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rLAMMPS lammps
compute_ackland_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: G. Ziegenhain, gerolf@ziegenhain.com
Copyright (C) 2007
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_ackland_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.h>
using
namespace
LAMMPS_NS
;
enum
{
UNKNOWN
,
BCC
,
FCC
,
HCP
,
ICO
};
/* ---------------------------------------------------------------------- */
ComputeAcklandAtom
::
ComputeAcklandAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal compute ackland/atom command"
);
peratom_flag
=
1
;
size_peratom_cols
=
0
;
nmax
=
0
;
structure
=
NULL
;
maxneigh
=
0
;
distsq
=
NULL
;
nearest
=
NULL
;
nearest_n0
=
NULL
;
nearest_n1
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeAcklandAtom
::~
ComputeAcklandAtom
()
{
memory
->
destroy
(
structure
);
memory
->
destroy
(
distsq
);
memory
->
destroy
(
nearest
);
memory
->
destroy
(
nearest_n0
);
memory
->
destroy
(
nearest_n1
);
}
/* ---------------------------------------------------------------------- */
void
ComputeAcklandAtom
::
init
()
{
// 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
,
"ackland/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute ackland/atom"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeAcklandAtom
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeAcklandAtom
::
compute_peratom
()
{
int
i
,
j
,
ii
,
jj
,
k
,
n
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
chi
[
8
];
invoked_peratom
=
update
->
ntimestep
;
// grow structure array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
structure
);
nmax
=
atom
->
nmax
;
memory
->
create
(
structure
,
nmax
,
"compute/ackland/atom:ackland"
);
vector_atom
=
structure
;
}
// 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 structure parameter for each atom in group
// use full neighbor list
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
double
cutsq
=
force
->
pair
->
cutforce
*
force
->
pair
->
cutforce
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
// ensure distsq and nearest arrays are long enough
if
(
jnum
>
maxneigh
)
{
memory
->
destroy
(
distsq
);
memory
->
destroy
(
nearest
);
memory
->
destroy
(
nearest_n0
);
memory
->
destroy
(
nearest_n1
);
maxneigh
=
jnum
;
memory
->
create
(
distsq
,
maxneigh
,
"compute/ackland/atom:distsq"
);
memory
->
create
(
nearest
,
maxneigh
,
"compute/ackland/atom:nearest"
);
memory
->
create
(
nearest_n0
,
maxneigh
,
"compute/ackland/atom:nearest_n0"
);
memory
->
create
(
nearest_n1
,
maxneigh
,
"compute/ackland/atom:nearest_n1"
);
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
n
=
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
[
n
]
=
rsq
;
nearest
[
n
++
]
=
j
;
}
}
// Select 6 nearest neighbors
select2
(
6
,
n
,
distsq
,
nearest
);
// Mean squared separation
double
r0_sq
=
0.
;
for
(
j
=
0
;
j
<
6
;
j
++
)
r0_sq
+=
distsq
[
j
];
r0_sq
/=
6.
;
// n0 near neighbors with: distsq<1.45*r0_sq
// n1 near neighbors with: distsq<1.55*r0_sq
double
n0_dist_sq
=
1.45
*
r0_sq
,
n1_dist_sq
=
1.55
*
r0_sq
;
int
n0
=
0
,
n1
=
0
;
for
(
j
=
0
;
j
<
n
;
j
++
)
{
if
(
distsq
[
j
]
<
n1_dist_sq
)
{
nearest_n1
[
n1
++
]
=
nearest
[
j
];
if
(
distsq
[
j
]
<
n0_dist_sq
)
{
nearest_n0
[
n0
++
]
=
nearest
[
j
];
}
}
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with:
// distsq < 1.45*r0_sq
double
bond_angle
;
double
norm_j
,
norm_k
;
chi
[
0
]
=
chi
[
1
]
=
chi
[
2
]
=
chi
[
3
]
=
chi
[
4
]
=
chi
[
5
]
=
chi
[
6
]
=
chi
[
7
]
=
0
;
double
x_ij
,
y_ij
,
z_ij
,
x_ik
,
y_ik
,
z_ik
;
for
(
j
=
0
;
j
<
n0
;
j
++
)
{
x_ij
=
x
[
i
][
0
]
-
x
[
nearest_n0
[
j
]][
0
];
y_ij
=
x
[
i
][
1
]
-
x
[
nearest_n0
[
j
]][
1
];
z_ij
=
x
[
i
][
2
]
-
x
[
nearest_n0
[
j
]][
2
];
norm_j
=
sqrt
(
x_ij
*
x_ij
+
y_ij
*
y_ij
+
z_ij
*
z_ij
);
if
(
norm_j
<=
0.
)
continue
;
for
(
k
=
j
+
1
;
k
<
n0
;
k
++
)
{
x_ik
=
x
[
i
][
0
]
-
x
[
nearest_n0
[
k
]][
0
];
y_ik
=
x
[
i
][
1
]
-
x
[
nearest_n0
[
k
]][
1
];
z_ik
=
x
[
i
][
2
]
-
x
[
nearest_n0
[
k
]][
2
];
norm_k
=
sqrt
(
x_ik
*
x_ik
+
y_ik
*
y_ik
+
z_ik
*
z_ik
);
if
(
norm_k
<=
0.
)
continue
;
bond_angle
=
(
x_ij
*
x_ik
+
y_ij
*
y_ik
+
z_ij
*
z_ik
)
/
(
norm_j
*
norm_k
);
// Histogram for identifying the relevant peaks
if
(
bond_angle
<
-
0.945
)
chi
[
0
]
++
;
else
if
(
bond_angle
<
-
0.915
)
chi
[
1
]
++
;
else
if
(
bond_angle
<
-
0.755
)
chi
[
2
]
++
;
else
if
(
bond_angle
<
-
0.195
)
chi
[
3
]
++
;
else
if
(
bond_angle
<
0.195
)
chi
[
4
]
++
;
else
if
(
bond_angle
<
0.245
)
chi
[
5
]
++
;
else
if
(
bond_angle
<
0.795
)
chi
[
6
]
++
;
else
chi
[
7
]
++
;
}
}
if
(
chi
[
7
]
>
0
||
n0
<
11
)
structure
[
i
]
=
UNKNOWN
;
else
if
(
chi
[
0
]
==
7
)
structure
[
i
]
=
BCC
;
else
if
(
chi
[
0
]
==
6
)
structure
[
i
]
=
FCC
;
else
if
(
chi
[
0
]
==
3
)
structure
[
i
]
=
HCP
;
else
{
// Deviations from the different lattice structures
double
delta_cp
=
fabs
(
1.
-
(
double
)
chi
[
6
]
/
24.
);
// ensure we do not get divide by zero
// and if we will, make delta_bcc irrelevant
double
delta_bcc
=
delta_cp
+
1.0
;
int
chi56m4
=
chi
[
5
]
+
chi
[
6
]
-
chi
[
4
];
// note that chi[7] presumed zero
if
(
chi56m4
!=
0
)
delta_bcc
=
0.35
*
chi
[
4
]
/
(
double
)
chi56m4
;
double
delta_fcc
=
0.61
*
(
fabs
((
double
)(
chi
[
0
]
+
chi
[
1
]
-
6
))
+
(
double
)
chi
[
2
])
/
6.0
;
double
delta_hcp
=
(
fabs
((
double
)
chi
[
0
]
-
3.
)
+
fabs
((
double
)
chi
[
0
]
+
(
double
)
chi
[
1
]
+
(
double
)
chi
[
2
]
+
(
double
)
chi
[
3
]
-
9.0
))
/
12.0
;
// Identification of the local structure according to the reference
if
(
delta_bcc
>=
0.1
&&
delta_cp
>=
0.1
&&
delta_fcc
>=
0.1
&&
delta_hcp
>=
0.1
)
structure
[
i
]
=
UNKNOWN
;
// not part of Ackland-Jones 2006; included for backward compatibility
if
(
chi
[
4
]
<
3.
&&
n1
==
12
)
structure
[
i
]
=
ICO
;
else
{
if
(
delta_bcc
<=
delta_cp
&&
n1
>
10
&&
n1
<
13
)
structure
[
i
]
=
BCC
;
else
{
if
(
n0
>
12
)
structure
[
i
]
=
UNKNOWN
;
else
{
if
(
delta_fcc
<
delta_hcp
)
structure
[
i
]
=
FCC
;
else
structure
[
i
]
=
HCP
;
}
}
}
}
}
else
structure
[
i
]
=
0.0
;
}
}
/* ----------------------------------------------------------------------
2 select routines from Numerical Recipes (slightly modified)
find k smallest values in array of length n
2nd routine sorts auxiliary array at same time
------------------------------------------------------------------------- */
#define SWAP(a,b) tmp = a; a = b; b = tmp;
#define ISWAP(a,b) itmp = a; a = b; b = itmp;
void
ComputeAcklandAtom
::
select
(
int
k
,
int
n
,
double
*
arr
)
{
int
i
,
ir
,
j
,
l
,
mid
;
double
a
,
tmp
;
arr
--
;
l
=
1
;
ir
=
n
;
for
(;;)
{
if
(
ir
<=
l
+
1
)
{
if
(
ir
==
l
+
1
&&
arr
[
ir
]
<
arr
[
l
])
{
SWAP
(
arr
[
l
],
arr
[
ir
])
}
return
;
}
else
{
mid
=
(
l
+
ir
)
>>
1
;
SWAP
(
arr
[
mid
],
arr
[
l
+
1
])
if
(
arr
[
l
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
],
arr
[
ir
])
}
if
(
arr
[
l
+
1
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
+
1
],
arr
[
ir
])
}
if
(
arr
[
l
]
>
arr
[
l
+
1
])
{
SWAP
(
arr
[
l
],
arr
[
l
+
1
])
}
i
=
l
+
1
;
j
=
ir
;
a
=
arr
[
l
+
1
];
for
(;;)
{
do
i
++
;
while
(
arr
[
i
]
<
a
);
do
j
--
;
while
(
arr
[
j
]
>
a
);
if
(
j
<
i
)
break
;
SWAP
(
arr
[
i
],
arr
[
j
])
}
arr
[
l
+
1
]
=
arr
[
j
];
arr
[
j
]
=
a
;
if
(
j
>=
k
)
ir
=
j
-
1
;
if
(
j
<=
k
)
l
=
i
;
}
}
}
/* ---------------------------------------------------------------------- */
void
ComputeAcklandAtom
::
select2
(
int
k
,
int
n
,
double
*
arr
,
int
*
iarr
)
{
int
i
,
ir
,
j
,
l
,
mid
,
ia
,
itmp
;
double
a
,
tmp
;
arr
--
;
iarr
--
;
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
])
}
return
;
}
else
{
mid
=
(
l
+
ir
)
>>
1
;
SWAP
(
arr
[
mid
],
arr
[
l
+
1
])
ISWAP
(
iarr
[
mid
],
iarr
[
l
+
1
])
if
(
arr
[
l
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
],
arr
[
ir
])
ISWAP
(
iarr
[
l
],
iarr
[
ir
])
}
if
(
arr
[
l
+
1
]
>
arr
[
ir
])
{
SWAP
(
arr
[
l
+
1
],
arr
[
ir
])
ISWAP
(
iarr
[
l
+
1
],
iarr
[
ir
])
}
if
(
arr
[
l
]
>
arr
[
l
+
1
])
{
SWAP
(
arr
[
l
],
arr
[
l
+
1
])
ISWAP
(
iarr
[
l
],
iarr
[
l
+
1
])
}
i
=
l
+
1
;
j
=
ir
;
a
=
arr
[
l
+
1
];
ia
=
iarr
[
l
+
1
];
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
])
}
arr
[
l
+
1
]
=
arr
[
j
];
arr
[
j
]
=
a
;
iarr
[
l
+
1
]
=
iarr
[
j
];
iarr
[
j
]
=
ia
;
if
(
j
>=
k
)
ir
=
j
-
1
;
if
(
j
<=
k
)
l
=
i
;
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeAcklandAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
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