172 lines
5.6 KiB
C
172 lines
5.6 KiB
C
/*
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* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <parameter.h>
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#ifndef __ATOM_H_
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#define __ATOM_H_
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#define DELTA 20000
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// Nbnxn layouts (as of GROMACS):
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// Simd4xN: M=4, N=VECTOR_WIDTH
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// Simd2xNN: M=4, N=(VECTOR_WIDTH/2)
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// Cuda: M=8, N=VECTOR_WIDTH
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#ifdef CUDA_TARGET
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# undef VECTOR_WIDTH
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# define VECTOR_WIDTH 8
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# define KERNEL_NAME "CUDA"
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# define CLUSTER_M 8
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# define CLUSTER_N VECTOR_WIDTH
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# define UNROLL_J 1
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# define computeForceLJ computeForceLJ_cuda
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# define initialIntegrate cudaInitialIntegrate
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# define finalIntegrate cudaFinalIntegrate
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# define updatePbc cudaUpdatePbc
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#else
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# define CLUSTER_M 4
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// Simd2xNN (here used for single-precision)
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# if VECTOR_WIDTH > CLUSTER_M * 2
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# define KERNEL_NAME "Simd2xNN"
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# define CLUSTER_N (VECTOR_WIDTH / 2)
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# define UNROLL_I 4
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# define UNROLL_J 2
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# define computeForceLJ computeForceLJ_2xnn
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// Simd4xN
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# else
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# define KERNEL_NAME "Simd4xN"
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# define CLUSTER_N VECTOR_WIDTH
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# define UNROLL_I 4
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# define UNROLL_J 1
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# define computeForceLJ computeForceLJ_4xn
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# endif
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# ifdef USE_REFERENCE_VERSION
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# undef KERNEL_NAME
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# undef computeForceLJ
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# define KERNEL_NAME "Reference"
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# define computeForceLJ computeForceLJ_ref
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# endif
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# define initialIntegrate cpuInitialIntegrate
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# define finalIntegrate cpuFinalIntegrate
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# define updatePbc cpuUpdatePbc
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#endif
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#if CLUSTER_M == CLUSTER_N
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# define CJ0_FROM_CI(a) (a)
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# define CJ1_FROM_CI(a) (a)
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# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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#elif CLUSTER_M == CLUSTER_N * 2 // M > N
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# define CJ0_FROM_CI(a) ((a) << 1)
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# define CJ1_FROM_CI(a) (((a) << 1) | 0x1)
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# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_M * (b))
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# define CJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1))
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#elif CLUSTER_M == CLUSTER_N / 2 // M < N
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# define CJ0_FROM_CI(a) ((a) >> 1)
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# define CJ1_FROM_CI(a) ((a) >> 1)
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# define CI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1))
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# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
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#else
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# error "Invalid cluster configuration!"
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#endif
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#if CLUSTER_N != 2 && CLUSTER_N != 4 && CLUSTER_N != 8
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# error "Cluster N dimension can be only 2, 4 and 8"
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#endif
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#define CI_SCALAR_BASE_INDEX(a) (CI_BASE_INDEX(a, 1))
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#define CI_VECTOR_BASE_INDEX(a) (CI_BASE_INDEX(a, 3))
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#define CJ_SCALAR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 1))
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#define CJ_VECTOR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 3))
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#if CLUSTER_M >= CLUSTER_N
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# define CL_X_OFFSET (0 * CLUSTER_M)
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# define CL_Y_OFFSET (1 * CLUSTER_M)
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# define CL_Z_OFFSET (2 * CLUSTER_M)
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#else
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# define CL_X_OFFSET (0 * CLUSTER_N)
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# define CL_Y_OFFSET (1 * CLUSTER_N)
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# define CL_Z_OFFSET (2 * CLUSTER_N)
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#endif
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typedef struct {
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int natoms;
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MD_FLOAT bbminx, bbmaxx;
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MD_FLOAT bbminy, bbmaxy;
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MD_FLOAT bbminz, bbmaxz;
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} Cluster;
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typedef struct {
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int Natoms, Nlocal, Nghost, Nmax;
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int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
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MD_FLOAT *x, *y, *z;
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MD_FLOAT *vx, *vy, *vz;
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int *border_map;
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int *type;
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int ntypes;
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MD_FLOAT *epsilon;
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MD_FLOAT *sigma6;
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MD_FLOAT *cutforcesq;
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MD_FLOAT *cutneighsq;
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int *PBCx, *PBCy, *PBCz;
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// Data in cluster format
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MD_FLOAT *cl_x;
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MD_FLOAT *cl_v;
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MD_FLOAT *cl_f;
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int *cl_type;
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Cluster *iclusters, *jclusters;
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int *icluster_bin;
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int dummy_cj;
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MD_UINT *exclusion_filter;
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MD_FLOAT *diagonal_4xn_j_minus_i;
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MD_FLOAT *diagonal_2xnn_j_minus_i;
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unsigned int masks_2xnn_hn[8];
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unsigned int masks_2xnn_fn[8];
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unsigned int masks_4xn_hn[16];
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unsigned int masks_4xn_fn[16];
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} Atom;
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extern void initAtom(Atom*);
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extern void initMasks(Atom*);
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extern void createAtom(Atom*, Parameter*);
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extern int readAtom(Atom*, Parameter*);
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extern int readAtom_pdb(Atom*, Parameter*);
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extern int readAtom_gro(Atom*, Parameter*);
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extern int readAtom_dmp(Atom*, Parameter*);
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extern void growAtom(Atom*);
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extern void growClusters(Atom*);
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#ifdef AOS
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# define POS_DATA_LAYOUT "AoS"
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# define atom_x(i) atom->x[(i) * 3 + 0]
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# define atom_y(i) atom->x[(i) * 3 + 1]
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# define atom_z(i) atom->x[(i) * 3 + 2]
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/*
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# define atom_vx(i) atom->vx[(i) * 3 + 0]
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# define atom_vy(i) atom->vx[(i) * 3 + 1]
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# define atom_vz(i) atom->vx[(i) * 3 + 2]
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# define atom_fx(i) atom->fx[(i) * 3 + 0]
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# define atom_fy(i) atom->fx[(i) * 3 + 1]
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# define atom_fz(i) atom->fx[(i) * 3 + 2]
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*/
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#else
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# define POS_DATA_LAYOUT "SoA"
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# define atom_x(i) atom->x[i]
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# define atom_y(i) atom->y[i]
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# define atom_z(i) atom->z[i]
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#endif
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// TODO: allow to switch velocites and forces to AoS
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# define atom_vx(i) atom->vx[i]
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# define atom_vy(i) atom->vy[i]
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# define atom_vz(i) atom->vz[i]
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# define atom_fx(i) atom->fx[i]
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# define atom_fy(i) atom->fy[i]
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# define atom_fz(i) atom->fz[i]
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#endif
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