Energy, gradient, virial tensor, and number of interactions. More...

Typedefs
typedef std::map< std::string, int >	tinker::TimeScaleConfig

Functions
void	tinker::zeroEGV (int vers=rc_flag)
	Zero out all of the counts, energies, gradients, and virials on device. More...

void	tinker::scaleGradient (double scale, grad_prec g0x, grad_prec g0y, grad_prec *g0z)
	`g0 *= scale`. More...

void	tinker::sumGradient (grad_prec g0x, grad_prec g0y, grad_prec g0z, const grad_prec g1x, const grad_prec g1y, const grad_prec g1z)
	`g0 += g1`. More...

void	tinker::sumGradient (double scale, grad_prec g0x, grad_prec g0y, grad_prec g0z, const grad_prec g1x, const grad_prec g1y, const grad_prec g1z)
	`g0 += scale*g1`. More...

void	tinker::copyGradientSync (int vers, double grdx, double grdy, double grdz, const grad_prec gx_src, const grad_prec gy_src, const grad_prec gz_src, int queue)
	Copies the energy gradients from device to host. More...

void	tinker::copyGradient (int vers, double grdx, double grdy, double grdz, const grad_prec gx_src, const grad_prec gy_src, const grad_prec gz_src)
	Copies the energy gradients from device to host. More...

void	tinker::copyGradient (int vers, double grdx, double grdy, double *grdz)

void	tinker::copyEnergy (int vers, energy_prec *eng)

void	tinker::energy_core (int vers, unsigned tsflag, const TimeScaleConfig &tsconfig)

void	tinker::energy (int vers)

void	tinker::energy (int vers, unsigned tsflag, const TimeScaleConfig &tsconfig)

void	tinker::energyData (RcOp)
	Entry point to the setup functions of all the potential energy terms. More...

bool	tinker::useEnergyVdw ()
	Logical flag for use of VDW, repulsion, dispersion, etc. terms. More...

bool	tinker::useEnergyElec ()
	Logical flag for use of electrostatic terms. More...

void	tinker::egvData (RcOp)
	Sets up data on device. More...

const TimeScaleConfig &	tinker::defaultTSConfig ()

Variables
grad_prec *	tinker::gx
	Gradient of valence terms; also works as total gradient array. More...

grad_prec *	tinker::gy
	Gradient of valence terms; also works as total gradient array. More...

grad_prec *	tinker::gz
	Gradient of valence terms; also works as total gradient array. More...

grad_prec *	tinker::gx_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...

grad_prec *	tinker::gy_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...

grad_prec *	tinker::gz_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...

grad_prec *	tinker::gx_elec
	Gradient of electrostatic terms. More...

grad_prec *	tinker::gy_elec
	Gradient of electrostatic terms. More...

grad_prec *	tinker::gz_elec
	Gradient of electrostatic terms. More...

EnergyBuffer	tinker::eng_buf
	Energy buffer for the valence terms. More...

EnergyBuffer	tinker::eng_buf_vdw
	Energy buffer for the vdw terms. More...

EnergyBuffer	tinker::eng_buf_elec
	Energy buffer for the electrostatic terms. More...

VirialBuffer	tinker::vir_buf
	Virial buffer for the valence terms. More...

VirialBuffer	tinker::vir_buf_vdw
	Virial buffer for the vdw terms. More...

VirialBuffer	tinker::vir_buf_elec
	Virial buffer for the electrostatic terms. More...

energy_prec	tinker::esum
	Total potential energy. More...

energy_prec	tinker::energy_valence
	Total valence energy. More...

energy_prec	tinker::energy_vdw
	Total vdw energy. More...

energy_prec	tinker::energy_elec
	Total electrostatic energy. More...

virial_prec	tinker::vir [9]
	Total potential virial tensor. More...

virial_prec	tinker::virial_valence [9]
	Total valence virial tensor. More...

virial_prec	tinker::virial_vdw [9]
	Total vdw virial tensor. More...

virial_prec	tinker::virial_elec [9]
	Total electrostatic virial tensor. More...

Detailed Description

Energy, gradient, virial tensor, and number of interactions.

