Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81583535
compute_temp_deform_eff.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, Sep 6, 21:24
Size
9 KB
Mime Type
text/x-c
Expires
Sun, Sep 8, 21:24 (2 d)
Engine
blob
Format
Raw Data
Handle
20542463
Attached To
rLAMMPS lammps
compute_temp_deform_eff.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: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "compute_temp_deform_eff.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
NO_REMAP
,
X_REMAP
,
V_REMAP
};
// same as fix_deform.cpp
/* ---------------------------------------------------------------------- */
ComputeTempDeformEff
::
ComputeTempDeformEff
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal compute temp/deform/eff command"
);
if
(
!
atom
->
electron_flag
)
error
->
all
(
FLERR
,
"Compute temp/deform/eff requires atom style electron"
);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
6
;
extscalar
=
0
;
extvector
=
1
;
tempflag
=
1
;
tempbias
=
1
;
maxbias
=
0
;
vbiasall
=
NULL
;
vector
=
new
double
[
6
];
}
/* ---------------------------------------------------------------------- */
ComputeTempDeformEff
::~
ComputeTempDeformEff
()
{
memory
->
destroy
(
vbiasall
);
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
init
()
{
// check fix deform remap settings
int
i
;
for
(
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"deform"
)
==
0
)
{
if
(((
FixDeform
*
)
modify
->
fix
[
i
])
->
remapflag
==
X_REMAP
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Using compute temp/deform/eff with inconsistent "
"fix deform remap option"
);
break
;
}
if
(
i
==
modify
->
nfix
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Using compute temp/deform/eff with no fix deform defined"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
setup
()
{
dynamic
=
0
;
if
(
dynamic_user
||
group
->
dynamic
[
igroup
])
dynamic
=
1
;
dof_compute
();
}
/* ---------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
dof_compute
()
{
fix_dof
=
modify
->
adjust_dof_fix
(
igroup
);
double
natoms
=
group
->
count
(
igroup
);
dof
=
domain
->
dimension
*
natoms
;
dof
-=
extra_dof
+
fix_dof
;
// just include nuclear dof
int
*
spin
=
atom
->
spin
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
one
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
abs
(
spin
[
i
])
==
1
)
one
++
;
}
int
nelectrons
;
MPI_Allreduce
(
&
one
,
&
nelectrons
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
// Assume 3/2 k T per nucleus
dof
-=
domain
->
dimension
*
nelectrons
;
if
(
dof
>
0
)
tfactor
=
force
->
mvv2e
/
(
dof
*
force
->
boltz
);
else
tfactor
=
0.0
;
}
/* ---------------------------------------------------------------------- */
double
ComputeTempDeformEff
::
compute_scalar
()
{
double
lamda
[
3
],
vstream
[
3
],
vthermal
[
3
];
invoked_scalar
=
update
->
ntimestep
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
ervel
=
atom
->
ervel
;
double
*
mass
=
atom
->
mass
;
int
*
spin
=
atom
->
spin
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
mefactor
=
domain
->
dimension
/
4.0
;
// lamda = 0-1 triclinic lamda coords
// vstream = streaming velocity = Hrate*lamda + Hratelo
// vthermal = thermal velocity = v - vstream
double
*
h_rate
=
domain
->
h_rate
;
double
*
h_ratelo
=
domain
->
h_ratelo
;
double
t
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
x2lamda
(
x
[
i
],
lamda
);
vstream
[
0
]
=
h_rate
[
0
]
*
lamda
[
0
]
+
h_rate
[
5
]
*
lamda
[
1
]
+
h_rate
[
4
]
*
lamda
[
2
]
+
h_ratelo
[
0
];
vstream
[
1
]
=
h_rate
[
1
]
*
lamda
[
1
]
+
h_rate
[
3
]
*
lamda
[
2
]
+
h_ratelo
[
1
];
vstream
[
2
]
=
h_rate
[
2
]
*
lamda
[
2
]
+
h_ratelo
[
2
];
vthermal
[
0
]
=
v
[
i
][
0
]
-
vstream
[
0
];
vthermal
[
1
]
=
v
[
i
][
1
]
-
vstream
[
1
];
vthermal
[
2
]
=
v
[
i
][
2
]
-
vstream
[
2
];
if
(
mass
)
{
t
+=
(
vthermal
[
0
]
*
vthermal
[
0
]
+
vthermal
[
1
]
*
vthermal
[
1
]
+
vthermal
[
2
]
*
vthermal
[
2
])
*
mass
[
type
[
i
]];
if
(
abs
(
spin
[
i
])
==
1
)
t
+=
mefactor
*
mass
[
type
[
i
]]
*
ervel
[
i
]
*
ervel
[
i
];
}
}
MPI_Allreduce
(
&
t
,
&
scalar
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
dynamic
)
dof_compute
