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