t_state Class Reference

#include <gromacs/mdtypes/state.h>

Collaboration diagram for t_state:

Description

The microstate of the system.

The global state will contain complete data for all used entries. The local state with domain decomposition will have partial entries for which stateEntryIsAtomProperty() is true. Some entries that are used in the global state might not be present in the local state.

Todo:

Move pure observables history to ObservablesHistory.

Public Member Functions
int	numAtoms () const
	Returns the number of atoms represented by this state.
void	changeNumAtoms (int numAtoms)
	Change the number of atoms represented by this state, allocating memory as needed.
bool	hasEntry (StateEntry entry) const
	Returns whether entry entry is present.
void	addEntry (StateEntry entry)
	Set entry entry to present, resizes corresponding vector to numAtoms() when relevant.
int	flags () const
	Return an integer with bits set for entries that are present.
void	setFlags (int flags)
	Sets the present entries to the ones set in flags.

Public Attributes
int	ngtc
	The number of temperature coupling groups.
int	nnhpres
	The number of NH-chains for the MTTK barostat (always 1 or 0)
int	nhchainlength
	The NH-chain length for temperature coupling and MTTK barostat.
int	fep_state
	indicates which of the alchemical states we are in
gmx::EnumerationArray < FreeEnergyPerturbationCouplingType, real >	lambda
	Free-energy lambda vector.
matrix	box
	Matrix of box vectors.
matrix	box_rel
	Relative box vectors characteristic of the box shape, used to to preserve that box shape.
matrix	boxv
	Box velocities for Parrinello-Rahman P-coupling.
matrix	pres_prev
	Pressure of the previous step for pcoupl.
matrix	svir_prev
	Shake virial for previous step for pcoupl.
matrix	fvir_prev
	Force virial of the previous step for pcoupl.
std::vector< double >	nosehoover_xi
	Nose-Hoover coordinates (ngtc)
std::vector< double >	nosehoover_vxi
	Nose-Hoover velocities (ngtc)
std::vector< double >	nhpres_xi
	Pressure Nose-Hoover coordinates.
std::vector< double >	nhpres_vxi
	Pressure Nose-Hoover velocities.
std::vector< double >	therm_integral
	Work exterted N-H/V-rescale T-coupling (ngtc)
double	baros_integral
	For Berendsen P-coupling conserved quantity.
real	veta
	Trotter based isotropic P-coupling.
real	vol0
	Initial volume,required for computing MTTK conserved quantity.
PaddedHostVector< gmx::RVec >	x
	The coordinates (numAtoms_)
PaddedHostVector< gmx::RVec >	v
	The velocities (numAtoms_)
PaddedHostVector< gmx::RVec >	cg_p
	p vector for conjugate gradient minimization
ekinstate_t	ekinstate
	The state of the kinetic energy.
history_t	hist
	Time history for restraints.
df_history_t *	dfhist
	Free-energy history for free energy analysis.
std::shared_ptr< gmx::AwhHistory >	awhHistory
	Accelerated weight histogram history.
int	ddp_count
	The DD partitioning count for this state.
int	ddp_count_cg_gl
	The DD partitioning count for index_gl.
std::vector< int >	cg_gl
	The global cg number of the local cgs.
std::vector< double >	pull_com_prev_step
	The COM of the previous step of each pull group.

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

• src/gromacs/mdtypes/state.h
• src/gromacs/mdtypes/state.cpp