Gromacs
2022

#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  nalloc 
Number of elements 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.  
real *  massA 
Atomic mass in A state.  
real *  massB 
Atomic mass in B state.  
real *  massT 
Atomic mass in present state.  
real *  invmass 
Inverse atomic mass per atom, 0 for vsites and shells.  
rvec *  invMassPerDim 
Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions.  
real *  chargeA 
Atomic charge in A state.  
real *  chargeB 
Atomic charge in B state.  
real *  sqrt_c6A 
Dispersion constant C6 in A state.  
real *  sqrt_c6B 
Dispersion constant C6 in A state.  
real *  sigmaA 
Van der Waals radius sigma in the A state.  
real *  sigmaB 
Van der Waals radius sigma in the B state.  
real *  sigma3A 
Van der Waals radius sigma^3 in the A state.  
real *  sigma3B 
Van der Waals radius sigma^3 in the B state.  
bool *  bPerturbed 
Is this atom perturbed.  
int *  typeA 
Type of atom in the A state.  
int *  typeB 
Type of atom in the B state.  
ParticleType *  ptype 
Particle type.  
unsigned short *  cTC 
Group index for temperature coupling.  
unsigned short *  cENER 
Group index for energy matrix.  
unsigned short *  cACC 
Group index for acceleration.  
unsigned short *  cFREEZE 
Group index for freezing.  
unsigned short *  cVCM 
Group index for center of mass motion removal.  
unsigned short *  cU1 
Group index for user 1.  
unsigned short *  cU2 
Group index for user 2.  
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.  