Loading src/USER-REAXC/README +38 −26 Original line number Diff line number Diff line This package contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. The files in this directory are a user-contributed package for LAMMPS. The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which library was originally authored by Adri van Duin. The reax/c version should be somewhat faster and more scalable, particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. The person who created this package is Hasan Metin Aktulga, hmaktulga at lbl.gov, while at Purdue University. Contact him directly, or Aidan Thompson (Sandia) at athomps at sandia.gov, if you have questions. For technical details about this implemention of ReaxFF, see this paper: Loading @@ -21,34 +12,55 @@ Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, Parallel Computing, to appear (2011). See the doc page for the pair_style reax/c command for details of how to use it in LAMMPS. -------------------------------------- The person who created this package is Hasan Metin Aktulga (hmaktulga at lbl.gov), while at Purdue University. Contact him directly, or Aidan Thompson at Sandia (athomps at sandia.gov), if you have questions. Note that the files with names starting with "reaxc" in this package are from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its copyright info and authorship info are listed below. -------------------------------------- PACKAGE DESCRIPTION: Contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which was originally authored by Adri van Duin. The reax/c version should be somewhat faster and more scalable, particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues due to linking to a Fortran library. OTHERS FILES INCLUDED: User examples for pair_style reax/c are in examples/reax. Thanks to Steve Plimpton and Aidan Thompson for their input on the LAMMPS architecture and for their help in understanding and customizing some of the required LAMMPS interfaces. Note that files in the package with names starting with "reaxc" are from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its copyright info and authorship info are listed below. -------------------------------------- The reaxc files in this directory have the following header: PuReMD - Purdue ReaxFF Molecular Dynamics Program Copyright (2010) Purdue University Hasan Metin Aktulga, haktulga@cs.purdue.edu Hasan Metin Aktulga, hmaktulga@lbl.gov Joseph Fogarty, jcfogart@mail.usf.edu Sagar Pandit, pandit@usf.edu Ananth Y Grama, ayg@cs.purdue.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. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of Loading src/USER-REAXC/fix_qeq_reax.cpp +31 −13 Original line number Diff line number Diff line Loading @@ -13,6 +13,12 @@ /* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #include "math.h" Loading Loading @@ -401,9 +407,6 @@ void FixQEqReax::pre_force(int vflag) if (update->ntimestep % nevery) return; if( comm->me == 0 ) t_start = MPI_Wtime(); if (domain->xprd < swb || domain->yprd < swb || domain->zprd < swb) error->warning("FixQEqReax cutoff greater than periodic dimension"); n = atom->nlocal; N = atom->nlocal + atom->nghost; // grow arrays if necessary Loading Loading @@ -474,12 +477,13 @@ void FixQEqReax::init_matvec() void FixQEqReax::compute_H() { int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh; int i, j, ii, jj, temp, newnbr; int *type; double **x; int i, j, ii, jj, temp, newnbr, flag; int *type, *tag; double **x, SMALL = 0.0001; double dx, dy, dz, r_sqr; type = atom->type; tag = atom->tag; x = atom->x; inum = list->inum; Loading @@ -499,12 +503,26 @@ void FixQEqReax::compute_H() for( jj = 0; jj < jnum; jj++ ) { j = jlist[jj]; dx = x[i][0] - x[j][0]; dy = x[i][1] - x[j][1]; dz = x[i][2] - x[j][2]; 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); if( r_sqr <= SQR(swb) && (j < n || atom->tag[i] <= atom->tag[j]) ) { 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[m_fill] = j; H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] ); m_fill++; Loading src/USER-REAXC/fix_qeq_reax.h +10 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,16 @@ 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,FixQEqReax) Loading src/USER-REAXC/fix_reax_c.cpp +6 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,12 @@ /* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #include "fix_reax_c.h" Loading src/USER-REAXC/fix_reax_c.h +10 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,16 @@ 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(REAXC,FixReaxC) Loading Loading
