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36 #ifndef _nbnxn_atomdata_h
37 #define _nbnxn_atomdata_h
46 /* Default nbnxn allocation routine, allocates 32 byte aligned,
47 * which works for plain C and aligned SSE and AVX loads/stores.
49 void nbnxn_alloc_aligned(void **ptr, size_t nbytes);
51 /* Free function for memory allocated with nbnxn_alloc_aligned */
52 void nbnxn_free_aligned(void *ptr);
54 /* Reallocation wrapper function for nbnxn data structures */
55 void nbnxn_realloc_void(void **ptr,
56 int nbytes_copy, int nbytes_new,
60 /* Reallocate the nbnxn_atomdata_t for a size of n atoms */
61 void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n);
63 /* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
64 * and fills up to na_round using cx,cy,cz.
66 void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
67 rvec *x, int nbatFormat, real *xnb, int a0,
68 int cx, int cy, int cz);
71 enbnxninitcombruleDETECT, enbnxninitcombruleGEOM, enbnxninitcombruleLB, enbnxninitcombruleNONE
74 /* Initialize the non-bonded atom data structure.
75 * The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
76 * Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
77 * to the atom data structure.
78 * enbnxninitcombrule sets what combination rule data gets stored in nbat.
80 void nbnxn_atomdata_init(FILE *fp,
81 nbnxn_atomdata_t *nbat,
83 int enbnxninitcombrule,
84 int ntype, const real *nbfp,
90 /* Copy the atom data to the non-bonded atom data structure */
91 void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
93 const nbnxn_search_t nbs,
94 const t_mdatoms *mdatoms,
97 /* Copy the shift vectors to nbat */
98 void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box,
100 nbnxn_atomdata_t *nbat);
102 /* Copy x to nbat->x.
103 * FillLocal tells if the local filler particle coordinates should be zeroed.
105 void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
109 nbnxn_atomdata_t *nbat);
111 /* Add the forces stored in nbat to f, zeros the forces in nbat */
112 void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t nbs,
114 const nbnxn_atomdata_t *nbat,
117 /* Add the fshift force stored in nbat to fshift */
118 void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,