Merge branch 'patchy-sphere-model' of brandeis_desktop:projects/lammps-mine

/* -*- 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.

------------------------------------------------------------------------- */

#ifdef PAIR_CLASS

PairStyle(patchysphere,PairPatchySphere)

#else

#ifndef LMP_PAIR_PATCHY_SPHERE_H

#define LMP_PAIR_PATCHY_SPHERE_H

#include "pair.h"

namespace LAMMPS_NS {

class PairPatchySphere : public Pair {

 public:

  PairPatchySphere(LAMMPS *);

  virtual ~PairPatchySphere();

  virtual void compute(int, int);

  virtual void settings(int, char **);

  void coeff(int, char **);

  virtual void init_style();

  double init_one(int, int);

	//void write_restart(FILE *);

	//void read_restart(FILE *);

	//void write_restart_settings(FILE *);

	//void read_restart_settings(FILE *);

	//void write_data(FILE *);

	//void write_data_all(FILE *);

 protected:

  // enumerate the "encounter" possibilities.

  enum{SPHERE_SPHERE,SPHERE_PATCHY,PATCHY_SPHERE,PATCHY_PATCHY};

  double cut_global;

  double **cut;

  double **inner_cut;

  double **offset;

  double **epsilon, **sigma;

  // Whole bunch of stuff related to bond vectors...

  double **epsilon_b; // Patch binding strength.

  int n_bond_pairs;   // Number of bond pairs (combinations of alpha, beta, ...)

  int **bond_pairs;   // Enumerate bond pairs.

  double **phi_m, **theta_m; // Theta and phi scale factors.

  int n_bonds;            // Number of bond vectors.

  double **bond_vectors;  // Bond vectors.

  class AtomVecEllipsoid *avec;

  bool debug_output;

  void allocate();

  double bond_vec_analytic(const int i, const int j, double a1[3][3],

                           double a2[3][3], double *r12, const double rsq,

                           double *fforce, double *ttor, double *rtor);

  double bond_vec_theta_part(const int i, const int j,

                             const int itype, const int jtype,

                             const double *r12, const double *b_alp,

                             const double *b_bet, double *fforce, double *ttor,

                             double *rtor);

  double bond_vec_phi_part(const int i, const int j,

                           const int itype, const int jtype,

                           const double *r12, const double rsq,

                           const double *b_alp, const double *b_bet,

                           const double *b_gam, const double *b_eps,

                           double *fforce, double *ttor, double *rtor);

};

} // namespace

#endif // LMP_PAIR_PATCHY_SPHERE_H

#endif // PAIR_CLASS