From 49981c5ddda35e6defd63d860bccfbc66e7158ca Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 02 Jun 2016 10:13:11 +0000
Subject: [PATCH] ConstVol and ConstArea area+volume are now also in the snapshost. Fix in timing of writting the .status file to the disk.
---
src/timestep.c | 22 +++++++++++++---------
src/snapshot.c | 9 ++++++++-
src/restore.h | 2 ++
src/restore.c | 22 ++++++++++++++++++++++
src/snapshot.h | 1 +
5 files changed, 46 insertions(+), 10 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index 196df76..3a93d3f 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -168,6 +168,13 @@
if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
parseTrisurfNucleus(vesicle, doc, child);
}
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
+ parseTrisurfConstantVolume(doc, child);
+ }
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
+ parseTrisurfConstantArea(doc, child);
+ }
+
child = child->next;
}
@@ -182,6 +189,21 @@
/* Low level tags parsers */
+ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ char *n=(char *)cvol;
+ V0=atof(n);
+ xmlFree(cvol);
+ return TS_SUCCESS;
+}
+ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ char *n=(char *)carea;
+ A0=atof(n);
+ xmlFree(carea);
+ return TS_SUCCESS;
+}
+
ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
char *n=(char *)coords;
diff --git a/src/restore.h b/src/restore.h
index 934d6e8..cfc6b66 100644
--- a/src/restore.h
+++ b/src/restore.h
@@ -12,4 +12,6 @@
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
+ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur);
+ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur);
#endif
diff --git a/src/snapshot.c b/src/snapshot.c
index 8b71e83..fbb6d4b 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -33,6 +33,7 @@
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);
#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
@@ -127,10 +128,16 @@
ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
- ts_sprintf(data,"<nucleus>%.17e %.17e %.7e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
+ ts_sprintf(data,"<nucleus>%.17e %.17e %.17e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
}
return TS_SUCCESS;
}
+ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area){
+ ts_sprintf(data,"<constant_volume>%.17e</constant_volume>",volume);
+ ts_sprintf(data,"<constant_area>%.17e</constant_area>",area);
+
+ return TS_SUCCESS;
+}
/* UTILITIES */
diff --git a/src/snapshot.h b/src/snapshot.h
index 0db57f4..7bc617b 100644
--- a/src/snapshot.h
+++ b/src/snapshot.h
@@ -19,6 +19,7 @@
ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist);
ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist);
ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle);
+ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area);
/* UTILITIES */
char *base64_encode(const unsigned char *data, size_t input_length, size_t *output_length);
unsigned char *base64_decode(const char *data, size_t input_length, size_t *output_length);
diff --git a/src/timestep.c b/src/timestep.c
index df74c43..9f40e1c 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -65,8 +65,12 @@
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;
+ 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);
@@ -88,14 +92,7 @@
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_master_xml_file(command_line_args.output_fullfilename);
@@ -146,7 +143,14 @@
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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