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sjplimp
2012-10-29 14:35:48 +00:00
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84
src/USER-MISC/pair_meam_spline.cpp
View File

@ -12,46 +12,12 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom method (MEAM) potential routine.
*
* Copyright (2011) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-525797 All rights reserved.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
*
Contributing author: Alexander Stukowski (LLNL), alex@stukowski.com
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* File history of changes:
*
* 25-Oct-10 - AS: First code version.
* 17-Feb-11 - AS: Several optimizations (introduced MEAM2Body struct).
* 25-Mar-11 - AS: Fixed calculation of per-atom virial stress.
@ -729,3 +695,43 @@ void PairMEAMSpline::SplineFunction::writeGnuplot(const char* filename, const ch
fprintf(fp, "e\n");
fclose(fp);
}
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom method (MEAM) potential routine.
*
* Copyright (2011) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-525797 All rights reserved.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
------------------------------------------------------------------------- */

82
src/USER-MISC/pair_meam_spline.h
View File

@ -12,45 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom method (MEAM) potential routine.
*
* Copyright (2011) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-525797 All rights reserved.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
*
* See file 'pair_spline_meam.cpp' for history of changes.
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
@ -275,3 +237,45 @@ protected:
#endif
#endif
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom method (MEAM) potential routine.
*
* Copyright (2011) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-525797 All rights reserved.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
*
* See file 'pair_spline_meam.cpp' for history of changes.
------------------------------------------------------------------------- */

