From 6da644f98434d3eac8b4e19981754f6030a315a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 27 Jun 2018 12:05:32 +0000
Subject: [PATCH] Resolving the issues with restoring vesicles from vtu and fixing the volume. Dump to vtu has been repaired.
---
src/timestep.c | 57 ++++++++++++++++++++++++++++++++++++++++-----------------
1 files changed, 40 insertions(+), 17 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 59ff8c6..c74e3e1 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>
@@ -15,43 +16,59 @@
#include<gsl/gsl_complex.h>
#include<gsl/gsl_complex_math.h>
#include<string.h>
+#include <sys/stat.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=0,kc2=0,kc3=0,kc4=0;
ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
ts_ulong epochtime;
- FILE *fd1,*fd2=NULL;
+ FILE *fd1,*fd2=NULL,*fd3=NULL;
char filename[10000];
- strcpy(filename,command_line_args.path);
- strcat(filename,"statistics.csv");
- FILE *fd=fopen(filename,"w");
+ //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){
strcpy(filename,command_line_args.path);
strcat(filename,"ulm2.csv");
+// int result = stat(filename, &st);
+ if(start_iteration==0)
fd2=fopen(filename,"w");
- if(fd2==NULL){
- fatal("Cannot open ulm2.csv file for writing",1);
- }
+ 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
- vesicle_area(vesicle); //needed for constant area at this moment
- V0=vesicle->volume;
- A0=vesicle->area;
+ vesicle_area(vesicle); //needed for constant area and stretching energy 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);
@@ -73,15 +90,14 @@
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);
if(i>=inititer){
- write_vertex_xml_file(vesicle,i-inititer);
+ vesicle_volume(vesicle); //calculates just volume.
+ vesicle_area(vesicle); //calculates area.
+ 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.
- vesicle_area(vesicle); //calculates area.
r0=getR0(vesicle);
if(vesicle->sphHarmonics!=NULL){
preparationSh(vesicle,r0);
@@ -125,7 +141,14 @@
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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