Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-MISC/dihedral_table.h
0f6d21acda7befficient_neuronet

Last Change
Raw File

dihedral_table.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Andrew Jewett (jewett.aij at g mail)
------------------------------------------------------------------------- */
#ifdef DIHEDRAL_CLASS
DihedralStyle(table,DihedralTable)
#else
#ifndef LMP_DIHEDRAL_TABLE_H
#define LMP_DIHEDRAL_TABLE_H
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralTable : public Dihedral {
public:
DihedralTable(class LAMMPS *);
virtual ~DihedralTable();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
double single(int type, int i1, int i2, int i3, int i4);
protected:
int tabstyle,tablength;
// double *phi0; <- equilibrium angles not supported
char *checkU_fname;
char *checkF_fname;
struct Table {
int ninput;
//double phi0; <-equilibrium angles not supported
int f_unspecified; // boolean (but MPI does not like type "bool")
int use_degrees; // boolean (but MPI does not like type "bool")
double *phifile,*efile,*ffile;
double *e2file,*f2file;
double delta,invdelta,deltasq6;
double *phi,*e,*de,*f,*df,*e2,*f2;
};
int ntables;
Table *tables;
int *tabindex;
void allocate();
void null_table(Table *);
void free_table(Table *);
void read_table(Table *, char *, char *);
void bcast_table(Table *);
void spline_table(Table *);
void compute_table(Table *);
void param_extract(Table *, char *);
// --------------------------------------------
// ------------ inline functions --------------
// --------------------------------------------
// -----------------------------------------------------------
// uf_lookup()
// quickly calculate the potential u and force f at angle x,
// using the internal tables tb->e and tb->f (evenly spaced)
// -----------------------------------------------------------
enum{LINEAR,SPLINE};
inline void uf_lookup(int type, double x, double &u, double &f)
{
Table *tb = &tables[tabindex[type]];
double x_over_delta = x*tb->invdelta;
int i = static_cast<int> (x_over_delta);
double a;
double b = x_over_delta - i;
// Apply periodic boundary conditions to indices i and i+1
if (i >= tablength) i -= tablength;
int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength;
switch(tabstyle) {
case LINEAR:
u = tb->e[i] + b * tb->de[i];
f = tb->f[i] + b * tb->df[i]; //<--works even if tb->f_unspecified==true
break;
case SPLINE:
a = 1.0 - b;
u = a * tb->e[i] + b * tb->e[ip1] +
((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
tb->deltasq6;
if (tb->f_unspecified)
//Formula below taken from equation3.3.5 of "numerical recipes in c"
//"f"=-derivative of e with respect to x (or "phi" in this case)
f = (tb->e[i]-tb->e[ip1])*tb->invdelta +
((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0;
else
f = a * tb->f[i] + b * tb->f[ip1] +
((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) *
tb->deltasq6;
break;
} // switch(tabstyle)
} // uf_lookup()
// ----------------------------------------------------------
// u_lookup()
// quickly calculate the potential u at angle x using tb->e
//-----------------------------------------------------------
inline void u_lookup(int type, double x, double &u)
{
Table *tb = &tables[tabindex[type]];
int N = tablength;
// i = static_cast<int> ((x - tb->lo) * tb->invdelta); <-general version
double x_over_delta = x*tb->invdelta;
int i = static_cast<int> (x_over_delta);
double b = x_over_delta - i;
// Apply periodic boundary conditions to indices i and i+1
if (i >= N) i -= N;
int ip1 = i+1; if (ip1 >= N) ip1 -= N;
if (tabstyle == LINEAR) {
u = tb->e[i] + b * tb->de[i];
}
else if (tabstyle == SPLINE) {
double a = 1.0 - b;
u = a * tb->e[i] + b * tb->e[ip1] +
((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
tb->deltasq6;
}
} // u_lookup()
}; //class DihedralTable
} // namespace LAMMPS_NS
#endif //#ifndef LMP_DIHEDRAL_TABLE_H
#endif //#ifdef DIHEDRAL_CLASS ... #else
c4science · Help