Minimal class for computing the depth- and membrane-dependent electrostatics energy. More...

#include <ImplicitMembraneCoulomb.hh>

Inheritance diagram for core::energy_methods::ImplicitMembraneCoulomb:

Public Member Functions
	ImplicitMembraneCoulomb ()
	Default constructor. More...

	ImplicitMembraneCoulomb (ImplicitMembraneCoulomb const &src)
	Copy constructor. More...

	~ImplicitMembraneCoulomb () override
	Destructor. More...

ImplicitMembraneCoulombOP	clone () const
	Clone operation: make a copy of this object, and return an owning pointer to the copy. More...

void	initialize ()
	Initialize max distance and coulomb constants. More...

core::Real	compute_depth_and_bilayer_dep_dielectric (core::Real const fi, core::Real const fj, core::Real const d) const
	Compute depth- and bilayer-dependent dielectric constant. More...

core::Real	sigmoidal_eps (core::Real const sigmoid_D0, core::Real const sigmoid_D, core::Real const sigmoid_s, core::Real const d) const
	Compute the distance dependent sigmoid function. More...

core::Real	sigmoidal_deps_dr (core::Real const sigmoid_D0, core::Real const sigmoid_D, core::Real const sigmoid_s, core::Real const d) const

core::Real	compute_deps_dr (core::Real const fi, core::Real const fj, core::Real const d) const
	Compute the derivative of depth- and bilayer-dependent dielectric. More...

core::Real	eval_atom_atom_fa_elecE (core::Vector const &i_xyz, core::Real const i_charge, core::Real const i_hyd, core::Vector const &j_xyz, core::Real const j_charge, core::Real const j_hyd) const
	Evaluate atom pair electrostatics energy (pass through) More...

core::Real	eval_atom_atom_fa_elecE (core::Vector const &i_xyz, core::Real const i_charge, core::Real const i_hyd, core::Vector const &j_xyz, core::Real const j_charge, core::Real const j_hyd, DistanceSquared &d2) const
	Evaluate atom pair electrostatics energy. More...

core::Real	eval_dfa_elecE_dr_over_r (core::Real const dis2, core::Real const q1, core::Real const q2, core::Real const i_hyd, core::Real const j_hyd) const
	Get the key numeric value for derivative calculations. More...

core::Vector	eval_dfa_elecE_df (core::Real const dis2, core::Real const q1, core::Real const q2, core::Real const i_hyd, core::Real const j_hyd, core::Vector const di_hyd_df, core::Vector const dj_hyd_df) const
	Get the key numeric value for derivative calculations i.e. the derivative of energy with respect to membrane depth. More...

numeric::CubicPolynomial	compute_hipoly (core::Real const fi, core::Real const fj) const

numeric::CubicPolynomial	compute_lowpoly (core::Real const fi, core::Real const fj) const

core::Real	compute_min_dis_score (core::Real const fi, core::Real const fj) const

Detailed Description

Minimal class for computing the depth- and membrane-dependent electrostatics energy.

Author: rfalford12 (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om)

Constructor & Destructor Documentation

◆ ImplicitMembraneCoulomb() [1/2]

core::energy_methods::ImplicitMembraneCoulomb::ImplicitMembraneCoulomb ( )

Default constructor.

References initialize().

◆ ImplicitMembraneCoulomb() [2/2]

core::energy_methods::ImplicitMembraneCoulomb::ImplicitMembraneCoulomb ( ImplicitMembraneCoulomb const & src )

default

Copy constructor.

Copy constructor. Keep default unless deep copying is needed (and in that case, consider using DeepCopyOPs.)

◆ ~ImplicitMembraneCoulomb()

core::energy_methods::ImplicitMembraneCoulomb::~ImplicitMembraneCoulomb ( )

override

Destructor.

Member Function Documentation

◆ clone()

ImplicitMembraneCoulombOP core::energy_methods::ImplicitMembraneCoulomb::clone ( ) const

Clone operation: make a copy of this object, and return an owning pointer to the copy.

◆ compute_deps_dr()

core::Real core::energy_methods::ImplicitMembraneCoulomb::compute_deps_dr	(	core::Real const	fi,
		core::Real const	fj,
		core::Real const	d
	)		const

Compute the derivative of depth- and bilayer-dependent dielectric.

References sigmoidal_deps_dr().

Referenced by compute_hipoly(), compute_lowpoly(), and eval_dfa_elecE_dr_over_r().

◆ compute_depth_and_bilayer_dep_dielectric()

core::Real core::energy_methods::ImplicitMembraneCoulomb::compute_depth_and_bilayer_dep_dielectric	(	core::Real const	fi,
		core::Real const	fj,
		core::Real const	d
	)		const

Compute depth- and bilayer-dependent dielectric constant.

