mod_analytic Module Reference

Analytical expressions, store energy and force in precomputed array. More...

Data Types
type	analytic
	Define tyoe analytic interactions (Debye-Huckel/crowders). More...

Functions/Subroutines
subroutine	allocate_analytic (this)
	Allocate the object with default values, arrays filled by param_force_energy:init_analytic when all data (cutoff,..) are known.
subroutine	deallocate_analytic (this)
	Deallocate all analytic arrays. .
subroutine	set_analytic_params (this, h, max_size, epfct, dh_radius, vol_radius, rep_radius, surface_charge_dens, surf_prefct, gouy_chapman)
	fill the arrays, here need to setup dimension
subroutine	set_dh_params (this, opt_ionic)
	Initialize debye-huckel parameters.
subroutine	fill_array_dh (this, list_dh_radius)
subroutine	set_zeroes (this, cutoff)
	Specific to Debye-Huckel set zero for at distance where the grid is available Allow to call normal electrostatic and debye-huckel without taking care (hopefully).
real(kind=8) function	get_energy_analytic (this, bin, type_nb)
	Return precomputed energy values.
real(kind=8) function	get_force_analytic (this, bin, type_nb)
	Return precomputed force values.
real(kind=8) function	get_force_analytic_hom_charged_surf (this, bin, type_nb)
subroutine	print_analytic (this)
	Print values of array force and energy. Called by info_analytic.
subroutine	info_analytic (this, opt_print)
	Print info about analytical grids.
subroutine	print_analytic_external (this)
subroutine	print_analytic_external_hom_charged_surf (this)
subroutine	fill_array_rep (this, list_rep_radius, rep_bfct)
	Precompute values of the spherical repulsion array.

Detailed Description

Analytical expressions, store energy and force in precomputed array.

Todo

Extend to the case of a surface

Function/Subroutine Documentation

allocate_analytic()

subroutine mod_analytic::allocate_analytic

(

type ( analytic )

this

)

Allocate the object with default values, arrays filled by param_force_energy:init_analytic when all data (cutoff,..) are known.

Parameters

this	: instance of mod_analytic

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deallocate_analytic()

subroutine mod_analytic::deallocate_analytic

(

type ( analytic )

this

)

Deallocate all analytic arrays.
.

Parameters

this	: instance of mod_analytic

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fill_array_dh()

subroutine mod_analytic::fill_array_dh	(	type ( analytic )	this,
		real (kind=8), dimension(:)	list_dh_radius )

Convert to kT/A

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fill_array_rep()

subroutine mod_analytic::fill_array_rep	(	type(analytic), intent(inout)	this,
		real(kind=8), dimension(:), intent(in)	list_rep_radius,
		real(kind=8), intent(in)	rep_bfct )

Precompute values of the spherical repulsion array.

• In this model, the repulsion between a pair of spheres of radii a1 and a2 is V(r) = ((a1+a2)/(r-b(a1+a2)))^6 in units kT.
• NOTE: DH array is divided by two so interaction can be calculated in both directions, then added. Same done here for consistency.

Parameters

this	: instance of mod_analytic::analytic
list_rep_radius	: array containing the radii of all solutes.
rep_bfct	: the parameter b in the eqn above.

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get_energy_analytic()

real(kind=8) function mod_analytic::get_energy_analytic	(	type ( analytic )	this,
		integer	bin,
		integer	type_nb )

Return precomputed energy values.

Parameters

this	: instance of mod_analytic
bin	: integer bin number
type_nb	: integer number corresponding to the type of protein

get_force_analytic()

real(kind=8) function mod_analytic::get_force_analytic	(	type ( analytic )	this,
		integer	bin,
		integer	type_nb )

Return precomputed force values.

Parameters

this	: instance of mod_analytic
bin	: integer bin number
type_nb	: integer number corresponding to the type of protein

get_force_analytic_hom_charged_surf()

real(kind=8) function mod_analytic::get_force_analytic_hom_charged_surf	(	type ( analytic )	this,
		integer	bin,
		integer	type_nb )

info_analytic()

subroutine mod_analytic::info_analytic	(	type ( analytic )	this,
		logical, optional	opt_print )

Print info about analytical grids.

Should apply to all, not only D-H

Parameters

this	: instance of mod_analytic
opt_print	: optional, print full arrays

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print_analytic()

subroutine mod_analytic::print_analytic

(

type ( analytic )

this

)

Print values of array force and energy.
Called by info_analytic.

Parameters

this	: instance of mod_analytic

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print_analytic_external()

subroutine mod_analytic::print_analytic_external

(

type ( analytic )

this

)

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print_analytic_external_hom_charged_surf()

subroutine mod_analytic::print_analytic_external_hom_charged_surf

(

type ( analytic )

this

)

set_analytic_params()

subroutine mod_analytic::set_analytic_params	(	type ( analytic )	this,
		real(kind=8), intent(in)	h,
		real(kind=4), intent(in)	max_size,
		real(kind=8), intent(in)	epfct,
		real(kind=8), intent(in)	dh_radius,
		real(kind=8), intent(in)	vol_radius,
		real(kind=8), intent(in)	rep_radius,
		real(kind=8), intent(in)	surface_charge_dens,
		real(kind=8), intent(in)	surf_prefct,
		logical, intent(in)	gouy_chapman )

fill the arrays, here need to setup dimension

Parameters

this	: instance of mod_analytic
h	: bin size of the precomputed arrays
max_size	: extensiom of DH, half the box for sdamm, c-surface for sda_2proteins
epfct	: scaling factor for DH electrostatics. Like grid calcs, usually 0.5 to stop double counting
dh_radius	: radius of this solute used for dh cavity
vol_radius	: radius of this solute used for volume occupancy
rep_radius	: radius of this solute used for repulsive crowder interactions
surface_charge_dens	: charge density for DH charged surface routine.

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set_dh_params()

subroutine mod_analytic::set_dh_params	(	type ( analytic )	this,
		real(kind=4), optional	opt_ionic )

Initialize debye-huckel parameters.

Parameters

this	: instance of mod_analytic
opt_ionic	: optional, if present set the ionic strength

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set_zeroes()

subroutine mod_analytic::set_zeroes	(	type ( analytic )	this,
		real ( kind=4 )	cutoff )

Specific to Debye-Huckel set zero for at distance where the grid is available Allow to call normal electrostatic and debye-huckel without taking care (hopefully).

Parameters

this	: instance of mod_analytic
cutoff	: max distance to which the value is set to 0