Collaboration diagram for gmx::test::anonymous_namespace{bonded.cpp}::iListInput:

Description

Input structure for listed forces tests.

Public Member Functions
	iListInput ()
	Constructor.

	iListInput (float ftol, double dtol)
	Constructor with tolerance. More...

iListInput	setHarmonic (InteractionFunction ft, real rA, real krA, real rB, real krB)
	Set parameters for harmonic potential. More...

iListInput	setHarmonic (InteractionFunction ft, real rA, real krA)
	Set parameters for harmonic potential. More...

iListInput	setCubic (real b0, real kb, real kcub)
	Set parameters for cubic potential. More...

iListInput	setMorse (real b0A, real cbA, real betaA, real b0B, real cbB, real betaB)
	Set parameters for morse potential. More...

iListInput	setMorse (real b0A, real cbA, real betaA)
	Set parameters for morse potential. More...

iListInput	setFene (real bm, real kb)
	Set parameters for fene potential. More...

iListInput	setLinearAngle (real klinA, real aA, real klinB, real aB)
	Set parameters for linear angle potential. More...

iListInput	setLinearAngle (real klinA, real aA)
	Set parameters for linear angle potential. More...

iListInput	setUreyBradley (real thetaA, real kthetaA, real r13A, real kUBA, real thetaB, real kthetaB, real r13B, real kUBB)
	Set parameters for Urey Bradley potential. More...

iListInput	setUreyBradley (real thetaA, real kthetaA, real r13A, real kUBA)
	Set parameters for Urey Bradley potential. More...

iListInput	setCrossBondBonds (real r1e, real r2e, real krr)
	Set parameters for Cross Bond Bonds potential. More...

iListInput	setCrossBondAngles (real r1e, real r2e, real r3e, real krt)
	Set parameters for Cross Bond Angles potential. More...

iListInput	setQuarticAngles (real theta, const real c[5])
	Set parameters for Quartic Angles potential. More...

iListInput	setPDihedrals (InteractionFunction ft, real phiA, real cpA, int mult, real phiB, real cpB)
	Set parameters for proper dihedrals potential. More...

iListInput	setPDihedrals (InteractionFunction ft, real phiA, real cpA, int mult)
	Set parameters for proper dihedrals potential. More...

iListInput	setRbDihedrals (const real rbcA[NR_RBDIHS], const real rbcB[NR_RBDIHS])
	Set parameters for Ryckaert-Bellemans dihedrals potential. More...

iListInput	setRbDihedrals (const real rbc[NR_RBDIHS])
	Set parameters for Ryckaert-Bellemans dihedrals potential. More...

iListInput	setPolarization (real alpha)
	Set parameters for Polarization. More...

iListInput	setAnharmPolarization (real alpha, real drcut, real khyp)
	Set parameters for Anharmonic Polarization. More...

iListInput	setTholePolarization (real a, real alpha1, real alpha2)
	Set parameters for Thole Polarization. More...

iListInput	setWaterPolarization (real alpha_x, real alpha_y, real alpha_z, real rOH, real rHH, real rOD)
	Set parameters for Water Polarization. More...

Public Attributes
std::optional < InteractionFunction >	ftype
	Function type.

float	ftoler = 1e-6
	Tolerance for float evaluation.

double	dtoler = 1e-8
	Tolerance for double evaluation.

bool	fep = false
	Do free energy perturbation?

t_iparams	iparams = { { 0 } }
	Interaction parameters.

Friends
std::ostream &	operator<< (std::ostream &out, const iListInput &input)
	Prints the interaction and parameters to a stream.

Constructor & Destructor Documentation

gmx::test::anonymous_namespace{bonded.cpp}::iListInput::iListInput	(	float	ftol,
		double	dtol
	)

inline

Constructor with tolerance.

Parameters

[in]	ftol	Single precision tolerance
[in]	dtol	Double precision tolerance

Member Function Documentation

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setAnharmPolarization	(	real	alpha,
		real	drcut,
		real	khyp
	)

inline

Set parameters for Anharmonic Polarization.

Parameters

[in]	alpha	Polarizability (nm^3)
[in]	drcut	The cut-off distance (nm) after which the fourth power kicks in
[in]	khyp	The force constant for the fourth power

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setCrossBondAngles	(	real	r1e,
		real	r2e,
		real	r3e,
		real	krt
	)

inline

Set parameters for Cross Bond Angles potential.

Parameters

[in]	r1e	First bond length i-j
[in]	r2e	Second bond length j-k
[in]	r3e	Third bond length i-k
[in]	krt	The force constant

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setCrossBondBonds	(	real	r1e,
		real	r2e,
		real	krr
	)

inline

Set parameters for Cross Bond Bonds potential.

Parameters

[in]	r1e	First bond length i-j
[in]	r2e	Second bond length i-k
[in]	krr	The force constant

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setCubic	(	real	b0,
		real	kb,
		real	kcub
	)

inline

Set parameters for cubic potential.

Parameters

[in]	b0	Equilibrium bond length
[in]	kb	Harmonic force constant
[in]	kcub	Cubic force constant

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setFene	(	real	bm,
		real	kb
	)

inline

Set parameters for fene potential.

