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36 #ifndef _nbnxn_atomdata_h
37 #define _nbnxn_atomdata_h
40 #include "gromacs/mdlib/nbnxn_pairlist.h"
47 /* Default nbnxn allocation routine, allocates 32 byte aligned,
48 * which works for plain C and aligned SSE and AVX loads/stores.
50 void nbnxn_alloc_aligned(void **ptr, size_t nbytes);
52 /* Free function for memory allocated with nbnxn_alloc_aligned */
53 void nbnxn_free_aligned(void *ptr);
55 /* Reallocation wrapper function for nbnxn data structures */
56 void nbnxn_realloc_void(void **ptr,
57 int nbytes_copy, int nbytes_new,
61 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
62 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
64 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
65 * and fills up to na_round using cx,cy,cz.
67 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
68 rvec *x, int nbatFormat, real *xnb, int a0,
69 int cx, int cy, int cz);
72 enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
75 /* Initialize the non-bonded atom data structure.
76 * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
77 * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
78 * to the atom data structure.
79 * enbnxninitcombrule sets what combination rule data gets stored in nbat.
81 void nbnxn_atomdata_init(FILE *fp,
82 nbnxn_atomdata_t *nbat,
84 int enbnxninitcombrule,
85 int ntype, const real *nbfp,
91 /* Copy the atom data to the non-bonded atom data structure */
92 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
94 const nbnxn_search_t nbs,
95 const t_mdatoms *mdatoms,
98 /* Copy the shift vectors to nbat */
99 void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
101 nbnxn_atomdata_t *nbat);
103 /* Copy x to nbat->x.
104 * FillLocal tells if the local filler particle coordinates should be zeroed.
106 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
110 nbnxn_atomdata_t *nbat);
112 /* Add the forces stored in nbat to f, zeros the forces in nbat */
113 void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t nbs,
115 const nbnxn_atomdata_t *nbat,
118 /* Add the fshift force stored in nbat to fshift */
119 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,