src/gromacs/mdtypes/mdatom.h

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  38 /*! \brief
  39  * Declares mdatom data structure.
  40  *
  41  * \inpublicapi
  42  * \ingroup module_mdtypes
  43  */
  44 #ifndef GMX_MDTYPES_MDATOM_H
  45 #define GMX_MDTYPES_MDATOM_H
  46
  47 #include "gromacs/math/vectypes.h"
  48 #include "gromacs/utility/basedefinitions.h"
  49 #include "gromacs/utility/real.h"
  50
  51 typedef struct t_mdatoms
  52 {
  53     //! Total mass in state A
  54     real tmassA;
  55     //! Total mass in state B
  56     real tmassB;
  57     //! Total mass
  58     real tmass;
  59     //! Number of atoms in arrays
  60     int nr;
  61     //! Number of elements in arrays
  62     int nalloc;
  63     //! Number of energy groups
  64     int nenergrp;
  65     //! Do we have multiple center of mass motion removal groups
  66     gmx_bool bVCMgrps;
  67     //! Do we have any virtual sites?
  68     gmx_bool haveVsites;
  69     //! Do we have atoms that are frozen along 1 or 2 (not 3) dimensions?
  70     gmx_bool havePartiallyFrozenAtoms;
  71     //! Number of perturbed atoms
  72     int nPerturbed;
  73     //! Number of atoms for which the mass is perturbed
  74     int nMassPerturbed;
  75     //! Number of atoms for which the charge is perturbed
  76     int nChargePerturbed;
  77     //! Number of atoms for which the type is perturbed
  78     int nTypePerturbed;
  79     //! Do we have orientation restraints
  80     gmx_bool bOrires;
  81     //! Atomic mass in A state
  82     real* massA;
  83     //! Atomic mass in B state
  84     real* massB;
  85     //! Atomic mass in present state
  86     real* massT;
  87     //! Inverse atomic mass per atom, 0 for vsites and shells
  88     real* invmass;
  89     //! Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
  90     rvec* invMassPerDim;
  91     //! Atomic charge in A state
  92     real* chargeA;
  93     //! Atomic charge in B state
  94     real* chargeB;
  95     //! Dispersion constant C6 in A state
  96     real* sqrt_c6A;
  97     //! Dispersion constant C6 in A state
  98     real* sqrt_c6B;
  99     //! Van der Waals radius sigma in the A state
 100     real* sigmaA;
 101     //! Van der Waals radius sigma in the B state
 102     real* sigmaB;
 103     //! Van der Waals radius sigma^3 in the A state
 104     real* sigma3A;
 105     //! Van der Waals radius sigma^3 in the B state
 106     real* sigma3B;
 107     //! Is this atom perturbed
 108     gmx_bool* bPerturbed;
 109     //! Type of atom in the A state
 110     int* typeA;
 111     //! Type of atom in the B state
 112     int* typeB;
 113     //! Particle type
 114     unsigned short* ptype;
 115     //! Group index for temperature coupling
 116     unsigned short* cTC;
 117     //! Group index for energy matrix
 118     unsigned short* cENER;
 119     //! Group index for acceleration
 120     unsigned short* cACC;
 121     //! Group index for freezing
 122     unsigned short* cFREEZE;
 123     //! Group index for center of mass motion removal
 124     unsigned short* cVCM;
 125     //! Group index for user 1
 126     unsigned short* cU1;
 127     //! Group index for user 2
 128     unsigned short* cU2;
 129     //! Group index for orientation restraints
 130     unsigned short* cORF;
 131     //! Number of atoms on this processor. TODO is this still used?
 132     int homenr;
 133     //! The lambda value used to create the contents of the struct
 134     real lambda;
 135 } t_mdatoms;
 136
 137 #endif