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Merge pull request #3247 from vladgl/adp-kk

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Kokkos accelerated variant for adp pair style
This commit is contained in:
Axel Kohlmeyer
2022-05-04 13:05:29 -04:00
committed by GitHub
parent fef6c37ea7 7fa2fe134c
commit d4a93ff9c7
9 changed files with 1399 additions and 13 deletions
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2
doc/src/Commands_pair.rst
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@ -34,7 +34,7 @@ OPT.
*
*
*
* :doc:`adp (o) <pair_adp>`
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`

3
doc/src/pair_adp.rst
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@ -1,10 +1,11 @@
.. index:: pair_style adp
.. index:: pair_style adp/kk
.. index:: pair_style adp/omp
pair_style adp command
======================
Accelerator Variants: *adp/omp*
Accelerator Variants: *adp/kk*, *adp/omp*
Syntax
""""""

2
src/KOKKOS/Install.sh
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@ -214,6 +214,8 @@ action min_kokkos.h
action min_linesearch_kokkos.cpp
action min_linesearch_kokkos.h
action pack_kokkos.h pack.h
action pair_adp_kokkos.cpp pair_adp.cpp
action pair_adp_kokkos.h pair_adp.h
action pair_buck_coul_cut_kokkos.cpp
action pair_buck_coul_cut_kokkos.h
action pair_buck_coul_long_kokkos.cpp pair_buck_coul_long.cpp

1182
src/KOKKOS/pair_adp_kokkos.cpp Normal file
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203
src/KOKKOS/pair_adp_kokkos.h Normal file
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@ -0,0 +1,203 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Vladislav Galigerov (HSE), Vsevolod Nikolskiy (HSE)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(adp/kk,PairADPKokkos<LMPDeviceType>);
PairStyle(adp/kk/device,PairADPKokkos<LMPDeviceType>);
PairStyle(adp/kk/host,PairADPKokkos<LMPHostType>);
// clang-format on
#else
// clang-format off
#ifndef LMP_PAIR_ADP_KOKKOS_H
#define LMP_PAIR_ADP_KOKKOS_H
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_adp.h"
#include "neigh_list_kokkos.h"
namespace LAMMPS_NS {
struct TagPairADPPackForwardComm{};
struct TagPairADPUnpackForwardComm{};
struct TagPairADPInitialize{};
template<int NEIGHFLAG, int NEWTON_PAIR>
struct TagPairADPKernelA{};
template<int EFLAG>
struct TagPairADPKernelB{};
template<int EFLAG>
struct TagPairADPKernelAB{};
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
struct TagPairADPKernelC{};
template<class DeviceType>
class PairADPKokkos : public PairADP, public KokkosBase
{
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typedef EV_FLOAT value_type;
PairADPKokkos(class LAMMPS *);
~PairADPKokkos() override;
void compute(int, int) override;
void init_style() override;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPPackForwardComm, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPUnpackForwardComm, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPInitialize, const int&) const;
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelA<NEIGHFLAG,NEWTON_PAIR>, const int&) const;
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelB<EFLAG>, const int&, EV_FLOAT&) const;
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelB<EFLAG>, const int&) const;
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelAB<EFLAG>, const int&, EV_FLOAT&) const;
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelAB<EFLAG>, const int&) const;
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&, EV_FLOAT&) const;
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairADPKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&) const;
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void ev_tally_xyz(EV_FLOAT &ev, const int &i, const int &j,
const F_FLOAT &epair, const F_FLOAT &fx, const F_FLOAT &fy, const F_FLOAT &fz, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *) override;
void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&) override;
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
protected:
typename AT::t_x_array x;
typename AT::t_f_array f;
typename AT::t_int_1d type;
typename AT::t_tagint_1d tag;
DAT::tdual_efloat_1d k_eatom;
DAT::tdual_virial_array k_vatom;
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
int need_dup;
using KKDeviceType = typename KKDevice<DeviceType>::value;
template<typename DataType, typename Layout>
using DupScatterView = KKScatterView<DataType, Layout, KKDeviceType, KKScatterSum, KKScatterDuplicated>;
template<typename DataType, typename Layout>
using NonDupScatterView = KKScatterView<DataType, Layout, KKDeviceType, KKScatterSum, KKScatterNonDuplicated>;
DupScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout> dup_rho;
DupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> dup_mu;
DupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> dup_lambda;
DupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> dup_f;
DupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> dup_eatom;
DupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> dup_vatom;
NonDupScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout> ndup_rho;
NonDupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> ndup_mu;
NonDupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> ndup_lambda;
NonDupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> ndup_f;
NonDupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> ndup_eatom;
NonDupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> ndup_vatom;
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
DAT::tdual_f_array k_mu;
DAT::tdual_virial_array k_lambda;
typename AT::t_ffloat_1d d_rho;
typename AT::t_ffloat_1d d_fp;
typename AT::t_f_array d_mu;
typename AT::t_virial_array d_lambda;
HAT::t_ffloat_1d h_rho;
HAT::t_ffloat_1d h_fp;
HAT::t_f_array h_mu;
HAT::t_virial_array h_lambda;
typename AT::t_int_1d d_type2frho;
typename AT::t_int_2d_dl d_type2rhor;
typename AT::t_int_2d_dl d_type2z2r;
typename AT::t_int_2d_dl d_type2u2r;
typename AT::t_int_2d_dl d_type2w2r;
typedef Kokkos::DualView<F_FLOAT**[7],DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const t_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7;
t_ffloat_2d_n7 d_frho_spline;
t_ffloat_2d_n7 d_rhor_spline;
t_ffloat_2d_n7 d_z2r_spline;
t_ffloat_2d_n7 d_u2r_spline, d_w2r_spline;
void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
void file2array() override;
void array2spline() override;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d d_ilist;
typename AT::t_int_1d d_numneigh;
int iswap;
int first;
typename AT::t_int_2d d_sendlist;
typename AT::t_xfloat_1d_um v_buf;
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
friend void pair_virial_fdotr_compute<PairADPKokkos>(PairADPKokkos*);
};
}
#endif
#endif

