* of size nbytes.
* Error handling should be done within this function.
*/
-typedef void nbnxn_alloc_t(void **ptr,size_t nbytes);
+typedef void nbnxn_alloc_t (void **ptr, size_t nbytes);
/* Function that should free the memory pointed to by *ptr.
* NULL should not be passed to this function.
*/
-typedef void nbnxn_free_t(void *ptr);
+typedef void nbnxn_free_t (void *ptr);
typedef struct {
int cj; /* The j-cluster */
typedef struct {
unsigned imask; /* The i-cluster interactions mask for 1 warp */
- int excl_ind; /* Index into the exclusion array for 1 warp */
+ int excl_ind; /* Index into the exclusion array for 1 warp */
} nbnxn_im_ei_t;
typedef struct {
- int cj[4]; /* The 4 j-clusters */
+ int cj[4]; /* The 4 j-clusters */
nbnxn_im_ei_t imei[2]; /* The i-cluster mask data for 2 warps */
} nbnxn_cj4_t;
typedef struct {
gmx_cache_protect_t cp0;
- nbnxn_alloc_t *alloc;
- nbnxn_free_t *free;
-
- gmx_bool bSimple; /* Simple list has na_sc=na_s and uses cj *
- * Complex list uses cj4 */
-
- int na_ci; /* The number of atoms per i-cluster */
- int na_cj; /* The number of atoms per j-cluster */
- int na_sc; /* The number of atoms per super cluster */
- real rlist; /* The radius for constructing the list */
- int nci; /* The number of i-clusters in the list */
- nbnxn_ci_t *ci; /* The i-cluster list, size nci */
- int ci_nalloc; /* The allocation size of ci */
- int nsci; /* The number of i-super-clusters in the list */
- nbnxn_sci_t *sci; /* The i-super-cluster list */
- int sci_nalloc; /* The allocation size of sci */
-
- int ncj; /* The number of j-clusters in the list */
- nbnxn_cj_t *cj; /* The j-cluster list, size ncj */
- int cj_nalloc; /* The allocation size of cj */
-
- int ncj4; /* The total number of 4*j clusters */
- nbnxn_cj4_t *cj4; /* The 4*j cluster list, size ncj4 */
- int cj4_nalloc; /* The allocation size of cj4 */
- int nexcl; /* The count for excl */
- nbnxn_excl_t *excl; /* Atom interaction bits (non-exclusions) */
- int excl_nalloc; /* The allocation size for excl */
- int nci_tot; /* The total number of i clusters */
+ nbnxn_alloc_t *alloc;
+ nbnxn_free_t *free;
+
+ gmx_bool bSimple; /* Simple list has na_sc=na_s and uses cj *
+ * Complex list uses cj4 */
+
+ int na_ci; /* The number of atoms per i-cluster */
+ int na_cj; /* The number of atoms per j-cluster */
+ int na_sc; /* The number of atoms per super cluster */
+ real rlist; /* The radius for constructing the list */
+ int nci; /* The number of i-clusters in the list */
+ nbnxn_ci_t *ci; /* The i-cluster list, size nci */
+ int ci_nalloc; /* The allocation size of ci */
+ int nsci; /* The number of i-super-clusters in the list */
+ nbnxn_sci_t *sci; /* The i-super-cluster list */
+ int sci_nalloc; /* The allocation size of sci */
+
+ int ncj; /* The number of j-clusters in the list */
+ nbnxn_cj_t *cj; /* The j-cluster list, size ncj */
+ int cj_nalloc; /* The allocation size of cj */
+
+ int ncj4; /* The total number of 4*j clusters */
+ nbnxn_cj4_t *cj4; /* The 4*j cluster list, size ncj4 */
+ int cj4_nalloc; /* The allocation size of cj4 */
+ int nexcl; /* The count for excl */
+ nbnxn_excl_t *excl; /* Atom interaction bits (non-exclusions) */
+ int excl_nalloc; /* The allocation size for excl */
+ int nci_tot; /* The total number of i clusters */
struct nbnxn_list_work *work;
- gmx_cache_protect_t cp1;
+ gmx_cache_protect_t cp1;
} nbnxn_pairlist_t;
typedef struct {
- int nnbl; /* number of lists */
- nbnxn_pairlist_t **nbl; /* lists */
- gmx_bool bCombined; /* TRUE if lists get combined into one (the 1st) */
- gmx_bool bSimple; /* TRUE if the list of of type "simple"
- (na_sc=na_s, no super-clusters used) */
- int natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
- int natpair_lj; /* Total number of atom pairs for LJ kernel */
- int natpair_q; /* Total number of atom pairs for Q kernel */
+ int nnbl; /* number of lists */
+ nbnxn_pairlist_t **nbl; /* lists */
+ gmx_bool bCombined; /* TRUE if lists get combined into one (the 1st) */
+ gmx_bool bSimple; /* TRUE if the list of of type "simple"
+ (na_sc=na_s, no super-clusters used) */
+ int natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
+ int natpair_lj; /* Total number of atom pairs for LJ kernel */
+ int natpair_q; /* Total number of atom pairs for Q kernel */
} nbnxn_pairlist_set_t;
-enum { nbatXYZ, nbatXYZQ, nbatX4, nbatX8 };
+enum {
+ nbatXYZ, nbatXYZQ, nbatX4, nbatX8
+};
typedef struct {
real *f; /* f, size natoms*fstride */
real *fshift; /* Shift force array, size SHIFTS*DIM */