529
src/USER-MISC/pair_meam_sw_spline.cpp
View File

@ -15,273 +15,11 @@
Contributing author: Robert Rudd (LLNL), robert.rudd@llnl.gov
Based on the spline-based MEAM routine written by
Alexander Stukowski (LLNL), alex@stukowski.com
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
* Based on the spline-based MEAM routine written by
* Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
*
* The spline-based MEAM+SW format was first devised and used to develop
* potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
* and Hyoungki Park at The Ohio State University.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
*
* The precise terms and conditions for copying, distribution and modification
* follows.
*
* GNU Terms and Conditions for Copying, Distribution, and Modification
*
* 0. This License applies to any program or other work which contains a
* notice placed by the copyright holder saying it may be distributed under
* the terms of this General Public License. The "Program," below, refers to
* any such program or work, and a "work based on the Program" means either
* the Program or any derivative work under copyright law: that is to say, a
* work containing the Program or a portion of it, either verbatim or with
* modifications and/or translated into another language. (Hereinafter,
* translation is included without limitation in the term "modification".)
* Each licensee is addressed as "you."
*
* Activities other than copying, distribution and modification are not
* covered by this License; they are outside its scope. The act of running
* the Program is not restricted, and the output from the Program is covered
* only if its contents constitute a work based on the Program (independent of
* having been made by running the Program). Whether that is true depends on
* what the Program does.
*
* 1. You may copy and distribute verbatim copies of the Program's source
* code as you receive it, in any medium, provided that you conspicuously and
* appropriately publish on each copy an appropriate copyright notice and
* disclaimer of warranty; keep intact all the notices that refer to this
* License and to the absence of any warranty; and give any other recipients
* of the Program a copy of this License along with the Program.
*
* You may charge a fee for the physical act of transferring a copy, and you
* may at your option offer warranty protection in exchange for a fee.
*
* 2. You may modify your copy or copies of the Program or any portion of it,
* thus forming a work based on the Program, and copy and distribute such
* modifications or work under the terms of Section 1 above, provided that you
* also meet all of these conditions:
*
* a) You must cause the modified files to carry prominent notices stating
* that you changed the files and the date of any change.
*
* b) You must cause any work that you distribute or publish, that in whole
* or in part contains or is derived from the Program or any part thereof, to
* be licensed as a whole at no charge to all third parties under the terms
* of this License.
*
* c) If the modified program normally reads commands interactively when
* run, you must cause it, when started running for such interactive use in
* the most ordinary way, to print or display an announcement including an
* appropriate copyright notice and a notice that there is no warranty (or
* else, saying that you provide a warranty) and that users may redistribute
* the program under these conditions, and telling the user how to view a
* copy of this License. (Exception: if the Program itself is interactive
* but does not normally print such an announcement, your work based on the
* Program is not required to print an announcement.)
*
* These requirements apply to the modified work as a whole. If
* identifiable sections of that work are not derived from the Program, and
* can be reasonably considered independent and separate works in
* themselves, then this License, and its terms, do not apply to those
* sections when you distribute them as separate work. But when you
* distribute the same section as part of a whole which is a work based on
* the Program, the distribution of the whole must be on the terms of this
* License, whose permissions for other licensees extend to the entire
* whole, and thus to each and every part regardless of who wrote it.
*
* Thus, it is not the intent of this section to claim rights or contest
* your rights to work written entirely by you; rather, the intent is to
* exercise the right to control the distribution of derivative or
* collective works based on the Program.
*
* In addition, mere aggregation of another work not based on the Program
* with the Program (or with a work based on the Program) on a volume of a
* storage or distribution medium does not bring the other work under the
* scope of this License.
*
* 3. You may copy and distribute the Program (or a work based on it, under
* Section 2) in object code or executable form under the terms of Sections
* 1 and 2 above provided that you also do one of the following:
*
* a) Accompany it with the complete corresponding machine-readable source
* code, which must be distributed under the terms of Sections 1 and 2 above
* on a medium customarily used for software interchange; or,
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* b) Accompany it with a written offer, valid for at least three years,
* to give any third party, for a charge no more than your cost of
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* This section is intended to make thoroughly clear what is believed to be a
* consequence of the rest of this License.
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* 8. If the distribution and/or use of the Program is restricted in certain
* countries either by patents or by copyrighted interfaces, the original
* copyright holder who places the Program under this License may add an
* explicit geographical distribution limitation excluding those countries, so
* that distribution is permitted only in or among countries not thus
* excluded. In such case, this License incorporates the limitation as if
* written in the body of this License.
*
* 9. The Free Software Foundation may publish revised and/or new versions of
* the General Public License from time to time. Such new versions will be
* similar in spirit to the present version, but may differ in detail to
* address new problems or concerns.
*
* Each version is given a distinguishing version number. If the Program
* specifies a version number of this License which applies to it and "any
* later version," you have the option of following the terms and conditions
* either of that version of any later version published by the Free Software
* Foundation. If the Program does not specify a version number of this
* License, you may choose any version ever published by the Free Software
* Foundation.
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* 10. If you wish to incorporate parts of the Program into other free
* programs whose distribution conditions are different, write to the author
