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rLAMMPS lammps
domain_omp.cpp
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/* ----------------------------------------------------------------------
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 : Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "domain.h"
#include "accelerator_omp.h"
#include "atom.h"
using
namespace
LAMMPS_NS
;
typedef
struct
{
double
x
,
y
,
z
;
}
dbl3_t
;
/* ----------------------------------------------------------------------
enforce PBC and modify box image flags for each atom
called every reneighboring and by other commands that change atoms
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
if fix deform, remap velocity of fix group atoms by box edge velocities
for triclinic, atoms must be in lamda coords (0-1) before pbc is called
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */
void
DomainOMP
::
pbc
()
{
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
&
atom
->
x
[
0
][
0
];
dbl3_t
*
_noalias
const
v
=
(
dbl3_t
*
)
&
atom
->
v
[
0
][
0
];
const
double
*
_noalias
const
lo
=
(
triclinic
==
0
)
?
boxlo
:
boxlo_lamda
;
const
double
*
_noalias
const
hi
=
(
triclinic
==
0
)
?
boxhi
:
boxhi_lamda
;
const
double
*
_noalias
const
period
=
(
triclinic
==
0
)
?
prd
:
prd_lamda
;
const
int
*
_noalias
const
mask
=
atom
->
mask
;
imageint
*
_noalias
const
image
=
atom
->
image
;
const
int
nlocal
=
atom
->
nlocal
;
int
i
;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
imageint
idim
,
otherdims
;
if
(
xperiodic
)
{
if
(
x
[
i
].
x
<
lo
[
0
])
{
x
[
i
].
x
+=
period
[
0
];
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
v
[
i
].
x
+=
h_rate
[
0
];
idim
=
image
[
i
]
&
IMGMASK
;
otherdims
=
image
[
i
]
^
idim
;
idim
--
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
idim
;
}
if
(
x
[
i
].
x
>=
hi
[
0
])
{
x
[
i
].
x
-=
period
[
0
];
x
[
i
].
x
=
MAX
(
x
[
i
].
x
,
lo
[
0
]);
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
v
[
i
].
x
-=
h_rate
[
0
];
idim
=
image
[
i
]
&
IMGMASK
;
otherdims
=
image
[
i
]
^
idim
;
idim
++
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
idim
;
}
}
if
(
yperiodic
)
{
if
(
x
[
i
].
y
<
lo
[
1
])
{
x
[
i
].
y
+=
period
[
1
];
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
{
v
[
i
].
x
+=
h_rate
[
5
];
v
[
i
].
y
+=
h_rate
[
1
];
}
idim
=
(
image
[
i
]
>>
IMGBITS
)
&
IMGMASK
;
otherdims
=
image
[
i
]
^
(
idim
<<
IMGBITS
);
idim
--
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
(
idim
<<
IMGBITS
);
}
if
(
x
[
i
].
y
>=
hi
[
1
])
{
x
[
i
].
y
-=
period
[
1
];
x
[
i
].
y
=
MAX
(
x
[
i
].
y
,
lo
[
1
]);
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
{
v
[
i
].
x
-=
h_rate
[
5
];
v
[
i
].
y
-=
h_rate
[
1
];
}
idim
=
(
image
[
i
]
>>
IMGBITS
)
&
IMGMASK
;
otherdims
=
image
[
i
]
^
(
idim
<<
IMGBITS
);
idim
++
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
(
idim
<<
IMGBITS
);
}
}
if
(
zperiodic
)
{
if
(
x
[
i
].
z
<
lo
[
2
])
{
x
[
i
].
z
+=
period
[
2
];
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
{
v
[
i
].
x
+=
h_rate
[
4
];
v
[
i
].
y
+=
h_rate
[
3
];
v
[
i
].
z
+=
h_rate
[
2
];
}
idim
=
image
[
i
]
>>
IMG2BITS
;
otherdims
=
image
[
i
]
^
(
idim
<<
IMG2BITS
);
idim
--
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
(
idim
<<
IMG2BITS
);
}
if
(
x
[
i
].
z
>=
hi
[
2
])
{
x
[
i
].
z
-=
period
[
2
];
x
[
i
].
z
=
MAX
(
x
[
i
].
z
,
lo
[
2
]);
if
(
deform_vremap
&&
mask
[
i
]
&
deform_groupbit
)
{
v
[
i
].
x
-=
h_rate
[
4
];
v
[
i
].
y
-=
h_rate
[
3
];
v
[
i
].
z
-=
h_rate
[
2
];
}
idim
=
image
[
i
]
>>
IMG2BITS
;
otherdims
=
image
[
i
]
^
(
idim
<<
IMG2BITS
);
idim
++
;
idim
&=
IMGMASK
;
image
[
i
]
=
otherdims
|
(
idim
<<
IMG2BITS
);
}
}
}
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for all N atoms
x = H lamda + x0;
------------------------------------------------------------------------- */
void
DomainOMP
::
lamda2x
(
int
n
)
{
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
&
atom
->
x
[
0
][
0
];
const
int
num
=
n
;
int
i
;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for
(
i
=
0
;
i
<
num
;
i
++
)
{
x
[
i
].
x
=
h
[
0
]
*
x
[
i
].
x
+
h
[
5
]
*
x
[
i
].
y
+
h
[
4
]
*
x
[
i
].
z
+
boxlo
[
0
];
x
[
i
].
y
=
h
[
1
]
*
x
[
i
].
y
+
h
[
3
]
*
x
[
i
].
z
+
boxlo
[
1
];
x
[
i
].
z
=
h
[
2
]
*
x
[
i
].
z
+
boxlo
[
2
];
}
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for all N atoms
lamda = H^-1 (x - x0)
------------------------------------------------------------------------- */
void
DomainOMP
::
x2lamda
(
int
n
)
{
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
&
atom
->
x
[
0
][
0
];
const
int
num
=
n
;
int
i
;
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none) schedule(static)
#endif
for
(
i
=
0
;
i
<
num
;
i
++
)
{
double
delta0
=
x
[
i
].
x
-
boxlo
[
0
];
double
delta1
=
x
[
i
].
y
-
boxlo
[
1
];
double
delta2
=
x
[
i
].
z
-
boxlo
[
2
];
x
[
i
].
x
=
h_inv
[
0
]
*
delta0
+
h_inv
[
5
]
*
delta1
+
h_inv
[
4
]
*
delta2
;
x
[
i
].
y
=
h_inv
[
1
]
*
delta1
+
h_inv
[
3
]
*
delta2
;
x
[
i
].
z
=
h_inv
[
2
]
*
delta2
;
}
}
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