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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 //! Do we have any virtual sites?
67 //! Do we have atoms that are frozen along 1 or 2 (not 3) dimensions?
68 gmx_bool havePartiallyFrozenAtoms;
69 //! Number of perturbed atoms
71 //! Number of atoms for which the mass is perturbed
73 //! Number of atoms for which the charge is perturbed
75 //! Number of atoms for which the type is perturbed
77 //! Do we have orientation restraints
79 //! Atomic mass in A state
81 //! Atomic mass in B state
83 //! Atomic mass in present state
85 //! Inverse atomic mass per atom, 0 for vsites and shells
87 //! Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
89 //! Atomic charge in A state
91 //! Atomic charge in B state
93 //! Dispersion constant C6 in A state
95 //! Dispersion constant C6 in A state
97 //! Van der Waals radius sigma in the A state
99 //! Van der Waals radius sigma in the B state
101 //! Van der Waals radius sigma^3 in the A state
103 //! Van der Waals radius sigma^3 in the B state
105 //! Is this atom perturbed
106 gmx_bool *bPerturbed;
107 //! Type of atom in the A state
109 //! Type of atom in the B state
112 unsigned short *ptype;
113 //! Group index for temperature coupling
115 //! Group index for energy matrix
116 unsigned short *cENER;
117 //! Group index for acceleration
118 unsigned short *cACC;
119 //! Group index for freezing
120 unsigned short *cFREEZE;
121 //! Group index for center of mass motion removal
122 unsigned short *cVCM;
123 //! Group index for user 1
125 //! Group index for user 2
127 //! Group index for orientation restraints
128 unsigned short *cORF;
131 //! Number of atoms on this processor. TODO is this still used?
133 //! The lambda value used to create the contents of the struct