mod_rate_calculation Module Reference

Define type association_rate. More...

Data Types
type	association_rate
	General type used storing statistics about the runs. More...

Functions/Subroutines
subroutine	deallocate_rate_association (this)
	Delete arrays and reinitialize data members. More...
subroutine	update_escape (this, nb_traj, visited_windows, escape, sum_time, first_time)
	Update the arrays after each trajectory. More...
subroutine	allocate_rate_association (this, first_window, nb_window, width_window, nb_contact, bsurf, csurf, dm, ibootsp, ifpt, iboot_et, stop_traj, anal_corr, dh_rad_sum, real_net_charge_product, ionic)
	Initialize association_rate and allocate arrays. More...
subroutine	calc_rate_corr (brate, crate, bsurf, csurf, dh_rad_sum, real_net_charge_product, ionic, dm)
subroutine	write_boot_file (this, total_run)
	Write the bootstrap output files. More...
subroutine	print_table_rate (this, total_run, opt_koff)
	Print final results, could be used for restart or checkpoint. More...
subroutine	print_sumtime (this, norm)
	Print only the array_sumtime, implemented for sdamm and association_rate. More...

Detailed Description

Define type association_rate.

Used only with sda_2proteins

Function/Subroutine Documentation

allocate_rate_association()

subroutine mod_rate_calculation::allocate_rate_association	(	type ( association_rate )	this,
		real ( kind=4 ), intent(in)	first_window,
		integer, intent(in)	nb_window,
		real ( kind=4 ), intent(in)	width_window,
		integer, intent(in)	nb_contact,
		real ( kind=4 ), intent(in)	bsurf,
		real ( kind=4 ), intent(in)	csurf,
		real ( kind=8 ), intent(in)	dm,
		logical	ibootsp,
		logical	ifpt,
		logical	iboot_et,
		logical	stop_traj,
		logical	anal_corr,
		real ( kind=8 ), intent(in)	dh_rad_sum,
		real ( kind=8 ), intent(in)	real_net_charge_product,
		real ( kind=4 ), intent(in)	ionic
	)

Initialize association_rate and allocate arrays.

dm need to be the sum of the diffusion coeff.

Parameters

this	: instance of association_rate
first_window	: distance of the first window, in Angstrom
nb_window	: number of windows
width_window	: width of each window
nb_contact	: number of contacts to record, from 1 to nb_contact included
bsurf,csurf	: values of the b and c surface
dm	: use the sum of the diffusion terms, absolute trans. diff. coeff.
ibootsp,ifpt,iboot_et	: file descriptor for the bootstrap output files
stop_traj	: should trajectory end when most strict reaction criteria met
anal_corr	: should analytical correction be applied to account for interactions at b surface
dh_rad_sum	: sum of Debye-Hueckel cavity radii of two solutes
real_net_charge_product	: product of net charge of two solutes
ionic	: ionic strength

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calc_rate_corr()

subroutine mod_rate_calculation::calc_rate_corr	(	real(kind=8), intent(out)	brate,
		real(kind=8), intent(out)	crate,
		real(kind=4), intent(in)	bsurf,
		real(kind=4), intent(in)	csurf,
		real(kind=8), intent(in)	dh_rad_sum,
		real(kind=8), intent(in)	real_net_charge_product,
		real(kind=4), intent(in)	ionic,
		real(kind=8), intent(in)	dm
	)

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deallocate_rate_association()

subroutine mod_rate_calculation::deallocate_rate_association

(

type ( association_rate )

this

)

Delete arrays and reinitialize data members.

Parameters

this	: instance of association_rate

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print_sumtime()

subroutine mod_rate_calculation::print_sumtime	(	type ( association_rate )	this,
		real ( kind=4 )	norm
	)

Print only the array_sumtime, implemented for sdamm and association_rate.

Parameters

this	: instance of association_rate
norm	: normalisation factor

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print_table_rate()

subroutine mod_rate_calculation::print_table_rate	(	type ( association_rate )	this,
		integer	total_run,
		logical, optional	opt_koff
	)

Print final results, could be used for restart or checkpoint.

Print data in the main output file
opt_koff, will not print the rate, does not make sense
if sda_2proteins, print all

Parameters

this	: instance of association_rate
total_run	: total number of runs
opt_koff	: optionaly print association rates

update_escape()

subroutine mod_rate_calculation::update_escape	(	type ( association_rate )	this,
		integer, intent(in)	nb_traj,
		integer, dimension(:), intent(in)	visited_windows,
		real ( kind=8 ), dimension(:,:), intent(in)	escape,
		real ( kind=4 ), dimension (:,:), intent(in)	sum_time,
		real ( kind=4 ), dimension (:,:), intent(in)	first_time
	)

Update the arrays after each trajectory.

Update all arrays at the end of trajectories
Function is thread-safe, with the use of ATOMIC sections minimum overhead.

Parameters

this	: instance of association_rate
nb_traj	: the total number of trajectories
visited_windows	: array for association rate ( version with 4 integers )
escape	: array for electron transfert, cannot anymore share the format with association rate
sum_time,first_time	: external arrays belonging to each thread for updating global sumtime and firstime

write_boot_file()

subroutine mod_rate_calculation::write_boot_file	(	type ( association_rate )	this,
		integer	total_run
	)

Write the bootstrap output files.

Call only at the end of the computation,

Parameters

this	: instance of association_rate
total_run	: the total number of runs really done (case of intercepted signal)