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fix_nvt_sllod_omp.cpp
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Mon, Sep 30, 21:23
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Wed, Oct 2, 21:23 (2 d)
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rLAMMPS lammps
fix_nvt_sllod_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "fix_nvt_sllod_omp.h"
#include "math_extra.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "compute.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NO_REMAP
,
X_REMAP
,
V_REMAP
};
// same as fix_deform.cpp
typedef
struct
{
double
x
,
y
,
z
;
}
dbl3_t
;
/* ---------------------------------------------------------------------- */
FixNVTSllodOMP
::
FixNVTSllodOMP
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixNHOMP
(
lmp
,
narg
,
arg
)
{
if
(
!
tstat_flag
)
error
->
all
(
FLERR
,
"Temperature control must be used with fix nvt/sllod"
);
if
(
pstat_flag
)
error
->
all
(
FLERR
,
"Pressure control can not be used with fix nvt/sllod"
);
// default values
if
(
mtchain_default_flag
)
mtchain
=
1
;
// create a new compute temp style
// id = fix-ID + temp
int
n
=
strlen
(
id
)
+
6
;
id_temp
=
new
char
[
n
];
strcpy
(
id_temp
,
id
);
strcat
(
id_temp
,
"_temp"
);
char
**
newarg
=
new
char
*
[
3
];
newarg
[
0
]
=
id_temp
;
newarg
[
1
]
=
group
->
names
[
igroup
];
newarg
[
2
]
=
(
char
*
)
"temp/deform"
;
modify
->
add_compute
(
3
,
newarg
);
delete
[]
newarg
;
tflag
=
1
;
}
/* ---------------------------------------------------------------------- */
void
FixNVTSllodOMP
::
init
()
{
FixNHOMP
::
init
();
if
(
!
temperature
->
tempbias
)
error
->
all
(
FLERR
,
"Temperature for fix nvt/sllod/omp does not have a bias"
);
nondeformbias
=
0
;
if
(
strcmp
(
temperature
->
style
,
"temp/deform"
)
!=
0
)
nondeformbias
=
1
;
// 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
!=
V_REMAP
)
error
->
all
(
FLERR
,
"Using fix nvt/sllod/omp with inconsistent fix "
"deform remap option"
);
break
;
}
if
(
i
==
modify
->
nfix
)
error
->
all
(
FLERR
,
"Using fix nvt/sllod/omp with no fix deform defined"
);
}
/* ----------------------------------------------------------------------
perform half-step scaling of velocities
-----------------------------------------------------------------------*/
void
FixNVTSllodOMP
::
nh_v_temp
()
{
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
// for non temp/deform BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
atom
->
v
[
0
];
const
int
*
_noalias
const
mask
=
atom
->
mask
;
const
int
nlocal
=
(
igroup
==
atom
->
firstgroup
)
?
atom
->
nfirst
:
atom
->
nlocal
;
int
i
;
if
(
nondeformbias
)
temperature
->
compute_scalar
();
double
h_two
[
6
];
MathExtra
::
multiply_shape_shape
(
domain
->
h_rate
,
domain
->
h_inv
,
h_two
);
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) shared(h_two) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
double
vdelu0
,
vdelu1
,
vdelu2
,
buf
[
3
];
if
(
mask
[
i
]
&
groupbit
)
{
vdelu0
=
h_two
[
0
]
*
v
[
i
].
x
+
h_two
[
5
]
*
v
[
i
].
y
+
h_two
[
4
]
*
v
[
i
].
z
;
vdelu1
=
h_two
[
1
]
*
v
[
i
].
y
+
h_two
[
3
]
*
v
[
i
].
z
;
vdelu2
=
h_two
[
2
]
*
v
[
i
].
z
;
temperature
->
remove_bias
(
i
,
&
v
[
i
].
x
);
v
[
i
].
x
=
v
[
i
].
x
*
factor_eta
-
dthalf
*
vdelu0
;
v
[
i
].
y
=
v
[
i
].
y
*
factor_eta
-
dthalf
*
vdelu1
;
v
[
i
].
z
=
v
[
i
].
z
*
factor_eta
-
dthalf
*
vdelu2
;
temperature
->
restore_bias
(
i
,
&
v
[
i
].
x
);
}
}
}
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