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36 #ifndef _nbnxn_atomdata_h
37 #define _nbnxn_atomdata_h
41 #include "gromacs/math/vectypes.h"
42 #include "gromacs/mdlib/nbnxn_pairlist.h"
43 #include "gromacs/utility/basedefinitions.h"
44 #include "gromacs/utility/real.h"
53 /* Default nbnxn allocation routine, allocates 32 byte aligned,
54 * which works for plain C and aligned SSE and AVX loads/stores.
56 void nbnxn_alloc_aligned(void **ptr, size_t nbytes);
58 /* Free function for memory allocated with nbnxn_alloc_aligned */
59 void nbnxn_free_aligned(void *ptr);
61 /* Reallocation wrapper function for nbnxn data structures */
62 void nbnxn_realloc_void(void **ptr,
63 int nbytes_copy, int nbytes_new,
67 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
68 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
70 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
71 * and fills up to na_round with coordinates that are far away.
73 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
74 const rvec *x, int nbatFormat,
78 enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
81 /* Initialize the non-bonded atom data structure.
82 * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
83 * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
84 * to the atom data structure.
85 * enbnxninitcombrule sets what combination rule data gets stored in nbat.
87 void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
88 nbnxn_atomdata_t *nbat,
90 int enbnxninitcombrule,
91 int ntype, const real *nbfp,
97 /* Copy the atom data to the non-bonded atom data structure */
98 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
99 const nbnxn_search_t nbs,
100 const t_mdatoms *mdatoms,
103 /* Copy the shift vectors to nbat */
104 void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
106 nbnxn_atomdata_t *nbat);
108 /* Copy x to nbat->x.
109 * FillLocal tells if the local filler particle coordinates should be zeroed.
111 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
115 nbnxn_atomdata_t *nbat);
117 /* Add the forces stored in nbat to f, zeros the forces in nbat */
118 void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t nbs,
120 const nbnxn_atomdata_t *nbat,
123 /* Add the fshift force stored in nbat to fshift */
124 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,