mod_residencetime Module Reference

residence time and rdf statistics More...

Data Types
type	residence_time
	Arrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm. More...

Functions/Subroutines
subroutine	init_resid_time (this, fixe_bin_size, enum_str, format_resid3d, b_pair, nb_type)
	Initialize the instance. More...
subroutine	delete_resid_time (this)
	Delete arrays. More...
subroutine	copy_resid_time (this, new_rt, new_enum_rt)
	Not a real copy, data are modified when we want to create a 2D or a 1D form a 3D reisdence_time. More...
subroutine	set_array_rt (this, geom_resid, nb_xcell, nb_ycell, nb_zcell, xcell, ycell, zcell)
	Set grid parameters. More...
subroutine	set_array_rt_sdamm (this, geom_resid, nb_type, nb_xcell, nb_ycell, nb_zcell, xcell, ycell, zcell)
	Similar to set_array_rt but only for sdamm. More...
subroutine	apply_shift_to_rt (this, shift_x, shift_y, shift_z)
	Shift the origin of the residence_time grid. More...
subroutine	update_residence_time (this, pos_prot, dist, dtnow)
	Update residence_time. More...
subroutine	update_rdf (this, dist, type1, type2)
	Update the radial distribution function. More...
recursive integer function	print_residence_time (this, geom_resid, nrun)
	Print final residence_time. More...
subroutine	print_rdf (this, tab_protein, geom_resid, n_rdfs)
	Normalize and print radial distribution functions in RDF.log. More...
subroutine	write_resid_3d (this, shift_center)
	Write the 3d reisdence time grid to UHBD format. More...

Variables
integer, parameter	rt_off = 1
integer, parameter	rt_distance = 2
integer, parameter	rt_plan = 3
integer, parameter	rt_resid3d = 4

Detailed Description

residence time and rdf statistics

Function/Subroutine Documentation

apply_shift_to_rt()

subroutine mod_residencetime::apply_shift_to_rt	(	type ( residence_time )	this,
		real ( kind=4 )	shift_x,
		real ( kind=4 )	shift_y,
		real ( kind=4 )	shift_z
	)

Shift the origin of the residence_time grid.

Apply only to resid3d ??

Parameters

this	: instance of residence_time
shift_x,shift_y,shift_z	: shift to apply to the origin

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copy_resid_time()

subroutine mod_residencetime::copy_resid_time	(	type ( residence_time )	this,
		type ( residence_time )	new_rt,
		integer	new_enum_rt
	)

Not a real copy, data are modified when we want to create a 2D or a 1D form a 3D reisdence_time.

Only valable when resid3d and called by print_resid_time, NOT general
only to use if this == resid_3d, want to produce new_rt as distance or plan residence time

Parameters

this	: instance of residence_time, source of the copy
new_rt	: instance of residence_time, target of the copy
new_enum_rt	: type of the new_rt residence_time ( "plan" or "distance" )

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delete_resid_time()

subroutine mod_residencetime::delete_resid_time

(

type ( residence_time )

this

)

Delete arrays.

Parameters

this	: instance of residence_time

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init_resid_time()

subroutine mod_residencetime::init_resid_time	(	type ( residence_time )	this,
		integer, intent(in)	fixe_bin_size,
		character, dimension(*), intent(in)	enum_str,
		integer, intent(in)	format_resid3d,
		logical, intent(in)	b_pair,
		integer, intent(in)	nb_type
	)

Initialize the instance.

Parameters

this	: instance of residence_time
fixe_bin_size	: if the size of the bin is fixed
enum_str	: "off" / "distance" / "plan" / "resid_3d"
format_resid3d	: ascii or binary for the output of the grid
b_pair	: if more than type of solute is present in sdamm
nb_type	: number of different type of solutes in sdamm, will set the number of pairs ( ( nb_type * ( nb_type + 1 ) ) / 2 )

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print_rdf()

subroutine mod_residencetime::print_rdf	(	type ( residence_time ), target	this,
		type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom_resid,
		integer	n_rdfs
	)

Normalize and print radial distribution functions in RDF.log.