();
if
(
tfactor
==
0.0
&&
scalar
!=
0.0
)
error
->
all
(
FLERR
,
"Temperature compute degrees of freedom < 0"
);
scalar
*=
tfactor
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
compute_vector
()
{
double
lamda
[
3
],
vstream
[
3
],
vthermal
[
3
];
invoked_vector
=
update
->
ntimestep
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
ervel
=
atom
->
ervel
;
double
*
mass
=
atom
->
mass
;
int
*
spin
=
atom
->
spin
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
mefactor
=
domain
->
dimension
/
4.0
;
double
*
h_rate
=
domain
->
h_rate
;
double
*
h_ratelo
=
domain
->
h_ratelo
;
double
massone
,
t
[
6
];
for
(
int
i
=
0
;
i
<
6
;
i
++
)
t
[
i
]
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
x2lamda
(
x
[
i
],
lamda
);
vstream
[
0
]
=
h_rate
[
0
]
*
lamda
[
0
]
+
h_rate
[
5
]
*
lamda
[
1
]
+
h_rate
[
4
]
*
lamda
[
2
]
+
h_ratelo
[
0
];
vstream
[
1
]
=
h_rate
[
1
]
*
lamda
[
1
]
+
h_rate
[
3
]
*
lamda
[
2
]
+
h_ratelo
[
1
];
vstream
[
2
]
=
h_rate
[
2
]
*
lamda
[
2
]
+
h_ratelo
[
2
];
vthermal
[
0
]
=
v
[
i
][
0
]
-
vstream
[
0
];
vthermal
[
1
]
=
v
[
i
][
1
]
-
vstream
[
1
];
vthermal
[
2
]
=
v
[
i
][
2
]
-
vstream
[
2
];
massone
=
mass
[
type
[
i
]];
t
[
0
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
0
];
t
[
1
]
+=
massone
*
vthermal
[
1
]
*
vthermal
[
1
];
t
[
2
]
+=
massone
*
vthermal
[
2
]
*
vthermal
[
2
];
t
[
3
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
1
];
t
[
4
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
2
];
t
[
5
]
+=
massone
*
vthermal
[
1
]
*
vthermal
[
2
];
if
(
abs
(
spin
[
i
])
==
1
)
{
t
[
0
]
+=
mefactor
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
t
[
1
]
+=
mefactor
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
t
[
2
]
+=
mefactor
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
}
}
MPI_Allreduce
(
t
,
vector
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
6
;
i
++
)
vector
[
i
]
*=
force
->
mvv2e
;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
remove_bias
(
int
i
,
double
*
v
)
{
double
lamda
[
3
];
double
*
h_rate
=
domain
->
h_rate
;
double
*
h_ratelo
=
domain
->
h_ratelo
;
domain
->
x2lamda
(
atom
->
x
[
i
],
lamda
);
vbias
[
0
]
=
h_rate
[
0
]
*
lamda
[
0
]
+
h_rate
[
5
]
*
lamda
[
1
]
+
h_rate
[
4
]
*
lamda
[
2
]
+
h_ratelo
[
0
];
vbias
[
1
]
=
h_rate
[
1
]
*
lamda
[
1
]
+
h_rate
[
3
]
*
lamda
[
2
]
+
h_ratelo
[
1
];
vbias
[
2
]
=
h_rate
[
2
]
*
lamda
[
2
]
+
h_ratelo
[
2
];
v
[
0
]
-=
vbias
[
0
];
v
[
1
]
-=
vbias
[
1
];
v
[
2
]
-=
vbias
[
2
];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
NOTE: only removes translational velocity bias from electrons
------------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
remove_bias_all
()
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
>
maxbias
)
{
memory
->
destroy
(
vbiasall
);
maxbias
=
atom
->
nmax
;
memory
->
create
(
vbiasall
,
maxbias
,
3
,
"temp/deform/eff:vbiasall"
);
}
double
lamda
[
3
];
double
*
h_rate
=
domain
->
h_rate
;
double
*
h_ratelo
=
domain
->
h_ratelo
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
x2lamda
(
atom
->
x
[
i
],
lamda
);
vbiasall
[
i
][
0
]
=
h_rate
[
0
]
*
lamda
[
0
]
+
h_rate
[
5
]
*
lamda
[
1
]
+
h_rate
[
4
]
*
lamda
[
2
]
+
h_ratelo
[
0
];
vbiasall
[
i
][
1
]
=
h_rate
[
1
]
*
lamda
[
1
]
+
h_rate
[
3
]
*
lamda
[
2
]
+
h_ratelo
[
1
];
vbiasall
[
i
][
2
]
=
h_rate
[
2
]
*
lamda
[
2
]
+
h_ratelo
[
2
];
v
[
i
][
0
]
-=
vbiasall
[
i
][
0
];
v
[
i
][
1
]
-=
vbiasall
[
i
][
1
];
v
[
i
][
2
]
-=
vbiasall
[
i
][
2
];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
restore_bias
(
int
i
,
double
*
v
)
{
v
[
0
]
+=
vbias
[
0
];
v
[
1
]
+=
vbias
[
1
];
v
[
2
]
+=
vbias
[
2
];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void
ComputeTempDeformEff
::
restore_bias_all
()
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
v
[
i
][
0
]
+=
vbiasall
[
i
][
0
];
v
[
i
][
1
]
+=
vbiasall
[
i
][
1
];
v
[
i
][
2
]
+=
vbiasall
[
i
][
2
];
}
}
/* ---------------------------------------------------------------------- */
double
ComputeTempDeformEff
::
memory_usage
()
{
double
bytes
=
maxbias
*
sizeof
(
double
);
return
bytes
;
}
Event Timeline
Log In to Comment