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39 #ifndef _nbnxn_pairlist_h
40 #define _nbnxn_pairlist_h
46 /* A buffer data structure of 64 bytes
47 * to be placed at the beginning and end of structs
48 * to avoid cache invalidation of the real contents
49 * of the struct by writes to neighboring memory.
53 } gmx_cache_protect_t;
55 /* Abstract type for pair searching data */
56 typedef struct nbnxn_search * nbnxn_search_t;
58 /* Function that should return a pointer *ptr to memory
60 * Error handling should be done within this function.
62 typedef void nbnxn_alloc_t (void **ptr, size_t nbytes);
64 /* Function that should free the memory pointed to by *ptr.
65 * NULL should not be passed to this function.
67 typedef void nbnxn_free_t (void *ptr);
70 int cj; /* The j-cluster */
71 unsigned excl; /* The exclusion (interaction) bits */
74 /* In nbnxn_ci_t the integer shift contains the shift in the lower 7 bits.
75 * The upper bits contain information for non-bonded kernel optimization.
76 * Simply calculating LJ and Coulomb for all pairs in a cluster pair is fine.
77 * But three flags can be used to skip interactions, currently only for subc=0
78 * !(shift & NBNXN_CI_DO_LJ(subc)) => we can skip LJ for all pairs
79 * shift & NBNXN_CI_HALF_LJ(subc) => we can skip LJ for the second half of i
80 * !(shift & NBNXN_CI_DO_COUL(subc)) => we can skip Coulomb for all pairs
82 #define NBNXN_CI_SHIFT 127
83 #define NBNXN_CI_DO_LJ(subc) (1<<(7+3*(subc)))
84 #define NBNXN_CI_HALF_LJ(subc) (1<<(8+3*(subc)))
85 #define NBNXN_CI_DO_COUL(subc) (1<<(9+3*(subc)))
87 /* Simple pair-list i-unit */
89 int ci; /* i-cluster */
90 int shift; /* Shift vector index plus possible flags, see above */
91 int cj_ind_start; /* Start index into cj */
92 int cj_ind_end; /* End index into cj */
95 /* Grouped pair-list i-unit */
97 int sci; /* i-super-cluster */
98 int shift; /* Shift vector index plus possible flags */
99 int cj4_ind_start; /* Start index into cj4 */
100 int cj4_ind_end; /* End index into cj4 */
104 unsigned imask; /* The i-cluster interactions mask for 1 warp */
105 int excl_ind; /* Index into the exclusion array for 1 warp */
109 int cj[4]; /* The 4 j-clusters */
110 nbnxn_im_ei_t imei[2]; /* The i-cluster mask data for 2 warps */
114 unsigned pair[32]; /* Exclusion bits for one warp, *
115 * each unsigned has bit for 4*8 i clusters */
119 gmx_cache_protect_t cp0;
121 nbnxn_alloc_t *alloc;
124 gmx_bool bSimple; /* Simple list has na_sc=na_s and uses cj *
125 * Complex list uses cj4 */
127 int na_ci; /* The number of atoms per i-cluster */
128 int na_cj; /* The number of atoms per j-cluster */
129 int na_sc; /* The number of atoms per super cluster */
130 real rlist; /* The radius for constructing the list */
131 int nci; /* The number of i-clusters in the list */
132 nbnxn_ci_t *ci; /* The i-cluster list, size nci */
133 int ci_nalloc; /* The allocation size of ci */
134 int nsci; /* The number of i-super-clusters in the list */
135 nbnxn_sci_t *sci; /* The i-super-cluster list */
136 int sci_nalloc; /* The allocation size of sci */
138 int ncj; /* The number of j-clusters in the list */
139 nbnxn_cj_t *cj; /* The j-cluster list, size ncj */
140 int cj_nalloc; /* The allocation size of cj */
142 int ncj4; /* The total number of 4*j clusters */
143 nbnxn_cj4_t *cj4; /* The 4*j cluster list, size ncj4 */
144 int cj4_nalloc; /* The allocation size of cj4 */
145 int nexcl; /* The count for excl */
146 nbnxn_excl_t *excl; /* Atom interaction bits (non-exclusions) */
147 int excl_nalloc; /* The allocation size for excl */
148 int nci_tot; /* The total number of i clusters */
150 struct nbnxn_list_work *work;
152 gmx_cache_protect_t cp1;
156 int nnbl; /* number of lists */
157 nbnxn_pairlist_t **nbl; /* lists */
158 gmx_bool bCombined; /* TRUE if lists get combined into one (the 1st) */
159 gmx_bool bSimple; /* TRUE if the list of of type "simple"
160 (na_sc=na_s, no super-clusters used) */
161 int natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
162 int natpair_lj; /* Total number of atom pairs for LJ kernel */
163 int natpair_q; /* Total number of atom pairs for Q kernel */
164 } nbnxn_pairlist_set_t;
167 nbatXYZ, nbatXYZQ, nbatX4, nbatX8
171 real *f; /* f, size natoms*fstride */
172 real *fshift; /* Shift force array, size SHIFTS*DIM */
173 int nV; /* The size of *Vvdw and *Vc */
174 real *Vvdw; /* Temporary Van der Waals group energy storage */
175 real *Vc; /* Temporary Coulomb group energy storage */
176 int nVS; /* The size of *VSvdw and *VSc */
177 real *VSvdw; /* Temporary SIMD Van der Waals group energy storage */
178 real *VSc; /* Temporary SIMD Coulomb group energy storage */
179 } nbnxn_atomdata_output_t;
181 /* Block size in atoms for the non-bonded thread force-buffer reduction,
182 * should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8).
