From 37d14a0a50ed40f536cc3821b3584552e1b75c5c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@CAE-linux.(none)>
Date: Mon, 07 Apr 2014 19:55:16 +0000
Subject: [PATCH] added statistics output to the outer loop
---
src/Makefile.am | 10 +-
src/timestep.c | 45 +++++++++-----
src/stats.c | 77 +++++++++++++++++++++++++
src/stats.h | 6 ++
src/spherical_trisurf.c | 5 +
src/timestep.h | 2
src/spherical_trisurf_ff.c | 5 +
7 files changed, 124 insertions(+), 26 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index 59e7972..204da92 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,17 +1,17 @@
trisurfdir=../
trisurf_PROGRAMS = trisurf
-trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c gyration.c
+trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c
#trisurf_LDFLAGS = -lm -lconfuse
shdiscoverdir=../
shdiscover_PROGRAMS= shdiscover
-shdiscover_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c energy.c sh.c shdiscover.c poly.c gyration.c
+shdiscover_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c energy.c sh.c shdiscover.c poly.c stats.c
AM_CFLAGS = -Wall -Werror
co_testdir=../
co_test_PROGRAMS=co_test
-co_test_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c energy.c sh.c co_test.c frame.c bondflip.c poly.c gyration.c
+co_test_SOURCES= general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c energy.c sh.c co_test.c frame.c bondflip.c poly.c stats.c
spherical_trisurfdir=../
spherical_trisurf_PROGRAMS = spherical_trisurf
-spherical_trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c spherical_trisurf.c sh.c bondflip.c poly.c gyration.c
+spherical_trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c spherical_trisurf.c sh.c bondflip.c poly.c stats.c
spherical_trisurf_ffdir=../
spherical_trisurf_ff_PROGRAMS = spherical_trisurf_ff
-spherical_trisurf_ff_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c spherical_trisurf_ff.c sh.c bondflip.c poly.c gyration.c
+spherical_trisurf_ff_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c spherical_trisurf_ff.c sh.c bondflip.c poly.c stats.c
diff --git a/src/spherical_trisurf.c b/src/spherical_trisurf.c
index 7fa40f9..6c5946f 100644
--- a/src/spherical_trisurf.c
+++ b/src/spherical_trisurf.c
@@ -61,10 +61,11 @@
calculateUlm(vesicle);
//preloop:
+ts_double vmsr, bfsr;
for(i=0;i<1000;i++){
cell_occupation(vesicle);
for(j=0;j<1000;j++){
- single_timestep(vesicle);
+ single_timestep(vesicle, &vmsr, &bfsr);
}
centermass(vesicle);
fprintf(stderr, "Preloop %d completed.\n",i+1);
@@ -75,7 +76,7 @@
for(j=0;j<200;j++){
cell_occupation(vesicle);
for(k=0;k<5;k++){
- single_timestep(vesicle);
+ single_timestep(vesicle, &vmsr, &bfsr);
}
centermass(vesicle);
}
diff --git a/src/spherical_trisurf_ff.c b/src/spherical_trisurf_ff.c
index 867f37d..00a4cc0 100644
--- a/src/spherical_trisurf_ff.c
+++ b/src/spherical_trisurf_ff.c
@@ -44,10 +44,11 @@
preparationSh(vesicle,r0);
calculateYlmi(vesicle);
calculateUlm(vesicle);
+ts_double vmsr,bfsr;
for(i=0;i<500;i++){
cell_occupation(vesicle);
for(j=0;j<1000;j++){
- single_timestep(vesicle);
+ single_timestep(vesicle,&vmsr,&bfsr);
}
centermass(vesicle);
fprintf(stderr, "Preloop %d completed.\n",i+1);
@@ -62,7 +63,7 @@
for(i=0;i<10000;i++){
cell_occupation(vesicle);
for(j=0;j<1000;j++){
- single_timestep(vesicle);
+ single_timestep(vesicle,&vmsr,&bfsr);
}
centermass(vesicle);
vesicle_volume(vesicle);
diff --git a/src/stats.c b/src/stats.c
new file mode 100644
index 0000000..4648d29
--- /dev/null
+++ b/src/stats.c
@@ -0,0 +1,77 @@
+#include <stdio.h>
+#include <time.h>
+//#include <gsl/gsl_math.h>
+//#include <gsl/gsl_blas.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_sort_vector.h>
+#include "general.h"
+
+void gyration_eigen(ts_vesicle *vesicle, ts_double *l1, ts_double *l2, ts_double *l3){
+ gsl_matrix *matrix = gsl_matrix_alloc(3,3);
+ gsl_vector *eig = gsl_vector_alloc(3);
+ gsl_eigen_symm_workspace *workspace = gsl_eigen_symm_alloc(3);
+ ts_uint i,j,k;
+ ts_double mat[3][3];
+ ts_double vec[3];
+ for(i = 0; i < 3; i++)
+ for(j = 0; j < 3; j++)
+ mat[i][j]=0;
+
+
+ for(k=0;k<vesicle->vlist->n;k++){
+ vec[0]=vesicle->vlist->vtx[k]->x;
+ vec[1]=vesicle->vlist->vtx[k]->y;
+ vec[2]=vesicle->vlist->vtx[k]->z;
+ for(i = 0; i < 3; i++)
+ for(j = 0; j <= i; j++)
+ mat[i][j]+=vec[i]*vec[j];
+ }
+
+// diagonal elements are copied twice!
