From 5eefcc281fda031d322599fd7094da4fc8450948 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 25 Sep 2018 13:55:53 +0000
Subject: [PATCH] Debugged
---
src/timestep.c | 29 ++++++++++++++++++++++++-----
src/tape | 4 ++--
src/vertexmove.c | 7 ++++---
3 files changed, 30 insertions(+), 10 deletions(-)
diff --git a/src/tape b/src/tape
index 8e4cc9a..83b9c27 100644
--- a/src/tape
+++ b/src/tape
@@ -99,6 +99,6 @@
#plane confinement
plane_confinement_switch=1
#final plane distance (float in lmin)
-plane_d=10.0
+plane_d=10
#plane to vesicle repulsion force while closing
-plane_F=10
+plane_F=0
diff --git a/src/timestep.c b/src/timestep.c
index 204e9ba..767a675 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -24,7 +24,7 @@
ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
ts_ulong epochtime;
- ts_double max_z, min_z;
+ ts_double max_z=0, min_z=0;
FILE *fd1,*fd2=NULL,*fd3=NULL;
char filename[10000];
//struct stat st;
@@ -72,7 +72,21 @@
ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
epsarea=A0/(ts_double)vesicle->tlist->n;
-
+ if(vesicle->tape->plane_confinement_switch){
+ min_z=1e10;
+ max_z=-1e10;
+ for(k=0;k<vesicle->vlist->n;k++){
+ if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
+ if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
+ }
+ if(max_z-min_z<=vesicle->tape->plane_d) {
+ vesicle->confinement_plane.z_max=max_z;
+ vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
+ } else {
+ vesicle->confinement_plane.z_min=min_z;//-1e-5;
+ vesicle->confinement_plane.z_max=max_z;//+1e-5;
+ }
+ }
// fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
@@ -83,6 +97,10 @@
// plane confinement
if(vesicle->tape->plane_confinement_switch){
if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min<=vesicle->tape->plane_d){
+ ts_fprintf(stdout,"Force is off\n");
+ } else {
+ ts_fprintf(stdout,"Force is on\n");
+
min_z=1e10;
max_z=-1e10;
for(k=0;k<vesicle->vlist->n;k++){
@@ -93,10 +111,11 @@
vesicle->confinement_plane.z_max=max_z;
vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
} else {
- vesicle->confinement_plane.z_min=min_z-1e-5;
- vesicle->confinement_plane.z_max=max_z+1e-5;
+ vesicle->confinement_plane.z_min=min_z;//-1e-5;
+ vesicle->confinement_plane.z_max=max_z;//+1e-5;
}
- }
+ }
+ ts_fprintf(stdout,"Planes (zmin, zmax)=(%e,%e)\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
}
/* vesicle_volume(vesicle);
diff --git a/src/vertexmove.c b/src/vertexmove.c
index a6fb0e2..d2bac09 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -101,7 +101,7 @@
// plane confinement test
if(vesicle->tape->plane_confinement_switch){
- if(vtx->z >= vesicle->confinement_plane.z_max || vtx->z <= vesicle->confinement_plane.z_min){
+ 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;
}
@@ -211,8 +211,9 @@
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) ) );
+ //ts_fprintf(stderr,"force!!!\n");
+ delta_energy-=vesicle->tape->plane_F * ( 1.0/pow(backupvtx->z-vesicle->confinement_plane.z_min,2) + 1.0/pow(-backupvtx->z+vesicle->confinement_plane.z_max,2) );
+ delta_energy+=vesicle->tape->plane_F * ( 1.0/pow(vtx->z-vesicle->confinement_plane.z_min,2) + +1.0/pow(-vtx->z+vesicle->confinement_plane.z_max,2) );
}
}
--
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