/* * Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg. * All rights reserved. This file is part of MD-Bench. * Use of this source code is governed by a LGPL-3.0 * license that can be found in the LICENSE file. */ #include #ifndef __ATOM_H_ #define __ATOM_H_ #define DELTA 20000 // Nbnxn layouts (as of GROMACS): // Simd4xN: M=4, N=VECTOR_WIDTH // Simd2xNN: M=4, N=(VECTOR_WIDTH/2) // Cuda: M=8, N=VECTOR_WIDTH #ifdef CUDA_TARGET # undef VECTOR_WIDTH # define VECTOR_WIDTH 8 # define KERNEL_NAME "CUDA" # define CLUSTER_M 8 # define CLUSTER_N VECTOR_WIDTH #ifdef USE_SUPER_CLUSTERS # define XX 0 # define YY 1 # define ZZ 2 # define SCLUSTER_SIZE_X 2 # define SCLUSTER_SIZE_Y 2 # define SCLUSTER_SIZE_Z 2 # define SCLUSTER_SIZE (SCLUSTER_SIZE_X * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_Z) # define DIM_COORD(dim,coord) ((dim == XX) ? atom_x(coord) : ((dim == YY) ? atom_y(coord) : atom_z(coord))) # define MIN(a,b) ({int _a = (a), _b = (b); _a < _b ? _a : _b; }) # define SCLUSTER_M CLUSTER_M * SCLUSTER_SIZE # define computeForceLJ computeForceLJSup_cuda #else # define computeForceLJ computeForceLJ_cuda #endif //USE_SUPER_CLUSTERS # define initialIntegrate cudaInitialIntegrate # define finalIntegrate cudaFinalIntegrate # define updatePbc cudaUpdatePbc #else # define CLUSTER_M 4 // Simd2xNN (here used for single-precision) # if VECTOR_WIDTH > CLUSTER_M * 2 # define KERNEL_NAME "Simd2xNN" # define CLUSTER_N (VECTOR_WIDTH / 2) # define computeForceLJ computeForceLJ_2xnn // Simd4xN # else # define KERNEL_NAME "Simd4xN" # define CLUSTER_N VECTOR_WIDTH # define computeForceLJ computeForceLJ_4xn # endif # ifdef USE_REFERENCE_VERSION # undef KERNEL_NAME # undef computeForceLJ # define KERNEL_NAME "Reference" # define computeForceLJ computeForceLJ_ref # endif # define initialIntegrate cpuInitialIntegrate # define finalIntegrate cpuFinalIntegrate # define updatePbc cpuUpdatePbc #endif #if CLUSTER_M == CLUSTER_N # define CJ0_FROM_CI(a) (a) # define CJ1_FROM_CI(a) (a) # define CI_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b)) # define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b)) #ifdef USE_SUPER_CLUSTERS # define CJ1_FROM_SCI(a) (a) # define SCI_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b)) # define SCJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b)) #endif //USE_SUPER_CLUSTERS #elif CLUSTER_M == CLUSTER_N * 2 // M > N # define CJ0_FROM_CI(a) ((a) << 1) # define CJ1_FROM_CI(a) (((a) << 1) | 0x1) # define CI_BASE_INDEX(a,b) ((a) * CLUSTER_M * (b)) # define CJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1)) #ifdef USE_SUPER_CLUSTERS # define SCI_BASE_INDEX(a,b) ((a) * CLUSTER_M * SCLUSTER_SIZE * (b)) # define SCJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * SCLUSTER_SIZE * (b) + ((a) & 0x1) * (SCLUSTER_SIZE * CLUSTER_M >> 1)) #endif //USE_SUPER_CLUSTERS #elif CLUSTER_M == CLUSTER_N / 2 // M < N # define CJ0_FROM_CI(a) ((a) >> 1) # define CJ1_FROM_CI(a) ((a) >> 1) # define CI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1)) # define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b)) #ifdef USE_SUPER_CLUSTERS # define SCI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * SCLUSTER_SIZE * (b) + ((a) & 0x1) * (CLUSTER_N * SCLUSTER_SIZE >> 1)) # define SCJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b)) #endif //USE_SUPER_CLUSTERS #else # error "Invalid cluster configuration!" #endif #if CLUSTER_N != 2 && CLUSTER_N != 4 && CLUSTER_N != 8 # error "Cluster N dimension can be