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fix_evaporate.cpp
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Sat, Aug 17, 00:21
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rLAMMPS lammps
fix_evaporate.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.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_evaporate.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "domain.h"
#include "region.h"
#include "comm.h"
#include "group.h"
#include "random_park.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixEvaporate
::
FixEvaporate
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
7
)
error
->
all
(
"Illegal fix evaporate command"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
0
;
nevery
=
atoi
(
arg
[
3
]);
nflux
=
atoi
(
arg
[
4
]);
iregion
=
domain
->
find_region
(
arg
[
5
]);
int
seed
=
atoi
(
arg
[
6
]);
if
(
nevery
<=
0
||
nflux
<=
0
)
error
->
all
(
"Illegal fix evaporate command"
);
if
(
iregion
==
-
1
)
error
->
all
(
"Fix evaporate region ID does not exist"
);
if
(
seed
<=
0
)
error
->
all
(
"Illegal fix evaporate command"
);
// random number generator, same for all procs
random
=
new
RanPark
(
lmp
,
seed
);
// set up reneighboring
force_reneighbor
=
1
;
next_reneighbor
=
(
update
->
ntimestep
/
nevery
)
*
nevery
+
nevery
;
ndeleted
=
0
;
nmax
=
0
;
list
=
NULL
;
mark
=
NULL
;
}
/* ---------------------------------------------------------------------- */
FixEvaporate
::~
FixEvaporate
()
{
delete
random
;
memory
->
sfree
(
list
);
memory
->
sfree
(
mark
);
}
/* ---------------------------------------------------------------------- */
int
FixEvaporate
::
setmask
()
{
int
mask
=
0
;
mask
|=
PRE_EXCHANGE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixEvaporate
::
init
()
{
// check that no deletable atoms are in atom->firstgroup
// deleting such an atom would not leave firstgroup atoms first
if
(
atom
->
firstgroup
>=
0
)
{
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
firstgroupbit
=
group
->
bitmask
[
atom
->
firstgroup
];
int
flag
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
((
mask
[
i
]
&
groupbit
)
&&
(
mask
[
i
]
&&
firstgroupbit
))
flag
=
1
;
int
flagall
;
MPI_Allreduce
(
&
flag
,
&
flagall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flagall
)
error
->
all
(
"Cannot evaporate atoms in atom_modify first group"
);
}
}
/* ----------------------------------------------------------------------
perform particle deletion
done before exchange, borders, reneighbor
so that ghost atoms and neighbor lists will be correct
------------------------------------------------------------------------- */
void
FixEvaporate
::
pre_exchange
()
{
int
i
,
iwhichglobal
,
iwhichlocal
;
if
(
update
->
ntimestep
!=
next_reneighbor
)
return
;
// grow list and mark arrays if necessary
if
(
atom
->
nlocal
>
nmax
)
{
memory
->
sfree
(
list
);
memory
->
sfree
(
mark
);
nmax
=
atom
->
nmax
;
list
=
(
int
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
int
),
"evaporate:list"
);
mark
=
(
int
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
int
),
"evaporate:mark"
);
}
// nall = # of deletable atoms in region
// nbefore = # on procs before me
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
ncount
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
domain
->
regions
[
iregion
]
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
list
[
ncount
++
]
=
i
;
int
nall
,
nbefore
;
MPI_Allreduce
(
&
ncount
,
&
nall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
MPI_Scan
(
&
ncount
,
&
nbefore
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
nbefore
-=
ncount
;
// nwhack = total number of atoms to delete
// choose atoms randomly across all procs and mark them for deletion
// shrink local list of candidates as my atoms get marked for deletion
int
nwhack
=
MIN
(
nflux
,
nall
);
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
mark
[
i
]
=
0
;
for
(
i
=
0
;
i
<
nwhack
;
i
++
)
{
iwhichglobal
=
static_cast
<
int
>
(
nall
*
random
->
uniform
());
if
(
iwhichglobal
<
nbefore
)
nbefore
--
;
else
if
(
iwhichglobal
<
nbefore
+
ncount
)
{
iwhichlocal
=
iwhichglobal
-
nbefore
;
mark
[
list
[
iwhichlocal
]]
=
1
;
list
[
iwhichlocal
]
=
list
[
ncount
-
1
];
ncount
--
;
}
nall
--
;
}
// delete my marked atoms
// loop in reverse order to avoid copying marked atoms
AtomVec
*
avec
=
atom
->
avec
;
for
(
i
=
nlocal
-
1
;
i
>=
0
;
i
--
)
{
if
(
mark
[
i
])
{
avec
->
copy
(
atom
->
nlocal
-
1
,
i
);
atom
->
nlocal
--
;
}
}
// reset global natoms
// if global map exists, reset it now instead of waiting for comm
// since deleting atoms messes up ghosts
atom
->
natoms
-=
nwhack
;
if
(
nwhack
&&
atom
->
map_style
)
{
atom
->
nghost
=
0
;
atom
->
map_init
();
atom
->
map_set
();
}
// statistics
ndeleted
+=
nwhack
;
next_reneighbor
=
update
->
ntimestep
+
nevery
;
}
/* ----------------------------------------------------------------------
return number of deleted particles
------------------------------------------------------------------------- */
double
FixEvaporate
::
compute_scalar
()
{
return
1.0
*
ndeleted
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixEvaporate
::
memory_usage
()
{
double
bytes
=
2
*
nmax
*
sizeof
(
int
);
return
bytes
;
}
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