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
	t_state ()
	Constructor.

Public Attributes
int	natoms
	Number of atoms, local + non-local; this is the size of x, v and cg_p, when used.
int	ngtc
	The number of temperature coupling groups.
int	nnhpres
	The NH-chain length for the MTTK barostat.
int	nhchainlength
	The NH-chain length for temperature coupling.
int	flags
	Set of bit-flags telling which entries are present, see enum at the top of the file.
int	fep_state
	indicates which of the alchemical states we are in
std::array< real, efptNR >	lambda
	Free-energy lambda vector.
matrix	box
	Matrix of box vectors.
matrix	box_rel
	Relative box vectors to preserve 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.
gmx::HostVector< gmx::RVec >	x
	The coordinates (natoms)
PaddedRVecVector	v
	The velocities (natoms)
PaddedRVecVector	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.

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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