added statistics output to the outer loop

Samo Penic

2014-04-07 37d14a0a50ed40f536cc3821b3584552e1b75c5c

added statistics output to the outer loop

 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

 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);
    }    

 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);

 src/stats.c

New file
@@ -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;
} 

 src/stats.h

New file
@@ -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

 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;
}


 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