VDW

Van der Waals. More...

Enumerations
enum class	tinker::Vdw : int {   tinker::Vdw::DECOUPLE = 0 , tinker::Vdw::ANNIHILATE = 1 , tinker::Vdw::ATOM_TYPE = 10 , tinker::Vdw::ATOM_CLASS = 11 ,   tinker::Vdw::ARITHMETIC = 20 , tinker::Vdw::GEOMETRIC = 21 , tinker::Vdw::CUBIC_MEAN = 22 , tinker::Vdw::HHG = 23 ,   tinker::Vdw::W_H = 24 , tinker::Vdw::LJ , tinker::Vdw::BUCK , tinker::Vdw::MM3HB ,   tinker::Vdw::HAL , tinker::Vdw::GAUSS }
	Constant flags for the VDW energy functions. More...

Functions
void	tinker::vdwSoftcoreData (RcOp)
void	tinker::evdwData (RcOp)
void	tinker::evdw (int vers)
void	tinker::elj (int vers)
	Lennard-Jones 12-6 potential. More...
void	tinker::elj14 (int vers)
void	tinker::ebuck (int vers)
void	tinker::emm3hb (int vers)
void	tinker::egauss (int vers)
void	tinker::ehal (int vers)
	Halgren buffered 14-7 potential. More...
void	tinker::ehalReduceXyz ()
void	tinker::ehalResolveGradient ()
template<bool DO_G>
__device__ void	tinker::pair_hal (real rik, real rv, real eps, real vscalek, real vlambda, real ghal, real dhal, real scexp, real scalpha, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, int SCALE>
__device__ void	tinker::pair_hal_v2 (real r, real vscale, real rv, real eps, real evcut, real evoff, real vlambda, real ghal, real dhal, real scexp, real scalpha, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, bool SOFTCORE>
__device__ void	tinker::pair_lj_v0 (real r, real invr, real vlambda, real rad, real eps, real &__restrict__ ev, real &__restrict__ dev)
template<bool DO_G, bool SOFTCORE>
__device__ void	tinker::pair_lj_v1 (real rik, real vlambda, real rv, real eps, real vscalek, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, bool SOFTCORE, class RADRULE , class EPSRULE , int SCALE>
__device__ void	tinker::pair_lj_v2 (real r, real invr, real vlambda, real vscale, real radi, real epsi, real radk, real epsk, real evcut, real evoff, real &__restrict__ ev, real &__restrict__ dev)
template<bool DO_G, bool SOFTCORE, int SCALE>
__device__ void	tinker::pair_lj_v3 (real r, real invr, real vlambda, real vscale, real rad, real eps, real evcut, real evoff, real &__restrict__ ev, real &__restrict__ dev)
__device__ real	tinker::pair_vlambda (real vlam, Vdw vcouple, int imut, int kmut)

Variables
real	tinker::ghal
	Value of \( \gamma \) in buffered 14-7 vdw potential. More...
real	tinker::dhal
	Value of \( \delta \) in buffered 14-7 vdw potential. More...
energy_prec	tinker::elrc_vol
	Long-range energy correction (lrc), used as e += lrc/volume. More...
virial_prec	tinker::vlrc_vol
	Long-range virial correction (lrc), used as v(i,i) += lrc/volume. More...
int *	tinker::jvdw
	Type or class index into vdw parameters for each atom. The indices have been sorted and start from 0. More...
real *	tinker::xred
	Halgren buffered 14-7 reduced x, y, z coordinates for each atom. More...
real *	tinker::radmin
	Minimum energy distance (radmin) or well depth parameter (epsilon) for each jvdw pair. Element [j1][j2] is accessed by [njvdw*j1 + j2]. More...
real *	tinker::radmin4
	VDW 1-4 parameters: minimum energy distance and well depth. More...
int	tinker::njvdw
	Number of unique values in the jvdw array. More...
grad_prec *	tinker::gxred
	Halgren buffered 14-7 reduced vdw gradients for each atom. More...
real	tinker::scexp
	Exponential factor for soft core buffered 14-7 potential. More...
real	tinker::scalpha
	Scale factor \( \alpha \) for soft core buffered 14-7 potential. More...
int *	tinker::mut
	State weighting values (lambda) of all atoms for van der Waals potentials. More...

Detailed Description

Van der Waals.

Enumeration Type Documentation

Vdw

enum class tinker::Vdw : int

strong

Constant flags for the VDW energy functions.

Enumerator
DECOUPLE	VDW lambda type: decouple.
ANNIHILATE	VDW lambda type: annihilate.
ATOM_TYPE	Indexing mode.
ATOM_CLASS	Indexing mode.
ARITHMETIC	Combining rule.
GEOMETRIC	Combining rule.
CUBIC_MEAN	Combining rule.
HHG	Combining rule.
W_H	Combining rule.
LJ	Lennard-Jones 12-6 potential.
BUCK	Buckingham potential.
MM3HB	MM3 exp-6 potential.
HAL	Halgren buffered 14-7 potential.
GAUSS	Gaussian expansion VDW potential.

