Gromacs
2019
|
#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 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) | |
PaddedVector< gmx::RVec > | v |
The velocities (natoms) | |
PaddedVector< 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. | |