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gmx::anonymous_namespace{bonded.cpp}::iListInput Struct Reference

Description

Input structure for listed forces tests.

Public Member Functions

 iListInput ()
 Constructor.
 
 iListInput (float ftol, double dtol)
 Constructor with tolerance. More...
 
iListInput setHarmonic (int ft, real rA, real krA, real rB, real krB)
 Set parameters for harmonic potential. More...
 
iListInput setHarmonic (int 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 (int ft, real phiA, real cpA, int mult, real phiB, real cpB)
 Set parameters for proper dihedrals potential. More...
 
iListInput setPDihedrals (int 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, real rfac)
 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

int ftype = -1
 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::anonymous_namespace{bonded.cpp}::iListInput::iListInput ( float  ftol,
double  dtol 
)
inline

Constructor with tolerance.

Parameters
[in]ftolSingle precision tolerance
[in]dtolDouble precision tolerance

Member Function Documentation

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

Set parameters for Anharmonic Polarization.

Parameters
[in]alphaPolarizability (nm^3)
[in]drcutThe cut-off distance (nm) after which the fourth power kicks in
[in]khypThe force constant for the fourth power
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setCrossBondAngles ( real  r1e,
real  r2e,
real  r3e,
real  krt 
)
inline

Set parameters for Cross Bond Angles potential.

Parameters
[in]r1eFirst bond length i-j
[in]r2eSecond bond length j-k
[in]r3eThird bond length i-k
[in]krtThe force constant
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setCrossBondBonds ( real  r1e,
real  r2e,
real  krr 
)
inline

Set parameters for Cross Bond Bonds potential.

Parameters
[in]r1eFirst bond length i-j
[in]r2eSecond bond length i-k
[in]krrThe force constant
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setCubic ( real  b0,
real  kb,
real  kcub 
)
inline

Set parameters for cubic potential.

Parameters
[in]b0Equilibrium bond length
[in]kbHarmonic force constant
[in]kcubCubic force constant
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setFene ( real  bm,
real  kb 
)
inline

Set parameters for fene potential.

Parameters
[in]bmEquilibrium bond length
[in]kbForce constant
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setHarmonic ( int  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]ftFunction type
[in]rAEquilibrium value A
[in]krAForce constant A
[in]rBEquilibrium value B
[in]krBForce constant B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setHarmonic ( int  ft,
real  rA,
real  krA 
)
inline

Set parameters for harmonic potential.

Parameters
[in]ftFunction type
[in]rAEquilibrium value
[in]krAForce constant
Returns
The structure itself.
iListInput gmx::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]klinAForce constant A
[in]aAThe position of the central atom A
[in]klinBForce constant B
[in]aBThe position of the central atom B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setLinearAngle ( real  klinA,
real  aA 
)
inline

Set parameters for linear angle potential.

Parameters
[in]klinAForce constant
[in]aAThe position of the central atom
Returns
The structure itself.
iListInput gmx::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]b0AEquilibrium value A
[in]cbAForce constant A
[in]betaASteepness parameter A
[in]b0BEquilibrium value B
[in]cbBForce constant B
[in]betaBSteepness parameter B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setMorse ( real  b0A,
real  cbA,
real  betaA 
)
inline

Set parameters for morse potential.

Parameters
[in]b0AEquilibrium value
[in]cbAForce constant
[in]betaASteepness parameter
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setPDihedrals ( int  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]ftFunction type
[in]phiADihedral angle A
[in]cpAForce constant A
[in]multMultiplicity of the angle
[in]phiBDihedral angle B
[in]cpBForce constant B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setPDihedrals ( int  ft,
real  phiA,
real  cpA,
int  mult 
)
inline

Set parameters for proper dihedrals potential.

Parameters
[in]ftFunction type
[in]phiADihedral angle
[in]cpAForce constant
[in]multMultiplicity of the angle
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setPolarization ( real  alpha)
inline

Set parameters for Polarization.

Parameters
[in]alphaPolarizability
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setQuarticAngles ( real  theta,
const real  c[5] 
)
inline

Set parameters for Quartic Angles potential.

Parameters
[in]thetaAngle
[in]cArray of parameters
Returns
The structure itself.
iListInput gmx::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]rbcAForce constants A
[in]rbcBForce constants B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setRbDihedrals ( const real  rbc[NR_RBDIHS])
inline

Set parameters for Ryckaert-Bellemans dihedrals potential.

Parameters
[in]rbcForce constants
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setTholePolarization ( real  a,
real  alpha1,
real  alpha2,
real  rfac 
)
inline

Set parameters for Thole Polarization.

Parameters
[in]aThole factor
[in]alpha1Polarizability 1 (nm^3)
[in]alpha2Polarizability 2 (nm^3)
[in]rfacDistance factor
Returns
The structure itself.
iListInput gmx::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]thetaAEquilibrium angle A
[in]kthetaAForce constant A
[in]r13AThe distance between i and k atoms A
[in]kUBAThe force constant for 1-3 distance A
[in]thetaBEquilibrium angle B
[in]kthetaBForce constant B
[in]r13BThe distance between i and k atoms B
[in]kUBBThe force constant for 1-3 distance B
Returns
The structure itself.
iListInput gmx::anonymous_namespace{bonded.cpp}::iListInput::setUreyBradley ( real  thetaA,
real  kthetaA,
real  r13A,
real  kUBA 
)
inline

Set parameters for Urey Bradley potential.

Parameters
[in]thetaAEquilibrium angle
[in]kthetaAForce constant
[in]r13AThe distance between i and k atoms
[in]kUBAThe force constant for 1-3 distance
Returns
The structure itself.
iListInput gmx::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_xPolarizability X (nm^3)
[in]alpha_yPolarizability Y (nm^3)
[in]alpha_zPolarizability Z (nm^3)
[in]rOHOxygen-Hydrogen distance
[in]rHHHydrogen-Hydrogen distance
[in]rODOxygen-Dummy distance
Returns
The structure itself.

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