References sigmoidal_eps().

Referenced by compute_hipoly(), compute_lowpoly(), compute_min_dis_score(), eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), and eval_dfa_elecE_dr_over_r().

◆ compute_hipoly()

numeric::CubicPolynomial core::energy_methods::ImplicitMembraneCoulomb::compute_hipoly	(	core::Real const	fi,
		core::Real const	fj
	)		const

References C0_, C1_, compute_deps_dr(), compute_depth_and_bilayer_dep_dielectric(), hi_poly_end_, hi_poly_start_, and max_dis_.

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), and eval_dfa_elecE_dr_over_r().

◆ compute_lowpoly()

numeric::CubicPolynomial core::energy_methods::ImplicitMembraneCoulomb::compute_lowpoly	(	core::Real const	fi,
		core::Real const	fj
	)		const

References C0_, C1_, compute_deps_dr(), compute_depth_and_bilayer_dep_dielectric(), compute_min_dis_score(), low_poly_end_, low_poly_start_, and max_dis_.

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), and eval_dfa_elecE_dr_over_r().

◆ compute_min_dis_score()

core::Real core::energy_methods::ImplicitMembraneCoulomb::compute_min_dis_score	(	core::Real const	fi,
		core::Real const	fj
	)		const

References C1_, compute_depth_and_bilayer_dep_dielectric(), max_dis_, and min_dis_.

Referenced by compute_lowpoly(), and eval_atom_atom_fa_elecE().

◆ eval_atom_atom_fa_elecE() [1/2]

core::Real core::energy_methods::ImplicitMembraneCoulomb::eval_atom_atom_fa_elecE	(	core::Vector const &	i_xyz,
		core::Real const	i_charge,
		core::Real const	i_hyd,
		core::Vector const &	j_xyz,
		core::Real const	j_charge,
		core::Real const	j_hyd
	)		const

Evaluate atom pair electrostatics energy (pass through)

◆ eval_atom_atom_fa_elecE() [2/2]

core::Real core::energy_methods::ImplicitMembraneCoulomb::eval_atom_atom_fa_elecE	(	core::Vector const &	i_xyz,
		core::Real const	i_charge,
		core::Real const	i_hyd,
		core::Vector const &	j_xyz,
		core::Real const	j_charge,
		core::Real const	j_hyd,
		DistanceSquared &	d2
	)		const

Evaluate atom pair electrostatics energy.

References C0_, C1_, compute_depth_and_bilayer_dep_dielectric(), compute_hipoly(), compute_lowpoly(), compute_min_dis_score(), hi_poly_start2_, low_poly_end2_, low_poly_start2_, max_dis2_, and max_dis_.

◆ eval_dfa_elecE_df()

core::Vector core::energy_methods::ImplicitMembraneCoulomb::eval_dfa_elecE_df	(	core::Real const	dis2,
		core::Real const	q1,
		core::Real const	q2,
		core::Real const	i_hyd,
		core::Real const	j_hyd,
		core::Vector const	di_hyd_df,
		core::Vector const	dj_hyd_df
	)		const

Get the key numeric value for derivative calculations i.e. the derivative of energy with respect to membrane depth.

References C0_, compute_depth_and_bilayer_dep_dielectric(), compute_hipoly(), compute_lowpoly(), hi_poly_start2_, low_poly_end2_, low_poly_start2_, and max_dis2_.

◆ eval_dfa_elecE_dr_over_r()

core::Real core::energy_methods::ImplicitMembraneCoulomb::eval_dfa_elecE_dr_over_r	(	core::Real const	dis2,
		core::Real const	q1,
		core::Real const	q2,
		core::Real const	i_hyd,
		core::Real const	j_hyd
	)		const

Get the key numeric value for derivative calculations.

Get the key numeric value for derivative calculations i.e. the derivative of energy with respect to distance divided by the distance.

References compute_deps_dr(), compute_depth_and_bilayer_dep_dielectric(), compute_hipoly(), compute_lowpoly(), dEfac_, hi_poly_start2_, low_poly_end2_, low_poly_start2_, and max_dis2_.

◆ initialize()

void core::energy_methods::ImplicitMembraneCoulomb::initialize ( )

Initialize max distance and coulomb constants.

References C0_, C1_, dEfac_, hi_poly_end2_, hi_poly_end_, hi_poly_start2_, hi_poly_start_, low_poly_end2_, low_poly_end_, low_poly_start2_, low_poly_start_, max_dis2_, max_dis_, min_dis2_, and min_dis_.

Referenced by ImplicitMembraneCoulomb().

◆ sigmoidal_deps_dr()

core::Real core::energy_methods::ImplicitMembraneCoulomb::sigmoidal_deps_dr	(	core::Real const	sigmoid_D0,
		core::Real const	sigmoid_D,
		core::Real const	sigmoid_s,
		core::Real const	d
	)		const

Referenced by compute_deps_dr().

