MD-Bench/gromacs/includes/atom.h

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/*
* 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.
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*/
#include <parameter.h>
#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
# define UNROLL_J 1
# define computeForceLJ computeForceLJ_cuda
# 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 UNROLL_I 4
# define UNROLL_J 2
# define computeForceLJ computeForceLJ_2xnn
// Simd4xN
# else
# define KERNEL_NAME "Simd4xN"
# define CLUSTER_N VECTOR_WIDTH
# define UNROLL_I 4
# define UNROLL_J 1
# 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))
#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))
#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))
#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))
#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)
#else
# define CL_X_OFFSET (0 * CLUSTER_N)
# define CL_Y_OFFSET (1 * CLUSTER_N)
# define CL_Z_OFFSET (2 * CLUSTER_N)
#endif
typedef struct {
int natoms;
MD_FLOAT bbminx, bbmaxx;
MD_FLOAT bbminy, bbmaxy;
MD_FLOAT bbminz, bbmaxz;
} Cluster;
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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;
MD_UINT *exclusion_filter;
MD_FLOAT *diagonal_4xn_j_minus_i;
MD_FLOAT *diagonal_2xnn_j_minus_i;
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} Atom;
extern void initAtom(Atom*);
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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*);
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extern void growAtom(Atom*);
extern void growClusters(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]
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#endif