src/USER-REAXC/README +38 −26 Original line number Diff line number Diff line This package contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. The files in this directory are a user-contributed package for LAMMPS. The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which library was originally authored by Adri van Duin. The reax/c version should be somewhat faster and more scalable, particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. The person who created this package is Hasan Metin Aktulga, hmaktulga at lbl.gov, while at Purdue University. Contact him directly, or Aidan Thompson (Sandia) at athomps at sandia.gov, if you have questions. For technical details about this implemention of ReaxFF, see this paper: Loading @@ -21,34 +12,55 @@ Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, Parallel Computing, to appear (2011). See the doc page for the pair_style reax/c command for details of how to use it in LAMMPS. -------------------------------------- The person who created this package is Hasan Metin Aktulga (hmaktulga at lbl.gov), while at Purdue University. Contact him directly, or Aidan Thompson at Sandia (athomps at sandia.gov), if you have questions. Note that the files with names starting with "reaxc" in this package are from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its copyright info and authorship info are listed below. -------------------------------------- PACKAGE DESCRIPTION: Contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which was originally authored by Adri van Duin. The reax/c version should be somewhat faster and more scalable, particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues due to linking to a Fortran library. OTHERS FILES INCLUDED: User examples for pair_style reax/c are in examples/reax. Thanks to Steve Plimpton and Aidan Thompson for their input on the LAMMPS architecture and for their help in understanding and customizing some of the required LAMMPS interfaces. Note that files in the package with names starting with "reaxc" are from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its copyright info and authorship info are listed below. -------------------------------------- The reaxc files in this directory have the following header: PuReMD - Purdue ReaxFF Molecular Dynamics Program Copyright (2010) Purdue University Hasan Metin Aktulga, haktulga@cs.purdue.edu Hasan Metin Aktulga, hmaktulga@lbl.gov Joseph Fogarty, jcfogart@mail.usf.edu Sagar Pandit, pandit@usf.edu Ananth Y Grama, ayg@cs.purdue.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. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of Loading
src/USER-REAXC/fix_qeq_reax.cpp +31 −13 Original line number Diff line number Diff line Loading @@ -13,6 +13,12 @@ /* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #include "math.h" Loading Loading @@ -401,9 +407,6 @@ void FixQEqReax::pre_force(int vflag) if (update->ntimestep % nevery) return; if( comm->me == 0 ) t_start = MPI_Wtime(); if (domain->xprd < swb || domain->yprd < swb || domain->zprd < swb) error->warning("FixQEqReax cutoff greater than periodic dimension"); n = atom->nlocal; N = atom->nlocal + atom->nghost; // grow arrays if necessary Loading Loading @@ -474,12 +477,13 @@ void FixQEqReax::init_matvec() void FixQEqReax::compute_H() { int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh; int i, j, ii, jj, temp, newnbr; int *type; double **x; int i, j, ii, jj, temp, newnbr, flag; int *type, *tag; double **x, SMALL = 0.0001; double dx, dy, dz, r_sqr; type = atom->type; tag = atom->tag; x = atom->x; inum = list->inum; Loading @@ -499,12 +503,26 @@ void FixQEqReax::compute_H() for( jj = 0; jj < jnum; jj++ ) { j = jlist[jj]; dx = x[i][0] - x[j][0]; dy = x[i][1] - x[j][1]; dz = x[i][2] - x[j][2]; 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); if( r_sqr <= SQR(swb) && (j < n || atom->tag[i] <= atom->tag[j]) ) { 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[m_fill] = j; H.val[m_fill] = calculate_H( sqrt(r_sqr), shld[type[i]][type[j]] ); m_fill++; Loading
src/USER-REAXC/fix_qeq_reax.h +10 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,16 @@ 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,FixQEqReax) Loading
src/USER-REAXC/fix_reax_c.cpp +6 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,12 @@ /* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #include "fix_reax_c.h" Loading
src/USER-REAXC/fix_reax_c.h +10 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,16 @@ 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(REAXC,FixReaxC) Loading
