Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F68574813
compute_temp_asphere.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
Fri, Jun 28, 00:50
Size
6 KB
Mime Type
text/x-c
Expires
Sun, Jun 30, 00:50 (2 d)
Engine
blob
Format
Raw Data
Handle
18548434
Attached To
rLAMMPS lammps
compute_temp_asphere.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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "compute_temp_asphere.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
ComputeTempAsphere
::
ComputeTempAsphere
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
"Illegal compute temp command"
);
if
(
!
atom
->
quat_flag
||
!
atom
->
angmom_flag
)
error
->
all
(
"Compute temp/asphere requires atom attributes quat, angmom"
);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
6
;
extscalar
=
0
;
extvector
=
1
;
tempflag
=
1
;
vector
=
new
double
[
6
];
inertia
=
memory
->
create_2d_double_array
(
atom
->
ntypes
+
1
,
3
,
"fix_temp_sphere:inertia"
);
}
/* ---------------------------------------------------------------------- */
ComputeTempAsphere
::~
ComputeTempAsphere
()
{
delete
[]
vector
;
memory
->
destroy_2d_double_array
(
inertia
);
}
/* ---------------------------------------------------------------------- */
void
ComputeTempAsphere
::
init
()
{
fix_dof
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
fix_dof
+=
modify
->
fix
[
i
]
->
dof
(
igroup
);
recount
();
calculate_inertia
();
}
/* ---------------------------------------------------------------------- */
void
ComputeTempAsphere
::
recount
()
{
double
natoms
=
group
->
count
(
igroup
);
dof
=
domain
->
dimension
*
natoms
;
dof
-=
extra_dof
+
fix_dof
;
// add rotational degrees of freedom
// 0 for sphere, 2 for uniaxial, 3 for biaxial
double
**
shape
=
atom
->
shape
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
itype
;
int
rot_dof
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
itype
=
type
[
i
];
if
(
shape
[
itype
][
0
]
==
shape
[
itype
][
1
]
&&
shape
[
itype
][
1
]
==
shape
[
itype
][
2
])
continue
;
else
if
(
shape
[
itype
][
0
]
==
shape
[
itype
][
1
]
||
shape
[
itype
][
1
]
==
shape
[
itype
][
2
]
||
shape
[
itype
][
0
]
==
shape
[
itype
][
2
])
rot_dof
+=
2
;
else
rot_dof
+=
3
;
}
int
rot_total
;
MPI_Allreduce
(
&
rot_dof
,
&
rot_total
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
dof
+=
rot_total
;
if
(
dof
>
0
)
tfactor
=
force
->
mvv2e
/
(
dof
*
force
->
boltz
);
else
tfactor
=
0.0
;
}
/* ---------------------------------------------------------------------- */
double
ComputeTempAsphere
::
compute_scalar
()
{
invoked
|=
INVOKED_SCALAR
;
double
**
v
=
atom
->
v
;
double
**
quat
=
atom
->
quat
;
double
**
angmom
=
atom
->
angmom
;
double
*
mass
=
atom
->
mass
;
double
**
shape
=
atom
->
shape
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
itype
;
double
wbody
[
3
];
double
rot
[
3
][
3
];
double
t
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
// translational kinetic energy
itype
=
type
[
i
];
t
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
mass
[
itype
];
// wbody = angular velocity in body frame
if
(
!
(
shape
[
itype
][
0
]
==
shape
[
itype
][
1
]
&&
shape
[
itype
][
1
]
==
shape
[
itype
][
2
]))
{
MathExtra
::
quat_to_mat
(
quat
[
i
],
rot
);
MathExtra
::
transpose_times_column3
(
rot
,
angmom
[
i
],
wbody
);
wbody
[
0
]
/=
inertia
[
itype
][
0
];
wbody
[
1
]
/=
inertia
[
itype
][
1
];
wbody
[
2
]
/=
inertia
[
itype
][
2
];
// rotational kinetic energy
t
+=
inertia
[
itype
][
0
]
*
wbody
[
0
]
*
wbody
[
0
]
+
inertia
[
itype
][
1
]
*
wbody
[
1
]
*
wbody
[
1
]
+
inertia
[
itype
][
2
]
*
wbody
[
2
]
*
wbody
[
2
];
}
}
MPI_Allreduce
(
&
t
,
&
scalar
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
dynamic
)
recount
();
scalar
*=
tfactor
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempAsphere
::
compute_vector
()
{
int
i
;
invoked
|=
INVOKED_VECTOR
;
double
**
v
=
atom
->
v
;
double
**
quat
=
atom
->
quat
;
double
**
angmom
=
atom
->
angmom
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
itype
;
double
wbody
[
3
];
double
rot
[
3
][
3
];
double
massone
,
t
[
6
];
for
(
i
=
0
;
i
<
6
;
i
++
)
t
[
i
]
=
0.0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
// translational kinetic energy
itype
=
type
[
i
];
massone
=
mass
[
itype
];
t
[
0
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
0
];
t
[
1
]
+=
massone
*
v
[
i
][
1
]
*
v
[
i
][
1
];
t
[
2
]
+=
massone
*
v
[
i
][
2
]
*
v
[
i
][
2
];
t
[
3
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
1
];
t
[
4
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
2
];
t
[
5
]
+=
massone
*
v
[
i
][
1
]
*
v
[
i
][
2
];
// wbody = angular velocity in body frame
MathExtra
::
quat_to_mat
(
quat
[
i
],
rot
);
MathExtra
::
transpose_times_column3
(
rot
,
angmom
[
i
],
wbody
);
wbody
[
0
]
/=
inertia
[
itype
][
0
];
wbody
[
1
]
/=
inertia
[
itype
][
1
];
wbody
[
2
]
/=
inertia
[
itype
][
2
];
// rotational kinetic energy
t
[
0
]
+=
inertia
[
itype
][
0
]
*
wbody
[
0
]
*
wbody
[
0
];
t
[
1
]
+=
inertia
[
itype
][
1
]
*
wbody
[
1
]
*
wbody
[
1
];
t
[
2
]
+=
inertia
[
itype
][
2
]
*
wbody
[
2
]
*
wbody
[
2
];
t
[
3
]
+=
inertia
[
itype
][
0
]
*
wbody
[
0
]
*
wbody
[
1
];
t
[
4
]
+=
inertia
[
itype
][
1
]
*
wbody
[
0
]
*
wbody
[
2
];
t
[
5
]
+=
inertia
[
itype
][
2
]
*
wbody
[
1
]
*
wbody
[
2
];
}
MPI_Allreduce
(
t
,
vector
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
6
;
i
++
)
vector
[
i
]
*=
force
->
mvv2e
;
}
/* ----------------------------------------------------------------------
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void
ComputeTempAsphere
::
calculate_inertia
()
{
double
*
mass
=
atom
->
mass
;
double
**
shape
=
atom
->
shape
;
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
{
inertia
[
i
][
0
]
=
mass
[
i
]
*
(
shape
[
i
][
1
]
*
shape
[
i
][
1
]
+
shape
[
i
][
2
]
*
shape
[
i
][
2
])
/
5.0
;
inertia
[
i
][
1
]
=
mass
[
i
]
*
(
shape
[
i
][
0
]
*
shape
[
i
][
0
]
+
shape
[
i
][
2
]
*
shape
[
i
][
2
])
/
5.0
;
inertia
[
i
][
2
]
=
mass
[
i
]
*
(
shape
[
i
][
0
]
*
shape
[
i
][
0
]
+
shape
[
i
][
1
]
*
shape
[
i
][
1
])
/
5.0
;
}
}
Event Timeline
Log In to Comment