Gromacs  2018.8
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t_state Class Reference

#include <gromacs/mdtypes/state.h>

+ Collaboration diagram for t_state:


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.

Move pure observables history to ObservablesHistory.

Public Member Functions

 t_state ()

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::RVecx
 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.
 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.

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