183 * Should be small to reduce the reduction and zeroing cost,
184 * but too small will result in overhead.
185 * Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.
188 #define NBNXN_BUFFERFLAG_SIZE 8
190 #define NBNXN_BUFFERFLAG_SIZE 16
193 /* We currently store the reduction flags as bits in an unsigned int.
194 * In most cases this limits the number of flags to 32.
195 * The reduction will automatically disable the flagging and do a full
196 * reduction when the flags won't fit, but this will lead to very slow
197 * reduction. As we anyhow don't expect reasonable performance with
198 * more than 32 threads, we put in this hard limit.
199 * You can increase this number, but the reduction will be very slow.
201 #define NBNXN_BUFFERFLAG_MAX_THREADS 32
203 /* Flags for telling if threads write to force output buffers */
205 int nflag; /* The number of flag blocks */
206 unsigned *flag; /* Bit i is set when thread i writes to a cell-block */
207 int flag_nalloc; /* Allocation size of cxy_flag */
208 } nbnxn_buffer_flags_t;
210 /* LJ combination rules: geometric, Lorentz-Berthelot, none */
212 ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR
216 nbnxn_alloc_t *alloc;
218 int ntype; /* The number of different atom types */
219 real *nbfp; /* Lennard-Jones 6*C6 and 12*C12 params, size ntype^2*2 */
220 int comb_rule; /* Combination rule, see enum above */
221 real *nbfp_comb; /* LJ parameter per atom type, size ntype*2 */
222 real *nbfp_s4; /* As nbfp, but with stride 4, size ntype^2*4. This
223 * might suit 4-wide SIMD loads of two values (e.g.
224 * two floats in single precision on x86). */
225 int natoms; /* Number of atoms */
226 int natoms_local; /* Number of local atoms */
227 int *type; /* Atom types */
228 real *lj_comb; /* LJ parameters per atom for combining for pairs */
229 int XFormat; /* The format of x (and q), enum */
230 int FFormat; /* The format of f, enum */
231 real *q; /* Charges, can be NULL if incorporated in x */
232 int na_c; /* The number of atoms per cluster */
233 int nenergrp; /* The number of energy groups */
234 int neg_2log; /* Log2 of nenergrp */
235 int *energrp; /* The energy groups per cluster, can be NULL */
236 gmx_bool bDynamicBox; /* Do we need to update shift_vec every step? */
237 rvec *shift_vec; /* Shift vectors, copied from t_forcerec */
238 int xstride; /* stride for a coordinate in x (usually 3 or 4) */
239 int fstride; /* stride for a coordinate in f (usually 3 or 4) */
240 real *x; /* x and possibly q, size natoms*xstride */
241 real *simd_4xn_diag; /* indices to set the SIMD 4xN diagonal masks */
242 real *simd_2xnn_diag; /* indices to set the SIMD 2x(N+N)diagonal masks */
243 unsigned *simd_excl_mask; /* exclusion masks for SIMD topology exclusions */
244 int nout; /* The number of force arrays */
245 nbnxn_atomdata_output_t *out; /* Output data structures */
246 int nalloc; /* Allocation size of all arrays (for x/f *x/fstride) */
247 gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
248 nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */