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36 #ifndef GMX_NBNXN_ATOMDATA_H
37 #define GMX_NBNXN_ATOMDATA_H
41 #include "gromacs/math/vectypes.h"
42 #include "gromacs/utility/basedefinitions.h"
43 #include "gromacs/utility/real.h"
52 struct nbnxn_atomdata_t;
59 enum class KernelType;
62 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
63 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
65 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
66 * and fills up to na_round with coordinates that are far away.
68 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
69 const rvec *x, int nbatFormat,
73 enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
76 /* Initialize the non-bonded atom data structure.
77 * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
78 * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
79 * to the atom data structure.
80 * enbnxninitcombrule sets what combination rule data gets stored in nbat.
82 void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
83 nbnxn_atomdata_t *nbat,
84 Nbnxm::KernelType kernelType,
85 int enbnxninitcombrule,
86 int ntype, const real *nbfp,
90 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
91 const nbnxn_search *nbs,
92 const t_mdatoms *mdatoms,
95 /* Copy the shift vectors to nbat */
96 void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
98 nbnxn_atomdata_t *nbat);
100 /* Copy x to nbat->x.
101 * FillLocal tells if the local filler particle coordinates should be zeroed.
103 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search *nbs,
104 Nbnxm::AtomLocality locality,
107 nbnxn_atomdata_t *nbat,
108 gmx_wallcycle *wcycle);
110 /* Add the forces stored in nbat to f, zeros the forces in nbat */
111 void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search *nbs,
112 Nbnxm::AtomLocality locality,
113 nbnxn_atomdata_t *nbat,
115 gmx_wallcycle *wcycle);
117 /* Add the fshift force stored in nbat to fshift */
118 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,