#include <gromacs/mdlib/update.h>

Description

Contains data for update phase.

Classes
class	Impl
	pImpled implementation for Update More...

Public Member Functions
	Update (const t_inputrec &inputRecord, BoxDeformation *boxDeformation)
	Constructor. More...

	~Update ()
	Destructor.

PaddedVector< gmx::RVec > *	xp ()
	Get the pointer to updated coordinates. More...

BoxDeformation *	deform () const
	Getter to local copy of box deformation class. More...

void	updateAfterPartition (int numAtoms, gmx::ArrayRef< const unsigned short > cFREEZE, gmx::ArrayRef< const unsigned short > cTC, gmx::ArrayRef< const unsigned short > cAcceleration)
	Sets data that changes only at domain decomposition time. More...

void	update_coords (const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const rvec > invMassPerDim, t_state state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata fcdata, const gmx_ekindata_t ekind, const matrix M, int updatePart, const t_commrec cr, bool haveConstraints)
	Perform numerical integration step. More...

void	finish_update (const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, t_state state, gmx_wallcycle wcycle, bool haveConstraints)
	Finalize the coordinate update. More...

void	update_sd_second_half (const t_inputrec &inputRecord, int64_t step, real dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state state, const t_commrec cr, t_nrnb nrnb, gmx_wallcycle wcycle, gmx::Constraints constr, bool do_log, bool do_ene)
	Secong part of the SD integrator. More...

void	update_for_constraint_virial (const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const rvec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind)
	Performs a leap-frog update without updating `state` so the constrain virial can be computed.

void	update_temperature_constants (const t_inputrec &inputRecord)
	Update pre-computed constants that depend on the reference temperature for coupling. More...

const std::vector< bool > &	getAndersenRandomizeGroup () const
	Getter for the list of the randomize groups. More...

const std::vector< real > &	getBoltzmanFactor () const
	Getter for the list of the Boltzmann factors. More...

Constructor & Destructor Documentation

Update::Update	(	const t_inputrec &	inputRecord,
		BoxDeformation *	boxDeformation
	)

Constructor.

Parameters

[in]	inputRecord	Input record, used to construct SD object.
[in]	boxDeformation	Periodic box deformation object.

Member Function Documentation

BoxDeformation * Update::deform ( ) const

Getter to local copy of box deformation class.

Returns: handle to box deformation class

void Update::finish_update	(	const t_inputrec &	inputRecord,
		bool	havePartiallyFrozenAtoms,
		int	homenr,
		t_state *	state,
		gmx_wallcycle *	wcycle,
		bool	haveConstraints
	)

Finalize the coordinate update.

Copy the updated coordinates to the main coordinates buffer for the atoms that are not frozen.

Parameters

[in]	inputRecord	Input record.
[in]	havePartiallyFrozenAtoms	Whether atoms are frozen along 1 or 2 (not 3) dimensions?
[in]	homenr	The number of atoms on this processor.
[in]	state	System state object.
[in]	wcycle	Wall-clock cycle counter.
[in]	haveConstraints	If the system has constraints.

const std::vector< bool > & Update::getAndersenRandomizeGroup ( ) const

Getter for the list of the randomize groups.

Needed for Andersen temperature control.

Returns: Reference to the groups from the SD data object.

const std::vector< real > & Update::getBoltzmanFactor ( ) const

Getter for the list of the Boltzmann factors.

Needed for Andersen temperature control.

Returns: Reference to the Boltzmann factors from the SD data object.

void Update::update_coords	(	const t_inputrec &	inputRecord,
		int64_t	step,
		int	homenr,
		bool	havePartiallyFrozenAtoms,
		gmx::ArrayRef< const ParticleType >	ptype,
		gmx::ArrayRef< const real >	invMass,
		gmx::ArrayRef< const rvec >	invMassPerDim,
		t_state *	state,
		const gmx::ArrayRefWithPadding< const gmx::RVec > &	f,
		t_fcdata *	fcdata,
		const gmx_ekindata_t *	ekind,
		const matrix	M,
		int	updatePart,
		const t_commrec *	cr,
		bool	haveConstraints
	)

Perform numerical integration step.

Selects the appropriate integrator, based on the input record and performs a numerical integration step.

Parameters

[in]	inputRecord	Input record.
[in]	step	Current timestep.
[in]	homenr	The number of atoms on this processor.
[in]	havePartiallyFrozenAtoms	Whether atoms are frozen along 1 or 2 (not 3) dimensions?
[in]	ptype	The list of particle types.
[in]	invMass	Inverse atomic mass per atom, 0 for vsites and shells.
[in]	invMassPerDim	Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
[in]	state	System state object.
[in]	f	Buffer with atomic forces for home particles.
[in]	fcdata	Force calculation data to update distance and orientation restraints.
[in]	ekind	Kinetic energy data (for temperature coupling, energy groups, etc.).
[in]	M	Parrinello-Rahman velocity scaling matrix.
[in]	updatePart	What should be updated, coordinates or velocities. This enum only used in VV integrator.
[in]	cr	Comunication record (Old comment: these shouldn't be here – need to think about it).
[in]	haveConstraints	If the system has constraints.

void Update::update_sd_second_half	(	const t_inputrec &	inputRecord,
		int64_t	step,
		real *	dvdlambda,
		int	homenr,
		gmx::ArrayRef< const ParticleType >	ptype,
		gmx::ArrayRef< const real >	invMass,
		t_state *	state,
		const t_commrec *	cr,
		t_nrnb *	nrnb,
		gmx_wallcycle *	wcycle,
		gmx::Constraints *	constr,
		bool	do_log,
		bool	do_ene
	)

Secong part of the SD integrator.

The first part of integration is performed in the update_coords(...) method.

Parameters

[in]	inputRecord	Input record.
[in]	step	Current timestep.
[in]	dvdlambda	Free energy derivative. Contribution to be added to the bonded interactions.
[in]	homenr	The number of atoms on this processor.
[in]	ptype	The list of particle types.
[in]	invMass	Inverse atomic mass per atom, 0 for vsites and shells.
[in]	state	System state object.
[in]	cr	Comunication record.
[in]	nrnb	Cycle counters.
[in]	wcycle	Wall-clock cycle counter.
[in]	constr	Constraints object. The constraints are applied on coordinates after update.
[in]	do_log	If this is logging step.
[in]	do_ene	If this is an energy evaluation step.

void Update::update_temperature_constants ( const t_inputrec & inputRecord )

Update pre-computed constants that depend on the reference temperature for coupling.

This could change e.g. in simulated annealing.

Parameters

[in] inputRecord Input record.

void Update::updateAfterPartition	(	int	numAtoms,
		gmx::ArrayRef< const unsigned short >	cFREEZE,
		gmx::ArrayRef< const unsigned short >	cTC,
		gmx::ArrayRef< const unsigned short >	cAcceleration
	)

Sets data that changes only at domain decomposition time.

Parameters

[in]	numAtoms	Updated number of atoms.
[in]	cFREEZE	Group index for freezing
[in]	cTC	Group index for center of mass motion removal
[in]	cAcceleration	Group index for constant acceleration groups

PaddedVector< RVec > * Update::xp ( )

Get the pointer to updated coordinates.

Update saves the updated coordinates into separate buffer, so that constraints will have access to both updated and not update coordinates. For that, update owns a separate buffer. See finish_update(...) for details.

Returns: The pointer to the intermediate coordinates buffer.

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

src/gromacs/mdlib/update.h
src/gromacs/mdlib/update.cpp

Description

Classes

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation