mod_set_parameters Module Reference

Group functions to compute the cutoff, allocate dummy_array and energy array.
used by all types of simulations. More...

Functions/Subroutines
subroutine	set_dummy_array_and_logical (tab_protein, dummy_array, iflex)
	General function to setup the dummy_array and logical variable lennard-jones is missing here.
subroutine	set_array_energy (type_calc, o_record, nb_prot, array_energy, opt_max_energy_terms, opt_size_array_energy, opt_force_large_array)
subroutine	set_rhit (tab_prot, param_probe, rhit)
	To compute rhit, maximum distance where we need to check for overlap. .
subroutine	set_cut_array (tab_protein, geom, cut2_max)
	Routine to generate an interaction cut off specific to each grid type. .
subroutine	alloc_fill_cut_array (tab_protein, cur_sogrid, cur_prot)
	Routine to allocate and fill a grid specific cut off array for each solute/conformation.
subroutine	set_hi_rad (tab_protein, geom, input_rad, hi_rad)
	Routine to find the Rcut value. – This is the radius used to define local volume in mean-field hydrodynamic approach. – At present, it finds the largest vol_radius of any solute, and multiplies this by a factor. – Does not use factor any more. Radius set in input file. This routine now just checks that chosen radius is larger than the largest vol_radius of any solute.

Detailed Description

Group functions to compute the cutoff, allocate dummy_array and energy array.
used by all types of simulations.

Function/Subroutine Documentation

alloc_fill_cut_array()

subroutine mod_set_parameters::alloc_fill_cut_array	(	type(array_protein_type), intent(in)	tab_protein,
		type(sogrid), intent(in), pointer	cur_sogrid,
		integer, intent(in)	cur_prot
	)

Routine to allocate and fill a grid specific cut off array for each solute/conformation.

Parameters

tab_protein	: instance of mod_array_protein::array_protein_type
cur_sogrid	: instance of mod_setofgrid::sogrid
cur_prot	: integer used as index to get protein data from mod_array_protein::array_protein_type::array

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set_array_energy()

subroutine mod_set_parameters::set_array_energy	(	type ( type_calculation ), intent(in)	type_calc,
		type ( record ), intent(in)	o_record,
		integer, intent(in)	nb_prot,
		real ( kind=8 ), dimension(:,:), pointer	array_energy,
		integer, intent(out), optional	opt_max_energy_terms,
		integer, intent(out), optional	opt_size_array_energy,
		logical, intent(in), optional	opt_force_large_array
	)

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set_cut_array()

subroutine mod_set_parameters::set_cut_array	(	type ( array_protein_type ), intent(in)	tab_protein,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(out)	cut2_max
	)

Routine to generate an interaction cut off specific to each grid type.
.

Using cut offs specific to each grid saves time by removing uneccessary calculations of zero interactions with small grids.
For each solute type, it checks to see if the solute has multiple conformations.
-If it does it calls /ref mod_set_parameters::alloc_fill_cut_array for each conformation.
-Else it calls once.

Parameters

tab_protein	: instance of mod_array_protein::array_protein_type
geom	: instance of mod_geometry::geometry
cut2_max	: maximum cut-off of all interactions

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set_dummy_array_and_logical()

subroutine mod_set_parameters::set_dummy_array_and_logical	(	type ( array_protein_type ), intent(in)	tab_protein,
		real ( kind=8 ), dimension( : ), pointer	dummy_array,
		logical, intent(inout)	iflex
	)

General function to setup the dummy_array and logical variable lennard-jones is missing here.

Set only shared variable, can be called in serial part. Apply to both sda_2proteins, and sdamm. certainly param_force_energy would be needed later.

Parameters

tab_protein	: : instance of mod_array_protein
dummy_array	: array of dummy atoms to allocate
iflex	: indicates if additional tests must be done for flexibility

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set_hi_rad()

subroutine mod_set_parameters::set_hi_rad	(	type ( array_protein_type ), intent(in)	tab_protein,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(in)	input_rad,
		real ( kind=4 ), intent(out)	hi_rad
	)

Routine to find the Rcut value.
– This is the radius used to define local volume in mean-field hydrodynamic approach.
– At present, it finds the largest vol_radius of any solute, and multiplies this by a factor. – Does not use factor any more. Radius set in input file. This routine now just checks that chosen radius is larger than the largest vol_radius of any solute.

Parameters

tab_protein	: instance of mod_array_protein::array_protein_type
geom	: instance of mod_geometry::geometry
input_rad	: Input radius set by lvol_cut in the input file
hi_rad	: radius Rcut used in hydrodynamic calculations. If test passed, will be equal to input_rad on exit.

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set_rhit()

subroutine mod_set_parameters::set_rhit	(	type ( array_protein_type )	tab_prot,
		type ( probe_type )	param_probe,
		real ( kind=4 )	rhit
	)

To compute rhit, maximum distance where we need to check for overlap.
.

Apply only for sda_2proteins type ( not sdamm )
if surface, dist_max correctly updated when reading input, no need to modification
limit to protein1 is a surface, but protein2 can be flexible

Parameters

tab_prot	: instance of mod_array_protein
param_probe	: instance of sda_com::param_probe
rhit	: distance to set for chaecking overlap

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