Underlying arrays used in energy, gradient, and viria calculation

Electrostatic terms

	.not. analyz	analyz
ebuf_elec	new array	nullptr
vbuf_elec	new array	nullptr
g_elec	new array	new array
em	alias ebuf_elec	new array
vir_em	alias vbuf_elec	new array
dem	alias g_elec	new array

VDW terms

	.not. analyz	analyz
ebuf_vdw	new array	nullptr
vbuf_vdw	new array	nullptr
g_vdw	new array	new array
ev	alias ebuf_vdw	new array
vir_ev	alias vbuf_vdw	new array
dev	alias g_vdw	new array

Valence terms

	.not. analyz	analyz
ebuf	new array	nullptr
vbuf	new array	nullptr
g	new array	new array
eb	alias ebuf	new array
vir_eb	alias vbuf	new array
deb	alias g	new array

Typedef Documentation

◆ TimeScaleConfig

typedef std::map<std::string, int> tinker::TimeScaleConfig

Time scale configuration that assigns a group number to every energy term. Up to 32 different group numbers are supported, from 0 to 31.

This class must:

implement a C++ style .at(arg) member function where arg is the name of an energy term;
return the group to which arg belongs;
throw an exception if arg is an invalid energy name.

If the k-th bit of the flag is set, all of the energies in Group k will be calculated.

Example 1.

Every energy term in the Verlet integrator is computed at every time-step. Therefore, all of the terms are in the same group. This group (G) can be any number from 0 to 31. Accordingly, the flag must be \( 2^G \).

Example 2.

There are usually two groups, "high frequency" (fast) and "low frequency" (slow), of energy terms in the RESPA integrator. If one decides to assign 3 and 5 to these two groups, respectively, tsconfig.at("ebond") shall return 3 and tsconfig.at("evdw") shall return 5.

The values of flags shall be:

8 ( \( 2^3 \)) for only the fast terms;
32 ( \( 2^5 \)) for only the slow terms;
40 (8 + 32) for both groups.

Note: To use a new energy term in an existing integrator, the force field developers are responsible to update the time scale configuration of this integrator.

Function Documentation

◆ copyEnergy()

void tinker::copyEnergy	(	int	vers,
		energy_prec *	eng
	)

Copies the total potential energy to another variable on host. Avoid accessing esum directly because the potential energy may not be evaluated on the current MD step.

◆ copyGradient() [1/2]

void tinker::copyGradient	(	int	vers,
		double *	grdx,
		double *	grdy,
		double *	grdz
	)

Copies the energy gradients from gx, gy, gz to host.

See also: gx; gy; gz

◆ copyGradient() [2/2]

void tinker::copyGradient	(	int	vers,
		double *	grdx,
		double *	grdy,
		double *	grdz,
		const grad_prec *	gx_src,
		const grad_prec *	gy_src,
		const grad_prec *	gz_src
	)

Copies the energy gradients from device to host.

◆ copyGradientSync()

void tinker::copyGradientSync	(	int	vers,
		double *	grdx,
		double *	grdy,
		double *	grdz,
		const grad_prec *	gx_src,
		const grad_prec *	gy_src,
		const grad_prec *	gz_src,
		int	queue
	)

Copies the energy gradients from device to host.

◆ defaultTSConfig()

const TimeScaleConfig & tinker::defaultTSConfig ( )

Returns: The default TimeScaleConfig object. All of the energy terms are in group 0, and can only be accessed via flag 1.

◆ egvData()

void tinker::egvData ( RcOp )

Sets up data on device.

◆ energy() [1/2]

void tinker::energy ( int vers )

First, energy buffers, virial buffers, gradient arrays, and count buffers are set to 0. Then, evaluate energies, gradients, virials, and count interactions. Last, update the global energy and virial tensor variables. Counts are not updated until countReduce() is explicitly called. May skip some steps based on the version parameter.

◆ energy() [2/2]

void tinker::energy	(	int	vers,
		unsigned	tsflag,
		const TimeScaleConfig &	tsconfig
	)

Initializes to zero and evaluates potential energy with time scale configuration.

See also: TimeScaleConfig

◆ energy_core()

void tinker::energy_core	(	int	vers,
		unsigned	tsflag,
		const TimeScaleConfig &	tsconfig
	)

Evaluates potential energy.

Parameters

vers	Flag to select the version of energy routines.
tsflag	Time scale flag, a 32-bit encrypted integer.
tsconfig	Constant reference to a TimeScaleConfig object.

See also: TimeScaleConfig

◆ energyData()

void tinker::energyData ( RcOp )

Entry point to the setup functions of all the potential energy terms.

◆ scaleGradient()

void tinker::scaleGradient	(	double	scale,
		grad_prec *	g0x,
		grad_prec *	g0y,
		grad_prec *	g0z
	)

g0 *= scale.

◆ sumGradient() [1/2]

void tinker::sumGradient	(	double	scale,
		grad_prec *	g0x,
		grad_prec *	g0y,
		grad_prec *	g0z,
		const grad_prec *	g1x,
		const grad_prec *	g1y,
		const grad_prec *	g1z
	)

g0 += scale*g1.

