src/gromacs/mdtypes/mdatom.h

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  37 /*! \brief
  38  * Declares mdatom data structure.
  39  *
  40  * \inpublicapi
  41  * \ingroup module_mdtypes
  42  */
  43 #ifndef GMX_MDTYPES_MDATOM_H
  44 #define GMX_MDTYPES_MDATOM_H
  45
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/real.h"
  48
  49 typedef struct t_mdatoms {
  50     //! Total mass in state A
  51     real                   tmassA;
  52     //! Total mass in state B
  53     real                   tmassB;
  54     //! Total mass
  55     real                   tmass;
  56     //! Number of atoms in arrays
  57     int                    nr;
  58     //! Number of elements in arrays
  59     int                    nalloc;
  60     //! Number of energy groups
  61     int                    nenergrp;
  62     //! Do we have multiple center of mass motion removal groups
  63     gmx_bool               bVCMgrps;
  64     //! Number of perturbed atoms
  65     int                    nPerturbed;
  66     //! Number of atoms for which the mass is perturbed
  67     int                    nMassPerturbed;
  68     //! Number of atoms for which the charge is perturbed
  69     int                    nChargePerturbed;
  70     //! Number of atoms for which the type is perturbed
  71     int                    nTypePerturbed;
  72     //! Do we have orientation restraints
  73     gmx_bool               bOrires;
  74     //! Atomic mass in A state
  75     real                  *massA;
  76     //! Atomic mass in B state
  77     real                  *massB;
  78     //! Atomic mass in present state
  79     real                  *massT;
  80     //! Inverse atomic mass
  81     real                  *invmass;
  82     //! Atomic charge in A state
  83     real                  *chargeA;
  84     //! Atomic charge in B state
  85     real                  *chargeB;
  86     //! Dispersion constant C6 in A state
  87     real                  *sqrt_c6A;
  88     //! Dispersion constant C6 in A state
  89     real                  *sqrt_c6B;
  90     //! Van der Waals radius sigma in the A state
  91     real                  *sigmaA;
  92     //! Van der Waals radius sigma in the B state
  93     real                  *sigmaB;
  94     //! Van der Waals radius sigma^3 in the A state
  95     real                  *sigma3A;
  96     //! Van der Waals radius sigma^3 in the B state
  97     real                  *sigma3B;
  98     //! Is this atom perturbed
  99     gmx_bool              *bPerturbed;
 100     //! Type of atom in the A state
 101     int                   *typeA;
 102     //! Type of atom in the B state
 103     int                   *typeB;
 104     //! Particle type
 105     unsigned short        *ptype;
 106     //! Group index for temperature coupling
 107     unsigned short        *cTC;
 108     //! Group index for energy matrix
 109     unsigned short        *cENER;
 110     //! Group index for acceleration
 111     unsigned short        *cACC;
 112     //! Group index for freezing
 113     unsigned short        *cFREEZE;
 114     //! Group index for center of mass motion removal
 115     unsigned short        *cVCM;
 116     //! Group index for user 1
 117     unsigned short        *cU1;
 118     //! Group index for user 2
 119     unsigned short        *cU2;
 120     //! Group index for orientation restraints
 121     unsigned short        *cORF;
 122     //! QMMM atoms
 123     gmx_bool              *bQM;
 124     //! Number of atoms on this processor. TODO is this still used?
 125     int                    homenr;
 126     //! The lambda value used to create the contents of the struct
 127     real                   lambda;
 128 } t_mdatoms;
 129
 130 #endif