Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/MANYBODY/pair_lcbop.h
49804d97059fefficient_neuronet

Last Change
Raw File

pair_lcbop.h
View Options

/* -*- 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(lcbop,PairLCBOP)
#else
#ifndef LMP_PAIR_LCBOP_H
#define LMP_PAIR_LCBOP_H
#include "pair.h"
#include "my_page.h"
#include <math.h>
#include "math_const.h"
namespace LAMMPS_NS {
class PairLCBOP : public Pair {
public:
PairLCBOP(class LAMMPS *);
virtual ~PairLCBOP();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
double memory_usage();
protected:
int **pages; // neighbor list pages
int *map; // 0 (C) or -1 (NULL) for each type
int me;
double cutLR; // LR cutoff
double cutLRsq; // LR cutoff squared
double cut3rebo; // maximum distance for 3rd SR neigh
int maxlocal; // size of numneigh, firstneigh arrays
int maxpage; // # of pages currently allocated
int pgsize; // size of neighbor page
int oneatom; // max # of neighbors for one atom
MyPage<int> *ipage; // neighbor list pages
int *SR_numneigh; // # of pair neighbors for each atom
int **SR_firstneigh; // ptr to 1st neighbor of each atom
double *N; // sum of cutoff fns ( f_C ) with SR neighs
double *M; // sum_j f_C_ij*F(N_j - f_C_ij)
double
r_1, r_2, gamma_1, A, B_1, B_2, alpha, beta_1, beta_2,
d, C_1, C_4, C_6, L, kappa, R_0, R_1,
r_0, r_1_LR, r_2_LR,
v_1, v_2, eps_1, eps_2, lambda_1, lambda_2, eps, delta;
double r_2_sq;
// splines coefficients
struct TF_conj_field {
double
f_00,
f_01,
f_10,
f_11,
f_x_00,
f_x_01,
f_x_10,
f_x_11,
f_y_00,
f_y_01,
f_y_10,
f_y_11;
} F_conj_field[3][3][2];
double F_conj_data[4][4][2][3]; // temporary data from file
double gX[6]; // x coordinates for described points[# of points];
double gC[5+1][6-1]; // coefficients for each period between described points [degree of polynomial+1][# of points-1]
void SR_neigh();
void FSR(int, int);
void FLR(int, int);
void FNij( int, int, double, double**, int );
void FMij( int, int, double, double**, int );
double bondorder( int, int, double*, double, double, double**, int );
double b ( int, int, double*, double, double, double**, int );
double gSpline( double, double* );
double hSpline( double, double* );
void g_decompose_x( double, size_t*, double* );
double F_conj( double, double, double, double*, double*, double* );
void read_file( char * );
void spline_init();
void allocate();
// ----------------------------------------------------------------------
// S'(t) and S(t) cutoff functions
// added to header for inlining
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
short range cutoff function
return cutoff and dX = derivative
no side effects
------------------------------------------------------------------------- */
inline double f_c(double Xij, double Xmin, double Xmax, double *dX) const {
double cutoff;
double t = (Xij-Xmin) / (Xmax-Xmin);
if (t <= 0.0) {
cutoff = 1.0;
*dX = 0.0;
} else if (t >= 1.0) {
cutoff = 0.0;
*dX = 0.0;
} else {
double z = t*t*t-1;
cutoff = exp( gamma_1*t*t*t/z );
*dX = cutoff * (-3*gamma_1*t*t)/z/z / (Xmax-Xmin);
}
return cutoff;
};
/* ----------------------------------------------------------------------
long range cutoff function
return cutoff and dX = derivative
no side effects
------------------------------------------------------------------------- */
inline double f_c_LR(double Xij, double Xmin, double Xmax, double *dX) const {
double cutoff;
double t = (Xij-Xmin) / (Xmax-Xmin);
if (t <= 0.0) {
cutoff = 1.0;
//dX = 0.0; this way the derivative is inherited from previous cut off function call
} else if (t >= 1.0) {
cutoff = 0.0;
*dX = 0.0;
} else {
cutoff = ( 1.0+cos(MathConst::MY_PI*t) )/2.0;
*dX = -MathConst::MY_PI*sin(MathConst::MY_PI*t)/2/(Xmax-Xmin);
}
return cutoff;
};
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style LCBOP requires atom IDs
This is a requirement to use the LCBOP potential.
E: Pair style LCBOP requires newton pair on
See the newton command. This is a restriction to use the Tersoff
potential.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Neighbor list overflow, boost neigh_modify one
There are too many neighbors of a single atom. Use the neigh_modify
command to increase the max number of neighbors allowed for one atom.
You may also want to boost the page size.
E: Cannot open LCBOP potential file %s
The specified LCBOP potential file cannot be opened. Check that the
path and name are correct.
*/
c4science · Help