Merge pull request #571 from hasanmetin/reaxc-omp-credits-update (fc6c10c9) · Commits · 郑智淋 / lammps

src/USER-OMP/fix_qeq_reax_omp.cpp

+96 −84

Original line number	Diff line number	Diff line
		@@ -12,10 +12,23 @@
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Hasan Metin Aktulga, Purdue University
		(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
		Contributing author:
		Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu

		Hybrid and sub-group capabilities: Ray Shan (Sandia)
		Hybrid & sub-group capabilities added by Ray Shan (Materials Design)

		OpenMP based threading support for fix qeq/reax/omp added
		by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF),
		Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF)

		Integration of the pair_style reax/c/omp into the User-OMP package
		by Axel Kohlmeyer (Temple U.)

		Please cite the related publication:
		H. M. Aktulga, C. Knight, P. Coffman, K. A. O'Hearn, T. R. Shan,
		W. Jiang, "Optimizing the performance of reactive molecular dynamics
		simulations for multi-core architectures", International Journal of
		High Performance Computing Applications, to appear.
		------------------------------------------------------------------------- */

		#include <math.h>
		@@ -36,7 +49,6 @@
		#include "pair.h"
		#include "respa.h"
		#include "memory.h"
		#include "citeme.h"
		#include "error.h"
		#include "reaxc_defs.h"

src/USER-OMP/fix_qeq_reax_omp.h

+0 −10

Original line number	Diff line number	Diff line
		@@ -11,16 +11,6 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Hasan Metin Aktulga, Purdue University
		(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)

		Please cite the related publication:
		H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
		"Parallel Reactive Molecular Dynamics: Numerical Methods and
		Algorithmic Techniques", Parallel Computing, in press.
		------------------------------------------------------------------------- */

		#ifdef FIX_CLASS

		FixStyle(qeq/reax/omp,FixQEqReaxOMP)

src/USER-OMP/pair_reaxc_omp.cpp

+31 −6

Original line number	Diff line number	Diff line
		@@ -12,11 +12,25 @@
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Hasan Metin Aktulga, Purdue University
		(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
		Per-atom energy/virial added by Ray Shan (Sandia)
		Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by
		Ray Shan (Sandia)
		Contributing author:
		Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu

		Per-atom energy/virial added by Ray Shan (Materials Design, Inc.)
		Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added
		by Ray Shan (Materials Design)

		OpenMP based threading support for pair_style reax/c/omp added
		by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF),
		Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF)

		Integration of the pair_style reax/c/omp into the User-OMP package
		by Axel Kohlmeyer (Temple U.)

		Please cite the related publication:
		H. M. Aktulga, C. Knight, P. Coffman, K. A. O'Hearn, T. R. Shan,
		W. Jiang, "Optimizing the performance of reactive molecular dynamics
		simulations for multi-core architectures", International Journal of
		High Performance Computing Applications, to appear.
		------------------------------------------------------------------------- */

		#include "pair_reaxc_omp.h"
		@@ -62,10 +76,21 @@ int ompTimingCount[LASTTIMINGINDEX];
		int ompTimingCGCount[LASTTIMINGINDEX];
		#endif

		static const char cite_pair_reax_c_omp[] =
		"pair reax/c/omp and fix qeq/reax/omp command:\n\n"
		"@Article{Aktulga17,\n"
		" author = {H. M. Aktulga, C. Knight, P. Coffman, K. A. OHearn, T. R. Shan, W. Jiang},\n"
		" title = {Optimizing the performance of reactive molecular dynamics simulations for multi-core architectures},\n"
		" journal = {International Journal of High Performance Computing Applications},\n"
		" year = to appear\n"
		"}\n\n";

		/* ---------------------------------------------------------------------- */

		PairReaxCOMP::PairReaxCOMP(LAMMPS *lmp) : PairReaxC(lmp), ThrOMP(lmp, THR_PAIR)
		{
		if (lmp->citeme) lmp->citeme->add(cite_pair_reax_c_omp);

		suffix_flag \|= Suffix::OMP;
		system->pair_ptr = this;

src/USER-OMP/pair_reaxc_omp.h

+0 −10

Original line number	Diff line number	Diff line
		@@ -11,16 +11,6 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author: Hasan Metin Aktulga, Purdue University
		(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)

		Please cite the related publication:
		H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
		"Parallel Reactive Molecular Dynamics: Numerical Methods and
		Algorithmic Techniques", Parallel Computing, in press.
		------------------------------------------------------------------------- */

		#ifdef PAIR_CLASS

		PairStyle(reax/c/omp,PairReaxCOMP)

src/USER-OMP/reaxc_bond_orders_omp.cpp

+8 −6

Original line number	Diff line number	Diff line
		/*----------------------------------------------------------------------
		PuReMD - Purdue ReaxFF Molecular Dynamics Program
		Website: https://www.cs.purdue.edu/puremd

		Copyright (2010) Purdue University
		Hasan Metin Aktulga, hmaktulga@lbl.gov
		Joseph Fogarty, jcfogart@mail.usf.edu
		Sagar Pandit, pandit@usf.edu
		Ananth Y Grama, ayg@cs.purdue.edu

		Contributing authors:
		H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
		Corresponding author:
		Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu

		Please cite the related publication:
		H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
		"Parallel Reactive Molecular Dynamics: Numerical Methods and
		Algorithmic Techniques", Parallel Computing, in press.
		Algorithmic Techniques", Parallel Computing, 38 (4-5), 245-259

		This program is free software; you can redistribute it and/or
		modify it under the terms of the GNU General Public License as

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