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rLAMMPS lammps
compute_orientorder_atom.cpp
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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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "compute_orientorder_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
std
;
#ifdef DBL_EPSILON
#define MY_EPSILON (10.0*DBL_EPSILON)
#else
#define MY_EPSILON (10.0*2.220446049250313e-16)
#endif
/* ---------------------------------------------------------------------- */
ComputeOrientOrderAtom
::
ComputeOrientOrderAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
distsq
(
NULL
),
nearest
(
NULL
),
rlist
(
NULL
),
qlist
(
NULL
),
qnarray
(
NULL
),
qnm_r
(
NULL
),
qnm_i
(
NULL
)
{
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
// set default values for optional args
nnn
=
12
;
cutsq
=
0.0
;
// specify which orders to request
nqlist
=
5
;
memory
->
create
(
qlist
,
nqlist
,
"orientorder/atom:qlist"
);
qlist
[
0
]
=
4
;
qlist
[
1
]
=
6
;
qlist
[
2
]
=
8
;
qlist
[
3
]
=
10
;
qlist
[
4
]
=
12
;
qmax
=
12
;
// process optional args
int
iarg
=
3
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"nnn"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"NULL"
)
==
0
)
nnn
=
0
;
else
{
nnn
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
(
nnn
<=
0
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
}
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"degrees"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
nqlist
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
(
nqlist
<=
0
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
memory
->
destroy
(
qlist
);
memory
->
create
(
qlist
,
nqlist
,
"orientorder/atom:qlist"
);
iarg
+=
2
;
if
(
iarg
+
nqlist
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
qmax
=
0
;
for
(
int
iw
=
0
;
iw
<
nqlist
;
iw
++
)
{
qlist
[
iw
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
iw
]);
if
(
qlist
[
iw
]
<
0
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
if
(
qlist
[
iw
]
>
qmax
)
qmax
=
qlist
[
iw
];
}
iarg
+=
nqlist
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"cutoff"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
double
cutoff
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
(
cutoff
<=
0.0
)
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
cutsq
=
cutoff
*
cutoff
;
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal compute orientorder/atom command"
);
}
ncol
=
nqlist
;
peratom_flag
=
1
;
size_peratom_cols
=
ncol
;
nmax
=
0
;
maxneigh
=
0
;
}
/* ---------------------------------------------------------------------- */
ComputeOrientOrderAtom
::~
ComputeOrientOrderAtom
()
{
memory
->
destroy
(
qnarray
);
memory
->
destroy
(
distsq
);
memory
->
destroy
(
rlist
);
memory
->
destroy
(
nearest
);
memory
->
destroy
(
qlist
);
memory
->
destroy
(
qnm_r
);
memory
->
destroy
(
qnm_i
);
}
/* ---------------------------------------------------------------------- */
void
ComputeOrientOrderAtom
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Compute orientorder/atom requires a pair style be defined"
);
if
(
cutsq
==
0.0
)
cutsq
=
force
->
pair
->
cutforce
*
force
->
pair
->
cutforce
;
else
if
(
sqrt
(
cutsq
)
>
force
->
pair
->
cutforce
)
error
->
all
(
FLERR
,
"Compute orientorder/atom cutoff is longer than pairwise cutoff"
);
memory
->
create
(
qnm_r
,
qmax
,
2
*
qmax
+
1
,
"orientorder/atom:qnm_r"
);
memory
->
create
(
qnm_i
,
qmax
,
2
*
qmax
+
1
,
"orientorder/atom:qnm_i"
);
// need an occasional full neighbor list
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"orientorder/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute orientorder/atom"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeOrientOrderAtom
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeOrientOrderAtom
::
compute_peratom
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
invoked_peratom
=
update
->
ntimestep
;
// grow order parameter array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
qnarray
);
nmax
=
atom
->
nmax
;
memory
->
create
(
qnarray
,
nmax
,
ncol
,
"orientorder/atom:qnarray"
);
array_atom
=
qnarray
;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor
->
build_one
(
list
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// compute order parameter for each atom in group
// use full neighbor list to count atoms less than cutoff
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
double
*
qn
=
qnarray
[
i
];
if
(
mask
[
i
]
&
groupbit
)
{
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
// insure distsq and nearest arrays are long enough
if
(
jnum
>
maxneigh
)
{
memory
->
destroy
(
distsq
);
memory
->
destroy
(
rlist
);
memory
->
destroy
(
nearest
);
maxneigh
=
jnum
;
memory
->
create
(
distsq
,
maxneigh
,
"orientorder/atom:distsq"
);
memory
->
create
(
rlist
,
maxneigh
,
3
,
"orientorder/atom:rlist"
);
memory
->
create
(
nearest
,
maxneigh
,
"orientorder/atom:nearest"
);
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// rlist[] = distance vector to each
// nearest[] = atom indices of neighbors
int
ncount
=
0
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
<
cutsq
)
{
distsq
[
ncount
]
=
rsq
;
rlist
[
ncount
][
0
]
=
delx
;
rlist
[
ncount
][
1
]
=
dely
;
rlist
[
ncount
][
2
]
=
delz
;
nearest
[
ncount
++
]
=
j
;
}
}
// if not nnn neighbors, order parameter = 0;
if
((
ncount
==
0
)
||
(
ncount
<
nnn
))
{
for
(
int
iw
=
0
;
iw
<
nqlist
;
iw
++
)
qn
[
iw
]
=
0.0
;
continue
;
}
// if nnn > 0, use only nearest nnn neighbors
if
(
nnn
>
0
)
{
select3
(
nnn
,
ncount
,
distsq
,
nearest
,
rlist
);
ncount
=
nnn
;
}
calc_boop
(
rlist
,
ncount
,
qn
,
qlist
,
nqlist
);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeOrientOrderAtom
::
memory_usage
()
{
double
bytes
=
ncol
*
nmax
*
sizeof
(
double
);
bytes
+=
(
qmax
*
(
2
*
qmax
+
1
)
+
maxneigh
*
4
)
*
sizeof
(
double
);
bytes
+=
(
nqlist
+
maxneigh
)
*
sizeof
(
int
);
return
bytes
;
}
/* ----------------------------------------------------------------------
select3 routine from Numerical Recipes (slightly modified)
find k smallest values in array of length n
sort auxiliary arrays at same time
------------------------------------------------------------------------- */
// Use no-op do while to create single statement
#define SWAP(a,b) do { \
tmp = a; a = b; b = tmp; \
} while(0)
#define ISWAP(a,b) do { \
itmp = a; a = b; b = itmp; \
} while(0)
#define SWAP3(a,b) do { \
tmp = a[0]; a[0] = b[0]; b[0] = tmp; \
tmp = a[1]; a[1] = b[1]; b[1] = tmp; \
tmp = a[2]; a[2] = b[2]; b[2] = tmp; \
} while(0)
/* ---------------------------------------------------------------------- */
void
ComputeOrientOrderAtom
::
select3
(
int
k
,
int
n
,
double
*
arr
,
int
*
iarr
,
double
**
arr3
)
{
int
i
,
ir
,
j
,
l
,
mid
,
ia
,
itmp
;
double
a
,
tmp
,
a3
[
3
];
arr
--
;
iarr
--
;
arr3
--
;
l
=
1
;
ir
=
n
;
for
(;;)
{
if
(
ir
<=
l
+
1
)
{
if
(
ir
==
l
+
1
&&
arr
[
ir
]
<
arr
[
l
])
{
SWAP
(
arr
[
l
],
arr
[
ir
]);
ISWAP
(
iarr
[
l
],
iarr
[
ir
]);
SWAP3
(
arr3
[
l
],
arr3
[
ir
]);
}
return
;
}
else
{
mid
=
(
l
+
ir
)
>>
1
;
SWAP
(
arr
[
mid
],
arr
[
l
+
1
]);
ISWAP
(
iarr
[
mid
],
iarr
[
l
+
1
]);
SWAP3
(
arr3
[
mid
],
arr3
[
l
+
1
]);
if
(
arr
[
l
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
],
arr
[
ir
]);
ISWAP
(
iarr
[
l
],
iarr
[
ir
]);
SWAP3
(
arr3
[
l
],
arr3
[
ir
]);
}
if
(
arr
[
l
+
1
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
+
1
],
arr
[
ir
]);
ISWAP
(
iarr
[
l
+
1
],
iarr
[
ir
]);
SWAP3
(
arr3
[
l
+
1
],
arr3
[
ir
]);
}
if
(
arr
[
l
]
>
arr
[
l
+
1
])
{
SWAP
(
arr
[
l
],
arr
[
l
+
1
]);
ISWAP
(
iarr
[
l
],
iarr
[
l
+
1
]);
SWAP3
(
arr3
[
l
],
arr3
[
l
+
1
]);
}
i
=
l
+
1
;
j
=
ir
;
a
=
arr
[
l
+
1
];
ia
=
iarr
[
l
+
1
];
a3
[
0
]
=
arr3
[
l
+
1
][
0
];
a3
[
1
]
=
arr3
[
l
+
1
][
1
];
a3
[
2
]
=
arr3
[
l
+
1
][
2
];
for
(;;)
{
do
i
++
;
while
(
arr
[
i
]
<
a
);
do
j
--
;
while
(
arr
[
j
]
>
a
);
if
(
j
<
i
)
break
;
SWAP
(
arr
[
i
],
arr
[
j
]);
ISWAP
(
iarr
[
i
],
iarr
[
j
]);
SWAP3
(
arr3
[
i
],
arr3
[
j
]);
}
arr
[
l
+
1
]
=
arr
[
j
];
arr
[
j
]
=
a
;
iarr
[
l
+
1
]
=
iarr
[
j
];
iarr
[
j
]
=
ia
;
arr3
[
l
+
1
][
0
]
=
arr3
[
j
][
0
];
arr3
[
l
+
1
][
1
]
=
arr3
[
j
][
1
];
arr3
[
l
+
1
][
2
]
=
arr3
[
j
][
2
];
arr3
[
j
][
0
]
=
a3
[
0
];
arr3
[
j
][
1
]
=
a3
[
1
];
arr3
[
j
][
2
]
=
a3
[
2
];
if
(
j
>=
k
)
ir
=
j
-
1
;
if
(
j
<=
k
)
l
=
i
;
}
}
}
/* ----------------------------------------------------------------------
calculate the bond orientational order parameters
------------------------------------------------------------------------- */
void
ComputeOrientOrderAtom
::
calc_boop
(
double
**
rlist
,
int
ncount
,
double
qn
[],
int
qlist
[],
int
nqlist
)
{
for
(
int
iw
=
0
;
iw
<
nqlist
;
iw
++
)
{
int
n
=
qlist
[
iw
];
qn
[
iw
]
=
0.0
;
for
(
int
m
=
0
;
m
<
2
*
n
+
1
;
m
++
)
{
qnm_r
[
iw
][
m
]
=
0.0
;
qnm_i
[
iw
][
m
]
=
0.0
;
}
}
for
(
int
ineigh
=
0
;
ineigh
<
ncount
;
ineigh
++
)
{
const
double
*
const
r
=
rlist
[
ineigh
];
double
rmag
=
dist
(
r
);
if
(
rmag
<=
MY_EPSILON
)
{
return
;
}
double
costheta
=
r
[
2
]
/
rmag
;
double
expphi_r
=
r
[
0
];
double
expphi_i
=
r
[
1
];
double
rxymag
=
sqrt
(
expphi_r
*
expphi_r
+
expphi_i
*
expphi_i
);
if
(
rxymag
<=
MY_EPSILON
)
{
expphi_r
=
1.0
;
expphi_i
=
0.0
;
}
else
{
double
rxymaginv
=
1.0
/
rxymag
;
expphi_r
*=
rxymaginv
;
expphi_i
*=
rxymaginv
;
}
for
(
int
iw
=
0
;
iw
<
nqlist
;
iw
++
)
{
int
n
=
qlist
[
iw
];
qnm_r
[
iw
][
n
]
+=
polar_prefactor
(
n
,
0
,
costheta
);
double
expphim_r
=
expphi_r
;
double
expphim_i
=
expphi_i
;
for
(
int
m
=
1
;
m
<=
+
n
;
m
++
)
{
double
prefactor
=
polar_prefactor
(
n
,
m
,
costheta
);
double
c_r
=
prefactor
*
expphim_r
;
double
c_i
=
prefactor
*
expphim_i
;
qnm_r
[
iw
][
m
+
n
]
+=
c_r
;
qnm_i
[
iw
][
m
+
n
]
+=
c_i
;
if
(
m
&
1
)
{
qnm_r
[
iw
][
-
m
+
n
]
-=
c_r
;
qnm_i
[
iw
][
-
m
+
n
]
+=
c_i
;
}
else
{
qnm_r
[
iw
][
-
m
+
n
]
+=
c_r
;
qnm_i
[
iw
][
-
m
+
n
]
-=
c_i
;
}
double
tmp_r
=
expphim_r
*
expphi_r
-
expphim_i
*
expphi_i
;
double
tmp_i
=
expphim_r
*
expphi_i
+
expphim_i
*
expphi_r
;
expphim_r
=
tmp_r
;
expphim_i
=
tmp_i
;
}
}
}
double
fac
=
sqrt
(
MY_4PI
)
/
ncount
;
for
(
int
iw
=
0
;
iw
<
nqlist
;
iw
++
)
{
int
n
=
qlist
[
iw
];
double
qm_sum
=
0.0
;
for
(
int
m
=
0
;
m
<
2
*
n
+
1
;
m
++
)
{
qm_sum
+=
qnm_r
[
iw
][
m
]
*
qnm_r
[
iw
][
m
]
+
qnm_i
[
iw
][
m
]
*
qnm_i
[
iw
][
m
];
// printf("Ylm^2 = %d %d %g\n",n,m,
// qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]);
}
qn
[
iw
]
=
fac
*
sqrt
(
qm_sum
/
(
2
*
n
+
1
));
}
}
/* ----------------------------------------------------------------------
calculate scalar distance
------------------------------------------------------------------------- */
double
ComputeOrientOrderAtom
::
dist
(
const
double
r
[])
{
return
sqrt
(
r
[
0
]
*
r
[
0
]
+
r
[
1
]
*
r
[
1
]
+
r
[
2
]
*
r
[
2
]);
}
/* ----------------------------------------------------------------------
polar prefactor for spherical harmonic Y_l^m, where
Y_l^m (theta, phi) = prefactor(l, m, cos(theta)) * exp(i*m*phi)
------------------------------------------------------------------------- */
double
ComputeOrientOrderAtom
::
polar_prefactor
(
int
l
,
int
m
,
double
costheta
)
{
const
int
mabs
=
abs
(
m
);
double
prefactor
=
1.0
;
for
(
int
i
=
l
-
mabs
+
1
;
i
<
l
+
mabs
+
1
;
++
i
)
prefactor
*=
static_cast
<
double
>
(
i
);
prefactor
=
sqrt
(
static_cast
<
double
>
(
2
*
l
+
1
)
/
(
MY_4PI
*
prefactor
))
*
associated_legendre
(
l
,
mabs
,
costheta
);
if
((
m
<
0
)
&&
(
m
%
2
))
prefactor
=
-
prefactor
;
return
prefactor
;
}
/* ----------------------------------------------------------------------
associated legendre polynomial
------------------------------------------------------------------------- */
double
ComputeOrientOrderAtom
::
associated_legendre
(
int
l
,
int
m
,
double
x
)
{
if
(
l
<
m
)
return
0.0
;
double
p
(
1.0
),
pm1
(
0.0
),
pm2
(
0.0
);
if
(
m
!=
0
)
{
const
double
sqx
=
sqrt
(
1.0
-
x
*
x
);
for
(
int
i
=
1
;
i
<
m
+
1
;
++
i
)
p
*=
static_cast
<
double
>
(
2
*
i
-
1
)
*
sqx
;
}
for
(
int
i
=
m
+
1
;
i
<
l
+
1
;
++
i
)
{
pm2
=
pm1
;
pm1
=
p
;
p
=
(
static_cast
<
double
>
(
2
*
i
-
1
)
*
x
*
pm1
-
static_cast
<
double
>
(
i
+
m
-
1
)
*
pm2
)
/
static_cast
<
double
>
(
i
-
m
);
}
return
p
;
}
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