9
src/KOKKOS/pair_eam_kokkos.cpp
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@ -54,10 +54,10 @@ PairEAMKokkos<DeviceType>::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp)
template<class DeviceType>
PairEAMKokkos<DeviceType>::~PairEAMKokkos()
{
if (!copymode) {
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
if (copymode) return;
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
/* ---------------------------------------------------------------------- */
@ -640,6 +640,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>, const int
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);

5
src/KOKKOS/pair_eam_kokkos.h
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@ -59,7 +59,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
~PairEAMKokkos() override;
void compute(int, int) override;
void init_style() override;
void *extract(const char *, int &) override { return nullptr; }
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMPackForwardComm, const int&) const;
@ -161,21 +160,18 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
t_ffloat_2d_n7 d_rhor_spline;
t_ffloat_2d_n7 d_z2r_spline;
void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
void file2array() override;
void array2spline() override;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d d_ilist;
typename AT::t_int_1d d_numneigh;
//NeighListKokkos<DeviceType> k_list;
int iswap;
int first;
typename AT::t_int_2d d_sendlist;
typename AT::t_xfloat_1d_um v_buf;
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
@ -183,7 +179,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
};
}
#endif
#endif

2
src/MANYBODY/pair_adp.cpp
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@ -76,6 +76,8 @@ PairADP::PairADP(LAMMPS *lmp) : Pair(lmp)
PairADP::~PairADP()
{
if (copymode) return;
memory->destroy(rho);
memory->destroy(fp);
memory->destroy(mu);

4
src/MANYBODY/pair_adp.h
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@ -78,11 +78,11 @@ class PairADP : public Pair {
Setfl *setfl;
void allocate();
void array2spline();
virtual void array2spline();
void interpolate(int, double, double *, double **);
void read_file(char *);
void file2array();
virtual void file2array();
};
} // namespace LAMMPS_NS