- int nV; /* The size of *Vvdw and *Vc */
+ int nV; /* The size of *Vvdw and *Vc */
real *Vvdw; /* Temporary Van der Waals group energy storage */
real *Vc; /* Temporary Coulomb group energy storage */
- int nVS; /* The size of *VSvdw and *VSc */
+ int nVS; /* The size of *VSvdw and *VSc */
real *VSvdw; /* Temporary SIMD Van der Waals group energy storage */
real *VSc; /* Temporary SIMD Coulomb group energy storage */
} nbnxn_atomdata_output_t;
/* Flags for telling if threads write to force output buffers */
typedef struct {
- int nflag; /* The number of flag blocks */
- unsigned *flag; /* Bit i is set when thread i writes to a cell-block */
- int flag_nalloc; /* Allocation size of cxy_flag */
+ int nflag; /* The number of flag blocks */
+ unsigned *flag; /* Bit i is set when thread i writes to a cell-block */
+ int flag_nalloc; /* Allocation size of cxy_flag */
} nbnxn_buffer_flags_t;
/* LJ combination rules: geometric, Lorentz-Berthelot, none */
-enum { ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR };
+enum {
+ ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR
+};
typedef struct {
- nbnxn_alloc_t *alloc;
- nbnxn_free_t *free;
- int ntype; /* The number of different atom types */
- real *nbfp; /* Lennard-Jones 6*C6 and 12*C12 params, size ntype^2*2 */
- int comb_rule; /* Combination rule, see enum above */
- real *nbfp_comb; /* LJ parameter per atom type, size ntype*2 */
- real *nbfp_s4; /* As nbfp, but with stride 4, size ntype^2*4 */
- int natoms; /* Number of atoms */
- int natoms_local; /* Number of local atoms */
- int *type; /* Atom types */
- real *lj_comb; /* LJ parameters per atom for combining for pairs */
- int XFormat; /* The format of x (and q), enum */
- int FFormat; /* The format of f, enum */
- real *q; /* Charges, can be NULL if incorporated in x */
- int na_c; /* The number of atoms per cluster */
- int nenergrp; /* The number of energy groups */
- int neg_2log; /* Log2 of nenergrp */
- int *energrp; /* The energy groups per cluster, can be NULL */
- gmx_bool bDynamicBox; /* Do we need to update shift_vec every step? */
- rvec *shift_vec; /* Shift vectors, copied from t_forcerec */
- int xstride; /* stride for a coordinate in x (usually 3 or 4) */
- int fstride; /* stride for a coordinate in f (usually 3 or 4) */
- real *x; /* x and possibly q, size natoms*xstride */
- real *simd_4xn_diag; /* indices to set the SIMD 4xN diagonal masks */
- real *simd_2xnn_diag; /* indices to set the SIMD 2x(N+N)diagonal masks */
- int nout; /* The number of force arrays */
- nbnxn_atomdata_output_t *out; /* Output data structures */
- int nalloc; /* Allocation size of all arrays (for x/f *x/fstride) */
- gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
- nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
+ nbnxn_alloc_t *alloc;
+ nbnxn_free_t *free;
+ int ntype; /* The number of different atom types */
+ real *nbfp; /* Lennard-Jones 6*C6 and 12*C12 params, size ntype^2*2 */
+ int comb_rule; /* Combination rule, see enum above */
+ real *nbfp_comb; /* LJ parameter per atom type, size ntype*2 */
+ real *nbfp_s4; /* As nbfp, but with stride 4, size ntype^2*4 */
+ int natoms; /* Number of atoms */
+ int natoms_local; /* Number of local atoms */
+ int *type; /* Atom types */
+ real *lj_comb; /* LJ parameters per atom for combining for pairs */
+ int XFormat; /* The format of x (and q), enum */
+ int FFormat; /* The format of f, enum */
+ real *q; /* Charges, can be NULL if incorporated in x */
+ int na_c; /* The number of atoms per cluster */
+ int nenergrp; /* The number of energy groups */
+ int neg_2log; /* Log2 of nenergrp */
+ int *energrp; /* The energy groups per cluster, can be NULL */
+ gmx_bool bDynamicBox; /* Do we need to update shift_vec every step? */
+ rvec *shift_vec; /* Shift vectors, copied from t_forcerec */
+ int xstride; /* stride for a coordinate in x (usually 3 or 4) */
+ int fstride; /* stride for a coordinate in f (usually 3 or 4) */
+ real *x; /* x and possibly q, size natoms*xstride */
+ real *simd_4xn_diag; /* indices to set the SIMD 4xN diagonal masks */
+ real *simd_2xnn_diag; /* indices to set the SIMD 2x(N+N)diagonal masks */
+ int nout; /* The number of force arrays */
+ nbnxn_atomdata_output_t *out; /* Output data structures */
+ int nalloc; /* Allocation size of all arrays (for x/f *x/fstride) */
+ gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
+ nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
} nbnxn_atomdata_t;
#ifdef __cplusplus
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff