From fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 17:33:28 +0000
Subject: [PATCH] First attempt in solving an issue of dense packed internal pegs. They are recreated as many times as needed.
---
src/vertexmove.c | 83 ++++++++++++++++++++++++++++++++++++-----
1 files changed, 72 insertions(+), 11 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 36cf993..fb74a06 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;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=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;
@@ -41,7 +42,7 @@
// vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
// vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
- //random move in a sphere with radius stepsize:
+//random move in a sphere with radius stepsize:
r=vesicle->stepsize*rn[0];
phi=rn[1]*2*M_PI;
costheta=2*rn[2]-1;
@@ -51,12 +52,12 @@
vtx->z=vtx->z+r*costheta;
- //distance with neighbours check
+//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;
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
}
}
@@ -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
@@ -87,14 +100,19 @@
}
- //if all the tests are successful, then energy for vtx and neighbours is calculated
+//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));
}
- if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch==1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
- };
+ }
+
+ if(vesicle->tape->constareaswitch==2){
+ for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
+
+ }
delta_energy=0;
@@ -113,11 +131,43 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch == 1){
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
};
+ if(vesicle->tape->constareaswitch==2){
+ /* check whether the darea is gt epsarea */
+ for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
+ if(fabs(vesicle->area+darea-A0)>epsarea){
+ //restore old state.
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //fprintf(stderr,"fajlam!\n");
+ return TS_FAIL;
+ }
+
+
+ }
+
+ if(vesicle->tape->constvolswitch==2){
+ /*check whether the dvol is gt than epsvol */
+ //fprintf(stderr,"DVOL=%1.16e\n",dvol);
+ if(fabs(vesicle->volume+dvol-V0)>epsvol){
+ //restore old state.
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //fprintf(stderr,"fajlam!\n");
+ return TS_FAIL;
+ }
+
+ } else
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
if(vesicle->tape->constvolswitch == 1){
@@ -150,7 +200,7 @@
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
- if(exp(-delta_energy)< drand48() )
+ if(exp(-delta_energy)< drand48())
#endif
#ifdef TS_DOUBLE_FLOAT
if(expf(-delta_energy)< (ts_float)drand48())
@@ -174,6 +224,8 @@
constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
}
// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
return TS_FAIL;
}
}
@@ -187,11 +239,20 @@
}
+ if(vesicle->tape->constvolswitch == 2){
+ vesicle->volume+=dvol;
+ } else
if(vesicle->tape->constvolswitch == 1){
constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
}
+
+ if(vesicle->tape->constareaswitch==2){
+ vesicle->area+=darea;
+ }
// if(oldcellidx);
//END MONTE CARLOOOOOOO
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
return TS_SUCCESS;
}
--
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