mod_force_energy Module Reference

Only one single object of this module should be initialized. More...

Data Types
type	type_force_energy
	Store the grid number to use for computing interaction and theirs types. More...

Functions/Subroutines
subroutine	init_force_energy (this, tab_protein, type_calc, imetal)
	Initilaize the oobject newer version, include asymetry, so need tab_protein to be general ( and sdamm case ) with sdamm need to modify shift, inter-type interactions, need type calculation.
subroutine	init_image_charge (this, tab_protein)
	Initialize array for image charge. Couyld be used for metal desolv as well. Make separate for the moment, allocate different array, but could be combined to init_force_energy img_chg can be found by tab_protein, important for sdamm to optimize to integrate init init_force, to test with sdamm.
subroutine	init_analytic (this, tab_protein, cut_off, surf_cut, h_anal, surf_prefct, opt_ionic, gouy_chapman)
	Initialize specificaly analytical interactions. .
subroutine	delete_force_energy (this)
	Initialization of one analytic of sogrid done in this subfunction, in module so_grid.
subroutine	print_info_param_fe (this)
	Print info about global settings. Would need a check for sdamm, array_grid_calc not used .
pure subroutine	force_atom_uhbd (x, f, tgrid)
	Compute the derivative of the energy of position x. Will be used to compute the force on an atom at position x Pass an instance of type_grid as parameter, so it can apply to any grid This version can deal with both uhbd and dtgrid. Overhead estimated to 10 %.
subroutine	potential_atom_uhbd (x, u, tgrid)
	Compute the energy of position x of grid tgrid.
subroutine	init_crowder (this, tab_protein, ionic, rep_bfct, h_size, max_dist, ionic_known)
	Initialise the array that lists crowder molecules – then calls one of two initialisation functions depending on crowder type Following similar logic to img_chg and and analtical.
subroutine	init_sphere_crowder (this, tab_protein, ionic, rep_bfct, h_size, max_dist)

Variables
integer, parameter	symetric = 0
	enumeration type for symetry of asymetry of interactions c2g1 : charge of protein2 in grid of solute 1 lennard-jones with surface is c1g2
integer, parameter	c2g1 = -1
integer, parameter	c1g2 = 1

Detailed Description

Only one single object of this module should be initialized.

Function/Subroutine Documentation

delete_force_energy()

subroutine mod_force_energy::delete_force_energy

(

type ( type_force_energy )

this

)

Initialization of one analytic of sogrid done in this subfunction, in module so_grid.

Deallocate all arrays.

Parameters

this	: instance of this class

force_atom_uhbd()

pure subroutine mod_force_energy::force_atom_uhbd	(	real ( kind=8 ), dimension(3), intent(in)	x,
		real ( kind=8 ), dimension(3), intent(out)	f,
		type (type_grid ), intent(in)	tgrid
	)

Compute the derivative of the energy of position x.
Will be used to compute the force on an atom at position x
Pass an instance of type_grid as parameter, so it can apply to any grid
This version can deal with both uhbd and dtgrid. Overhead estimated to 10 %.

Parameters

x	: position of the atom
f	: return force ( rather derivative of the energy ) computed at x
tgrid	: instance of the grid used for computation
voxel	: voxel list containing 8 potential values

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init_analytic()

subroutine mod_force_energy::init_analytic	(	type ( type_force_energy )	this,
		type ( array_protein_type ), intent(in)	tab_protein,
		real (kind=4), intent(in)	cut_off,
		real (kind=4), intent(in)	surf_cut,
		real (kind=4), intent(in)	h_anal,
		real (kind=8), intent(in)	surf_prefct,
		real (kind=4), intent(in), optional	opt_ionic,
		logical, optional, value	gouy_chapman
	)

Initialize specificaly analytical interactions.
.

Parameters

this	: instance of this class
tab_protein	: instance of mod_array_protein
cut_off	: indicates the maximum distance, half the box for sdamm, c-surface for sda_2proteins
surf_cut	: For a charged surface, its cut off is c-surf for 2prot, z extent for sdamm
h_anal	: bin size of analytical arrays
opt_ionic	: optional, used only for the ionic strength at the moment

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init_crowder()

subroutine mod_force_energy::init_crowder	(	type(type_force_energy), intent(inout)	this,
		type(array_protein_type), intent(in)	tab_protein,
		real(kind=4), intent(in)	ionic,
		real(kind=4), intent(in)	rep_bfct,
		real(kind=4), intent(in)	h_size,
		real(kind=4), intent(in)	max_dist,
		logical, intent(in)	ionic_known
	)

Initialise the array that lists crowder molecules – then calls one of two initialisation functions depending on crowder type Following similar logic to img_chg and and analtical.

Parameters

this	: instance of /ref mod_force_energy::type_force_energy
tab_protein	: instance of /ref mod_array_protein::array_protein_type
ionic	: ionic strnegth in Molar
rep_bfct	: Factor to define where hard core is in repulsive potential
h_size	: resolution of the analytical grids
max_dist	: Absolute maximum distance for analytical interactions. Smaller dist can be set later per interaction.

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init_force_energy()

subroutine mod_force_energy::init_force_energy	(	type ( type_force_energy )	this,
		type ( array_protein_type ), intent(in)	tab_protein,
		type ( type_calculation ), intent(in)	type_calc,
		logical, intent(in)	imetal
	)

Initilaize the oobject newer version, include asymetry, so need tab_protein to be general ( and sdamm case ) with sdamm need to modify shift, inter-type interactions, need type calculation.

Parameters

this	: instance of this class
tab_protein	: instance of mod_array_protein
type_calc	: instance of type_calc
imetal	: logical set metal desolvation

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init_image_charge()

subroutine mod_force_energy::init_image_charge	(	type ( type_force_energy )	this,
		type ( array_protein_type ), intent(in)	tab_protein
	)

Initialize array for image charge.
Couyld be used for metal desolv as well.
Make separate for the moment, allocate different array, but could be combined to init_force_energy img_chg can be found by tab_protein, important for sdamm to optimize to integrate init init_force, to test with sdamm.

Parameters

this	: instance of this class
tab_protein	: instance of mod_array_protein

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init_sphere_crowder()

subroutine mod_force_energy::init_sphere_crowder	(	type(type_force_energy), intent(inout)	this,
		type(array_protein_type), intent(in)	tab_protein,
		real(kind=4), intent(in)	ionic,
		real(kind=4), intent(in)	rep_bfct,
		real(kind=4), intent(in)	h_size,
		real(kind=4), intent(in)	max_dist
	)

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potential_atom_uhbd()

subroutine mod_force_energy::potential_atom_uhbd	(	real ( kind=8 ), dimension(3), intent(in)	x,
		real ( kind=8 ), intent(out)	u,
		type (type_grid ), intent(in)	tgrid
	)

Compute the energy of position x of grid tgrid.

This version can deal with both uhbd and dtgrid

Parameters

x	: position of the atom
U	: return the computed potential
tgrid	: instance of the grid to use for the computation

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print_info_param_fe()

subroutine mod_force_energy::print_info_param_fe

(

type ( type_force_energy )

this

)

Print info about global settings.
Would need a check for sdamm, array_grid_calc not used
.

Parameters

this	: instance of type_force_energy

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Variable Documentation

c1g2

integer, parameter mod_force_energy::c1g2 = 1

c2g1

integer, parameter mod_force_energy::c2g1 = -1

symetric

integer, parameter mod_force_energy::symetric = 0

enumeration type for symetry of asymetry of interactions c2g1 : charge of protein2 in grid of solute 1 lennard-jones with surface is c1g2