Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F88112560
fix_orient_fcc.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, Oct 16, 20:54
Size
17 KB
Mime Type
text/x-c
Expires
Fri, Oct 18, 20:54 (2 d)
Engine
blob
Format
Raw Data
Handle
21718872
Attached To
rLAMMPS lammps
fix_orient_fcc.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 authors: Koenraad Janssens and David Olmsted (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include <mpi.h>
#include "fix_orient_fcc.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "output.h"
#include "force.h"
#include "math_const.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
using
namespace
MathConst
;
#define BIG 1000000000
static
const
char
cite_fix_orient_fcc
[]
=
"fix orient/fcc command:
\n\n
"
"@Article{Janssens06,
\n
"
" author = {K. G. F. Janssens, D. Olmsted, E.A. Holm, S. M. Foiles, S. J. Plimpton, and P. M. Derlet},
\n
"
" title = {Computing the Mobility of Grain Boundaries},
\n
"
" journal = {Nature Materials},
\n
"
" year = 2006,
\n
"
" volume = 5,
\n
"
" pages = {124--127}
\n
"
"}
\n\n
"
;
/* ---------------------------------------------------------------------- */
FixOrientFCC
::
FixOrientFCC
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
lmp
->
citeme
)
lmp
->
citeme
->
add
(
cite_fix_orient_fcc
);
MPI_Comm_rank
(
world
,
&
me
);
if
(
narg
!=
11
)
error
->
all
(
FLERR
,
"Illegal fix orient/fcc command"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
1
;
peratom_flag
=
1
;
size_peratom_cols
=
2
;
peratom_freq
=
1
;
respa_level_support
=
1
;
ilevel_respa
=
0
;
nstats
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
direction_of_motion
=
force
->
inumeric
(
FLERR
,
arg
[
4
]);
a
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
Vxi
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
uxif_low
=
force
->
numeric
(
FLERR
,
arg
[
7
]);
uxif_high
=
force
->
numeric
(
FLERR
,
arg
[
8
]);
if
(
direction_of_motion
==
0
)
{
int
n
=
strlen
(
arg
[
9
])
+
1
;
chifilename
=
new
char
[
n
];
strcpy
(
chifilename
,
arg
[
9
]);
n
=
strlen
(
arg
[
10
])
+
1
;
xifilename
=
new
char
[
n
];
strcpy
(
xifilename
,
arg
[
10
]);
}
else
if
(
direction_of_motion
==
1
)
{
int
n
=
strlen
(
arg
[
9
])
+
1
;
xifilename
=
new
char
[
n
];
strcpy
(
xifilename
,
arg
[
9
]);
n
=
strlen
(
arg
[
10
])
+
1
;
chifilename
=
new
char
[
n
];
strcpy
(
chifilename
,
arg
[
10
]);
}
else
error
->
all
(
FLERR
,
"Illegal fix orient/fcc command"
);
// initializations
half_fcc_nn
=
6
;
use_xismooth
=
false
;
double
xicutoff
=
1.57
;
xicutoffsq
=
xicutoff
*
xicutoff
;
cutsq
=
0.5
*
a
*
a
*
xicutoffsq
;
nmax
=
0
;
// read xi and chi reference orientations from files
if
(
me
==
0
)
{
char
line
[
IMGMAX
];
char
*
result
;
int
count
;
FILE
*
infile
=
fopen
(
xifilename
,
"r"
);
if
(
infile
==
NULL
)
error
->
one
(
FLERR
,
"Fix orient/fcc file open failed"
);
for
(
int
i
=
0
;
i
<
6
;
i
++
)
{
result
=
fgets
(
line
,
IMGMAX
,
infile
);
if
(
!
result
)
error
->
one
(
FLERR
,
"Fix orient/fcc file read failed"
);
count
=
sscanf
(
line
,
"%lg %lg %lg"
,
&
Rxi
[
i
][
0
],
&
Rxi
[
i
][
1
],
&
Rxi
[
i
][
2
]);
if
(
count
!=
3
)
error
->
one
(
FLERR
,
"Fix orient/fcc file read failed"
);
}
fclose
(
infile
);
infile
=
fopen
(
chifilename
,
"r"
);
if
(
infile
==
NULL
)
error
->
one
(
FLERR
,
"Fix orient/fcc file open failed"
);
for
(
int
i
=
0
;
i
<
6
;
i
++
)
{
result
=
fgets
(
line
,
IMGMAX
,
infile
);
if
(
!
result
)
error
->
one
(
FLERR
,
"Fix orient/fcc file read failed"
);
count
=
sscanf
(
line
,
"%lg %lg %lg"
,
&
Rchi
[
i
][
0
],
&
Rchi
[
i
][
1
],
&
Rchi
[
i
][
2
]);
if
(
count
!=
3
)
error
->
one
(
FLERR
,
"Fix orient/fcc file read failed"
);
}
fclose
(
infile
);
}
MPI_Bcast
(
&
Rxi
[
0
][
0
],
18
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Rchi
[
0
][
0
],
18
,
MPI_DOUBLE
,
0
,
world
);
// make copy of the reference vectors
for
(
int
i
=
0
;
i
<
6
;
i
++
)
for
(
int
j
=
0
;
j
<
3
;
j
++
)
{
half_xi_chi_vec
[
0
][
i
][
j
]
=
Rxi
[
i
][
j
];
half_xi_chi_vec
[
1
][
i
][
j
]
=
Rchi
[
i
][
j
];
}
// compute xiid,xi0,xi1 for all 12 neighbors
// xi is the favored crystal
// want order parameter when actual is Rchi
double
xi_sq
,
dxi
[
3
],
rchi
[
3
];
xiid
=
0.0
;
for
(
int
i
=
0
;
i
<
6
;
i
++
)
{
rchi
[
0
]
=
Rchi
[
i
][
0
];
rchi
[
1
]
=
Rchi
[
i
][
1
];
rchi
[
2
]
=
Rchi
[
i
][
2
];
find_best_ref
(
rchi
,
0
,
xi_sq
,
dxi
);
xiid
+=
sqrt
(
xi_sq
);
for
(
int
j
=
0
;
j
<
3
;
j
++
)
rchi
[
j
]
=
-
rchi
[
j
];
find_best_ref
(
rchi
,
0
,
xi_sq
,
dxi
);
xiid
+=
sqrt
(
xi_sq
);
}
xiid
/=
12.0
;
xi0
=
uxif_low
*
xiid
;
xi1
=
uxif_high
*
xiid
;
// set comm size needed by this Fix
// NOTE: doesn't seem that use_xismooth is ever true
if
(
use_xismooth
)
comm_forward
=
62
;
else
comm_forward
=
50
;
added_energy
=
0.0
;
nmax
=
atom
->
nmax
;
nbr
=
(
Nbr
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
Nbr
),
"orient/fcc:nbr"
);
memory
->
create
(
order
,
nmax
,
2
,
"orient/fcc:order"
);
array_atom
=
order
;
// zero the array since a variable may access it before first run
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
order
[
i
][
0
]
=
order
[
i
][
1
]
=
0.0
;
}
/* ---------------------------------------------------------------------- */
FixOrientFCC
::~
FixOrientFCC
()
{
delete
[]
xifilename
;
delete
[]
chifilename
;
memory
->
sfree
(
nbr
);
memory
->
destroy
(
order
);
}
/* ---------------------------------------------------------------------- */
int
FixOrientFCC
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
THERMO_ENERGY
;
mask
|=
POST_FORCE_RESPA
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
init
()
{
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
{
ilevel_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
-
1
;
if
(
respa_level
>=
0
)
ilevel_respa
=
MIN
(
respa_level
,
ilevel_respa
);
}
// need a full neighbor list
// perpetual list, built whenever re-neighboring occurs
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
fix
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
setup
(
int
vflag
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
ilevel_respa
);
post_force_respa
(
vflag
,
ilevel_respa
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
ilevel_respa
);
}
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
post_force
(
int
vflag
)
{
int
i
,
j
,
k
,
ii
,
jj
,
inum
,
jnum
,
m
,
n
,
nn
,
nsort
;
tagint
id_self
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
edelta
,
omega
;
double
dx
,
dy
,
dz
,
rsq
,
xismooth
,
xi_sq
,
duxi
,
duxi_other
;
double
dxi
[
3
];
double
*
dxiptr
;
bool
found_myself
;
// set local ptrs
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
tagint
*
tag
=
atom
->
tag
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// insure nbr and order data structures are adequate size
if
(
nall
>
nmax
)
{
nmax
=
nall
;
memory
->
destroy
(
nbr
);
memory
->
destroy
(
order
);
nbr
=
(
Nbr
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
Nbr
),
"orient/fcc:nbr"
);
memory
->
create
(
order
,
nmax
,
2
,
"orient/fcc:order"
);
array_atom
=
order
;
}
// loop over owned atoms and build Nbr data structure of neighbors
// use full neighbor list
added_energy
=
0.0
;
int
count
=
0
;
int
mincount
=
BIG
;
int
maxcount
=
0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
if
(
jnum
<
mincount
)
mincount
=
jnum
;
if
(
jnum
>
maxcount
)
{
if
(
maxcount
)
delete
[]
sort
;
sort
=
new
Sort
[
jnum
];
maxcount
=
jnum
;
}
// loop over all neighbors of atom i
// for those within cutsq, build sort data structure
// store local id, rsq, delta vector, xismooth (if included)
nsort
=
0
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
count
++
;
dx
=
x
[
i
][
0
]
-
x
[
j
][
0
];
dy
=
x
[
i
][
1
]
-
x
[
j
][
1
];
dz
=
x
[
i
][
2
]
-
x
[
j
][
2
];
rsq
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
if
(
rsq
<
cutsq
)
{
sort
[
nsort
].
id
=
j
;
sort
[
nsort
].
rsq
=
rsq
;
sort
[
nsort
].
delta
[
0
]
=
dx
;
sort
[
nsort
].
delta
[
1
]
=
dy
;
sort
[
nsort
].
delta
[
2
]
=
dz
;
if
(
use_xismooth
)
{
xismooth
=
(
xicutoffsq
-
2.0
*
rsq
/
(
a
*
a
))
/
(
xicutoffsq
-
1.0
);
sort
[
nsort
].
xismooth
=
1.0
-
fabs
(
1.0
-
xismooth
);
}
nsort
++
;
}
}
// sort neighbors by rsq distance
// no need to sort if nsort <= 12
if
(
nsort
>
12
)
qsort
(
sort
,
nsort
,
sizeof
(
Sort
),
compare
);
// copy up to 12 nearest neighbors into nbr data structure
// operate on delta vector via find_best_ref() to compute dxi
n
=
MIN
(
12
,
nsort
);
nbr
[
i
].
n
=
n
;
if
(
n
==
0
)
continue
;
double
xi_total
=
0.0
;
for
(
j
=
0
;
j
<
n
;
j
++
)
{
find_best_ref
(
sort
[
j
].
delta
,
0
,
xi_sq
,
dxi
);
xi_total
+=
sqrt
(
xi_sq
);
nbr
[
i
].
id
[
j
]
=
sort
[
j
].
id
;
nbr
[
i
].
dxi
[
j
][
0
]
=
dxi
[
0
]
/
n
;
nbr
[
i
].
dxi
[
j
][
1
]
=
dxi
[
1
]
/
n
;
nbr
[
i
].
dxi
[
j
][
2
]
=
dxi
[
2
]
/
n
;
if
(
use_xismooth
)
nbr
[
i
].
xismooth
[
j
]
=
sort
[
j
].
xismooth
;
}
xi_total
/=
n
;
order
[
i
][
0
]
=
xi_total
;
// compute potential derivative to xi
if
(
xi_total
<
xi0
)
{
nbr
[
i
].
duxi
=
0.0
;
edelta
=
0.0
;
order
[
i
][
1
]
=
0.0
;
}
else
if
(
xi_total
>
xi1
)
{
nbr
[
i
].
duxi
=
0.0
;
edelta
=
Vxi
;
order
[
i
][
1
]
=
1.0
;
}
else
{
omega
=
MY_PI2
*
(
xi_total
-
xi0
)
/
(
xi1
-
xi0
);
nbr
[
i
].
duxi
=
MY_PI
*
Vxi
*
sin
(
2.0
*
omega
)
/
(
2.0
*
(
xi1
-
xi0
));
edelta
=
Vxi
*
(
1
-
cos
(
2.0
*
omega
))
/
2.0
;
order
[
i
][
1
]
=
omega
/
MY_PI2
;
}
added_energy
+=
edelta
;
}
if
(
maxcount
)
delete
[]
sort
;
// communicate to acquire nbr data for ghost atoms
comm
->
forward_comm_fix
(
this
);
// compute grain boundary force on each owned atom
// skip atoms not in group
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
n
=
nbr
[
i
].
n
;
duxi
=
nbr
[
i
].
duxi
;
for
(
j
=
0
;
j
<
n
;
j
++
)
{
dxiptr
=
&
nbr
[
i
].
dxi
[
j
][
0
];
if
(
use_xismooth
)
{
xismooth
=
nbr
[
i
].
xismooth
[
j
];
f
[
i
][
0
]
+=
duxi
*
dxiptr
[
0
]
*
xismooth
;
f
[
i
][
1
]
+=
duxi
*
dxiptr
[
1
]
*
xismooth
;
f
[
i
][
2
]
+=
duxi
*
dxiptr
[
2
]
*
xismooth
;
}
else
{
f
[
i
][
0
]
+=
duxi
*
dxiptr
[
0
];
f
[
i
][
1
]
+=
duxi
*
dxiptr
[
1
];
f
[
i
][
2
]
+=
duxi
*
dxiptr
[
2
];
}
// m = local index of neighbor
// id_self = ID for atom I in atom M's neighbor list
// if M is local atom, id_self will be local ID of atom I
// if M is ghost atom, id_self will be global ID of atom I
m
=
nbr
[
i
].
id
[
j
];
if
(
m
<
nlocal
)
id_self
=
i
;
else
id_self
=
tag
[
i
];
found_myself
=
false
;
nn
=
nbr
[
m
].
n
;
for
(
k
=
0
;
k
<
nn
;
k
++
)
{
if
(
id_self
==
nbr
[
m
].
id
[
k
])
{
if
(
found_myself
)
error
->
one
(
FLERR
,
"Fix orient/fcc found self twice"
);
found_myself
=
true
;
duxi_other
=
nbr
[
m
].
duxi
;
dxiptr
=
&
nbr
[
m
].
dxi
[
k
][
0
];
if
(
use_xismooth
)
{
xismooth
=
nbr
[
m
].
xismooth
[
k
];
f
[
i
][
0
]
-=
duxi_other
*
dxiptr
[
0
]
*
xismooth
;
f
[
i
][
1
]
-=
duxi_other
*
dxiptr
[
1
]
*
xismooth
;
f
[
i
][
2
]
-=
duxi_other
*
dxiptr
[
2
]
*
xismooth
;
}
else
{
f
[
i
][
0
]
-=
duxi_other
*
dxiptr
[
0
];
f
[
i
][
1
]
-=
duxi_other
*
dxiptr
[
1
];
f
[
i
][
2
]
-=
duxi_other
*
dxiptr
[
2
];
}
}
}
}
}
// print statistics every nstats timesteps
if
(
nstats
&&
update
->
ntimestep
%
nstats
==
0
)
{
int
total
;
MPI_Allreduce
(
&
count
,
&
total
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
double
ave
=
static_cast
<
double
>
(
total
)
/
atom
->
natoms
;
int
min
,
max
;
MPI_Allreduce
(
&
mincount
,
&
min
,
1
,
MPI_INT
,
MPI_MIN
,
world
);
MPI_Allreduce
(
&
maxcount
,
&
max
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
if
(
me
==
0
)
{
if
(
screen
)
fprintf
(
screen
,
"orient step "
BIGINT_FORMAT
": "
BIGINT_FORMAT
" atoms have %d neighbors
\n
"
,
update
->
ntimestep
,
atom
->
natoms
,
total
);
if
(
logfile
)
fprintf
(
logfile
,
"orient step "
BIGINT_FORMAT
": "
BIGINT_FORMAT
" atoms have %d neighbors
\n
"
,
update
->
ntimestep
,
atom
->
natoms
,
total
);
if
(
screen
)
fprintf
(
screen
,
" neighs: min = %d, max = %d, ave = %g
\n
"
,
min
,
max
,
ave
);
if
(
logfile
)
fprintf
(
logfile
,
" neighs: min = %d, max = %d, ave = %g
\n
"
,
min
,
max
,
ave
);
}
}
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
ilevel_respa
)
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
double
FixOrientFCC
::
compute_scalar
()
{
double
added_energy_total
;
MPI_Allreduce
(
&
added_energy
,
&
added_energy_total
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
return
added_energy_total
;
}
/* ---------------------------------------------------------------------- */
int
FixOrientFCC
::
pack_forward_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
k
,
num
;
tagint
id
;
tagint
*
tag
=
atom
->
tag
;
int
nlocal
=
atom
->
nlocal
;
int
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
k
=
list
[
i
];
num
=
nbr
[
k
].
n
;
buf
[
m
++
]
=
num
;
buf
[
m
++
]
=
nbr
[
k
].
duxi
;
for
(
j
=
0
;
j
<
num
;
j
++
)
{
if
(
use_xismooth
)
buf
[
m
++
]
=
nbr
[
k
].
xismooth
[
j
];
buf
[
m
++
]
=
nbr
[
k
].
dxi
[
j
][
0
];
buf
[
m
++
]
=
nbr
[
k
].
dxi
[
j
][
1
];
buf
[
m
++
]
=
nbr
[
k
].
dxi
[
j
][
2
];
// id stored in buf needs to be global ID
// if k is a local atom, it stores local IDs, so convert to global
// if k is a ghost atom (already comm'd), its IDs are already global
id
=
nbr
[
k
].
id
[
j
];
if
(
k
<
nlocal
)
id
=
tag
[
id
];
buf
[
m
++
]
=
id
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
unpack_forward_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
j
,
num
;
int
last
=
first
+
n
;
int
m
=
0
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
nbr
[
i
].
n
=
num
=
static_cast
<
int
>
(
buf
[
m
++
]);
nbr
[
i
].
duxi
=
buf
[
m
++
];
for
(
j
=
0
;
j
<
num
;
j
++
)
{
if
(
use_xismooth
)
nbr
[
i
].
xismooth
[
j
]
=
buf
[
m
++
];
nbr
[
i
].
dxi
[
j
][
0
]
=
buf
[
m
++
];
nbr
[
i
].
dxi
[
j
][
1
]
=
buf
[
m
++
];
nbr
[
i
].
dxi
[
j
][
2
]
=
buf
[
m
++
];
nbr
[
i
].
id
[
j
]
=
static_cast
<
tagint
>
(
buf
[
m
++
]);
}
}
}
/* ---------------------------------------------------------------------- */
void
FixOrientFCC
::
find_best_ref
(
double
*
displs
,
int
which_crystal
,
double
&
xi_sq
,
double
*
dxi
)
{
int
i
;
double
dot
,
tmp
;
double
best_dot
=
-
1.0
;
// best is biggest (smallest angle)
int
best_i
=
-
1
;
int
best_sign
=
0
;
for
(
i
=
0
;
i
<
half_fcc_nn
;
i
++
)
{
dot
=
displs
[
0
]
*
half_xi_chi_vec
[
which_crystal
][
i
][
0
]
+
displs
[
1
]
*
half_xi_chi_vec
[
which_crystal
][
i
][
1
]
+
displs
[
2
]
*
half_xi_chi_vec
[
which_crystal
][
i
][
2
];
if
(
fabs
(
dot
)
>
best_dot
)
{
best_dot
=
fabs
(
dot
);
best_i
=
i
;
if
(
dot
<
0.0
)
best_sign
=
-
1
;
else
best_sign
=
1
;
}
}
xi_sq
=
0.0
;
for
(
i
=
0
;
i
<
3
;
i
++
)
{
tmp
=
displs
[
i
]
-
best_sign
*
half_xi_chi_vec
[
which_crystal
][
best_i
][
i
];
xi_sq
+=
tmp
*
tmp
;
}
if
(
xi_sq
>
0.0
)
{
double
xi
=
sqrt
(
xi_sq
);
for
(
i
=
0
;
i
<
3
;
i
++
)
dxi
[
i
]
=
(
best_sign
*
half_xi_chi_vec
[
which_crystal
][
best_i
][
i
]
-
displs
[
i
])
/
xi
;
}
else
dxi
[
0
]
=
dxi
[
1
]
=
dxi
[
2
]
=
0.0
;
}
/* ----------------------------------------------------------------------
compare two neighbors I and J in sort data structure
called via qsort in post_force() method
is a static method so can't access sort data structure directly
return -1 if I < J, 0 if I = J, 1 if I > J
do comparison based on rsq distance
------------------------------------------------------------------------- */
int
FixOrientFCC
::
compare
(
const
void
*
pi
,
const
void
*
pj
)
{
FixOrientFCC
::
Sort
*
ineigh
=
(
FixOrientFCC
::
Sort
*
)
pi
;
FixOrientFCC
::
Sort
*
jneigh
=
(
FixOrientFCC
::
Sort
*
)
pj
;
if
(
ineigh
->
rsq
<
jneigh
->
rsq
)
return
-
1
;
else
if
(
ineigh
->
rsq
>
jneigh
->
rsq
)
return
1
;
return
0
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixOrientFCC
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
Nbr
);
bytes
+=
2
*
nmax
*
sizeof
(
double
);
return
bytes
;
}
Event Timeline
Log In to Comment