mod_hydrodynamics Module Reference

Module Hydrodynamics.
Only contain function, state independent. More...

Functions/Subroutines
subroutine	scale_diffusion_coefficients (tab_protein, geom, cutoff_phi)
	Wrapper function.
subroutine	scale_diffusion_coefficients_surface (tab_protein, geom, force_energy, surface_h, current_step)
subroutine	scale_diffusion_coefficients_sdamm (tab_protein, geom, cutoff_phi)
subroutine	scale_diffusion_coefficients_sdamm_surface (tab_protein, geom, force_energy, surface_h, current_step)
subroutine	scale_diffusion_coefficients_sda2prot (tab_protein, geom, cutoff_phi)
subroutine	scale_diffusion_coefficients_sda2prot_surface (tab_protein, geom, cutoff_phi, surface_h)
subroutine	local_volume_fraction (prot2, dist2, cutoff_phi, vol_occ)
	compute volume fraction
subroutine	local_trans_diff_scaling (dm_init, vol_occ, dm_scaled)
	Scale the translation diffusion coefficient according to.
subroutine	local_rot_diff_scaling (dr_init, vol_occ, dr_scaled)
	Scale the rotational diffusion coefficient according to.

Detailed Description

Module Hydrodynamics.
Only contain function, state independent.

Function/Subroutine Documentation

local_rot_diff_scaling()

subroutine mod_hydrodynamics::local_rot_diff_scaling	(	real ( kind=8 ), intent(in)	dr_init,
		real ( kind=8 ), intent(in)	vol_occ,
		real ( kind=8 ), intent(out)	dr_scaled )

Scale the rotational diffusion coefficient according to.

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local_trans_diff_scaling()

subroutine mod_hydrodynamics::local_trans_diff_scaling	(	real ( kind=8 ), intent(in)	dm_init,
		real ( kind=8 ), intent(in)	vol_occ,
		real ( kind=8 ), intent(out)	dm_scaled )

Scale the translation diffusion coefficient according to.

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local_volume_fraction()

subroutine mod_hydrodynamics::local_volume_fraction	(	type ( protein ), intent(in)	prot2,
		real ( kind=8 ), intent(in)	dist2,
		real ( kind=8 ), intent(in)	cutoff_phi,
		real ( kind=8 ), intent(inout)	vol_occ )

compute volume fraction

• NJB: Subroutine computes fraction of a volume spherical occupied by a single protein and adds it to the input vol_occ to the occupied volume fraction can be summed in calling routine.

Parameters

prot2	: second solute
dist2	: distance square
cutoff_phi	: cutoff distance
vol_occ	: summation variable to which fraction of volume occupied by prot2 is added

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scale_diffusion_coefficients()

subroutine mod_hydrodynamics::scale_diffusion_coefficients	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		real (kind=8), intent(in)	cutoff_phi )

Wrapper function.

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scale_diffusion_coefficients_sda2prot()

subroutine mod_hydrodynamics::scale_diffusion_coefficients_sda2prot	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		real (kind=8), intent(in)	cutoff_phi )

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scale_diffusion_coefficients_sda2prot_surface()

subroutine mod_hydrodynamics::scale_diffusion_coefficients_sda2prot_surface	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		real (kind=8), intent(in)	cutoff_phi,
		real (kind=8), intent(in)	surface_h )

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scale_diffusion_coefficients_sdamm()

subroutine mod_hydrodynamics::scale_diffusion_coefficients_sdamm	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		real (kind=8), intent(in)	cutoff_phi )

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scale_diffusion_coefficients_sdamm_surface()

subroutine mod_hydrodynamics::scale_diffusion_coefficients_sdamm_surface	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		type(type_force_energy), intent(in)	force_energy,
		real (kind=8), intent(in)	surface_h,
		integer, intent(in)	current_step )

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scale_diffusion_coefficients_surface()

subroutine mod_hydrodynamics::scale_diffusion_coefficients_surface	(	type ( array_protein_type )	tab_protein,
		type ( geometry ), intent(in)	geom,
		type (type_force_energy), intent(in)	force_energy,
		real (kind=8), intent(in)	surface_h,
		integer, intent(in)	current_step )

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