From b4e2e6dbd5049ae279f0f74838cd21b625148c72 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 11 Oct 2018 10:34:25 +0000
Subject: [PATCH] Changes in plates movement
---
src/timestep.c | 69 ++++++++++++++++++++++++++++------
1 files changed, 56 insertions(+), 13 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 6972015..af8859c 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=0, min_z=0, cm_backup[3];
FILE *fd1,*fd2=NULL,*fd3=NULL;
char filename[10000];
//struct stat st;
@@ -49,22 +50,16 @@
fd2=fopen(filename,"w");
else
fd2=fopen(filename,"a");
- if(fd2==NULL){
- fatal("Cannot open ulm2.csv file for writing",1);
- }
- if(start_iteration==0) //file does not exist
- fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
-
+ if(fd2==NULL){
+ fatal("Cannot open ulm2.csv file for writing",1);
+ }
+ if(start_iteration==0) //file does not exist
+ fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
}
/* RANDOM SEED SET BY CURRENT TIME */
epochtime=get_epoch();
srand48(epochtime);
-/*Nir Gov: randomly add spontaneous curvature for some vertices */
- for(i=0;i<200;i++){
- int b=rand() % vesicle->vlist->n;
- vesicle->vlist->vtx[b]->c=-0.1;
- }
centermass(vesicle);
cell_occupation(vesicle);
vesicle_volume(vesicle); //needed for constant volume at this moment
@@ -74,14 +69,32 @@
ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
if(A0<0.000001)
A0=vesicle->area;
- ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
+ 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);
for(i=start_iteration;i<inititer+iterations;i++){
vmsr=0.0;
bfsr=0.0;
+
+
/* vesicle_volume(vesicle);
fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
for(j=0;j<mcsweeps;j++){
@@ -94,11 +107,41 @@
fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
vmsr/=(ts_double)mcsweeps;
bfsr/=(ts_double)mcsweeps;
+ for (k=0;k<3;k++) cm_backup[k]=vesicle->cm[k];
+
centermass(vesicle);
cell_occupation(vesicle);
+
+ // 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++){
+ 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+=(vesicle->cm[2]-cm_backup[2]);
+ vesicle->confinement_plane.z_min+=(vesicle->cm[2]-cm_backup[2]);
+ //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;
+ }
+ }
+ ts_fprintf(stdout,"Planes (zmin, zmax)=(%e,%e)\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
+ }
+ // end plane confinement
+
dump_state(vesicle,i);
if(i>=inititer){
- write_vertex_xml_file(vesicle,i-inititer);
+ write_vertex_xml_file(vesicle,i-inititer,NULL);
write_master_xml_file(command_line_args.output_fullfilename);
epochtime=get_epoch();
gyration_eigen(vesicle, &l1, &l2, &l3);
--
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