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compute_centro_atom.cpp
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Wed, Sep 4, 14:49
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8 KB
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text/x-c
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Fri, Sep 6, 14:49 (2 d)
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blob
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rLAMMPS lammps
compute_centro_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: 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 "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeCentroAtom
::
ComputeCentroAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
4
)
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
]);
if
(
nnn
<=
0
||
nnn
%
2
)
error
->
all
(
FLERR
,
"Illegal neighbor value for compute centro/atom command"
);
peratom_flag
=
1
;
size_peratom_cols
=
0
;
nmax
=
0
;
centro
=
NULL
;
maxneigh
=
0
;
distsq
=
NULL
;
nearest
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeCentroAtom
::~
ComputeCentroAtom
()
{
memory
->
destroy
(
centro
);
memory
->
destroy
(
distsq
);
memory
->
destroy
(
nearest
);
}
/* ---------------------------------------------------------------------- */
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
);
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
if
(
atom
->
nlocal
>
nmax
)
{
memory
->
destroy
(
centro
);
nmax
=
atom
->
nmax
;
memory
->
create
(
centro
,
nmax
,
"centro/atom:centro"
);
vector_atom
=
centro
;
}
// 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
;
}
}
// 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
;
}
}
// 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
;
}
delete
[]
pairs
;
}
/* ----------------------------------------------------------------------
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
;
}
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