From dd4e182bc818974b3ad529422e631aa6a0764f2f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Jul 2016 10:18:24 +0000
Subject: [PATCH] Merge branch 'nirgov' of bitbucket.org:samop/trisurf-ng into nirgov
---
src/Makefile.am | 5 +
src/main.c | 1
src/initial_distribution.h | 2
src/initial_distribution.c | 17 ++-
src/restore.h | 1
src/restore.c | 49 +++++++++++
src/tspoststat.c | 119 +++++++++++++++++++++++++++++
src/tsmeasure.c | 1
8 files changed, 184 insertions(+), 11 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index 04ad1c7..19449c4 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,4 +1,4 @@
-bin_PROGRAMS = trisurf tsmeasure
+bin_PROGRAMS = trisurf tsmeasure tspoststat
trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
GITVERSION:=$(shell git --no-pager describe --tags --always --dirty)
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline
@@ -20,5 +20,8 @@
tsmeasure_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c tsmeasure.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
tsmeasure_LDADD = ${libcurl_LIBS} ${libxml2_LIBS}
+
+tspoststat_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c tspoststat.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
+tspoststat_LDADD = ${libcurl_LIBS} ${libxml2_LIBS}
#gitversion.c: .git/HEAD .git/index
# echo "const char *gitversion = \"$(shell git rev-parse HEAD)\";" > $@
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index d8e917f..dbdd0c4 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -44,6 +44,7 @@
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
vesicle->tape=tape;
set_vesicle_values_from_tape(vesicle);
+ initial_population_with_c0(vesicle,tape);
return vesicle;
}
@@ -111,7 +112,14 @@
vesicle->sphHarmonics=NULL;
}
- int rndvtx;
+
+ return TS_SUCCESS;
+
+}
+
+
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
+ int rndvtx,i,j;
if(tape->number_of_vertices_with_c0>0){
ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
j=0;
@@ -133,13 +141,8 @@
sweep_attraction_bond_energy(vesicle);
}
}
-
- return TS_SUCCESS;
-
+ return TS_SUCCESS;
}
-
-
-
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
diff --git a/src/initial_distribution.h b/src/initial_distribution.h
index b1a20e1..e54ee08 100644
--- a/src/initial_distribution.h
+++ b/src/initial_distribution.h
@@ -15,6 +15,8 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape);
ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle);
+
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape);
/** Sets the initial position of the vertexes to dipyramid
*
* @param *vlist is a pointer to list of vertices
diff --git a/src/main.c b/src/main.c
index 7c1ff29..55c27ba 100644
--- a/src/main.c
+++ b/src/main.c
@@ -127,6 +127,7 @@
}
//printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
+ //write_vertex_xml_file(vesicle,1000);
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/restore.c b/src/restore.c
index 3a93d3f..a490d53 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -54,6 +54,10 @@
if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
cur2=cur1->xmlChildrenNode;
while(cur2!=NULL){
+ if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){
+ if(vesicle!=NULL)
+ parseXMLPointData(vesicle,doc,cur2);
+ }
if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
//fprintf(stderr,"Found point data\n");
if(vesicle!=NULL)
@@ -81,6 +85,7 @@
init_normal_vectors(vesicle->tlist);
mean_curvature_and_energy(vesicle);
+ sweep_attraction_bond_energy(vesicle);
/* TODO: filaments */
@@ -182,7 +187,6 @@
vesicle->tape=tape;
set_vesicle_values_from_tape(vesicle);
-
return vesicle;
}
@@ -318,7 +322,48 @@
return TS_SUCCESS;
}
-
+/* this parses the data for vertices (like spontaneous curvature, etc.) */
+ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
+ xmlNodePtr child = cur->xmlChildrenNode;
+ xmlChar *property_name;
+ xmlChar *values;
+ char *vals;
+ char *token;
+ int idx, polyidx, monoidx, filidx, fonoidx;
+ while (child != NULL) {
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
+ property_name=xmlGetProp(child, (xmlChar *)"Name");
+ // fprintf(stderr,"Name: %s\n", property_name);
+ if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
+ values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
+ vals=(char *)values;
+ token=strtok(vals," ");
+ idx=0;
