132 lines
4.2 KiB
C
132 lines
4.2 KiB
C
/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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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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#define CLUSTER_M 4
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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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// Simd2XNN (here used for single-precision)
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#if VECTOR_WIDTH > CLUSTER_M * 2
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# define CLUSTER_N (VECTOR_WIDTH / 2)
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// Simd4xN
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#else
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# define CLUSTER_N VECTOR_WIDTH
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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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} Atom;
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extern void initAtom(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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#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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#endif
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