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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

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
< FreeEnergyPerturbationCouplingType,
 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::RVecx
 The coordinates (numAtoms_)
PaddedHostVector< gmx::RVecv
 The velocities (numAtoms_)
PaddedHostVector< gmx::RVeccg_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.
std::vector< double > pull_com_prev_step
 The COM of the previous step of each pull group.

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