Parameters

this	: instance of residence_time
tab_protein	: instance array_protein_type
geom_resid	: instance of geometry
n_rdfs	: number of radial distribution functions

print_residence_time()

recursive integer function mod_residencetime::print_residence_time	(	type ( residence_time )	this,
		type ( geometry ), intent(in)	geom_resid,
		integer	nrun
	)

Print final residence_time.

Use recursive function : if the 3d residence time has been computed, 2d and 1d will be computed and printed

Parameters

this	: instance residence_time
geom_resid	: instance of geometry
nrun	: total number of runs, used for the normalization

Returns

status : error status

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set_array_rt()

subroutine mod_residencetime::set_array_rt	(	type ( residence_time )	this,
		type ( geometry ), intent(in)	geom_resid,
		integer, intent(in)	nb_xcell,
		integer, intent(in)	nb_ycell,
		integer, intent(in)	nb_zcell,
		real ( kind=4 ), intent(in)	xcell,
		real ( kind=4 ), intent(in)	ycell,
		real ( kind=4 ), intent(in)	zcell
	)

Set grid parameters.

Can specify the size of the cells or the number of cells for each axis or both
But it is an UHBD format which accepts only a fixed cell spacing for all 3 dimensions
The grid can be produced correctly, but not visualized in VMD

Modified origin, for the shift a grid spacing is missing

Parameters

this	: instance of residence_time
geom_resid	: instance of geometry
nb_xcell,nb_ycell,nb_zcell	: number of cell for each axis
xcell,ycell,zcell	: size of the cells for each axis

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set_array_rt_sdamm()

subroutine mod_residencetime::set_array_rt_sdamm	(	type ( residence_time )	this,
		type ( geometry ), intent(in)	geom_resid,
		integer, intent(in)	nb_type,
		integer, intent(in)	nb_xcell,
		integer, intent(in)	nb_ycell,
		integer, intent(in)	nb_zcell,
		real ( kind=4 ), intent(in)	xcell,
		real ( kind=4 ), intent(in)	ycell,
		real ( kind=4 ), intent(in)	zcell
	)

Similar to set_array_rt but only for sdamm.

Additionaly allocate the array for the radial distribution functions

Parameters

this	: instance of residence_time
geom_resid	: instance of geometry
nb_type	: number of different type of solutes, needed for rdf
nb_xcell,nb_ycell,nb_zcell	: number of cell for each axis
xcell,ycell,zcell	: size of the cells for each axis

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update_rdf()

subroutine mod_residencetime::update_rdf	(	type ( residence_time )	this,
		real ( kind=8 ), intent(in)	dist,
		integer	type1,
		integer	type2
	)

Update the radial distribution function.

Only used with sdamm

Parameters

this	: instance of residence_time
dist	: distance between the 2 solutes
type1,type2	: type of the solutes

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update_residence_time()

subroutine mod_residencetime::update_residence_time	(	type ( residence_time )	this,
		real ( kind=8 ), dimension ( 3 )	pos_prot,
		real ( kind=4 )	dist,
		real ( kind=8 )	dtnow
	)

Update residence_time.

Only used by sda_2proteins
Update all arrays, done every steps in sda_2proteins
This function must be thread-safe

Parameters

this	: instance of residence_time
pos_prot	: position of one solute
dist	: distance, used only for sda_2proteins
dtnow	: current value of the timestep ( variable for sda_2proteins )

write_resid_3d()

subroutine mod_residencetime::write_resid_3d	(	type ( residence_time ), target	this,
		real ( kind=8 ), dimension(3)	shift_center
	)

Write the 3d reisdence time grid to UHBD format.

Need to shift to the center of the solute 1 for visualisation

Parameters

this	: instance of residence_time
shift_center	: center of solute 1 ?

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Variable Documentation

rt_distance

integer, parameter mod_residencetime::rt_distance = 2

rt_off

integer, parameter mod_residencetime::rt_off = 1

rt_plan

integer, parameter mod_residencetime::rt_plan = 3

rt_resid3d

integer, parameter mod_residencetime::rt_resid3d = 4