◆ sigmoidal_eps()

core::Real core::energy_methods::ImplicitMembraneCoulomb::sigmoidal_eps	(	core::Real const	sigmoid_D0,
		core::Real const	sigmoid_D,
		core::Real const	sigmoid_s,
		core::Real const	d
	)		const

Compute the distance dependent sigmoid function.

Referenced by compute_depth_and_bilayer_dep_dielectric().

Member Data Documentation

◆ C0_

core::Real core::energy_methods::ImplicitMembraneCoulomb::C0_

private

Referenced by compute_hipoly(), compute_lowpoly(), eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), and initialize().

◆ C1_

core::Real core::energy_methods::ImplicitMembraneCoulomb::C1_

private

Referenced by compute_hipoly(), compute_lowpoly(), compute_min_dis_score(), eval_atom_atom_fa_elecE(), and initialize().

◆ dEfac_

core::Real core::energy_methods::ImplicitMembraneCoulomb::dEfac_

private

Referenced by eval_dfa_elecE_dr_over_r(), and initialize().

◆ hi_poly_end2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::hi_poly_end2_

private

Referenced by initialize().

◆ hi_poly_end_

core::Real core::energy_methods::ImplicitMembraneCoulomb::hi_poly_end_

private

Referenced by compute_hipoly(), and initialize().

◆ hi_poly_start2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::hi_poly_start2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), eval_dfa_elecE_dr_over_r(), and initialize().

◆ hi_poly_start_

core::Real core::energy_methods::ImplicitMembraneCoulomb::hi_poly_start_

private

Referenced by compute_hipoly(), and initialize().

◆ low_poly_end2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::low_poly_end2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), eval_dfa_elecE_dr_over_r(), and initialize().

◆ low_poly_end_

core::Real core::energy_methods::ImplicitMembraneCoulomb::low_poly_end_

private

Referenced by compute_lowpoly(), and initialize().

◆ low_poly_start2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::low_poly_start2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), eval_dfa_elecE_dr_over_r(), and initialize().

◆ low_poly_start_

core::Real core::energy_methods::ImplicitMembraneCoulomb::low_poly_start_

private

Referenced by compute_lowpoly(), and initialize().

◆ max_dis2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::max_dis2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_df(), eval_dfa_elecE_dr_over_r(), and initialize().

◆ max_dis_

core::Real core::energy_methods::ImplicitMembraneCoulomb::max_dis_

private

Referenced by compute_hipoly(), compute_lowpoly(), compute_min_dis_score(), eval_atom_atom_fa_elecE(), and initialize().

◆ min_dis2_

core::Real core::energy_methods::ImplicitMembraneCoulomb::min_dis2_

private

Referenced by initialize().

◆ min_dis_

core::Real core::energy_methods::ImplicitMembraneCoulomb::min_dis_

private

Referenced by compute_min_dis_score(), and initialize().

The documentation for this class was generated from the following files:

src/core/energy_methods/ImplicitMembraneCoulomb.hh
src/core/energy_methods/ImplicitMembraneCoulomb.cc

Private Attributes
core::Real	max_dis_

core::Real	max_dis2_

core::Real	min_dis_

core::Real	min_dis2_

core::Real	low_poly_start_

core::Real	low_poly_start2_

core::Real	low_poly_end_

core::Real	low_poly_end2_

core::Real	hi_poly_start_

core::Real	hi_poly_start2_

core::Real	hi_poly_end_

core::Real	hi_poly_end2_

core::Real	C0_

core::Real	C1_

core::Real	dEfac_

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ImplicitMembraneCoulomb() [1/2]

◆ ImplicitMembraneCoulomb() [2/2]

◆ ~ImplicitMembraneCoulomb()

Member Function Documentation

◆ clone()

◆ compute_deps_dr()

◆ compute_depth_and_bilayer_dep_dielectric()

◆ compute_hipoly()

◆ compute_lowpoly()

◆ compute_min_dis_score()

◆ eval_atom_atom_fa_elecE() [1/2]

◆ eval_atom_atom_fa_elecE() [2/2]

◆ eval_dfa_elecE_df()

◆ eval_dfa_elecE_dr_over_r()

◆ initialize()

◆ sigmoidal_deps_dr()

◆ sigmoidal_eps()

Member Data Documentation

◆ C0_

◆ C1_

◆ dEfac_

◆ hi_poly_end2_

◆ hi_poly_end_

◆ hi_poly_start2_

◆ hi_poly_start_

◆ low_poly_end2_

◆ low_poly_end_

◆ low_poly_start2_

◆ low_poly_start_

◆ max_dis2_

◆ max_dis_

◆ min_dis2_

◆ min_dis_