◆ sumGradient() [2/2]

void tinker::sumGradient	(	grad_prec *	g0x,
		grad_prec *	g0y,
		grad_prec *	g0z,
		const grad_prec *	g1x,
		const grad_prec *	g1y,
		const grad_prec *	g1z
	)

g0 += g1.

◆ useEnergyElec()

bool tinker::useEnergyElec ( )

Logical flag for use of electrostatic terms.

◆ useEnergyVdw()

bool tinker::useEnergyVdw ( )

Logical flag for use of VDW, repulsion, dispersion, etc. terms.

◆ zeroEGV()

void tinker::zeroEGV ( int vers = rc_flag )

Zero out all of the counts, energies, gradients, and virials on device.

Variable Documentation

◆ energy_elec

energy_prec tinker::energy_elec

extern

Total electrostatic energy.

◆ energy_valence

energy_prec tinker::energy_valence

extern

Total valence energy.

◆ energy_vdw

energy_prec tinker::energy_vdw

extern

Total vdw energy.

◆ eng_buf

EnergyBuffer tinker::eng_buf

extern

Energy buffer for the valence terms.

◆ eng_buf_elec

EnergyBuffer tinker::eng_buf_elec

extern

Energy buffer for the electrostatic terms.

◆ eng_buf_vdw

EnergyBuffer tinker::eng_buf_vdw

extern

Energy buffer for the vdw terms.

◆ esum

energy_prec tinker::esum

extern

Total potential energy.

◆ gx

grad_prec* tinker::gx

extern

Gradient of valence terms; also works as total gradient array.

◆ gx_elec

grad_prec* tinker::gx_elec

extern

Gradient of electrostatic terms.

◆ gx_vdw

grad_prec* tinker::gx_vdw

extern

Gradient of VDW, repulsion, dispersion, etc. terms.

◆ gy

grad_prec* tinker::gy

extern

Gradient of valence terms; also works as total gradient array.

◆ gy_elec

grad_prec* tinker::gy_elec

extern

Gradient of electrostatic terms.

◆ gy_vdw

grad_prec* tinker::gy_vdw

extern

Gradient of VDW, repulsion, dispersion, etc. terms.

◆ gz

grad_prec* tinker::gz

extern

Gradient of valence terms; also works as total gradient array.

◆ gz_elec

grad_prec* tinker::gz_elec

extern

Gradient of electrostatic terms.

◆ gz_vdw

grad_prec* tinker::gz_vdw

extern

Gradient of VDW, repulsion, dispersion, etc. terms.

◆ vir

virial_prec tinker::vir[9]

extern

Total potential virial tensor.

◆ vir_buf

VirialBuffer tinker::vir_buf

extern

Virial buffer for the valence terms.

◆ vir_buf_elec

VirialBuffer tinker::vir_buf_elec

extern

Virial buffer for the electrostatic terms.

◆ vir_buf_vdw

VirialBuffer tinker::vir_buf_vdw

extern

Virial buffer for the vdw terms.

◆ virial_elec

virial_prec tinker::virial_elec[9]

extern

Total electrostatic virial tensor.

◆ virial_valence

virial_prec tinker::virial_valence[9]

extern

Total valence virial tensor.

◆ virial_vdw

virial_prec tinker::virial_vdw[9]

extern

Total vdw virial tensor.

Typedefs

Functions

Variables

Detailed Description

Underlying arrays used in energy, gradient, and viria calculation

Electrostatic terms

VDW terms

Valence terms

Typedef Documentation

◆ TimeScaleConfig

Example 1.

Example 2.

Function Documentation

◆ copyEnergy()

◆ copyGradient() [1/2]

◆ copyGradient() [2/2]

◆ copyGradientSync()

◆ defaultTSConfig()

◆ egvData()

◆ energy() [1/2]

◆ energy() [2/2]

◆ energy_core()

◆ energyData()

◆ scaleGradient()

◆ sumGradient() [1/2]

◆ sumGradient() [2/2]

◆ useEnergyElec()

◆ useEnergyVdw()

◆ zeroEGV()

Variable Documentation

◆ energy_elec

◆ energy_valence

◆ energy_vdw

◆ eng_buf

◆ eng_buf_elec

◆ eng_buf_vdw

◆ esum

◆ gx

◆ gx_elec

◆ gx_vdw

◆ gy

◆ gy_elec

◆ gy_vdw

◆ gz

◆ gz_elec

◆ gz_vdw

◆ vir

◆ vir_buf

◆ vir_buf_elec

◆ vir_buf_vdw

◆ virial_elec

◆ virial_valence

◆ virial_vdw