Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F91994875
compute_omega_chunk.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
Sat, Nov 16, 11:28
Size
12 KB
Mime Type
text/x-c
Expires
Mon, Nov 18, 11:28 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
22360491
Attached To
rLAMMPS lammps
compute_omega_chunk.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.
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_omega_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk
::
ComputeOmegaChunk
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
idchunk
(
NULL
),
massproc
(
NULL
),
masstotal
(
NULL
),
com
(
NULL
),
comall
(
NULL
),
inertia
(
NULL
),
inertiaall
(
NULL
),
angmom
(
NULL
),
angmomall
(
NULL
),
omega
(
NULL
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Illegal compute omega/chunk command"
);
array_flag
=
1
;
size_array_cols
=
3
;
size_array_rows
=
0
;
size_array_rows_variable
=
1
;
extarray
=
0
;
// ID of compute chunk/atom
int
n
=
strlen
(
arg
[
3
])
+
1
;
idchunk
=
new
char
[
n
];
strcpy
(
idchunk
,
arg
[
3
]);
init
();
// chunk-based data
nchunk
=
1
;
maxchunk
=
0
;
allocate
();
}
/* ---------------------------------------------------------------------- */
ComputeOmegaChunk
::~
ComputeOmegaChunk
()
{
delete
[]
idchunk
;
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
com
);
memory
->
destroy
(
comall
);
memory
->
destroy
(
angmom
);
memory
->
destroy
(
angmomall
);
memory
->
destroy
(
inertia
);
memory
->
destroy
(
inertiaall
);
memory
->
destroy
(
omega
);
}
/* ---------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
init
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Chunk/atom compute does not exist for "
"compute omega/chunk"
);
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
if
(
strcmp
(
cchunk
->
style
,
"chunk/atom"
)
!=
0
)
error
->
all
(
FLERR
,
"Compute omega/chunk does not use chunk/atom compute"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
compute_array
()
{
int
i
,
j
,
m
,
index
;
double
dx
,
dy
,
dz
,
massone
;
double
unwrap
[
3
];
invoked_array
=
update
->
ntimestep
;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
cchunk
->
compute_ichunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
if
(
nchunk
>
maxchunk
)
allocate
();
size_array_rows
=
nchunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
massproc
[
i
]
=
0.0
;
com
[
i
][
0
]
=
com
[
i
][
1
]
=
com
[
i
][
2
]
=
0.0
;
for
(
j
=
0
;
j
<
6
;
j
++
)
inertia
[
i
][
j
]
=
0.0
;
angmom
[
i
][
0
]
=
angmom
[
i
][
1
]
=
angmom
[
i
][
2
]
=
0.0
;
omega
[
i
][
0
]
=
omega
[
i
][
1
]
=
omega
[
i
][
2
]
=
0.0
;
}
// compute COM for each chunk
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
massproc
[
index
]
+=
massone
;
com
[
index
][
0
]
+=
unwrap
[
0
]
*
massone
;
com
[
index
][
1
]
+=
unwrap
[
1
]
*
massone
;
com
[
index
][
2
]
+=
unwrap
[
2
]
*
massone
;
}
MPI_Allreduce
(
massproc
,
masstotal
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
MPI_Allreduce
(
&
com
[
0
][
0
],
&
comall
[
0
][
0
],
3
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
if
(
masstotal
[
i
]
>
0.0
)
{
comall
[
i
][
0
]
/=
masstotal
[
i
];
comall
[
i
][
1
]
/=
masstotal
[
i
];
comall
[
i
][
2
]
/=
masstotal
[
i
];
}
}
// compute inertia tensor for each chunk
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
comall
[
index
][
0
];
dy
=
unwrap
[
1
]
-
comall
