diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h
index d13968067..d16a321cb 100644
--- a/src/USER-MISC/pair_meam_spline.h
+++ b/src/USER-MISC/pair_meam_spline.h
@@ -1,281 +1,281 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(meam/spline,PairMEAMSpline)
#else
#ifndef LMP_PAIR_MEAM_SPLINE_H
#define LMP_PAIR_MEAM_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_MEAM_SUPPORT_NON_GRID_SPLINES 0
class PairMEAMSpline : public Pair
{
public:
PairMEAMSpline(class LAMMPS *);
virtual ~PairMEAMSpline();
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_forward_comm(int, int *, double *, int, int *);
void unpack_forward_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;
+ 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_MEAM_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);
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_MEAM_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);
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 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)
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 (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.
------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/USER-MISC/pair_meam_sw_spline.h
index 23dd1724f..383104df4 100644
--- a/src/USER-MISC/pair_meam_sw_spline.h
+++ b/src/USER-MISC/pair_meam_sw_spline.h
@@ -1,510 +1,510 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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_forward_comm(int, int *, double *, int, int *);
void unpack_forward_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;
+ 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.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
* Based on the spline 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
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* 4. You may not copy, modify, sublicense, or distribute the Program except
* as expressly provided under this License. Any attempt otherwise to copy,
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* automatically terminate your rights under this License. However, parties
* who have received copies, or rights, from you under this License will not
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* 5. You are not required to accept this License, since you have not signed
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* 7. If, as a consequence of a court judgment or allegation of patent
* infringement or for any other reason (not limited to patent
* issues), conditions are imposed on you (whether by court
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* If any portion of this section is held invalid or unenforceable under any
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* It is not the purpose to this section to induce you to infringe any patents
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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
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* 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.
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* Each version is given a distinguishing version number. If the Program
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* 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
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* Foundation.
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* 10. If you wish to incorporate parts of the Program into other free
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* NO WARRANTY
*
* 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
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* OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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* 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,
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* END OF TERMS AND CONDITIONS
------------------------------------------------------------------------- */