rdf.f90 File Reference

Compute the radial distribution function. More...

Functions/Subroutines
program	rdf
	Program rdf. More...
subroutine	calc_frame_rdf (rdf_hist, position, start_centre, end_centre, start_dist, end_dist, box_dim)
	Calculate the rdf of a single trajectory frame. More...
subroutine	normalise_rdf (unnormalised_rdf, normalised_rdf, counter, nb_centre, dens)
	Normalise radial distribution function. More...
subroutine	virial (rdf_hist, virial_integral, rdf_integral)
	Subroutine find osmotic second virial coefficients by integration of RDF. More...
subroutine	write_rdf_log (log_fileno, rdf_hist, virial_int, rdf_int)
	Subroutine to write normalised RDF to file. More...

Detailed Description

Compute the radial distribution function.

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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Function/Subroutine Documentation

calc_frame_rdf()

subroutine calc_frame_rdf	(	type(type_int_hist), intent(inout)	rdf_hist,
		real(kind=8), dimension(:,:), intent(in)	position,
		integer, intent(in)	start_centre,
		integer, intent(in)	end_centre,
		integer, intent(in)	start_dist,
		integer, intent(in)	end_dist,
		real(kind=8), dimension(3), intent(in)	box_dim
	)

Calculate the rdf of a single trajectory frame.

Parameters

rdf_hist	: instance of mod_histogram::type_int_hist used to store RDF
tab_prot	: array to store the positions of all solutes in current frame
start_centre	: Index to first solute of central type
end_centre	: Index to last solute of central type
start_dist	: Index to first solute of distribution type
end_dist	: Index to last solute of distribution type
box_dim	: Array to store xyz box dimensions

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normalise_rdf()

subroutine normalise_rdf	(	type(type_int_hist), intent(in)	unnormalised_rdf,
		type(type_real_hist), intent(out)	normalised_rdf,
		integer, intent(in)	counter,
		integer, intent(in)	nb_centre,
		real(kind=8), intent(in)	dens
	)

Normalise radial distribution function.

Parameters

unnormalised_rdf	: mod_histogram::type_int_hist instance used to store input RDF
normalised_rdf	: mod_histogram::type_real_hist instance used to store normalised output RDF
counter	: Number of frames used in generating distribution
nb_centre	: Number of central solutes used to create distribution
protein_array	: Needed to calculate number density of each solute

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virial()

subroutine virial	(	type(type_real_hist), intent(in)	rdf_hist,
		real(kind=8), intent(out)	virial_integral,
		real(kind=8), intent(out)	rdf_integral
	)

Subroutine find osmotic second virial coefficients by integration of RDF.

Parameters

rdf_hist	: normalised real RDF histogram
virial_integral	: integral \( \int \left( g\left(r\right) - 1\right)r^2 \textrm{d}r \) over histogram length
rdf_integral	: integral \( \int \left( g\left(r\right) - 1\right) \textrm{d}r \) over histogram length

Integrates bins by midpoint rectangular quadrature

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write_rdf_log()

subroutine write_rdf_log	(	integer, intent(in)	log_fileno,
		type(type_real_hist), intent(in)	rdf_hist,
		real(kind=8), intent(in)	virial_int,
		real(kind=8), intent(in)	rdf_int
	)

Subroutine to write normalised RDF to file.

Parameters

log_fileno	: File number to write log file. File already opened in calling routine
rdf_hist	: Normalised RDF stored in mod_histogram::type_real_hist instance

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