From 7ec6fb63c690080d0624c7bf138d0fd84fe7664e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 15 May 2018 16:11:14 +0000
Subject: [PATCH] First working version, not debugged and energy assigned to vesicles on timesteps
---
src/vertexmove.c | 42 +++++++++++++++++++++++++++++++++++++++---
1 files changed, 39 insertions(+), 3 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index c552a87..401dddf 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"
@@ -20,7 +21,7 @@
ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
@@ -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
@@ -100,7 +113,10 @@
for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
}
-
+ //stretching energy 1 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy/3.0;
+ }
delta_energy=0;
// vesicle_volume(vesicle);
@@ -176,6 +192,19 @@
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);
+
+ //stretching energy 2 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle, vtx->tristar[i]);
+ dstretchenergy+=vtx->tristar[i]->energy/3.0;
+ }
+ }
+
+ delta_energy+=dstretchenergy;
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -185,6 +214,7 @@
*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
+// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
if(exp(-delta_energy)< drand48())
@@ -205,6 +235,12 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //stretching energy 3 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle,vtx->tristar[i]);
+ }
+ }
// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
if(vesicle->tape->constvolswitch == 1){
--
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