lammps-sys 0.6.0

/* -*- 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 get_coeff(double *, double *);
  double pair_density(int );
  double three_body_density(int );
  void init_style();
  void init_list(int, class NeighList *);
  double init_one(int, int);

  // helper functions for compute()

  int ij_to_potl(const int itype, const int jtype, const int ntypes) const {
    return  jtype - 1 + (itype-1)*ntypes - (itype-1)*itype/2;
  }
  int i_to_potl(const int itype) const { return itype-1; }


  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;
      deriv0 = _deriv0;
      derivN = _derivN;
      // if (X) delete[] X;
      // if (Xs) delete[] Xs;
      // if (Y) delete[] Y;
      // if (Y2) delete[] Y2;
      // if (Ydelta) 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, bool isNewFormat);

    /// 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 regular grid, we 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 regular grid, we 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;  // holds the index of the second atom (j)
    double r;
    double f, fprime;
    double del[3];
  };

  SplineFunction* phis; // Phi_i(r_ij)
  SplineFunction* rhos; // Rho_ij(r_ij)
  SplineFunction* fs;   // f_i(r_ij)
  SplineFunction* Us;   // U_i(rho)
  SplineFunction* gs;   // g_ij(cos_theta)
  double* zero_atom_energies; // 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.
------------------------------------------------------------------------- */