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Set interaction masks as gromacs does

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2023-03-23 00:58:25 +01:00
parent f5fd3e265a
commit 296a4c4e01
9 changed files with 171 additions and 57 deletions
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4
gromacs/includes/atom.h
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@@ -22,6 +22,7 @@
# define KERNEL_NAME "CUDA"
# define CLUSTER_M 8
# define CLUSTER_N VECTOR_WIDTH
# define UNROLL_J 1
# define computeForceLJ computeForceLJ_cuda
# define initialIntegrate cudaInitialIntegrate
# define finalIntegrate cudaFinalIntegrate
@@ -32,11 +33,13 @@
# if VECTOR_WIDTH > CLUSTER_M * 2
# define KERNEL_NAME "Simd2xNN"
# define CLUSTER_N (VECTOR_WIDTH / 2)
# define UNROLL_J 2
# define computeForceLJ computeForceLJ_2xnn
// Simd4xN
# else
# define KERNEL_NAME "Simd4xN"
# define CLUSTER_N VECTOR_WIDTH
# define UNROLL_J 1
# define computeForceLJ computeForceLJ_4xn
# endif
# ifdef USE_REFERENCE_VERSION
@@ -116,6 +119,7 @@ typedef struct {
Cluster *iclusters, *jclusters;
int *icluster_bin;
int dummy_cj;
MD_UINT *exclusion_filter;
} Atom;
extern void initAtom(Atom*);

23
gromacs/includes/neighbor.h
View File

@@ -9,13 +9,34 @@
#ifndef __NEIGHBOR_H_
#define __NEIGHBOR_H_
// Interaction masks from GROMACS, things to remember (maybe these confused just me):
// 1. These are not "exclusion" masks as the name suggests in GROMACS, but rather
// interaction masks (1 = interaction, 0 = no interaction)
// 2. These are inverted (maybe because that is how you use in AVX2/AVX512 masking),
// so read them from right to left (least significant to most significant bit)
// All interaction mask is the same for all kernels
#define NBNXN_INTERACTION_MASK_ALL 0xffffffffU
// 4x4 kernel diagonal mask
#define NBNXN_INTERACTION_MASK_DIAG 0x08ceU
// 4x2 kernel diagonal masks
#define NBNXN_INTERACTION_MASK_DIAG_J2_0 0x0002U
#define NBNXN_INTERACTION_MASK_DIAG_J2_1 0x002fU
// 4x8 kernel diagonal masks
#define NBNXN_INTERACTION_MASK_DIAG_J8_0 0xf0f8fcfeU
#define NBNXN_INTERACTION_MASK_DIAG_J8_1 0x0080c0e0U
typedef struct {
int cj;
unsigned int imask;
} NeighborCluster;
typedef struct {
int every;
int ncalls;
int* neighbors;
int maxneighs;
int* numneigh;
int half_neigh;
NeighborCluster* neighbors;
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);