From 6c274defd904dedd6cb89c002f5eeced6c079d47 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 11 Dec 2018 11:42:22 +0000
Subject: [PATCH] Added stretching variables
---
src/timestep.c | 73 ++++++++++++++++++++++++++----------
1 files changed, 53 insertions(+), 20 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index df74c43..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;
@@ -49,31 +50,63 @@
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);
-
centermass(vesicle);
cell_occupation(vesicle);
vesicle_volume(vesicle); //needed for constant volume at this moment
- vesicle_area(vesicle); //needed for constant area at this moment
- V0=vesicle->volume;
- A0=vesicle->area;
+ vesicle_area(vesicle); //needed for constant area at this moment
+ if(V0<0.000001)
+ V0=vesicle->volume;
+ 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);
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;
- // fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
+ epsarea=A0/(ts_double)vesicle->tlist->n;
+
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++){
@@ -88,16 +121,9 @@
bfsr/=(ts_double)mcsweeps;
centermass(vesicle);
cell_occupation(vesicle);
- ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
dump_state(vesicle,i);
- fd3=fopen(".status","w");
- if(fd3==NULL){
- fatal("Cannot open .status file for writing",1);
- }
- fprintf(fd3,"%d",i);
- fclose(fd3);
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);
@@ -146,7 +172,14 @@
fflush(fd);
// sprintf(filename,"timestep-%05d.pov",i-inititer);
// write_pov_file(vesicle,filename);
+ } //end if(inititer....)
+ fd3=fopen(".status","w"); //write status file when everything is written to disk.
+ if(fd3==NULL){
+ fatal("Cannot open .status file for writing",1);
}
+ fprintf(fd3,"%d",i);
+ fclose(fd3);
+ ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
}
fclose(fd);
if(fd2!=NULL) fclose(fd2);
--
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