From 267cf14b1ced6fce480e4292131a987a1802e28a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 23 Sep 2018 08:32:24 +0000
Subject: [PATCH] Confinement planes, not debugged
---
src/vertexmove.c | 36 ++++++++++++++++++++++++++++++++++--
1 files changed, 34 insertions(+), 2 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index c552a87..a6fb0e2 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -71,11 +72,23 @@
// 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){
+//#define SQ(x) x*x
+if(vesicle->R_nucleus>0.0){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+} else if(vesicle->R_nucleusX>0.0){
+// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
+// if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+// if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
+}
+//#undef SQ
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
@@ -86,7 +99,13 @@
return TS_FAIL;
}
-
+// plane confinement test
+ if(vesicle->tape->plane_confinement_switch){
+ if(vtx->z >= vesicle->confinement_plane.z_max || vtx->z <= vesicle->confinement_plane.z_min){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
//if all the tests are successful, then energy for vtx and neighbours is calculated
for(i=0;i<vtx->neigh_no;i++){
memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
@@ -176,6 +195,8 @@
delta_energy+=delta_energy_cv;
// fprintf(stderr,"Denergy after=%e\n",delta_energy);
}
+/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
+ delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -185,6 +206,17 @@
*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
+// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
+// plane confinement
+ if(vesicle->tape->plane_confinement_switch){
+ //if planes are not close enough, then repusion force is on
+ if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min > vesicle->tape->plane_d){
+ delta_energy+=vesicle->tape->plane_F * 1.0/( (backupvtx->z-vesicle->confinement_plane.z_min) + (backupvtx->z-vesicle->confinement_plane.z_max) );
+ delta_energy+=-(vesicle->tape->plane_F * 1.0/( (vtx->z-vesicle->confinement_plane.z_min) + (vtx->z-vesicle->confinement_plane.z_max) ) );
+
+ }
+ }
+// end plane confinement
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
if(exp(-delta_energy)< drand48())
--
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