only 2, 4 and 8" #endif #define CI_SCALAR_BASE_INDEX(a) (CI_BASE_INDEX(a, 1)) #define CI_VECTOR_BASE_INDEX(a) (CI_BASE_INDEX(a, 3)) #define CJ_SCALAR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 1)) #define CJ_VECTOR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 3)) #ifdef USE_SUPER_CLUSTERS #define SCI_SCALAR_BASE_INDEX(a) (SCI_BASE_INDEX(a, 1)) #define SCI_VECTOR_BASE_INDEX(a) (SCI_BASE_INDEX(a, 3)) #define SCJ_SCALAR_BASE_INDEX(a) (SCJ_BASE_INDEX(a, 1)) #define SCJ_VECTOR_BASE_INDEX(a) (SCJ_BASE_INDEX(a, 3)) #endif //USE_SUPER_CLUSTERS #if CLUSTER_M >= CLUSTER_N # define CL_X_OFFSET (0 * CLUSTER_M) # define CL_Y_OFFSET (1 * CLUSTER_M) # define CL_Z_OFFSET (2 * CLUSTER_M) #ifdef USE_SUPER_CLUSTERS # define SCL_CL_X_OFFSET(ci) (ci * CLUSTER_M + 0 * SCLUSTER_M) # define SCL_CL_Y_OFFSET(ci) (ci * CLUSTER_M + 1 * SCLUSTER_M) # define SCL_CL_Z_OFFSET(ci) (ci * CLUSTER_M + 2 * SCLUSTER_M) # define SCL_X_OFFSET (0 * SCLUSTER_M) # define SCL_Y_OFFSET (1 * SCLUSTER_M) # define SCL_Z_OFFSET (2 * SCLUSTER_M) #endif //USE_SUPER_CLUSTERS #else # define CL_X_OFFSET (0 * CLUSTER_N) # define CL_Y_OFFSET (1 * CLUSTER_N) # define CL_Z_OFFSET (2 * CLUSTER_N) #ifdef USE_SUPER_CLUSTERS # define SCL_X_OFFSET (0 * SCLUSTER_SIZE * CLUSTER_N) # define SCL_Y_OFFSET (1 * SCLUSTER_SIZE * CLUSTER_N) # define SCL_Z_OFFSET (2 * SCLUSTER_SIZE * CLUSTER_N) #endif //USE_SUPER_CLUSTERS #endif typedef struct { int natoms; MD_FLOAT bbminx, bbmaxx; MD_FLOAT bbminy, bbmaxy; MD_FLOAT bbminz, bbmaxz; } Cluster; typedef struct { int nclusters; MD_FLOAT bbminx, bbmaxx; MD_FLOAT bbminy, bbmaxy; MD_FLOAT bbminz, bbmaxz; } SuperCluster; typedef struct { int Natoms, Nlocal, Nghost, Nmax; int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max; MD_FLOAT *x, *y, *z; MD_FLOAT *vx, *vy, *vz; int *border_map; int *type; int ntypes; MD_FLOAT *epsilon; MD_FLOAT *sigma6; MD_FLOAT *cutforcesq; MD_FLOAT *cutneighsq; int *PBCx, *PBCy, *PBCz; // Data in cluster format MD_FLOAT *cl_x; MD_FLOAT *cl_v; MD_FLOAT *cl_f; int *cl_type; Cluster *iclusters, *jclusters; int *icluster_bin; int dummy_cj; #ifdef USE_SUPER_CLUSTERS int Nsclusters, Nsclusters_local, Nsclusters_ghost, Nsclusters_max; MD_FLOAT *scl_x; MD_FLOAT *scl_v; MD_FLOAT *scl_f; int *scl_type; int *icluster_idx; SuperCluster *siclusters; int *sicluster_bin; #endif //USE_SUPER_CLUSTERS } Atom; extern void initAtom(Atom*); extern void createAtom(Atom*, Parameter*); extern int readAtom(Atom*, Parameter*); extern int readAtom_pdb(Atom*, Parameter*); extern int readAtom_gro(Atom*, Parameter*); extern int readAtom_dmp(Atom*, Parameter*); extern void growAtom(Atom*); extern void growClusters(Atom*); extern void growSuperClusters(Atom*); #ifdef AOS # define POS_DATA_LAYOUT "AoS" # define atom_x(i) atom->x[(i) * 3 + 0] # define atom_y(i) atom->x[(i) * 3 + 1] # define atom_z(i) atom->x[(i) * 3 + 2] /* # define atom_vx(i) atom->vx[(i) * 3 + 0] # define atom_vy(i) atom->vx[(i) * 3 + 1] # define atom_vz(i) atom->vx[(i) * 3 + 2] # define atom_fx(i) atom->fx[(i) * 3 + 0] # define atom_fy(i) atom->fx[(i) * 3 + 1] # define atom_fz(i) atom->fx[(i) * 3 + 2] */ #else # define POS_DATA_LAYOUT "SoA" # define atom_x(i) atom->x[i] # define atom_y(i) atom->y[i] # define atom_z(i) atom->z[i] #endif // TODO: allow to switch velocites and forces to AoS # define atom_vx(i) atom->vx[i] # define atom_vy(i) atom->vy[i] # define atom_vz(i) atom->vz[i] # define atom_fx(i) atom->fx[i] # define atom_fy(i) atom->fy[i] # define atom_fz(i) atom->fz[i] #endif