From 0dd5baa7166ab9abd7ef2d6b374e72beab03ef2a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 11 Dec 2018 10:58:51 +0000
Subject: [PATCH] First test successful
---
src/timestep.c | 40 +++++++++++++++----
src/tape | 4 +-
src/frame.c | 11 +++++
src/vertexmove.c | 19 +++++++++
4 files changed, 61 insertions(+), 13 deletions(-)
diff --git a/src/frame.c b/src/frame.c
index 68b8a84..5c473f7 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -9,6 +9,7 @@
ts_bool centermass(ts_vesicle *vesicle){
ts_uint i,j, n=vesicle->vlist->n;
ts_vertex **vtx=vesicle->vlist->vtx;
+ ts_double temp_z_cm=0;
vesicle->cm[0]=0;
vesicle->cm[1]=0;
vesicle->cm[2]=0;
@@ -20,6 +21,12 @@
vesicle->cm[0]/=(ts_float)n;
vesicle->cm[1]/=(ts_float)n;
vesicle->cm[2]/=(ts_float)n;
+
+ //center mass for z component does not change if we confine the vesicle with plates
+ if(vesicle->tape->plane_confinement_switch){
+ temp_z_cm=vesicle->cm[2];
+ vesicle->cm[2]=0;
+ }
for(i=0;i<n;i++){
vtx[i]->x-=vesicle->cm[0];
@@ -49,7 +56,9 @@
vesicle->cm[0]=0.0;
vesicle->cm[1]=0.0;
- vesicle->cm[2]=0.0;
+ if(vesicle->tape->plane_confinement_switch){
+ vesicle->cm[2]=temp_z_cm;
+ }
for(i=0;i<vesicle->tlist->n;i++){
triangle_normal_vector(vesicle->tlist->tria[i]);
diff --git a/src/tape b/src/tape
index cb09003..9d7363b 100644
--- a/src/tape
+++ b/src/tape
@@ -100,6 +100,6 @@
#plane confinement
plane_confinement_switch=1
#final plane distance (float in lmin)
-plane_d=15
+plane_d=10
#plane to vesicle repulsion force while closing
-plane_F=1000
+plane_F=10
diff --git a/src/timestep.c b/src/timestep.c
index d8440d0..6430597 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -24,6 +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;
FILE *fd1,*fd2=NULL,*fd3=NULL;
char filename[10000];
//struct stat st;
@@ -72,19 +73,40 @@
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;
- //plane confinement part 1
-
- if(vesicle->tape->plane_confinement_switch){
- vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
- vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
- ts_fprintf(stderr,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
- }
-
- // 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);
for(i=start_iteration;i<inititer+iterations;i++){
vmsr=0.0;
bfsr=0.0;
+
+ //plane confinement
+ 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;
+ }
+ vesicle->confinement_plane.force_switch=0;
+ if(max_z>=vesicle->tape->plane_d/2.0){
+ ts_fprintf(stdout, "Max vertex out of bounds (z>=%e). Plane set to max_z = %e.\n",vesicle->tape->plane_d/2.0,max_z);
+ vesicle->confinement_plane.z_max = max_z;
+ vesicle->confinement_plane.force_switch=1;
+ } else {
+ vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
+ }
+ if(min_z<=-vesicle->tape->plane_d/2.0){
+ ts_fprintf(stdout, "Min vertex out of bounds (z<=%e). Plane set to min_z = %e.\n",-vesicle->tape->plane_d/2.0,min_z);
+ vesicle->confinement_plane.z_min = min_z;
+ vesicle->confinement_plane.force_switch=1;
+ } else {
+ vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
+ }
+ ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
+ if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
+ }
+
+ //end plane confinement
+
/* vesicle_volume(vesicle);
fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
for(j=0;j<mcsweeps;j++){
diff --git a/src/vertexmove.c b/src/vertexmove.c
index a3244b2..eec552e 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -123,7 +123,8 @@
}
delta_energy=0;
-
+
+
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
@@ -206,6 +207,22 @@
pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
}
*/
+
+// plane confinement energy due to compressing force
+ if(vesicle->tape->plane_confinement_switch){
+ if(vesicle->confinement_plane.force_switch){
+ //substract old energy
+ if(abs(vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_max)>1e-10) {
+ delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-backupvtx[0].z,2);
+ delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-vtx->z,2);
+ }
+ if(abs(-vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_min)>1e-10) {
+ delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-backupvtx[0].z,2);
+ delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-vtx->z,2);
+ }
+ }
+ }
+
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
--
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