[
index
][
1
];
dz
=
unwrap
[
2
]
-
comall
[
index
][
2
];
inertia
[
index
][
0
]
+=
massone
*
(
dy
*
dy
+
dz
*
dz
);
inertia
[
index
][
1
]
+=
massone
*
(
dx
*
dx
+
dz
*
dz
);
inertia
[
index
][
2
]
+=
massone
*
(
dx
*
dx
+
dy
*
dy
);
inertia
[
index
][
3
]
-=
massone
*
dx
*
dy
;
inertia
[
index
][
4
]
-=
massone
*
dy
*
dz
;
inertia
[
index
][
5
]
-=
massone
*
dx
*
dz
;
}
MPI_Allreduce
(
&
inertia
[
0
][
0
],
&
inertiaall
[
0
][
0
],
6
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
// compute angmom for each chunk
double
**
v
=
atom
->
v
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
comall
[
index
][
0
];
dy
=
unwrap
[
1
]
-
comall
[
index
][
1
];
dz
=
unwrap
[
2
]
-
comall
[
index
][
2
];
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
angmom
[
index
][
0
]
+=
massone
*
(
dy
*
v
[
i
][
2
]
-
dz
*
v
[
i
][
1
]);
angmom
[
index
][
1
]
+=
massone
*
(
dz
*
v
[
i
][
0
]
-
dx
*
v
[
i
][
2
]);
angmom
[
index
][
2
]
+=
massone
*
(
dx
*
v
[
i
][
1
]
-
dy
*
v
[
i
][
0
]);
}
MPI_Allreduce
(
&
angmom
[
0
][
0
],
&
angmomall
[
0
][
0
],
3
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
// compute omega for each chunk
double
determinant
,
invdeterminant
;
double
idiag
[
3
],
ex
[
3
],
ey
[
3
],
ez
[
3
],
cross
[
3
];
double
ione
[
3
][
3
],
inverse
[
3
][
3
],
evectors
[
3
][
3
];
double
*
iall
,
*
mall
;
for
(
m
=
0
;
m
<
nchunk
;
m
++
)
{
// determinant = triple product of rows of inertia matrix
iall
=
&
inertiaall
[
m
][
0
];
determinant
=
iall
[
0
]
*
(
iall
[
1
]
*
iall
[
2
]
-
iall
[
4
]
*
iall
[
4
])
+
iall
[
3
]
*
(
iall
[
4
]
*
iall
[
5
]
-
iall
[
3
]
*
iall
[
2
])
+
iall
[
5
]
*
(
iall
[
3
]
*
iall
[
4
]
-
iall
[
1
]
*
iall
[
5
]);
ione
[
0
][
0
]
=
iall
[
0
];
ione
[
1
][
1
]
=
iall
[
1
];
ione
[
2
][
2
]
=
iall
[
2
];
ione
[
0
][
1
]
=
ione
[
1
][
0
]
=
iall
[
3
];
ione
[
1
][
2
]
=
ione
[
2
][
1
]
=
iall
[
4
];
ione
[
0
][
2
]
=
ione
[
2
][
0
]
=
iall
[
5
];
// non-singular I matrix
// use L = Iw, inverting I to solve for w
if
(
determinant
>
EPSILON
)
{
inverse
[
0
][
0
]
=
ione
[
1
][
1
]
*
ione
[
2
][
2
]
-
ione
[
1
][
2
]
*
ione
[
2
][
1
];
inverse
[
0
][
1
]
=
-
(
ione
[
0
][
1
]
*
ione
[
2
][
2
]
-
ione
[
0
][
2
]
*
ione
[
2
][
1
]);
inverse
[
0
][
2
]
=
ione
[
0
][
1
]
*
ione
[
1
][
2
]
-
ione
[
0
][
2
]
*
ione
[
1
][
1
];
inverse
[
1
][
0
]
=
-
(
ione
[
1
][
0
]
*
ione
[
2
][
2
]
-
ione
[
1
][
2
]
*
ione
[
2
][
0
]);
inverse
[
1
][
1
]
=
ione
[
0
][
0
]
*
ione
[
2
][
2
]
-
ione
[
0
][
2
]
*
ione
[
2
][
0
];
inverse
[
1
][
2
]
=
-
(
ione
[
0
][
0
]
*
ione
[
1
][
2
]
-
ione
[
0
][
2
]
*
ione
[
1
][
0
]);
inverse
[
2
][
0
]
=
ione
[
1
][
0
]
*
ione
[
2
][
1
]
-
ione
[
1
][
1
]
*
ione
[
2
][
0
];
inverse
[
2
][
1
]
=
-
(
ione
[
0
][
0
]
*
ione
[
2
][
1
]
-
ione
[
0
][
1
]
*
ione
[
2
][
0
]);
inverse
[
2
][
2
]
=
ione
[
0
][
0
]
*
ione
[
1
][
1
]
-
ione
[
0
][
1
]
*
ione
[
1
][
0
];
invdeterminant
=
1.0
/
determinant
;
for
(
i
=
0
;
i
<
3
;
i
++
)
for
(
j
=
0
;
j
<
3
;
j
++
)
inverse
[
i
][
j
]
*=
invdeterminant
;
mall
=
&
angmomall
[
m
][
0
];
omega
[
m
][
0
]
=
inverse
[
0
][
0
]
*
mall
[
0
]
+
inverse
[
0
][
1
]
*
mall
[
1
]
+
inverse
[
0
][
2
]
*
mall
[
2
];
omega
[
m
][
1
]
=
inverse
[
1
][
0
]
*
mall
[
0
]
+
inverse
[
1
][
1
]
*
mall
[
1
]
+
inverse
[
1
][
2
]
*
mall
[
2
];
omega
[
m
][
2
]
=
inverse
[
2
][
0
]
*
mall
[
0
]
+
inverse
[
2
][
1
]
*
mall
[
1