Function Documentation

ebuck()

void tinker::ebuck

(

int

vers

)

egauss()

void tinker::egauss

(

int

vers

)

ehal()

void tinker::ehal

(

int

vers

)

Halgren buffered 14-7 potential.

\[ U(r|r_m,\epsilon) = \epsilon \left(\frac{1+\gamma}{\rho^m+\gamma}-2\right) \left(\frac{1+\delta}{\rho+\delta}\right)^{n-m} \]

\[ \rho = r/r_m,\ n=14,\ m=7,\ \gamma=0.12,\ \delta=0.07 \]

Soft core buffered 14-7 potential.

\[ U(r|\lambda) = \lambda^t\epsilon \left(\frac{1.12}{\alpha(1-\lambda)^2+\rho^7+0.12}-2\right) \frac{1.07^5}{\alpha(1-\lambda)^2+(\rho+0.07)^7} \]

\[ t=5,\ \alpha=0.7 \]

ehalReduceXyz()

void tinker::ehalReduceXyz

(

)

ehalResolveGradient()

void tinker::ehalResolveGradient

(

)

elj()

void tinker::elj

(

int

vers

)

Lennard-Jones 12-6 potential.

\[ U(r|r_m,\epsilon) = \epsilon [(r_m/r)^{12} - 2(r_m/r)^6] \]

elj14()

void tinker::elj14

(

int

vers

)

emm3hb()

void tinker::emm3hb

(

int

vers

)

evdw()

void tinker::evdw

(

int

vers

)

evdwData()

void tinker::evdwData

(

RcOp

)

pair_hal()

template<bool DO_G>

__device__ void tinker::pair_hal	(	real	rik,
		real	rv,
		real	eps,
		real	vscalek,
		real	vlambda,
		real	ghal,
		real	dhal,
		real	scexp,
		real	scalpha,
		real &__restrict__	e,
		real &__restrict__	de
	)

pair_hal_v2()

template<bool DO_G, int SCALE>

__device__ void tinker::pair_hal_v2	(	real	r,
		real	vscale,
		real	rv,
		real	eps,
		real	evcut,
		real	evoff,
		real	vlambda,
		real	ghal,
		real	dhal,
		real	scexp,
		real	scalpha,
		real &__restrict__	e,
		real &__restrict__	de
	)

pair_lj_v0()

template<bool DO_G, bool SOFTCORE>

__device__ void tinker::pair_lj_v0	(	real	r,
		real	invr,
		real	vlambda,
		real	rad,
		real	eps,
		real &__restrict__	ev,
		real &__restrict__	dev
	)

pair_lj_v1()

template<bool DO_G, bool SOFTCORE>

__device__ void tinker::pair_lj_v1	(	real	rik,
		real	vlambda,
		real	rv,
		real	eps,
		real	vscalek,
		real &__restrict__	e,
		real &__restrict__	de
	)

pair_lj_v2()

template<bool DO_G, bool SOFTCORE, class RADRULE , class EPSRULE , int SCALE>

__device__ void tinker::pair_lj_v2	(	real	r,
		real	invr,
		real	vlambda,
		real	vscale,
		real	radi,
		real	epsi,
		real	radk,
		real	epsk,
		real	evcut,
		real	evoff,
		real &__restrict__	ev,
		real &__restrict__	dev
	)

pair_lj_v3()

template<bool DO_G, bool SOFTCORE, int SCALE>

__device__ void tinker::pair_lj_v3	(	real	r,
		real	invr,
		real	vlambda,
		real	vscale,
		real	rad,
		real	eps,
		real	evcut,
		real	evoff,
		real &__restrict__	ev,
		real &__restrict__	dev
	)

pair_vlambda()

__device__ real tinker::pair_vlambda ( real  vlam, Vdw  vcouple, int  imut, int  kmut  )

inline

vdwSoftcoreData()

void tinker::vdwSoftcoreData

(

RcOp

)

Variable Documentation

dhal

real tinker::dhal

extern

Value of \( \delta \) in buffered 14-7 vdw potential.

elrc_vol

energy_prec tinker::elrc_vol

extern

Long-range energy correction (lrc), used as e += lrc/volume.

Note

Must be 0 if system is unbound.

ghal

real tinker::ghal

extern

Value of \( \gamma \) in buffered 14-7 vdw potential.

gxred

grad_prec* tinker::gxred

extern

Halgren buffered 14-7 reduced vdw gradients for each atom.

jvdw

int* tinker::jvdw

extern

Type or class index into vdw parameters for each atom. The indices have been sorted and start from 0.

mut

int* tinker::mut

extern

State weighting values (lambda) of all atoms for van der Waals potentials.

njvdw

int tinker::njvdw

extern

Number of unique values in the jvdw array.

radmin

real* tinker::radmin

extern

Minimum energy distance (radmin) or well depth parameter (epsilon) for each jvdw pair. Element [j1][j2] is accessed by [njvdw*j1 + j2].

See also

njvdw

radmin4

real* tinker::radmin4

extern

VDW 1-4 parameters: minimum energy distance and well depth.

See also

radmin epsilon

scalpha

real tinker::scalpha

extern

Scale factor \( \alpha \) for soft core buffered 14-7 potential.

scexp

real tinker::scexp

extern

Exponential factor for soft core buffered 14-7 potential.

vlrc_vol

virial_prec tinker::vlrc_vol

extern

Long-range virial correction (lrc), used as v(i,i) += lrc/volume.

Note

Must be 0 if system is unbound.

xred

real* tinker::xred

extern

Halgren buffered 14-7 reduced x, y, z coordinates for each atom.