+ for(i = 0; i < 3; i++)
+ for(j = 0; j <= i; j++){
+ gsl_matrix_set(matrix,i,j,mat[i][j]);
+ gsl_matrix_set(matrix,j,i,mat[i][j]);
+ }
+/*
+for(i = 0; i < 3; i++)
+ {
+ for(j = 0; j < 3; j++)
+ printf("%g ", gsl_matrix_get(matrix, i, j));
+ printf("\n");
+ }
+ printf("\n");
+*/
+ gsl_eigen_symm(matrix, eig, workspace);
+ gsl_sort_vector(eig);
+/* printf("** eigenvalues \n");
+ for(i = 0; i < 3; i++){
+ printf("%3d %25.17e\n", i, gsl_vector_get(eig, i));
+} */
+ *l1=gsl_vector_get(eig,0);
+ *l2=gsl_vector_get(eig,1);
+ *l3=gsl_vector_get(eig,2);
+
+ gsl_eigen_symm_free(workspace);
+ gsl_matrix_free(matrix);
+ gsl_vector_free(eig);
+}
+
+ts_ulong get_epoch(){
+ time_t currTime;
+ currTime = time(NULL);
+ return (ts_ulong)currTime;
+}
+
+ts_bool get_area_volume(ts_vesicle *vesicle, ts_double *area, ts_double *volume){
+ ts_uint i;
+ *volume=0.0;
+ *area=0.0;
+ for(i=0;i<vesicle->tlist->n;i++){
+ *volume+=vesicle->tlist->tria[i]->volume;
+ *area+=vesicle->tlist->tria[i]->area;
+ }
+ return TS_SUCCESS;
+}
diff --git a/src/stats.h b/src/stats.h
new file mode 100644
index 0000000..223a99b
--- /dev/null
+++ b/src/stats.h
@@ -0,0 +1,6 @@
+#ifndef _H_STATS
+#define _H_STATS
+void gyration_eigen(ts_vesicle *vesicle, ts_double *l1, ts_double *l2, ts_double *l3);
+ts_ulong get_epoch();
+ts_bool get_area_volume(ts_vesicle *vesicle, ts_double *area, ts_double *volume);
+#endif
diff --git a/src/timestep.c b/src/timestep.c
index c136d64..9ab60fd 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -8,59 +8,71 @@
#include "bondflip.h"
#include "frame.h"
#include "io.h"
-#include "gyration.h"
+#include "stats.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;
- ts_double l1,l2,l3;
+ ts_double l1,l2,l3,volume=0.0,area=0.0,vmsr,bfsr, vmsrt, bfsrt;
+ ts_ulong epochtime;
// char filename[255];
-
+ FILE *fd=fopen("statistics.csv","w");
+ if(fd==NULL){
+ fatal("Cannot open statistics.csv file for writing",1);
+ }
+ fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lmabda3\n");
centermass(vesicle);
cell_occupation(vesicle);
if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
for(i=start_iteration;i<inititer+iterations;i++){
+ vmsr=0.0;
+ bfsr=0.0;
for(j=0;j<mcsweeps;j++){
- single_timestep(vesicle);
+ single_timestep(vesicle, &vmsrt, &bfsrt);
+ vmsr+=vmsrt;
+ bfsr+=bfsrt;
}
+ vmsr/=(ts_double)mcsweeps;
+ bfsr/=(ts_double)mcsweeps;
centermass(vesicle);
cell_occupation(vesicle);
- gyration_eigen(vesicle, &l1, &l2, &l3);
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);
- write_master_xml_file("test.pvd");
-
+ write_master_xml_file("test.pvd");
+ epochtime=get_epoch();
+ gyration_eigen(vesicle, &l1, &l2, &l3);
+ get_area_volume(vesicle, &area,&volume);
+ fprintf(fd, "%lu %u %e %e %e %e %e %e %e\n",epochtime,i,vmsr,bfsr,volume, area,l1,l2,l3);
+
// sprintf(filename,"timestep-%05d.pov",i-inititer);
// write_pov_file(vesicle,filename);
}
}
+ fclose(fd);
return TS_SUCCESS;
}
-ts_bool single_timestep(ts_vesicle *vesicle){
+ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
ts_bool retval;
ts_double rnvec[3];
ts_uint i,j,b;
+ ts_uint vmsrcnt=0;
for(i=0;i<vesicle->vlist->n;i++){
rnvec[0]=drand48();
rnvec[1]=drand48();
rnvec[2]=drand48();
retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
+ if(retval==TS_SUCCESS) vmsrcnt++;
}
-// ts_int cnt=0;
+ ts_int bfsrcnt=0;
for(i=0;i<3*vesicle->vlist->n;i++){
-//why is rnvec needed in bondflip?
-/* rnvec[0]=drand48();
- rnvec[1]=drand48();
- rnvec[2]=drand48();
-*/
b=rand() % vesicle->blist->n;
//find a bond and return a pointer to a bond...
//call single_bondflip_timestep...
retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
-// if(retval==TS_SUCCESS) cnt++;
+ if(retval==TS_SUCCESS) bfsrcnt++;
}
for(i=0;i<vesicle->poly_list->n;i++){
@@ -84,7 +96,8 @@
// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
- if(retval);
+ *vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
+ *bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
return TS_SUCCESS;
}
diff --git a/src/timestep.h b/src/timestep.h
index dd18481..0d8dc74 100644
--- a/src/timestep.h
+++ b/src/timestep.h
@@ -1,5 +1,5 @@
#ifndef _TIMESTEP_H
#define _TIMESTEP_H
-ts_bool single_timestep(ts_vesicle *vesicle);
+ts_bool single_timestep(ts_vesicle *vesicle, ts_double *vmsr, ts_double *bfsr);
ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_simulation);
#endif
--
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