utils_diffusion.f90 File Reference

Functions/Subroutines
subroutine	print_acf (acf, time_snapshot, b_type, value_type, title)
	General function for printing ACFs type, in a single file.
subroutine	print_coeffd_msd (d_coeff, region_fit, b_type, value_type, dt, b_trans, b_deriv, io_msd)
	Print coefficient from the msd fit method.
subroutine	fit_msd_by_regions (input, nb_region, dt, b_trans, io_dt)
	Fit the MSD graph.
subroutine	fit_msd_derivative (input, d_coeff, shift_step, array_limit)
	Fit the derivative of the MSD.

Detailed Description

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade

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Common functions used by diffusion program tools

Function/Subroutine Documentation

fit_msd_by_regions()

subroutine fit_msd_by_regions	(	real ( kind=8 ), dimension(:), intent(in)	input,
		integer, intent(in)	nb_region,
		real ( kind=4 ), intent(in)	dt,
		logical, intent(in)	b_trans,
		integer, intent(in)	io_dt
	)

Fit the MSD graph.

Parameters

input	: 1 dimension array
nb_region	: how many blocks are divided
dt	: time between each frame
io_dt	: file unit of the output file. Should be opened / close by calller
b_trans	: parameter trans / rot for factor 4 or 6

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fit_msd_derivative()

subroutine fit_msd_derivative	(	real ( kind=8 ), dimension(:), intent(in)	input,
		real ( kind=8 ), dimension(4)	d_coeff,
		integer	shift_step,
		integer, dimension(4)	array_limit
	)

Fit the derivative of the MSD.

Different method
To add array for storing limit of fit, will be easier to print out

Parameters

input	: 1D array with values to fit
D_COEFF	: array to store the results
shift_step	: ??
array_limit	: store the fitted region

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print_acf()

subroutine print_acf	(	real ( kind=8 ), dimension (:,:,:), intent(in)	acf,
		real ( kind=4 ), intent(in)	time_snapshot,
		logical, intent(in)	b_type,
		integer, intent(in)	value_type,
		character, dimension(*), intent(in)	title
	)

General function for printing ACFs type, in a single file.

Parameters

ACF	: 3 diemsional array for autocorrelation function ( "x,y,z", protein_nb, time )
time_snapshot	: timestep between the frames
b_type	: if true, there is different types of solutes in the simulation
value_type	: indicates which type if b_type is true
title	: filename for the output

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print_coeffd_msd()

subroutine print_coeffd_msd	(	real ( kind=8 ), dimension (:,:,:)	d_coeff,
		integer, dimension(:,:)	region_fit,
		logical	b_type,
		integer	value_type,
		real ( kind=4 )	dt,
		logical	b_trans,
		logical	b_deriv,
		integer	io_msd
	)

Print coefficient from the msd fit method.

Give io_msd to append the data to the main log file

Parameters

D_COEFF	: contains the computed values
region_fit	: info about the fitting
b_type	: if true, there is different types of solutes in the simulation
value_type	: indicates which type if b_type is true
dt	: timestep
b_trans	: true if translation, false rotation
b_deriv	: true if exact derivation, false simplified derivative ( MSD/time )
io_msd	: file descriptor

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