]
+
inverse
[
2
][
2
]
*
mall
[
2
];
// handle each (nearly) singular I matrix
// due to 2-atom chunk or linear molecule
// use jacobi() and angmom_to_omega() to calculate valid omega
}
else
{
int
ierror
=
MathExtra
::
jacobi
(
ione
,
idiag
,
evectors
);
if
(
ierror
)
error
->
all
(
FLERR
,
"Insufficient Jacobi rotations for omega/chunk"
);
ex
[
0
]
=
evectors
[
0
][
0
];
ex
[
1
]
=
evectors
[
1
][
0
];
ex
[
2
]
=
evectors
[
2
][
0
];
ey
[
0
]
=
evectors
[
0
][
1
];
ey
[
1
]
=
evectors
[
1
][
1
];
ey
[
2
]
=
evectors
[
2
][
1
];
ez
[
0
]
=
evectors
[
0
][
2
];
ez
[
1
]
=
evectors
[
1
][
2
];
ez
[
2
]
=
evectors
[
2
][
2
];
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra
::
cross3
(
ex
,
ey
,
cross
);
if
(
MathExtra
::
dot3
(
cross
,
ez
)
<
0.0
)
MathExtra
::
negate3
(
ez
);
// if any principal moment < scaled EPSILON, set to 0.0
double
max
;
max
=
MAX
(
idiag
[
0
],
idiag
[
1
]);
max
=
MAX
(
max
,
idiag
[
2
]);
if
(
idiag
[
0
]
<
EPSILON
*
max
)
idiag
[
0
]
=
0.0
;
if
(
idiag
[
1
]
<
EPSILON
*
max
)
idiag
[
1
]
=
0.0
;
if
(
idiag
[
2
]
<
EPSILON
*
max
)
idiag
[
2
]
=
0.0
;
// calculate omega using diagonalized inertia matrix
MathExtra
::
angmom_to_omega
(
&
angmomall
[
m
][
0
],
ex
,
ey
,
ez
,
idiag
,
&
omega
[
m
][
0
]);
}
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
lock_enable
()
{
cchunk
->
lockcount
++
;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
lock_disable
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
>=
0
)
{
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
cchunk
->
lockcount
--
;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int
ComputeOmegaChunk
::
lock_length
()
{
nchunk
=
cchunk
->
setup_chunks
();
return
nchunk
;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
lock
(
Fix
*
fixptr
,
bigint
startstep
,
bigint
stopstep
)
{
cchunk
->
lock
(
fixptr
,
startstep
,
stopstep
);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
unlock
(
Fix
*
fixptr
)
{
cchunk
->
unlock
(
fixptr
);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void
ComputeOmegaChunk
::
allocate
()
{
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
com
);
memory
->
destroy
(
comall
);
memory
->
destroy
(
inertia
);
memory
->
destroy
(
inertiaall
);
memory
->
destroy
(
angmom
);
memory
->
destroy
(
angmomall
);
memory
->
destroy
(
omega
);
maxchunk
=
nchunk
;
memory
->
create
(
massproc
,
maxchunk
,
"omega/chunk:massproc"
);
memory
->
create
(
masstotal
,
maxchunk
,
"omega/chunk:masstotal"
);
memory
->
create
(
com
,
maxchunk
,
3
,
"omega/chunk:com"
);
memory
->
create
(
comall
,
maxchunk
,
3
,
"omega/chunk:comall"
);
memory
->
create
(
inertia
,
maxchunk
,
6
,
"omega/chunk:inertia"
);
memory
->
create
(
inertiaall
,
maxchunk
,
6
,
"omega/chunk:inertiaall"
);
memory
->
create
(
angmom
,
maxchunk
,
3
,
"omega/chunk:angmom"
);
memory
->
create
(
angmomall
,
maxchunk
,
3
,
"omega/chunk:angmomall"
);
memory
->
create
(
omega
,
maxchunk
,
3
,
"omega/chunk:omega"
);
array
=
omega
;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeOmegaChunk
::
memory_usage
()
{
double
bytes
=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
3
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
6
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
3
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
3
*
sizeof
(
double
);
return
bytes
;
}
Event Timeline
Log In to Comment