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 | 26 ++++++++++----------------
1 files changed, 10 insertions(+), 16 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 6328b0f..c74e3e1 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -49,32 +49,26 @@
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<20;i++){
- int b=rand() % vesicle->vlist->n;
- vesicle->vlist->vtx[b]->c=-0.5;
- }
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
+ 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);
+ 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);
@@ -98,12 +92,12 @@
cell_occupation(vesicle);
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);
--
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