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2026.0-dev-20251111-8c1ac59
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Gromacs
2026.0-dev-20251111-8c1ac59
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#include <gromacs/mdtypes/mdatom.h>
Collaboration diagram for t_mdatoms: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. | |
1.8.5