SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
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. More...
 
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. More...
 
subroutine fit_msd_by_regions (input, nb_region, dt, b_trans, io_dt)
 Fit the MSD graph. More...
 
subroutine fit_msd_derivative (input, D_COEFF, shift_step, array_limit)
 Fit the derivative of the MSD. 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


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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