Parameters

[in]	bm	Equilibrium bond length
[in]	kb	Force constant

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setHarmonic	(	InteractionFunction	ft,
		real	rA,
		real	krA,
		real	rB,
		real	krB
	)

inline

Set parameters for harmonic potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	ft	Function type
[in]	rA	Equilibrium value A
[in]	krA	Force constant A
[in]	rB	Equilibrium value B
[in]	krB	Force constant B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setHarmonic	(	InteractionFunction	ft,
		real	rA,
		real	krA
	)

inline

Set parameters for harmonic potential.

Parameters

[in]	ft	Function type
[in]	rA	Equilibrium value
[in]	krA	Force constant

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setLinearAngle	(	real	klinA,
		real	aA,
		real	klinB,
		real	aB
	)

inline

Set parameters for linear angle potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	klinA	Force constant A
[in]	aA	The position of the central atom A
[in]	klinB	Force constant B
[in]	aB	The position of the central atom B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setLinearAngle	(	real	klinA,
		real	aA
	)

inline

Set parameters for linear angle potential.

Parameters

[in]	klinA	Force constant
[in]	aA	The position of the central atom

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setMorse	(	real	b0A,
		real	cbA,
		real	betaA,
		real	b0B,
		real	cbB,
		real	betaB
	)

inline

Set parameters for morse potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	b0A	Equilibrium value A
[in]	cbA	Force constant A
[in]	betaA	Steepness parameter A
[in]	b0B	Equilibrium value B
[in]	cbB	Force constant B
[in]	betaB	Steepness parameter B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setMorse	(	real	b0A,
		real	cbA,
		real	betaA
	)

inline

Set parameters for morse potential.

Parameters

[in]	b0A	Equilibrium value
[in]	cbA	Force constant
[in]	betaA	Steepness parameter

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setPDihedrals	(	InteractionFunction	ft,
		real	phiA,
		real	cpA,
		int	mult,
		real	phiB,
		real	cpB
	)

inline

Set parameters for proper dihedrals potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	ft	Function type
[in]	phiA	Dihedral angle A
[in]	cpA	Force constant A
[in]	mult	Multiplicity of the angle
[in]	phiB	Dihedral angle B
[in]	cpB	Force constant B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setPDihedrals	(	InteractionFunction	ft,
		real	phiA,
		real	cpA,
		int	mult
	)

inline

Set parameters for proper dihedrals potential.

Parameters

[in]	ft	Function type
[in]	phiA	Dihedral angle
[in]	cpA	Force constant
[in]	mult	Multiplicity of the angle

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setPolarization ( real alpha )

inline

Set parameters for Polarization.

Parameters

[in] alpha Polarizability

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setQuarticAngles	(	real	theta,
		const real	c[5]
	)

inline

Set parameters for Quartic Angles potential.

Parameters

[in]	theta	Angle
[in]	c	Array of parameters

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setRbDihedrals	(	const real	rbcA[NR_RBDIHS],
		const real	rbcB[NR_RBDIHS]
	)

inline

Set parameters for Ryckaert-Bellemans dihedrals potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	rbcA	Force constants A
[in]	rbcB	Force constants B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setRbDihedrals ( const real rbc[NR_RBDIHS] )

inline

Set parameters for Ryckaert-Bellemans dihedrals potential.

Parameters

[in] rbc Force constants

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setTholePolarization	(	real	a,
		real	alpha1,
		real	alpha2
	)

inline

Set parameters for Thole Polarization.

Parameters

[in]	a	Thole factor
[in]	alpha1	Polarizability 1 (nm^3)
[in]	alpha2	Polarizability 2 (nm^3)

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setUreyBradley	(	real	thetaA,
		real	kthetaA,
		real	r13A,
		real	kUBA,
		real	thetaB,
		real	kthetaB,
		real	r13B,
		real	kUBB
	)

inline

Set parameters for Urey Bradley potential.

Free energy perturbation is turned on when A and B parameters are different.

Parameters

[in]	thetaA	Equilibrium angle A
[in]	kthetaA	Force constant A
[in]	r13A	The distance between i and k atoms A
[in]	kUBA	The force constant for 1-3 distance A
[in]	thetaB	Equilibrium angle B
[in]	kthetaB	Force constant B
[in]	r13B	The distance between i and k atoms B
[in]	kUBB	The force constant for 1-3 distance B

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setUreyBradley	(	real	thetaA,
		real	kthetaA,
		real	r13A,
		real	kUBA
	)

inline

Set parameters for Urey Bradley potential.

Parameters

[in]	thetaA	Equilibrium angle
[in]	kthetaA	Force constant
[in]	r13A	The distance between i and k atoms
[in]	kUBA	The force constant for 1-3 distance

Returns: The structure itself.

iListInput gmx::test::anonymous_namespace{bonded.cpp}::iListInput::setWaterPolarization	(	real	alpha_x,
		real	alpha_y,
		real	alpha_z,
		real	rOH,
		real	rHH,
		real	rOD
	)

inline

Set parameters for Water Polarization.

Parameters

[in]	alpha_x	Polarizability X (nm^3)
[in]	alpha_y	Polarizability Y (nm^3)
[in]	alpha_z	Polarizability Z (nm^3)
[in]	rOH	Oxygen-Hydrogen distance
[in]	rHH	Hydrogen-Hydrogen distance
[in]	rOD	Oxygen-Dummy distance

Returns: The structure itself.

The documentation for this struct was generated from the following file:

src/gromacs/listed_forces/tests/bonded.cpp

Description

Public Member Functions

Public Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation