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rLAMMPS lammps
pair_polymorphic.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
(
polymorphic
,
PairPolymorphic
)
#else
#ifndef LMP_PAIR_POLYMORPHIC_H
#define LMP_PAIR_POLYMORPHIC_H
#include "pair.h"
namespace
LAMMPS_NS
{
class
PairPolymorphic
:
public
Pair
{
public:
PairPolymorphic
(
class
LAMMPS
*
);
virtual
~
PairPolymorphic
();
virtual
void
compute
(
int
,
int
);
void
settings
(
int
,
char
**
);
void
coeff
(
int
,
char
**
);
void
init_style
();
double
init_one
(
int
,
int
);
protected:
class
tabularFunction
{
public:
tabularFunction
()
{
size
=
0
;
xmin
=
0.0
;
xmax
=
0.0
;
xmaxsq
=
xmax
*
xmax
;
vmax
=
0.0
;
xs
=
NULL
;
ys
=
NULL
;
ys1
=
NULL
;
ys2
=
NULL
;
ys3
=
NULL
;
ys4
=
NULL
;
ys5
=
NULL
;
ys6
=
NULL
;
}
tabularFunction
(
int
n
)
{
size
=
n
;
xmin
=
0.0
;
xmax
=
0.0
;
xmaxsq
=
xmax
*
xmax
;
xs
=
new
double
[
n
];
ys
=
new
double
[
n
];
ys1
=
new
double
[
n
];
ys2
=
new
double
[
n
];
ys3
=
new
double
[
n
];
ys4
=
new
double
[
n
];
ys5
=
new
double
[
n
];
ys6
=
new
double
[
n
];
}
tabularFunction
(
int
n
,
double
x1
,
double
x2
)
{
size
=
n
;
xmin
=
x1
;
xmax
=
x2
;
xmaxsq
=
xmax
*
xmax
;
xs
=
new
double
[
n
];
ys
=
new
double
[
n
];
ys1
=
new
double
[
n
];
ys2
=
new
double
[
n
];
ys3
=
new
double
[
n
];
ys4
=
new
double
[
n
];
ys5
=
new
double
[
n
];
ys6
=
new
double
[
n
];
}
virtual
~
tabularFunction
()
{
if
(
xs
)
delete
[]
xs
;
if
(
ys
)
delete
[]
ys
;
if
(
ys1
)
delete
[]
ys1
;
if
(
ys2
)
delete
[]
ys2
;
if
(
ys3
)
delete
[]
ys3
;
if
(
ys4
)
delete
[]
ys4
;
if
(
ys5
)
delete
[]
ys5
;
if
(
ys6
)
delete
[]
ys6
;
}
void
set_xrange
(
double
x1
,
double
x2
)
{
xmin
=
x1
;
xmax
=
x2
;
xmaxsq
=
xmax
*
xmax
;
}
void
set_values
(
int
n
,
double
x1
,
double
x2
,
double
*
values
,
double
epsilon
)
{
int
i0
;
i0
=
n
-
1
;
// shrink (remove near zero points) reduces cutoff radius, and therefore computational cost
// do not shrink when x2 < 1.1 (angular function) or x2 > 20.0 (non-radial function)
if
(
x2
>=
1.1
&&
x2
<=
20.0
)
{
for
(
int
i
=
n
-
1
;
i
>=
0
;
i
--
)
{
if
(
fabs
(
values
[
i
])
>
epsilon
)
{
i0
=
i
;
break
;
}
}
}
// do not shrink when when list is abnormally small
if
(
i0
<
10
/
n
)
{
i0
=
n
-
1
;
}
else
if
(
i0
<
n
-
1
)
{
values
[
i0
]
=
0.0
;
i0
=
i0
+
1
;
values
[
i0
]
=
0.0
;
}
xmin
=
x1
;
xmax
=
x1
+
(
x2
-
x1
)
/
(
n
-
1
)
*
i0
;
xmaxsq
=
xmax
*
xmax
;
n
=
i0
+
1
;
resize
(
n
);
memcpy
(
ys
,
values
,
n
*
sizeof
(
double
));
initialize
();
}
void
value
(
double
x
,
double
&
y
,
int
ny
,
double
&
y1
,
int
ny1
)
{
double
ps
=
(
x
-
xmin
)
*
rdx
;
int
ks
=
ps
+
0.5
;
if
(
ks
>
size
-
1
)
ks
=
size
-
1
;
if
(
ks
<
0
)
ks
=
0
;
ps
=
ps
-
ks
;
if
(
ny
)
y
=
((
ys3
[
ks
]
*
ps
+
ys2
[
ks
])
*
ps
+
ys1
[
ks
])
*
ps
+
ys
[
ks
];
if
(
ny1
)
y1
=
(
ys6
[
ks
]
*
ps
+
ys5
[
ks
])
*
ps
+
ys4
[
ks
];
}
void
print_value
()
{
printf
(
"%d %f %f %f
\n
"
,
size
,
xmin
,
xmax
,
rdx
);
printf
(
"
\n
"
);
for
(
int
i
=
0
;
i
<
size
;
i
++
)
{
printf
(
"%f %f
\n
"
,
xs
[
i
],
ys
[
i
]);
}
}
double
get_xmin
()
{
return
xmin
;
}
double
get_xmax
()
{
return
xmax
;
}
double
get_xmaxsq
()
{
return
xmaxsq
;
}
double
get_rdx
()
{
return
rdx
;
}
double
get_vmax
()
{
return
vmax
;
}
protected:
void
resize
(
int
n
)
{
if
(
n
!=
size
)
{
size
=
n
;
if
(
xs
)
delete
[]
xs
;
xs
=
new
double
[
n
];
if
(
ys
)
delete
[]
ys
;
ys
=
new
double
[
n
];
if
(
ys1
)
delete
[]
ys1
;
ys1
=
new
double
[
n
];
if
(
ys2
)
delete
[]
ys2
;
ys2
=
new
double
[
n
];
if
(
ys3
)
delete
[]
ys3
;
ys3
=
new
double
[
n
];
if
(
ys4
)
delete
[]
ys4
;
ys4
=
new
double
[
n
];
if
(
ys5
)
delete
[]
ys5
;
ys5
=
new
double
[
n
];
if
(
ys6
)
delete
[]
ys6
;
ys6
=
new
double
[
n
];
}
}
void
initialize
()
{
int
n
=
size
;
rdx
=
(
xmax
-
xmin
)
/
(
n
-
1.0
);
vmax
=
0.0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
if
(
fabs
(
ys
[
i
])
>
vmax
)
vmax
=
fabs
(
ys
[
i
]);
}
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
xs
[
i
]
=
xmin
+
i
*
rdx
;
}
rdx
=
1.0
/
rdx
;
ys1
[
0
]
=
ys
[
1
]
-
ys
[
0
];
ys1
[
1
]
=
0.5
*
(
ys
[
2
]
-
ys
[
0
]);
ys1
[
n
-
2
]
=
0.5
*
(
ys
[
n
-
1
]
-
ys
[
n
-
3
]);
ys1
[
n
-
1
]
=
ys
[
n
-
1
]
-
ys
[
n
-
2
];
for
(
int
i
=
2
;
i
<
n
-
2
;
i
++
)
{
ys1
[
i
]
=
((
ys
[
i
-
2
]
-
ys
[
i
+
2
])
+
8.0
*
(
ys
[
i
+
1
]
-
ys
[
i
-
1
]))
/
12.0
;
}
for
(
int
i
=
0
;
i
<
n
-
1
;
i
++
)
{
ys2
[
i
]
=
3.0
*
(
ys
[
i
+
1
]
-
ys
[
i
])
-
2.0
*
ys1
[
i
]
-
ys1
[
i
+
1
];
ys3
[
i
]
=
ys1
[
i
]
+
ys1
[
i
+
1
]
-
2.0
*
(
ys
[
i
+
1
]
-
ys
[
i
]);
}
ys2
[
n
-
1
]
=
0.0
;
ys3
[
n
-
1
]
=
0.0
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
ys4
[
i
]
=
ys1
[
i
]
*
rdx
;
ys5
[
i
]
=
2.0
*
ys2
[
i
]
*
rdx
;
ys6
[
i
]
=
3.0
*
ys3
[
i
]
*
rdx
;
}
}
int
size
;
double
xmin
,
xmax
,
xmaxsq
,
rdx
,
vmax
;
double
*
ys
,
*
ys1
,
*
ys2
,
*
ys3
,
*
ys4
,
*
ys5
,
*
ys6
;
double
*
xs
;
};
struct
PairParameters
{
double
cut
;
double
cutsq
;
bool
xi
;
// "indicator"
class
tabularFunction
*
U
;
class
tabularFunction
*
V
;
class
tabularFunction
*
W
;
class
tabularFunction
*
P
;
class
tabularFunction
*
F
;
PairParameters
()
{
cut
=
0.0
;
cutsq
=
0.0
;
xi
=
true
;
U
=
NULL
;
V
=
NULL
;
W
=
NULL
;
P
=
NULL
;
F
=
NULL
;
};
};
struct
TripletParameters
{
class
tabularFunction
*
G
;
TripletParameters
()
{
G
=
NULL
;
};
};
double
epsilon
;
bool
eta
;
// global indicator
int
nx
,
nr
,
ng
;
// table sizes
double
maxX
;
// parameter sets
PairParameters
*
pairParameters
;
// for I-J interaction
TripletParameters
*
tripletParameters
;
// for I-J-K interaction
int
neighsize
,
numneighV
,
numneighW
,
numneighW1
;
int
*
firstneighV
,
*
firstneighW
,
*
firstneighW1
;
double
*
delxV
,
*
delyV
,
*
delzV
,
*
drV
;
double
*
delxW
,
*
delyW
,
*
delzW
,
*
drW
;
char
**
elements
;
// names of unique elements
int
**
elem2param
;
// map: element pairs to parameters
int
***
elem3param
;
// map: element triplets to parameters
int
*
map
;
// mapping from atom types to elements
double
cutmax
;
// max cutoff for all elements
double
cutmaxsq
;
int
nelements
;
// # of unique elements
int
npair
,
ntriple
;
int
*
match
;
void
allocate
();
void
grab
(
FILE
*
,
int
,
double
*
);
virtual
void
read_file
(
char
*
);
void
setup_params
();
void
write_tables
(
int
);
void
attractive
(
PairParameters
*
,
TripletParameters
*
,
double
,
double
,
double
,
double
*
,
double
*
,
double
*
,
double
*
,
double
*
);
void
ters_zetaterm_d
(
double
,
double
*
,
double
,
double
*
,
double
,
double
*
,
double
*
,
double
*
,
PairParameters
*
,
TripletParameters
*
);
void
costheta_d
(
double
*
,
double
,
double
*
,
double
,
double
*
,
double
*
,
double
*
);
// inlined functions for efficiency
inline
double
vec3_dot
(
const
double
x
[
3
],
const
double
y
[
3
])
const
{
return
x
[
0
]
*
y
[
0
]
+
x
[
1
]
*
y
[
1
]
+
x
[
2
]
*
y
[
2
];
}
inline
void
vec3_add
(
const
double
x
[
3
],
const
double
y
[
3
],
double
*
const
z
)
const
{
z
[
0
]
=
x
[
0
]
+
y
[
0
];
z
[
1
]
=
x
[
1
]
+
y
[
1
];
z
[
2
]
=
x
[
2
]
+
y
[
2
];
}
inline
void
vec3_scale
(
const
double
k
,
const
double
x
[
3
],
double
y
[
3
])
const
{
y
[
0
]
=
k
*
x
[
0
];
y
[
1
]
=
k
*
x
[
1
];
y
[
2
]
=
k
*
x
[
2
];
}
inline
void
vec3_scaleadd
(
const
double
k
,
const
double
x
[
3
],
const
double
y
[
3
],
double
*
const
z
)
const
{
z
[
0
]
=
k
*
x
[
0
]
+
y
[
0
];
z
[
1
]
=
k
*
x
[
1
]
+
y
[
1
];
z
[
2
]
=
k
*
x
[
2
]
+
y
[
2
];
}
};
}
#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 polymorphic requires atom IDs
This is a requirement to use the polymorphic potential.
E: Pair style polymorphic requires newton pair on
See the newton command. This is a restriction to use the polymorphic
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: Cannot open polymorphic potential file %s
The specified polymorphic potential file cannot be opened. Check that
the path and name are correct.
E: Incorrect number of elements in potential file
Self-explanatory.
E: Element not defined in potential file
The specified element is not in the potential file.
*/
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