From 3006183b769f2e126b1a96e6bf697c2b7f657df7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 26 Apr 2020 17:35:26 +0000
Subject: [PATCH] Code for incremental adding of inclusions done
---
src/timestep.c | 166 +++++++++++++++++++++++++++++++++++--------------------
1 files changed, 105 insertions(+), 61 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 98b47dc..fe0ca24 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<stdio.h>
#include<math.h>
@@ -14,46 +15,111 @@
#include "vesicle.h"
#include<gsl/gsl_complex.h>
#include<gsl/gsl_complex_math.h>
-
+#include<string.h>
+#include <sys/stat.h>
+#include "initial_distribution.h"
ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
- ts_uint i, j,k,l,m;
- ts_double r0,kc1,kc2,kc3,kc4;
- ts_double l1,l2,l3,volume=0.0,area=0.0,vmsr,bfsr, vmsrt, bfsrt;
+ ts_uint i, j,k; //,l,m;
+ ts_double kc1=0,kc2=0,kc3=0,kc4=0;
+ ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
ts_ulong epochtime;
- FILE *fd1,*fd2=NULL;
-// char filename[255];
- FILE *fd=fopen("statistics.csv","w");
+ ts_double max_z,min_z;
+ FILE *fd3=NULL;
+ char filename[10000];
+ //struct stat st;
+ strcpy(filename,command_line_args.path);
+ strcat(filename,"statistics.csv");
+ //int result = stat(filename, &st);
+ FILE *fd;
+ if(start_iteration==0)
+ fd=fopen(filename,"w");
+ else
+ fd=fopen(filename,"a");
if(fd==NULL){
fatal("Cannot open statistics.csv file for writing",1);
}
- fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
+ if(start_iteration==0)
+ fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
- if(vesicle->sphHarmonics!=NULL){
- fd2=fopen("ulm2.csv","w");
- if(fd2==NULL){
- fatal("Cannot open ulm2.csv file for writing",1);
- }
+/* if(vesicle->sphHarmonics!=NULL){
+ strcpy(filename,command_line_args.path);
+ strcat(filename,"ulm2.csv");
+// int result = stat(filename, &st);
+ if(start_iteration==0)
+ 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");
-
}
+*/
/* 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
- V0=vesicle->volume;
+ 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);
- // fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
+// printf("epsvol=%e\n",epsvol);
+ epsarea=A0/(ts_double)vesicle->tlist->n;
+
+ int delta_number_c0=ceil((float)vesicle->tape->number_of_vertices_with_c0/(float)(iterations-1));
+ ts_fprintf(stdout, "Adding additional %d inclusions every %d iterations (%d times, total=%d).\n",delta_number_c0, mcsweeps, (vesicle->tape->number_of_vertices_with_c0)/delta_number_c0,(vesicle->tape->number_of_vertices_with_c0/delta_number_c0)*delta_number_c0);
+
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); */
+
+ if(i*delta_number_c0<vesicle->tape->number_of_vertices_with_c0){
+ fprintf(stdout, "Adding %d inclusions.\n", delta_number_c0);
+ add_vertices_with_c0(vesicle, delta_number_c0, vesicle->tape->c0, vesicle->tape->w);
+ }
for(j=0;j<mcsweeps;j++){
single_timestep(vesicle, &vmsrt, &bfsrt);
vmsr+=vmsrt;
@@ -66,61 +132,39 @@
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);
+/* BINARY DUMPS ARE OBSOLETE. SHOULD WORK AS OF MAR 2020, BUT NO LONGER MAINTAINED */
+// dump_state(vesicle,i);
+ vesicle_volume(vesicle); //calculates just volume.
+ vesicle_area(vesicle); //calculates area.
+ if(vesicle->tape->constvolswitch==0){
+ V0=vesicle->volume;
+ }
+ if(vesicle->tape->constareaswitch==0){
+ A0=vesicle->area;
+ }
if(i>=inititer){
- write_vertex_xml_file(vesicle,i-inititer);
- write_master_xml_file("test.pvd");
+ 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);
- vesicle_volume(vesicle); //calculates just volume. Area is not added to ts_vesicle yet!
- get_area_volume(vesicle, &area,&volume); //that's why I must recalculate area (and volume for no particular reason).
- r0=getR0(vesicle);
- if(vesicle->sphHarmonics!=NULL){
- preparationSh(vesicle,r0);
- //calculateYlmi(vesicle);
- calculateUlmComplex(vesicle);
- storeUlmComplex2(vesicle);
- saveAvgUlm2(vesicle);
- kc1=calculateKc(vesicle, 2,9);
- kc2=calculateKc(vesicle, 6,9);
- kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
- kc4=calculateKc(vesicle, 3,6);
-
- fd1=fopen("state.dat","w");
- fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
- for(k=0;k<vesicle->vlist->n;k++){
- fprintf(fd1,"%e %e %e %e %e\n",
- vesicle->vlist->vtx[k]->x,
- vesicle->vlist->vtx[k]->y,
- vesicle->vlist->vtx[k]->z,
- vesicle->vlist->vtx[k]->solAngle,
- vesicle->vlist->vtx[k]->relR
- );
- }
- fclose(fd1);
-
- fprintf(fd2,"%u ", i);
- for(l=0;l<vesicle->sphHarmonics->l;l++){
- for(m=l;m<2*l+1;m++){
- fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
- }
- }
- fprintf(fd2,"\n");
-
- fflush(fd2);
+ //r0=getR0(vesicle);
- }
-
- fprintf(fd, "%lu %u %e %e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e\n",epochtime,i,vmsr,bfsr,volume, area,l1,l2,l3,kc1, kc2, kc3,kc4);
+ fprintf(fd, "%lu %u %e %e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e\n",epochtime,i,vmsr,bfsr,vesicle->volume, vesicle->area,l1,l2,l3,kc1, kc2, kc3,kc4);
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);
+// if(fd2!=NULL) fclose(fd2);
return TS_SUCCESS;
}
--
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