Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F75033044
compute_centro_atom.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Jul 31, 00:17
Size
10 KB
Mime Type
text/x-c
Expires
Fri, Aug 2, 00:17 (2 d)
Engine
blob
Format
Raw Data
Handle
19435537
Attached To
rLAMMPS lammps
compute_centro_atom.cpp
View Options
/* ----------------------------------------------------------------------
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: Michel Perez (U Lyon) for non-fcc lattices
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "compute_centro_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 "math_extra.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeCentroAtom
::
ComputeCentroAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
distsq
(
NULL
),
nearest
(
NULL
),
centro
(
NULL
)
{
if
(
narg
<
4
||
narg
>
6
)
error
->
all
(
FLERR
,
"Illegal compute centro/atom command"
);
if
(
strcmp
(
arg
[
3
],
"fcc"
)
==
0
)
nnn
=
12
;
else
if
(
strcmp
(
arg
[
3
],
"bcc"
)
==
0
)
nnn
=
8
;
else
nnn
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
// default values
axes_flag
=
0
;
// optional keywords
int
iarg
=
4
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"axes"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute centro/atom command3"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
axes_flag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
axes_flag
=
0
;
else
error
->
all
(
FLERR
,
"Illegal compute centro/atom command2"
);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal compute centro/atom command1"
);
}
if
(
nnn
<=
0
||
nnn
%
2
)
error
->
all
(
FLERR
,
"Illegal neighbor value for compute centro/atom command"
);
peratom_flag
=
1
;
if
(
!
axes_flag
)
size_peratom_cols
=
0
;
else
size_peratom_cols
=
10
;
nmax
=
0
;
maxneigh
=
0
;
}
/* ---------------------------------------------------------------------- */
ComputeCentroAtom
::~
ComputeCentroAtom
()
{
memory
->
destroy
(
centro
);
memory
->
destroy
(
distsq
);
memory
->
destroy
(
nearest
);
if
(
axes_flag
)
memory
->
destroy
(
array_atom
);
}
/* ---------------------------------------------------------------------- */
void
ComputeCentroAtom
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Compute centro/atom requires a pair style be defined"
);
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"centro/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute centro/atom"
);
// 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
;
}
/* ---------------------------------------------------------------------- */
void
ComputeCentroAtom
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeCentroAtom
::
compute_peratom
()
{
int
i
,
j
,
k
,
ii
,
jj
,
kk
,
n
,
inum
,
jnum
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
,
value
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
invoked_peratom
=
update
->
ntimestep
;
// grow centro array if necessary
// grow array_atom array if axes_flag set
if
(
atom
->
nmax
>
nmax
)
{
if
(
!
axes_flag
)
{
memory
->
destroy
(
centro
);
nmax
=
atom
->
nmax
;
memory
->
create
(
centro
,
nmax
,
"centro/atom:centro"
);
vector_atom
=
centro
;
}
else
{
memory
->
destroy
(
centro
);
memory
->
destroy
(
array_atom
);
nmax
=
atom
->
nmax
;
memory
->
create
(
centro
,
nmax
,
"centro/atom:centro"
);
memory
->
create
(
array_atom
,
nmax
,
size_peratom_cols
,
"centro/atom:array_atom"
);
}
}
// 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
;
// npairs = number of unique pairs
int
nhalf
=
nnn
/
2
;
int
npairs
=
nnn
*
(
nnn
-
1
)
/
2
;
double
*
pairs
=
new
double
[
npairs
];
// compute centro-symmetry 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
];
// insure distsq and nearest arrays are long enough
if
(
jnum
>
maxneigh
)
{
memory
->
destroy
(
distsq
);
memory
->
destroy
(
nearest
);
maxneigh
=
jnum
;
memory
->
create
(
distsq
,
maxneigh
,
"centro/atom:distsq"
);
memory
->
create
(
nearest
,
maxneigh
,
"centro/atom:nearest"
);
}
// 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
;
}
}
// check whether to include local crystal symmetry axes
if
(
!
axes_flag
)
{
// if not nnn neighbors, centro = 0.0
if
(
n
<
nnn
)
{
centro
[
i
]
=
0.0
;
continue
;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2
(
nnn
,
n
,
distsq
,
nearest
);
// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
// pairs = squared length of each R
n
=
0
;
for
(
j
=
0
;
j
<
nnn
;
j
++
)
{
jj
=
nearest
[
j
];
for
(
k
=
j
+
1
;
k
<
nnn
;
k
++
)
{
kk
=
nearest
[
k
];
delx
=
x
[
jj
][
0
]
+
x
[
kk
][
0
]
-
2.0
*
xtmp
;
dely
=
x
[
jj
][
1
]
+
x
[
kk
][
1
]
-
2.0
*
ytmp
;
delz
=
x
[
jj
][
2
]
+
x
[
kk
][
2
]
-
2.0
*
ztmp
;
pairs
[
n
++
]
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
}
}
}
else
{
// calculate local crystal symmetry axes
// rsq1, rsq2 are two smallest values of R^2
// R1, R2 are corresponding vectors Ri - Rj
// R3 is normal to R1, R2
double
rsq1
,
rsq2
;
double
*
r1
=
&
array_atom
[
i
][
1
];
double
*
r2
=
&
array_atom
[
i
][
4
];
double
*
r3
=
&
array_atom
[
i
][
7
];
if
(
n
<
nnn
)
{
centro
[
i
]
=
0.0
;
MathExtra
::
zero3
(
r1
);
MathExtra
::
zero3
(
r2
);
MathExtra
::
zero3
(
r3
);
continue
;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2
(
nnn
,
n
,
distsq
,
nearest
);
n
=
0
;
rsq1
=
rsq2
=
cutsq
;
for
(
j
=
0
;
j
<
nnn
;
j
++
)
{
jj
=
nearest
[
j
];
for
(
k
=
j
+
1
;
k
<
nnn
;
k
++
)
{
kk
=
nearest
[
k
];
delx
=
x
[
jj
][
0
]
+
x
[
kk
][
0
]
-
2.0
*
xtmp
;
dely
=
x
[
jj
][
1
]
+
x
[
kk
][
1
]
-
2.0
*
ytmp
;
delz
=
x
[
jj
][
2
]
+
x
[
kk
][
2
]
-
2.0
*
ztmp
;
double
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
pairs
[
n
++
]
=
rsq
;
if
(
rsq
<
rsq2
)
{
if
(
rsq
<
rsq1
)
{
rsq2
=
rsq1
;
MathExtra
::
copy3
(
r1
,
r2
);
rsq1
=
rsq
;
MathExtra
::
sub3
(
x
[
jj
],
x
[
kk
],
r1
);
}
else
{
rsq2
=
rsq
;
MathExtra
::
sub3
(
x
[
jj
],
x
[
kk
],
r2
);
}
}
}
}
MathExtra
::
cross3
(
r1
,
r2
,
r3
);
MathExtra
::
norm3
(
r1
);
MathExtra
::
norm3
(
r2
);
MathExtra
::
norm3
(
r3
);
}
// store nhalf smallest pair distances in 1st nhalf locations of pairs
select
(
nhalf
,
npairs
,
pairs
);
// centrosymmetry = sum of nhalf smallest squared values
value
=
0.0
;
for
(
j
=
0
;
j
<
nhalf
;
j
++
)
value
+=
pairs
[
j
];
centro
[
i
]
=
value
;
}
else
{
centro
[
i
]
=
0.0
;
if
(
axes_flag
)
{
MathExtra
::
zero3
(
&
array_atom
[
i
][
1
]);
MathExtra
::
zero3
(
&
array_atom
[
i
][
4
]);
MathExtra
::
zero3
(
&
array_atom
[
i
][
7
]);
}
}
}
delete
[]
pairs
;
if
(
axes_flag
)
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
array_atom
[
i
][
0
]
=
centro
[
i
];
}
}
/* ----------------------------------------------------------------------
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
ComputeCentroAtom
::
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
ComputeCentroAtom
::
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
ComputeCentroAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
Event Timeline
Log In to Comment