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Merge pull request #571 from hasanmetin/reaxc-omp-credits-update 

updated the credits and citations for pair style reaxc/omp and qeq/reax/omp
This commit is contained in:
sjplimp 2017-07-13 11:27:18 -06:00 committed by GitHub
parent a3a0c9b144 f7f4a24930
commit fc6c10c9a9
22 changed files with 270 additions and 217 deletions
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178
src/USER-OMP/fix_qeq_reax_omp.cpp
View File

@ -12,11 +12,24 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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>
#include <stdio.h>
@ -36,7 +49,6 @@
#include "pair.h"
#include "respa.h"
#include "memory.h"
#include "citeme.h"
#include "error.h"
#include "reaxc_defs.h"
@ -192,46 +204,46 @@ void FixQEqReaxOMP::compute_H()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
jnum = numneigh[i];
mfill = H.firstnbr[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < n) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
else if (fabs(dz) < SMALL) {
if (dy > SMALL) flag = 1;
else if (fabs(dy) < SMALL && dx > SMALL) flag = 1;
}
}
}
if (flag) {
H.jlist[mfill] = j;
H.val[mfill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
mfill++;
}
}
H.numnbrs[i] = mfill - H.firstnbr[i];
jlist = firstneigh[i];
jnum = numneigh[i];
mfill = H.firstnbr[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < n) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
else if (fabs(dz) < SMALL) {
if (dy > SMALL) flag = 1;
else if (fabs(dy) < SMALL && dx > SMALL) flag = 1;
}
}
}
if (flag) {
H.jlist[mfill] = j;
H.val[mfill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] );
mfill++;
}
}
H.numnbrs[i] = mfill - H.firstnbr[i];
}
}
if (mfill >= H.m) {
char str[128];
sprintf(str,"H matrix size has been exceeded: mfill=%d H.m=%d\n",
mfill, H.m);
mfill, H.m);
error->warning(FLERR,str);
error->all(FLERR,"Fix qeq/reax/omp has insufficient QEq matrix size");
}
@ -301,7 +313,7 @@ void FixQEqReaxOMP::pre_force(int vflag)
if (dual_enabled) {
matvecs = dual_CG(b_s, b_t, s, t); // OMP_TIMING inside dual_CG
} else {
matvecs_s = CG(b_s, s); // CG on s - parallel
matvecs_s = CG(b_s, s); // CG on s - parallel
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
@ -311,7 +323,7 @@ void FixQEqReaxOMP::pre_force(int vflag)
startTimeBase = endTimeBase;
#endif
matvecs_t = CG(b_t, t); // CG on t - parallel
matvecs_t = CG(b_t, t); // CG on t - parallel
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
@ -378,23 +390,23 @@ void FixQEqReaxOMP::init_matvec()
for (int ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -chi[ atom->type[i] ];
b_t[i] = -1.0;
// Predictor Step
double tp = 0.0;
double sp = 0.0;
for (int j=0; j<aspc_order+2; j++) {
tp+= aspc_b[j] * t_hist[i][j];
sp+= aspc_b[j] * s_hist[i][j];
}
// Corrector Step
t[i] = aspc_omega * t_hist[i][0] + m_aspc_omega * tp;
s[i] = aspc_omega * s_hist[i][0] + m_aspc_omega * sp;
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -chi[ atom->type[i] ];
b_t[i] = -1.0;
// Predictor Step
double tp = 0.0;
double sp = 0.0;
for (int j=0; j<aspc_order+2; j++) {
tp+= aspc_b[j] * t_hist[i][j];
sp+= aspc_b[j] * s_hist[i][j];
}
// Corrector Step
t[i] = aspc_omega * t_hist[i][0] + m_aspc_omega * tp;
s[i] = aspc_omega * s_hist[i][0] + m_aspc_omega * sp;
}
}
@ -406,23 +418,23 @@ void FixQEqReaxOMP::init_matvec()
for (int ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -chi[ atom->type[i] ];
b_t[i] = -1.0;
/* linear extrapolation for s & t from previous solutions */
//s[i] = 2 * s_hist[i][0] - s_hist[i][1];
//t[i] = 2 * t_hist[i][0] - t_hist[i][1];
/* quadratic extrapolation for s & t from previous solutions */
//s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
/* cubic extrapolation for s & t from previous solutions */
s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
//t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]);
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -chi[ atom->type[i] ];
b_t[i] = -1.0;
/* linear extrapolation for s & t from previous solutions */
//s[i] = 2 * s_hist[i][0] - s_hist[i][1];
//t[i] = 2 * t_hist[i][0] - t_hist[i][1];
/* quadratic extrapolation for s & t from previous solutions */
//s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
/* cubic extrapolation for s & t from previous solutions */
s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
//t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]);
}
}
}
@ -514,7 +526,7 @@ int FixQEqReaxOMP::CG( double *b, double *x)
#endif
{
MPI_Allreduce(&tmp1, &tmp2, 1, MPI_DOUBLE, MPI_SUM, world);
alpha = sig_new / tmp2;
tmp1 = 0.0;
}
@ -528,7 +540,7 @@ int FixQEqReaxOMP::CG( double *b, double *x)
if (atom->mask[ii] & groupbit) {
x[ii] += alpha * d[ii];
r[ii] -= alpha * q[ii];
// pre-conditioning
p[ii] = r[ii] * Hdia_inv[ii];
tmp1 += r[ii] * p[ii];
@ -616,7 +628,7 @@ void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b)
#if defined(_OPENMP)
#pragma omp barrier
#pragma omp for schedule(dynamic,50)
#endif
#endif
for (ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
@ -846,9 +858,9 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
{
my_buf[0] = tmp1;
my_buf[1] = tmp2;
MPI_Allreduce(&my_buf, &buf, 2, MPI_DOUBLE, MPI_SUM, world);
alpha_s = sig_new_s / buf[0];
alpha_t = sig_new_t / buf[1];
@ -865,14 +877,14 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
int indxI = 2 * ii;
x1[ii] += alpha_s * d[indxI ];
x2[ii] += alpha_t * d[indxI+1];
r[indxI ] -= alpha_s * q[indxI ];
r[indxI+1] -= alpha_t * q[indxI+1];
// pre-conditioning
p[indxI ] = r[indxI ] * Hdia_inv[ii];
p[indxI+1] = r[indxI+1] * Hdia_inv[ii];
tmp1 += r[indxI ] * p[indxI ];
tmp2 += r[indxI+1] * p[indxI+1];
}
@ -903,7 +915,7 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
ii = ilist[jj];
if (atom->mask[ii] & groupbit) {
int indxI = 2 * ii;
d[indxI ] = p[indxI ] + beta_s * d[indxI ];
d[indxI+1] = p[indxI+1] + beta_t * d[indxI+1];
}

10
src/USER-OMP/fix_qeq_reax_omp.h
View File

@ -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)

37
src/USER-OMP/pair_reaxc_omp.cpp
View File

@ -12,12 +12,26 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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"
#include "atom.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;

10
src/USER-OMP/pair_reaxc_omp.h
View File

@ -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)

14
src/USER-OMP/reaxc_bond_orders_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_bond_orders_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_bonds_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_bonds_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_forces_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_forces_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_hydrogen_bonds_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_init_md_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_init_md_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_multi_body_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_multi_body_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_nonbonded_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_nonbonded_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_torsion_angles_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_torsion_angles_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_valence_angles_omp.cpp
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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

14
src/USER-OMP/reaxc_valence_angles_omp.h
View File

@ -1,16 +1,18 @@
/*----------------------------------------------------------------------
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