;
+	}
+
 
 	//self avoidance check with distant vertices
 	cellidx=vertex_self_avoidance(vesicle, vtx);
 	//check occupation number
 	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
-	
 	if(retval==TS_FAIL){
 		vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
         return TS_FAIL;
@@ -305,26 +321,30 @@
 		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 +359,18 @@
     	{
 	//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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