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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 {
51 //! Total mass in state A
53 //! Total mass in state B
57 //! Number of atoms in arrays
59 //! Number of elements in arrays
61 //! Number of energy groups
63 //! Do we have multiple center of mass motion removal groups
65 //! Number of perturbed atoms
67 //! Number of atoms for which the mass is perturbed
69 //! Number of atoms for which the charge is perturbed
71 //! Number of atoms for which the type is perturbed
73 //! Do we have orientation restraints
75 //! Atomic mass in A state
77 //! Atomic mass in B state
79 //! Atomic mass in present state
81 //! Inverse atomic mass per atom, 0 for vsites and shells
83 //! Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
85 //! Atomic charge in A state
87 //! Atomic charge in B state
89 //! Dispersion constant C6 in A state
91 //! Dispersion constant C6 in A state
93 //! Van der Waals radius sigma in the A state
95 //! Van der Waals radius sigma in the B state
97 //! Van der Waals radius sigma^3 in the A state
99 //! Van der Waals radius sigma^3 in the B state
101 //! Is this atom perturbed
102 gmx_bool *bPerturbed;
103 //! Type of atom in the A state
105 //! Type of atom in the B state
108 unsigned short *ptype;
109 //! Group index for temperature coupling
111 //! Group index for energy matrix
112 unsigned short *cENER;
113 //! Group index for acceleration
114 unsigned short *cACC;
115 //! Group index for freezing
116 unsigned short *cFREEZE;
117 //! Group index for center of mass motion removal
118 unsigned short *cVCM;
119 //! Group index for user 1
121 //! Group index for user 2
123 //! Group index for orientation restraints
124 unsigned short *cORF;
127 //! Number of atoms on this processor. TODO is this still used?
129 //! The lambda value used to create the contents of the struct