Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78288212
fix_evaporate.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
Mon, Aug 19, 15:19
Size
11 KB
Mime Type
text/x-c
Expires
Wed, Aug 21, 15:19 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
19238719
Attached To
rLAMMPS lammps
fix_evaporate.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.
------------------------------------------------------------------------- */
#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 "force.h"
#include "group.h"
#include "random_park.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixEvaporate
::
FixEvaporate
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
7
)
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
0
;
nevery
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
nflux
=
force
->
inumeric
(
FLERR
,
arg
[
4
]);
iregion
=
domain
->
find_region
(
arg
[
5
]);
int
n
=
strlen
(
arg
[
5
])
+
1
;
idregion
=
new
char
[
n
];
strcpy
(
idregion
,
arg
[
5
]);
int
seed
=
force
->
inumeric
(
FLERR
,
arg
[
6
]);
if
(
nevery
<=
0
||
nflux
<=
0
)
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix evaporate does not exist"
);
if
(
seed
<=
0
)
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
// random number generator, same for all procs
random
=
new
RanPark
(
lmp
,
seed
);
// optional args
molflag
=
0
;
int
iarg
=
7
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"molecule"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
molflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
molflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix evaporate command"
);
}
// set up reneighboring
force_reneighbor
=
1
;
next_reneighbor
=
(
update
->
ntimestep
/
nevery
)
*
nevery
+
nevery
;
ndeleted
=
0
;
nmax
=
0
;
list
=
NULL
;
mark
=
NULL
;
}
/* ---------------------------------------------------------------------- */
FixEvaporate
::~
FixEvaporate
()
{
delete
[]
idregion
;
delete
random
;
memory
->
destroy
(
list
);
memory
->
destroy
(
mark
);
}
/* ---------------------------------------------------------------------- */
int
FixEvaporate
::
setmask
()
{
int
mask
=
0
;
mask
|=
PRE_EXCHANGE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixEvaporate
::
init
()
{
// set index and check validity of region
iregion
=
domain
->
find_region
(
idregion
);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix evaporate does not exist"
);
// 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
(
FLERR
,
"Cannot evaporate atoms in atom_modify first group"
);
}
// if molflag not set, warn if any deletable atom has a mol ID
if
(
molflag
==
0
&&
atom
->
molecule_flag
)
{
int
*
molecule
=
atom
->
molecule
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
flag
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
molecule
[
i
])
flag
=
1
;
int
flagall
;
MPI_Allreduce
(
&
flag
,
&
flagall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flagall
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Fix evaporate may delete atom with non-zero molecule ID"
);
}
if
(
molflag
&&
atom
->
molecule_flag
==
0
)
error
->
all
(
FLERR
,
"Fix evaporate molecule requires atom attribute molecule"
);
}
/* ----------------------------------------------------------------------
perform particle deletion
done before exchange, borders, reneighbor
so that ghost atoms and neighbor lists will be correct
------------------------------------------------------------------------- */
void
FixEvaporate
::
pre_exchange
()
{
int
i
,
j
,
m
,
iwhichglobal
,
iwhichlocal
;
int
ndel
,
ndeltopo
[
4
];
if
(
update
->
ntimestep
!=
next_reneighbor
)
return
;
// grow list and mark arrays if necessary
if
(
atom
->
nlocal
>
nmax
)
{
memory
->
destroy
(
list
);
memory
->
destroy
(
mark
);
nmax
=
atom
->
nmax
;
memory
->
create
(
list
,
nmax
,
"evaporate:list"
);
memory
->
create
(
mark
,
nmax
,
"evaporate:mark"
);
}
// ncount = # of deletable atoms in region that I own
// nall = # on all procs
// nbefore = # on procs before me
// list[ncount] = list of local indices of atoms I can delete
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
*
tag
=
atom
->
tag
;
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
;
// ndel = total # of atom deletions, in or out of region
// ndeltopo[1,2,3,4] = ditto for bonds, angles, dihedrals, impropers
// mark[] = 1 if deleted
