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pair_airebo.h
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rLAMMPS lammps
pair_airebo.h
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/* ----------------------------------------------------------------------
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
(
airebo
,
PairAIREBO
)
#else
#ifndef LMP_PAIR_AIREBO_H
#define LMP_PAIR_AIREBO_H
#include "pair.h"
#include "math.h"
#include "math_const.h"
namespace
LAMMPS_NS
{
class
PairAIREBO
:
public
Pair
{
public:
PairAIREBO
(
class
LAMMPS
*
);
virtual
~
PairAIREBO
();
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), 1 (H), or -1 (NULL) for each type
int
me
;
int
ljflag
,
torflag
;
// 0/1 if LJ,torsion terms included
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
double
cutlj
;
// user-specified LJ cutoff
double
cutljrebosq
;
// cut for when to compute
// REBO neighs of ghost atoms
double
**
cutljsq
;
// LJ cutoffs for C,H types
double
**
lj1
,
**
lj2
,
**
lj3
,
**
lj4
;
// pre-computed LJ coeffs for C,H types
double
cut3rebo
;
// maximum distance for 3rd REBO neigh
int
*
REBO_numneigh
;
// # of pair neighbors for each atom
int
**
REBO_firstneigh
;
// ptr to 1st neighbor of each atom
double
*
closestdistsq
;
// closest owned atom dist to each ghost
double
*
nC
,
*
nH
;
// sum of weighting fns with REBO neighs
double
smin
,
Nmin
,
Nmax
,
NCmin
,
NCmax
,
thmin
,
thmax
;
double
rcmin
[
2
][
2
],
rcmax
[
2
][
2
],
rcmaxsq
[
2
][
2
],
rcmaxp
[
2
][
2
];
double
Q
[
2
][
2
],
alpha
[
2
][
2
],
A
[
2
][
2
],
rho
[
2
][
2
],
BIJc
[
2
][
2
][
3
],
Beta
[
2
][
2
][
3
];
double
rcLJmin
[
2
][
2
],
rcLJmax
[
2
][
2
],
rcLJmaxsq
[
2
][
2
],
bLJmin
[
2
][
2
],
bLJmax
[
2
][
2
];
double
epsilon
[
2
][
2
],
sigma
[
2
][
2
],
epsilonT
[
2
][
2
];
// spline coefficients
double
gCdom
[
5
],
gC1
[
4
][
6
],
gC2
[
4
][
6
],
gHdom
[
4
],
gH
[
3
][
6
];
double
pCCdom
[
2
][
2
],
pCHdom
[
2
][
2
],
pCC
[
4
][
4
][
16
],
pCH
[
4
][
4
][
16
];
double
piCCdom
[
3
][
2
],
piCHdom
[
3
][
2
],
piHHdom
[
3
][
2
];
double
piCC
[
4
][
4
][
9
][
64
],
piCH
[
4
][
4
][
9
][
64
],
piHH
[
4
][
4
][
9
][
64
];
double
Tijdom
[
3
][
2
],
Tijc
[
4
][
4
][
9
][
64
];
// spline knot values
double
PCCf
[
5
][
5
],
PCCdfdx
[
5
][
5
],
PCCdfdy
[
5
][
5
],
PCHf
[
5
][
5
];
double
PCHdfdx
[
5
][
5
],
PCHdfdy
[
5
][
5
];
double
piCCf
[
5
][
5
][
11
],
piCCdfdx
[
5
][
5
][
11
];
double
piCCdfdy
[
5
][
5
][
11
],
piCCdfdz
[
5
][
5
][
11
];
double
piCHf
[
5
][
5
][
11
],
piCHdfdx
[
5
][
5
][
11
];
double
piCHdfdy
[
5
][
5
][
11
],
piCHdfdz
[
5
][
5
][
11
];
double
piHHf
[
5
][
5
][
11
],
piHHdfdx
[
5
][
5
][
11
];
double
piHHdfdy
[
5
][
5
][
11
],
piHHdfdz
[
5
][
5
][
11
];
double
Tf
[
5
][
5
][
10
],
Tdfdx
[
5
][
5
][
10
],
Tdfdy
[
5
][
5
][
10
],
Tdfdz
[
5
][
5
][
10
];
void
REBO_neigh
();
void
FREBO
(
int
,
int
);
void
FLJ
(
int
,
int
);
void
TORSION
(
int
,
int
);
double
bondorder
(
int
,
int
,
double
*
,
double
,
double
,
double
**
,
int
);
double
bondorderLJ
(
int
,
int
,
double
*
,
double
,
double
,
double
*
,
double
,
double
**
,
int
);
double
gSpline
(
double
,
double
,
int
,
double
*
,
double
*
);
double
PijSpline
(
double
,
double
,
int
,
int
,
double
*
);
double
piRCSpline
(
double
,
double
,
double
,
int
,
int
,
double
*
);
double
TijSpline
(
double
,
double
,
double
,
double
*
);
void
add_pages
(
int
howmany
=
1
);
void
read_file
(
char
*
);
double
Sp5th
(
double
,
double
*
,
double
*
);
double
Spbicubic
(
double
,
double
,
double
*
,
double
*
);
double
Sptricubic
(
double
,
double
,
double
,
double
*
,
double
*
);
void
spline_init
();
void
allocate
();
// ----------------------------------------------------------------------
// S'(t) and S(t) cutoff functions
// added to header for inlining
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
cutoff function Sprime
return cutoff and dX = derivative
no side effects
------------------------------------------------------------------------- */
inline
double
Sp
(
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
{
cutoff
=
0.5
*
(
1.0
+
cos
(
t
*
MathConst
::
MY_PI
));
dX
=
(
-
0.5
*
MathConst
::
MY_PI
*
sin
(
t
*
MathConst
::
MY_PI
))
/
(
Xmax
-
Xmin
);
}
return
cutoff
;
};
/* ----------------------------------------------------------------------
LJ cutoff function Sp2
return cutoff and dX = derivative
no side effects
------------------------------------------------------------------------- */
inline
double
Sp2
(
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
{
cutoff
=
(
1.0
-
(
t
*
t
*
(
3.0
-
2.0
*
t
)));
dX
=
6.0
*
(
t
*
t
-
t
)
/
(
Xmax
-
Xmin
);
}
return
cutoff
;
};
/* kronecker delta function returning a double */
inline
double
kronecker
(
const
int
a
,
const
int
b
)
const
{
return
(
a
==
b
)
?
1.0
:
0.0
;
};
};
}
#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 AIREBO requires atom IDs
This is a requirement to use the AIREBO potential.
E: Pair style AIREBO requires newton pair on
See the newton command. This is a restriction to use the AIREBO
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 or page
There are too many neighbors of a single atom. Use the neigh_modify
command to increase the neighbor page size and the max number of
neighbors allowed for one atom.
E: Cannot open AIREBO potential file %s
The specified AIREBO potential file cannot be opened. Check that the
path and name are correct.
*/
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