+ while(token!=NULL){
+ if(idx<vesicle->vlist->n){
+ vesicle->vlist->vtx[idx]->c=atof(token);
+ } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
+ polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
+ monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
+ vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=atof(token);
+ } else {
+ filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
+ fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
+ //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=atof(token);
+ }
+ idx++;
+ token=strtok(NULL," ");
+ }
+ xmlFree(values);
+ }
+ xmlFree(property_name);
+ }
+
+ child=child->next;
+ }
+ return TS_SUCCESS;
+}
/* this is a parser of vertex positions and bonds from main xml data */
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
xmlNodePtr child = cur->xmlChildrenNode;
diff --git a/src/restore.h b/src/restore.h
index cfc6b66..b05c6a8 100644
--- a/src/restore.h
+++ b/src/restore.h
@@ -9,6 +9,7 @@
ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
+ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
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);
diff --git a/src/tsmeasure.c b/src/tsmeasure.c
index 4ed39eb..beabc61 100644
--- a/src/tsmeasure.c
+++ b/src/tsmeasure.c
@@ -84,7 +84,6 @@
tape_free(vesicle->tape);
vesicle_free(vesicle);
}
- free(ent);
}
for (n = 0; n < count; n++)
{
diff --git a/src/tspoststat.c b/src/tspoststat.c
new file mode 100644
index 0000000..5fb1380
--- /dev/null
+++ b/src/tspoststat.c
@@ -0,0 +1,119 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+#include<stdio.h>
+#include<math.h>
+#include<stdlib.h>
+#include "general.h"
+//#include "vertex.h"
+//#include "bond.h"
+//#include "triangle.h"
+//#include "cell.h"
+#include "vesicle.h"
+#include "io.h"
+//#include "initial_distribution.h"
+//#include "frame.h"
+//#include "timestep.h"
+//#include "poly.h"
+#include "stats.h"
+#include "sh.h"
+#include "shcomplex.h"
+#include "dumpstate.h"
+#include "restore.h"
+#include <string.h>
+#include <getopt.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <errno.h>
+#include <snapshot.h>
+#include<gsl/gsl_complex.h>
+#include<gsl/gsl_complex_math.h>
+
+
+ts_vesicle *restoreVesicle(char *filename){
+ ts_vesicle *vesicle = parseDump(filename);
+ return vesicle;
+}
+
+void vesicle_calculate_ulm2(ts_vesicle *vesicle){
+ //complex_sph_free(vesicle->sphHarmonics);
+
+ //vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,21);
+ vesicle_volume(vesicle);
+ preparationSh(vesicle,getR0(vesicle));
+ calculateUlmComplex(vesicle);
+ ts_int i,j;
+ for(i=0;i<vesicle->sphHarmonics->l;i++){
+ for(j=i;j<2*i+1;j++){
+ printf("%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[i][j]));
+ }
+ }
+ printf("\n");
+
+}
+
+
+
+int count_bonds_with_energy(ts_bond_list *blist){
+
+ unsigned int i, cnt;
+ cnt=0;
+ for(i=0;i<blist->n;i++){
+ if(fabs(blist->bond[i]->energy)>1e-16) cnt++;
+ }
+ return cnt;
+}
+
+int main(){
+ ts_vesicle *vesicle;
+ ts_char *i,*j;
+ ts_uint tstep,n;
+ ts_char *number;
+ struct dirent **list;
+ ts_double l1,l2,l3;
+ int count;
+ ts_fprintf(stderr,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+
+ fprintf(stdout, "OuterLoop Volume Area lamdba1 lambda2 lambda3 Nbw/Nb\n");
+
+
+ count=scandir(".",&list,0,alphasort);
+ if(count<0){
+ fatal("Error, cannot open directory.",1);
+ }
+ tstep=0;
+ for(n=0;n<count;n++){
+ struct dirent *ent;
+ ent=list[n];
+ i=rindex(ent->d_name,'.');
+ if(i==NULL) {
+ continue;
+ }
+ if(strcmp(i+1,"vtu")==0){
+ j=rindex(ent->d_name,'_');
+ if(j==NULL) continue;
+ number=strndup(j+1,j-i);
+ quiet=1;
+ ts_fprintf(stdout,"timestep: %u filename: %s\n",atoi(number),ent->d_name);
+// printf("%u ",atoi(number));
+ vesicle=restoreVesicle(ent->d_name);
+// vesicle_calculate_ulm2(vesicle);
+ vesicle_volume(vesicle);
+ vesicle_area(vesicle);
+ gyration_eigen(vesicle,&l1,&l2,&l3);
+ fprintf(stdout,"%d %.17e %.17e %.17e %.17e %.17e %.17e\n",atoi(number),vesicle->volume, vesicle->area,l1,l2,l3, (ts_double)count_bonds_with_energy(vesicle->blist)/(ts_double)vesicle->blist->n),
+ tstep++;
+
+ free(number);
+ tape_free(vesicle->tape);
+ vesicle_free(vesicle);
+ }
+ }
+ for (n = 0; n < count; n++)
+ {
+ free(list[n]);
+ }
+
+ free(list);
+ return 0;
+}
+
--
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