diffusion_calc.f90 File Reference

Functions/Subroutines
program	diffusion_calc
	Program diffusion_calc. More...
subroutine	calculate_trans_msd (incoords, msd, max_steps, binned, bin_width, bin_offset, decomp, msd_decomp)
	Read in all coordinates and calculate the translational MSD. More...
subroutine	calculate_rot_msd (inorient, msd, max_steps, inheight, binned, bin_width, bin_offset)
	Read in all orientations and calculate the unbounded rotational MSD – See Mazza et al Phys. Rev. E (2007), 76, 031203. More...
subroutine	calculate_rot_acf (inorient, acf, max_steps, inheight, binned, bin_width, bin_offset)
	Read in all orientations and calculate the rotational autocorrelation function. More...
subroutine	write_function (io_data, funct, interval, binned, bin_width, bin_offset, desc)

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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Function/Subroutine Documentation

calculate_rot_acf()

subroutine calculate_rot_acf	(	real(kind=8), dimension(:,:,:,:), intent(in)	inorient,
		real(kind=8), dimension(:,:), intent(out)	acf,
		integer, intent(in)	max_steps,
		real(kind=8), dimension(:,:), intent(in)	inheight,
		logical	binned,
		real(kind=8), intent(in)	bin_width,
		real(kind=8), intent(in)	bin_offset
	)

Read in all orientations and calculate the rotational autocorrelation function.

Parameters

inorient	:: 4D array containing coordinates of each solute in each frame. Order (axis, axis vector, solute, frame)
msd	:: 2D array for storing the ACF, allows height binning. Order (msd,bin) – MUST BE ALLOCATED IN CALLER
max_steps	:: number of frames in the largest time interval over which ACF is calculated
inheight	:: 2D vector giving the height of each solute in each frame. Needed for binning
binned	:: is the ACF to be binned in z dimension
bin_width	:: If binning data in z, what is the width in Ang of the bins
bin_offset	:: If binning data in z, at what height does the first bin begin

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calculate_rot_msd()

subroutine calculate_rot_msd	(	real(kind=8), dimension(:,:,:,:), intent(in)	inorient,
		real(kind=8), dimension(:,:), intent(out)	msd,
		integer, intent(in)	max_steps,
		real(kind=8), dimension(:,:), intent(in)	inheight,
		logical	binned,
		real(kind=8), intent(in)	bin_width,
		real(kind=8), intent(in)	bin_offset
	)

Read in all orientations and calculate the unbounded rotational MSD – See Mazza et al Phys. Rev. E (2007), 76, 031203.

Uses z axis vector as principle axis

Parameters

inorient	:: 4D array containing coordinates of each solute in each frame. Order (axis, axis vector, solute, frame)
msd	:: 2D array for storing the MSD, allows height binning. Order (msd,bin) – MUST BE ALLOCATED IN CALLER
max_steps	:: number of frames in the largest time interval over which MSD is calculated
inheight	:: 2D vector giving the height of each solute in each frame. Needed for binning
binned	:: is the MSD to be binned in z dimension
bin_width	:: If binning data in z, what is the width in Ang of the bins
bin_offset	:: If binning data in z, at what height does the first bin begin

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calculate_trans_msd()

subroutine calculate_trans_msd	(	real(kind=8), dimension(:,:,:), intent(in)	incoords,
		real(kind=8), dimension(:,:), intent(out)	msd,
		integer, intent(in)	max_steps,
		logical	binned,
		real(kind=8), intent(in)	bin_width,
		real(kind=8), intent(in)	bin_offset,
		logical	decomp,
		real(kind=8), dimension(:,:,:), intent(out)	msd_decomp
	)

Read in all coordinates and calculate the translational MSD.

Parameters

incoords	:: 3D array containing coordinates of each solute in each frame. Order (x/y/z, solute, frame)
msd	:: 2D array for storing the MSD, allows height binning. Order (msd,bin) – MUST BE ALLOCATED IN CALLER
max_steps	:: number of frames in the largest time interval over which MSD is calculated
binned	:: is the MSD to be binned in z dimension
bin_width	:: If binning data in z, what is the width in Ang of the bins
bin_offset	:: If binning data in z, at what height does the first bin begin
decomp	:: Should diffusion be decomposed into 1D diffusion in z, and 2D diffusion in xy
msd_decomp	:: 3D array for storing the decomposed MSD, allows height binning. Order ([xy,z],msd,bin) – MUST BE ALLOCATED IN CALLER

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write_function()

subroutine write_function	(	integer, intent(in)	io_data,
		real(kind=8), dimension(:,:), intent(in)	funct,
		real(kind=8), intent(in)	interval,
		logical, intent(in)	binned,
		real(kind=8), intent(in)	bin_width,
		real(kind=8), intent(in)	bin_offset,
		character(76), intent(in)	desc
	)

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