rot_diffusion.f90 File Reference

Functions/Subroutines
program	rot_diffusion
	Program rot_diffusion. More...
subroutine	all_acf_rotation (orient_axis, tab_prot, ACF, nchunks, b_type, value_type)
	Compute all autocorrelation function of rotation. More...
subroutine	all_msd_rotation (orient_axis, tab_prot, ACF, nchunks, b_type, value_type, nb_region, dt, io_msd)
	This method uses rotational mean square displacement ( rmsd ) computed with a trick from above reference. More...
subroutine	autocorrelation_orient (input_data, output_data, size_input)
	Make autocorrelation of the orientation, simplest form. More...
subroutine	rmsd_orient (input_data, output_data, dt)
	Different implementation, as an usual msd ( 2 loops over t ) dt only needed in check, could be deleted. More...
subroutine	print_acfrot_sdamm (ACF, time_snapshot, b_type, value_type, io_acf)
	Version with output similar to sdamm, need to produce more files. More...

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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Compute the autocorrelation function of the rotation and the rotational diffusion coefficients

Function/Subroutine Documentation

all_acf_rotation()

subroutine all_acf_rotation	(	real ( kind=8 ), dimension (:,:,:,:)	orient_axis,
		type ( array_protein_type )	tab_prot,
		real ( kind=8 ), dimension (:,:,:), allocatable	ACF,
		integer	nchunks,
		logical	b_type,
		integer	value_type
	)

Compute all autocorrelation function of rotation.

Can deal with splitting the trajectory with nchunks

Parameters

orient_axis	: array containing the orientation of the solute during the trajectory
tab_prot	: instance of array_protein_type
ACF	: return, autocorrelation functions
nchunks	: how many parts the simulation is splitted
b_type	: logical, compute for different type of proteins if .true.
value_type	: if 0 compute for all proteins AND for all types of proteins, if > 0 compute only for this type could improve, read in orient_axis only for this type and forget about this argument

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all_msd_rotation()

subroutine all_msd_rotation	(	real ( kind=8 ), dimension (:,:,:,:), intent(in)	orient_axis,
		type ( array_protein_type ), intent(in)	tab_prot,
		real ( kind=8 ), dimension (:,:,:), allocatable	ACF,
		integer, intent(in)	nchunks,
		logical, intent(in)	b_type,
		integer, intent(in)	value_type,
		integer, intent(in)	nb_region,
		real ( kind=4 ), intent(in)	dt,
		integer, intent(in)	io_msd
	)

This method uses rotational mean square displacement ( rmsd ) computed with a trick from above reference.

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autocorrelation_orient()

subroutine autocorrelation_orient	(	real ( kind=8 ), dimension (:,:,:,:), intent(in)	input_data,
		real ( kind=8 ), dimension (:), intent(out)	output_data,
		integer, intent(in)	size_input
	)

Make autocorrelation of the orientation, simplest form.

Version using the maximum number of data points
Large tau have a poor statistic
Here can use OpenMP

Parameters

input_data	: trajectory of the orientation
output_data	: return, 1 dimensional autocorrelation function
size_input	: size of input

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print_acfrot_sdamm()

subroutine print_acfrot_sdamm	(	real ( kind=8 ), dimension (:,:,:)	ACF,
		real (kind=4)	time_snapshot,
		logical	b_type,
		integer	value_type,
		integer	io_acf
	)

Version with output similar to sdamm, need to produce more files.

For use with octave script

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rmsd_orient()

subroutine rmsd_orient	(	real ( kind=8 ), dimension (:,:,:,:), intent(in)	input_data,
		real ( kind=8 ), dimension (:), intent(out)	output_data,
		real ( kind=4 ), intent(in)	dt
	)

Different implementation, as an usual msd ( 2 loops over t ) dt only needed in check, could be deleted.

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