Gromacs
2024.4
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#include <gromacs/mdtypes/state.h>
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.
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. | |