ndel
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
mark
[
i
]
=
0
;
// atomic deletions
// choose atoms randomly across all procs and mark them for deletion
// shrink eligible list as my atoms get marked
// keep ndel,ncount,nall,nbefore current after each atom deletion
if
(
molflag
==
0
)
{
while
(
nall
&&
ndel
<
nflux
)
{
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
--
;
}
ndel
++
;
nall
--
;
}
// molecule deletions
// choose one atom in one molecule randomly across all procs
// bcast mol ID and delete all atoms in that molecule on any proc
// update deletion count by total # of atoms in molecule
// shrink list of eligible candidates as any of my atoms get marked
// keep ndel,ndeltopo,ncount,nall,nbefore current after each mol deletion
}
else
{
int
me
,
proc
,
iatom
,
imolecule
,
ndelone
,
ndelall
;
int
*
molecule
=
atom
->
molecule
;
ndeltopo
[
0
]
=
ndeltopo
[
1
]
=
ndeltopo
[
2
]
=
ndeltopo
[
3
]
=
0
;
while
(
nall
&&
ndel
<
nflux
)
{
// pick an iatom,imolecule on proc me to delete
iwhichglobal
=
static_cast
<
int
>
(
nall
*
random
->
uniform
());
if
(
iwhichglobal
>=
nbefore
&&
iwhichglobal
<
nbefore
+
ncount
)
{
iwhichlocal
=
iwhichglobal
-
nbefore
;
iatom
=
list
[
iwhichlocal
];
imolecule
=
molecule
[
iatom
];
me
=
comm
->
me
;
}
else
me
=
-
1
;
// bcast mol ID to delete all atoms from
// if mol ID > 0, delete any atom in molecule and decrement counters
// if mol ID == 0, delete single iatom
// be careful to delete correct # of bond,angle,etc for newton on or off
MPI_Allreduce
(
&
me
,
&
proc
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
MPI_Bcast
(
&
imolecule
,
1
,
MPI_INT
,
proc
,
world
);
ndelone
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
imolecule
&&
molecule
[
i
]
==
imolecule
)
{
mark
[
i
]
=
1
;
ndelone
++
;
if
(
atom
->
avec
->
bonds_allow
)
{
if
(
force
->
newton_bond
)
ndeltopo
[
0
]
+=
atom
->
num_bond
[
i
];
else
{
for
(
j
=
0
;
j
<
atom
->
num_bond
[
i
];
j
++
)
{
if
(
tag
[
i
]
<
atom
->
bond_atom
[
i
][
j
])
ndeltopo
[
0
]
++
;
}
}
}
if
(
atom
->
avec
->
angles_allow
)
{
if
(
force
->
newton_bond
)
ndeltopo
[
1
]
+=
atom
->
num_angle
[
i
];
else
{
for
(
j
=
0
;
j
<
atom
->
num_angle
[
i
];
j
++
)
{
m
=
atom
->
map
(
atom
->
angle_atom2
[
i
][
j
]);
if
(
m
>=
0
&&
m
<
nlocal
)
ndeltopo
[
1
]
++
;
}
}
}
if
(
atom
->
avec
->
dihedrals_allow
)
{
if
(
force
->
newton_bond
)
ndeltopo
[
2
]
+=
atom
->
num_dihedral
[
i
];
else
{
for
(
j
=
0
;
j
<
atom
->
num_dihedral
[
i
];
j
++
)
{
m
=
atom
->
map
(
atom
->
dihedral_atom2
[
i
][
j
]);
if
(
m
>=
0
&&
m
<
nlocal
)
ndeltopo
[
2
]
++
;
}
}
}
if
(
atom
->
avec
->
impropers_allow
)
{
if
(
force
->
newton_bond
)
ndeltopo
[
3
]
+=
atom
->
num_improper
[
i
];
else
{
for
(
j
=
0
;
j
<
atom
->
num_improper
[
i
];
j
++
)
{
m
=
atom
->
map
(
atom
->
improper_atom2
[
i
][
j
]);
if
(
m
>=
0
&&
m
<
nlocal
)
ndeltopo
[
3
]
++
;
}
}
}
}
else
if
(
me
==
proc
&&
i
==
iatom
)
{
mark
[
i
]
=
1
;
ndelone
++
;
}
}
// remove any atoms marked for deletion from my eligible list
i
=
0
;
while
(
i
<
ncount
)
{
if
(
mark
[
list
[
i
]])
{
list
[
i
]
=
list
[
ncount
-
1
];
ncount
--
;
}
else
i
++
;
}
// update ndel,ncount,nall,nbefore
// ndelall is total atoms deleted on this iteration
// ncount is already correct, so resum to get nall and nbefore
MPI_Allreduce
(
&
ndelone
,
&
ndelall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
ndel
+=
ndelall
;
MPI_Allreduce
(
&
ncount
,
&
nall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
MPI_Scan
(
&
ncount
,
&
nbefore
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
nbefore
-=
ncount
;
}
}
// 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
,
1
);
atom
->
nlocal
--
;
}
}
// reset global natoms and bonds, angles, etc
// if global map exists, reset it now instead of waiting for comm
// since deleting atoms messes up ghosts
atom
->
natoms
-=
ndel
;
if
(
molflag
)
{
int
all
[
4
];
MPI_Allreduce
(
ndeltopo
,
all
,
4
,
MPI_INT
,
MPI_SUM
,
world
);
atom
->
nbonds
-=
all
[
0
];
atom
->
nangles
-=
all
[
1
];
atom
->
ndihedrals
-=
all
[
2
];
atom
->
nimpropers
-=
all
[
3
];
}
if
(
ndel
&&
atom
->
map_style
)
{
atom
->
nghost
=
0
;
atom
->
map_init
();
atom
->
map_set
();
}
// statistics
ndeleted
+=
ndel
;
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
;
}
Event Timeline
Log In to Comment