autocorr.cpp File Reference

#include "gmxpre.h"
#include "autocorr.h"
#include <cmath>
#include <cstdio>
#include <cstring>
#include <algorithm>
#include "gromacs/correlationfunctions/expfit.h"
#include "gromacs/correlationfunctions/integrate.h"
#include "gromacs/correlationfunctions/manyautocorrelation.h"
#include "gromacs/correlationfunctions/polynomials.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"

Include dependency graph for autocorr.cpp:

Description

Implements function to compute many autocorrelation functions.

Author

David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se

Macros
#define	MODE(x)   ((mode & (x)) == (x))
	Shortcut macro to select modes.

Enumerations
enum	{ enNorm, enCos, enSin }

Functions
static void	low_do_four_core (int nframes, real c1[], real cfour[], int nCos)
	Routine to compute ACF using FFT.
static void	do_ac_core (int nframes, int nout, real corr[], real c1[], int nrestart, unsigned long mode)
	Routine to comput ACF without FFT.
static void	normalize_acf (int nout, real corr[])
	Routine to normalize ACF, dividing by corr[0].
static void	average_acf (gmx_bool bVerbose, int n, int nitem, real **c1)
	Routine that averages ACFs.
static void	norm_and_scale_vectors (int nframes, real c1[], real scale)
	Normalize ACFs.
static void	dump_tmp (char *s, int n, real c[])
	Debugging.
static void	do_four_core (unsigned long mode, int nframes, real c1[], real csum[], real ctmp[])
	High level ACF routine.
void	low_do_autocorr (const char *fn, const gmx_output_env_t *oenv, const char *title, int nframes, int nitem, int nout, real **c1, real dt, unsigned long mode, int nrestart, gmx_bool bAver, gmx_bool bNormalize, gmx_bool bVerbose, real tbeginfit, real tendfit, int eFitFn)
	Low level computation of autocorrelation functions. More...
t_pargs *	add_acf_pargs (int *npargs, t_pargs *pa)
	Add commandline arguments related to autocorrelations to the existing array. *npargs must be initialised to the number of elements in pa, it will be incremented appropriately. More...
void	do_autocorr (const char *fn, const gmx_output_env_t *oenv, const char *title, int nframes, int nitem, real **c1, real dt, unsigned long mode, gmx_bool bAver)
	Calls low_do_autocorr (see below). add_acf_pargs has to be called before this can be used. More...
int	get_acfnout ()
	Returns the number of points to output from a correlation function. Works only AFTER do_auto_corr has been called! More...
int	get_acffitfn ()
	Returns the fitting function selected. Works only AFTER do_auto_corr has been called! More...

Variables
static gmx_bool	bACFinit = false
	Global variable set true if initialization routines are called.
static t_acf	acf
	Data structure for storing command line variables.
static const char *	Leg [] = { nullptr, "0", "1", "2", "3", nullptr }
	Legend for selecting Legendre polynomials.

Function Documentation

t_pargs* add_acf_pargs	(	int *	npargs,
		t_pargs *	pa
	)

Add commandline arguments related to autocorrelations to the existing array. *npargs must be initialised to the number of elements in pa, it will be incremented appropriately.

Parameters

	npargs	The number of arguments before and after (is changed in this function)
[in]	pa	The initial argument list

Returns

the new array

void do_autocorr	(	const char *	fn,
		const gmx_output_env_t *	oenv,
		const char *	title,
		int	nframes,
		int	nitem,
		real **	c1,
		real	dt,
		unsigned long	mode,
		gmx_bool	bAver
	)

Calls low_do_autocorr (see below). add_acf_pargs has to be called before this can be used.

Parameters

[in]	fn	File name for xvg output (may this be NULL)?
[in]	oenv	The output environment information
[in]	title	is the title in the output file
[in]	nframes	is the number of frames in the time series
[in]	nitem	is the number of items
[in,out]	c1	is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ] on output, this array is filled with the correlation function to reduce storage
[in]	dt	is the time between frames
[in]	mode	Different types of ACF can be done, see above
[in]	bAver	If set, all ndih C(t) functions are averaged into a single C(t)

int get_acffitfn

(

)

Returns the fitting function selected. Works only AFTER do_auto_corr has been called!

Returns

the fit function type.

int get_acfnout

(

)

Returns the number of points to output from a correlation function. Works only AFTER do_auto_corr has been called!

Returns

the output length for the correlation function

void low_do_autocorr	(	const char *	fn,
		const gmx_output_env_t *	oenv,
		const char *	title,
		int	nframes,
		int	nitem,
		int	nout,
		real **	c1,
		real	dt,
		unsigned long	mode,
		int	nrestart,
		gmx_bool	bAver,
		gmx_bool	bNormalize,
		gmx_bool	bVerbose,
		real	tbeginfit,
		real	tendfit,
		int	nfitparm
	)

Low level computation of autocorrelation functions.

do_autocorr calculates autocorrelation functions for many things. It takes a 2 d array containing nitem arrays of length nframes for each item the ACF is calculated.

A number of "modes" exist for computation of the ACF controlled by variable mode, with the following meaning.

Mode	Function
eacNormal	C(t) = < X (tau) * X (tau+t) >
eacCos	C(t) = < cos (X(tau) - X(tau+t)) >
eacIden	C(t) = < (X(tau) == X(tau+t)) > (not fully supported yet)
eacVector	C(t) = < X(tau) * X(tau+t)
eacP1	C(t) = < cos (X(tau) * X(tau+t) >
eacP2	C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
eacRcross	C(t) = < ( X(tau) * X(tau+t) )^2 >

For modes eacVector, eacP1, eacP2 and eacRcross the input should be 3 x nframes long, where each triplet is taken as a 3D vector

For mode eacCos inputdata must be in radians, not degrees!

Other parameters are:

Parameters

[in]	fn	is output filename (.xvg) where the correlation function(s) are printed
[in]	oenv	controls output file properties
[in]	title	is the title in the output file
[in]	nframes	is the number of frames in the time series
[in]	nitem	is the number of items
[in]	nout
[in,out]	c1	is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ] on output, this array is filled with the correlation function to reduce storage
[in]	dt	is the time between frames
[in]	mode	Different types of ACF can be done, see above
[in]	nrestart	is the number of steps between restarts for direct ACFs (i.e. without FFT) When set to 1 all points are used as time origin for averaging
[in]	bAver	If set, all ndih C(t) functions are averaged into a single C(t)
[in]	bNormalize	If set, all ACFs will be normalized to start at 0
[in]	bVerbose	If set output to console will be generated
[in]	tbeginfit	Time to start fitting to the ACF
[in]	tendfit	Time to end fitting to the ACF
[in]	nfitparm	Number of fitting parameters in a multi-exponential fit