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* 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
* FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
* OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
* PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
* OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
* MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
* TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
* PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
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* 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
* WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
* REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
* INCLUDING ANY GENERAL, SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
* OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
* TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
* YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
* PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGES.
*
* END OF TERMS AND CONDITIONS
*
* File history of changes:
*
* 01-Aug-12 - RER: First code version.
------------------------------------------------------------------------- */
@ -993,3 +731,268 @@ void PairMEAMSWSpline::SplineFunction::writeGnuplot(const char* filename, const
fprintf(fp, "e\n");
fclose(fp);
}
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus
* Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
* Based on the spline-based MEAM routine written by
* Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
*
* The spline-based MEAM+SW format was first devised and used to develop
* potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
* and Hyoungki Park at The Ohio State University.
*
* 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) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
*
* The precise terms and conditions for copying, distribution and modification
* follows.
*
* GNU Terms and Conditions for Copying, Distribution, and Modification
*
* 0. This License applies to any program or other work which contains a
* notice placed by the copyright holder saying it may be distributed under
* the terms of this General Public License. The "Program," below, refers to
* any such program or work, and a "work based on the Program" means either
* the Program or any derivative work under copyright law: that is to say, a
* work containing the Program or a portion of it, either verbatim or with
* modifications and/or translated into another language. (Hereinafter,
* translation is included without limitation in the term "modification".)
* Each licensee is addressed as "you."
*
* Activities other than copying, distribution and modification are not
* covered by this License; they are outside its scope. The act of running
* the Program is not restricted, and the output from the Program is covered
* only if its contents constitute a work based on the Program (independent of
* having been made by running the Program). Whether that is true depends on
* what the Program does.
*
* 1. You may copy and distribute verbatim copies of the Program's source
* code as you receive it, in any medium, provided that you conspicuously and
* appropriately publish on each copy an appropriate copyright notice and
* disclaimer of warranty; keep intact all the notices that refer to this
* License and to the absence of any warranty; and give any other recipients
* of the Program a copy of this License along with the Program.
*
* You may charge a fee for the physical act of transferring a copy, and you
* may at your option offer warranty protection in exchange for a fee.
*
* 2. You may modify your copy or copies of the Program or any portion of it,
* thus forming a work based on the Program, and copy and distribute such
* modifications or work under the terms of Section 1 above, provided that you
* also meet all of these conditions:
*
* a) You must cause the modified files to carry prominent notices stating
* that you changed the files and the date of any change.
*
* b) You must cause any work that you distribute or publish, that in whole
* or in part contains or is derived from the Program or any part thereof, to
* be licensed as a whole at no charge to all third parties under the terms
* of this License.
*
* c) If the modified program normally reads commands interactively when
* run, you must cause it, when started running for such interactive use in
* the most ordinary way, to print or display an announcement including an
* appropriate copyright notice and a notice that there is no warranty (or
* else, saying that you provide a warranty) and that users may redistribute
* the program under these conditions, and telling the user how to view a
* copy of this License. (Exception: if the Program itself is interactive
* but does not normally print such an announcement, your work based on the
* Program is not required to print an announcement.)
*
* These requirements apply to the modified work as a whole. If
* identifiable sections of that work are not derived from the Program, and
* can be reasonably considered independent and separate works in
* themselves, then this License, and its terms, do not apply to those
* sections when you distribute them as separate work. But when you
* distribute the same section as part of a whole which is a work based on
* the Program, the distribution of the whole must be on the terms of this
* License, whose permissions for other licensees extend to the entire
* whole, and thus to each and every part regardless of who wrote it.
*
* Thus, it is not the intent of this section to claim rights or contest
* your rights to work written entirely by you; rather, the intent is to
* exercise the right to control the distribution of derivative or
* collective works based on the Program.
*
* In addition, mere aggregation of another work not based on the Program
* with the Program (or with a work based on the Program) on a volume of a
* storage or distribution medium does not bring the other work under the
* scope of this License.
*
* 3. You may copy and distribute the Program (or a work based on it, under
* Section 2) in object code or executable form under the terms of Sections
* 1 and 2 above provided that you also do one of the following:
*
* a) Accompany it with the complete corresponding machine-readable source
* code, which must be distributed under the terms of Sections 1 and 2 above
* on a medium customarily used for software interchange; or,
*
* b) Accompany it with a written offer, valid for at least three years,
* to give any third party, for a charge no more than your cost of
* physically performing source distribution, a complete machine-readable
* copy of the corresponding source code, to be distributed under the terms
* of Sections 1 and 2 above on a medium customarily used for software
* interchange; or,
*
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------------------------------------------------------------------------- */

