Gromacs
2025-dev-20241002-88a4191
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#include <gromacs/mdtypes/mdatom.h>
Declares mdatom data structure.
Public Attributes | |
real | tmassA |
Total mass in state A. | |
real | tmassB |
Total mass in state B. | |
real | tmass |
Total mass. | |
int | nr |
Number of atoms in arrays. | |
int | nenergrp |
Number of energy groups. | |
bool | bVCMgrps |
Do we have multiple center of mass motion removal groups. | |
bool | haveVsites |
Do we have any virtual sites? | |
bool | havePartiallyFrozenAtoms |
Do we have atoms that are frozen along 1 or 2 (not 3) dimensions? | |
int | nPerturbed |
Number of perturbed atoms. | |
int | nMassPerturbed |
Number of atoms for which the mass is perturbed. | |
int | nChargePerturbed |
Number of atoms for which the charge is perturbed. | |
int | nTypePerturbed |
Number of atoms for which the type is perturbed. | |
bool | bOrires |
Do we have orientation restraints. | |
std::vector< real > | massA |
Atomic mass in A state. | |
std::vector< real > | massB |
Atomic mass in B state. | |
std::vector< real > | massT |
Atomic mass in present state. | |
gmx::PaddedVector< real > | invmass |
Inverse atomic mass per atom, 0 for vsites and shells. | |
std::vector< gmx::RVec > | invMassPerDim |
Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions. | |
gmx::ArrayRef< real > | chargeA |
Atomic charge in A state. | |
gmx::ArrayRef< real > | chargeB |
Atomic charge in B state. | |
std::vector< real > | sqrt_c6A |
Dispersion constant C6 in A state. | |
std::vector< real > | sqrt_c6B |
Dispersion constant C6 in A state. | |
std::vector< real > | sigmaA |
Van der Waals radius sigma in the A state. | |
std::vector< real > | sigmaB |
Van der Waals radius sigma in the B state. | |
std::vector< real > | sigma3A |
Van der Waals radius sigma^3 in the A state. | |
std::vector< real > | sigma3B |
Van der Waals radius sigma^3 in the B state. | |
std::vector< gmx::BoolType > | bPerturbed |
Is this atom perturbed? | |
std::vector< int > | typeA |
Type of atom in the A state. | |
std::vector< int > | typeB |
Type of atom in the B state. | |
std::vector< ParticleType > | ptype |
Particle type. | |
std::vector< unsigned short > | cTC |
Group index for temperature coupling. | |
std::vector< unsigned short > | cENER |
Group index for energy matrix. | |
std::vector< unsigned short > | cACC |
Group index for acceleration. | |
std::vector< unsigned short > | cFREEZE |
Group index for freezing. | |
std::vector< unsigned short > | cVCM |
Group index for center of mass motion removal. | |
std::vector< unsigned short > | cU1 |
Group index for user 1. | |
std::vector< unsigned short > | cU2 |
Group index for user 2. | |
std::vector< unsigned short > | cORF |
Group index for orientation restraints. | |
int | homenr |
Number of atoms on this processor. TODO is this still used? | |
real | lambda |
The lambda value used to create the contents of the struct. | |