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/main.c | 1 +
src/timestep.c | 4 ++--
src/snapshot.c | 12 ++++++++++--
src/vertexmove.c | 5 +++--
4 files changed, 16 insertions(+), 6 deletions(-)
diff --git a/src/main.c b/src/main.c
index 3f91f43..0d20cad 100644
--- a/src/main.c
+++ b/src/main.c
@@ -131,6 +131,7 @@
// exit(1);
//write_vertex_xml_file(vesicle,1000);
+ fprintf(stderr,"constvol=%ld, precision=%e\n", tape->constvolswitch, tape->constvolprecision);
run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
write_master_xml_file(command_line_args.output_fullfilename);
write_dout_fcompat_file(vesicle,"dout");
diff --git a/src/snapshot.c b/src/snapshot.c
index da21498..6c628b4 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -22,7 +22,7 @@
/* outputs additional data into paraview xml file */
ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle){
-
+ ts_double cvol_write=0, carea_write=0;
ts_string *data=(ts_string *)malloc(sizeof(ts_sprintf));
data->string=(char *)malloc(5120000*sizeof(char)); /*TODO: warning, can break if the string is to long */
data->beg=0;
@@ -33,7 +33,15 @@
xml_trisurf_vtx_neigh(data,vesicle->vlist);
xml_trisurf_vtx_tristar(data,vesicle->vlist);
xml_trisurf_nucleus(data,vesicle);
- xml_trisurf_constvolarea(data,V0,A0);
+ if(vesicle->tape->constvolswitch==0)
+ cvol_write=vesicle->volume;
+ else
+ cvol_write=V0;
+ if(vesicle->tape->constareaswitch==0)
+ carea_write=vesicle->area;
+ else
+ carea_write=A0;
+ xml_trisurf_constvolarea(data,cvol_write,carea_write);
#ifdef COMPRESSION
char *compressed;
ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
diff --git a/src/timestep.c b/src/timestep.c
index d4748e6..c74e3e1 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -92,12 +92,12 @@
cell_occupation(vesicle);
dump_state(vesicle,i);
if(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);
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 1d5d7fa..3483965 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -165,7 +165,7 @@
if(vesicle->tape->constvolswitch==2){
/*check whether the dvol is gt than epsvol */
- //fprintf(stderr,"DVOL=%1.16e\n",dvol);
+ //fprintf(stderr,"DVOL=%1.16e, V0=%1.16e, vesicleVolume=%1.16e, |volume+dvol-V0|=%1.16e\n",dvol, V0, vesicle->volume, fabs(vesicle->volume+dvol-V0));
if(fabs(vesicle->volume+dvol-V0)>epsvol){
//restore old state.
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
@@ -173,11 +173,12 @@
vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
}
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //fprintf(stderr,"fajlam!\n");
+ // fprintf(stderr,"fajlam!\n");
return TS_FAIL;
}
} else
+ //fprintf(stderr, "success\n");
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
if(vesicle->tape->constvolswitch == 1){
--
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