467
src/USER-MISC/pair_meam_sw_spline.h
View File

@ -12,7 +12,241 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus Stillinger-Weber (MEAM+SW) potential routine.
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(meam/sw/spline,PairMEAMSWSpline)
#else
#ifndef LMP_PAIR_MEAM_SW_SPLINE_H
#define LMP_PAIR_MEAM_SW_SPLINE_H
#include "pair.h"
namespace LAMMPS_NS {
/// Set this to 1 if you intend to use MEAM potentials with non-uniform spline knots.
/// Set this to 0 if you intend to use only MEAM potentials with spline knots on a uniform grid.
///
/// With SUPPORT_NON_GRID_SPLINES == 0, the code runs about 50% faster.
#define SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES 0
class PairMEAMSWSpline : public Pair
{
public:
PairMEAMSWSpline(class LAMMPS *);
virtual ~PairMEAMSWSpline();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
protected:
char **elements; // names of unique elements
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
class SplineFunction {
public:
/// Default constructor.
SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
/// Destructor.
~SplineFunction() {
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
}
/// Initialization of spline function.
void init(int _N, double _deriv0, double _derivN) {
N = _N;
deriv0 = _deriv0;
derivN = _derivN;
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
X = new double[N];
Xs = new double[N];
Y = new double[N];
Y2 = new double[N];
Ydelta = new double[N];
}
/// Adds a knot to the spline.
void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
/// Returns the number of knots.
int numKnots() const { return N; }
/// Parses the spline knots from a text file.
void parse(FILE* fp, Error* error);
/// Calculates the second derivatives of the cubic spline.
void prepareSpline(Error* error);
/// Evaluates the spline function at position x.
inline double eval(double x) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
//
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Evaluates the spline function and its first derivative at position x.
inline double eval(double x, double& deriv) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
deriv = deriv0;
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
deriv = derivN;
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
deriv = (Y[khi] - Y[klo]) / h + ((3.0*b*b - 1.0) * Y2[khi] - (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi] - (3.0*a*a - hsq) * Y2[klo]);
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Returns the number of bytes used by this function object.
double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
/// Returns the cutoff radius of this function.
double cutoff() const { return X[N-1]; }
/// Writes a Gnuplot script that plots the spline function.
void writeGnuplot(const char* filename, const char* title = NULL) const;
/// Broadcasts the spline function parameters to all processors.
void communicate(MPI_Comm& world, int me);
private:
double* X; // Positions of spline knots
double* Xs; // Shifted positions of spline knots
double* Y; // Function values at spline knots
double* Y2; // Second derivatives at spline knots
double* Ydelta; // If this is a grid spline, Ydelta[i] = (Y[i+1]-Y[i])/h
int N; // Number of spline knots
double deriv0; // First derivative at knot 0
double derivN; // First derivative at knot (N-1)
double xmin; // The beginning of the interval on which the spline function is defined.
double xmax; // The end of the interval on which the spline function is defined.
int isGridSpline; // Indicates that all spline knots are on a regular grid.
double h; // The distance between knots if this is a grid spline with equidistant knots.
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
};
/// Helper data structure for potential routine.
struct MEAM2Body {
int tag;
double r;
double f, fprime;
double F, Fprime;
double del[3];
};
SplineFunction phi; // Phi(r_ij)
SplineFunction rho; // Rho(r_ij)
SplineFunction f; // f(r_ij)
SplineFunction U; // U(rho)
SplineFunction g; // g(cos_theta)
SplineFunction F; // F(r_ij)
SplineFunction G; // G(cos_theta)
double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
double cutoff; // The cutoff radius
double* Uprime_values; // Used for temporary storage of U'(rho) values
int nmax; // Size of temporary array.
int maxNeighbors; // The last maximum number of neighbors a single atoms has.
MEAM2Body* twoBodyInfo; // Temporary array.
void read_file(const char* filename);
void allocate();
};
}
#endif
#endif
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus
* Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
@ -273,235 +507,4 @@
* POSSIBILITY OF SUCH DAMAGES.
*
* END OF TERMS AND CONDITIONS
*
* See file 'pair_meam_sw_spline.cpp' for history of changes.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(meam/sw/spline,PairMEAMSWSpline)
#else
#ifndef LMP_PAIR_MEAM_SW_SPLINE_H
#define LMP_PAIR_MEAM_SW_SPLINE_H
#include "pair.h"
namespace LAMMPS_NS {
/// Set this to 1 if you intend to use MEAM potentials with non-uniform spline knots.
/// Set this to 0 if you intend to use only MEAM potentials with spline knots on a uniform grid.
///
/// With SUPPORT_NON_GRID_SPLINES == 0, the code runs about 50% faster.
#define SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES 0
class PairMEAMSWSpline : public Pair
{
public:
PairMEAMSWSpline(class LAMMPS *);
virtual ~PairMEAMSWSpline();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
protected:
char **elements; // names of unique elements
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
class SplineFunction {
public:
/// Default constructor.
SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
/// Destructor.
~SplineFunction() {
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
}
/// Initialization of spline function.
void init(int _N, double _deriv0, double _derivN) {
N = _N;
deriv0 = _deriv0;
derivN = _derivN;
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
X = new double[N];
Xs = new double[N];
Y = new double[N];
Y2 = new double[N];
Ydelta = new double[N];
}
/// Adds a knot to the spline.
void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
/// Returns the number of knots.
int numKnots() const { return N; }
/// Parses the spline knots from a text file.
void parse(FILE* fp, Error* error);
/// Calculates the second derivatives of the cubic spline.
void prepareSpline(Error* error);
/// Evaluates the spline function at position x.
inline double eval(double x) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
//
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Evaluates the spline function and its first derivative at position x.
inline double eval(double x, double& deriv) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
deriv = deriv0;
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
deriv = derivN;
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
deriv = (Y[khi] - Y[klo]) / h + ((3.0*b*b - 1.0) * Y2[khi] - (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi] - (3.0*a*a - hsq) * Y2[klo]);
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Returns the number of bytes used by this function object.
double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
/// Returns the cutoff radius of this function.
double cutoff() const { return X[N-1]; }
/// Writes a Gnuplot script that plots the spline function.
void writeGnuplot(const char* filename, const char* title = NULL) const;
/// Broadcasts the spline function parameters to all processors.
void communicate(MPI_Comm& world, int me);
private:
double* X; // Positions of spline knots
double* Xs; // Shifted positions of spline knots
double* Y; // Function values at spline knots
double* Y2; // Second derivatives at spline knots
double* Ydelta; // If this is a grid spline, Ydelta[i] = (Y[i+1]-Y[i])/h
int N; // Number of spline knots
double deriv0; // First derivative at knot 0
double derivN; // First derivative at knot (N-1)
double xmin; // The beginning of the interval on which the spline function is defined.
double xmax; // The end of the interval on which the spline function is defined.
int isGridSpline; // Indicates that all spline knots are on a regular grid.
double h; // The distance between knots if this is a grid spline with equidistant knots.
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
};
/// Helper data structure for potential routine.
struct MEAM2Body {
int tag;
double r;
double f, fprime;
double F, Fprime;
double del[3];
};
SplineFunction phi; // Phi(r_ij)
SplineFunction rho; // Rho(r_ij)
SplineFunction f; // f(r_ij)
SplineFunction U; // U(rho)
SplineFunction g; // g(cos_theta)
SplineFunction F; // F(r_ij)
SplineFunction G; // G(cos_theta)
double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
double cutoff; // The cutoff radius
double* Uprime_values; // Used for temporary storage of U'(rho) values
int nmax; // Size of temporary array.
int maxNeighbors; // The last maximum number of neighbors a single atoms has.
MEAM2Body* twoBodyInfo; // Temporary array.
void read_file(const char* filename);
void allocate();
};
}
#endif
#endif