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38 * Declares mdatom data structure.
41 * \ingroup module_mdtypes
43 #ifndef GMX_MDTYPES_MDATOM_H
44 #define GMX_MDTYPES_MDATOM_H
46 #include "gromacs/math/vectypes.h"
47 #include "gromacs/utility/basedefinitions.h"
48 #include "gromacs/utility/real.h"
50 typedef struct t_mdatoms
52 //! Total mass in state A
54 //! Total mass in state B
58 //! Number of atoms in arrays
60 //! Number of elements in arrays
62 //! Number of energy groups
64 //! Do we have multiple center of mass motion removal groups
66 //! Do we have any virtual sites?
68 //! Do we have atoms that are frozen along 1 or 2 (not 3) dimensions?
69 gmx_bool havePartiallyFrozenAtoms;
70 //! Number of perturbed atoms
72 //! Number of atoms for which the mass is perturbed
74 //! Number of atoms for which the charge is perturbed
76 //! Number of atoms for which the type is perturbed
78 //! Do we have orientation restraints
80 //! Atomic mass in A state
82 //! Atomic mass in B state
84 //! Atomic mass in present state
86 //! Inverse atomic mass per atom, 0 for vsites and shells
88 //! Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
90 //! Atomic charge in A state
92 //! Atomic charge in B state
94 //! Dispersion constant C6 in A state
96 //! Dispersion constant C6 in A state
98 //! Van der Waals radius sigma in the A state
100 //! Van der Waals radius sigma in the B state
102 //! Van der Waals radius sigma^3 in the A state
104 //! Van der Waals radius sigma^3 in the B state
106 //! Is this atom perturbed
107 gmx_bool* bPerturbed;
108 //! Type of atom in the A state
110 //! Type of atom in the B state
113 unsigned short* ptype;
114 //! Group index for temperature coupling
116 //! Group index for energy matrix
117 unsigned short* cENER;
118 //! Group index for acceleration
119 unsigned short* cACC;
120 //! Group index for freezing
121 unsigned short* cFREEZE;
122 //! Group index for center of mass motion removal
123 unsigned short* cVCM;
124 //! Group index for user 1
126 //! Group index for user 2
128 //! Group index for orientation restraints
129 unsigned short* cORF;
132 //! Number of atoms on this processor. TODO is this still used?
134 //! The lambda value used to create the contents of the struct