Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78072121
compute.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
Sun, Aug 18, 06:18
Size
8 KB
Mime Type
text/x-c
Expires
Tue, Aug 20, 06:18 (2 d)
Engine
blob
Format
Raw Data
Handle
19819529
Attached To
rLAMMPS lammps
compute.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 "lmptype.h"
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "compute.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 4
#define BIG 2000000000
/* ---------------------------------------------------------------------- */
Compute
::
Compute
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Pointers
(
lmp
)
{
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal compute command"
);
// compute ID, group, and style
// ID must be all alphanumeric chars or underscores
int
n
=
strlen
(
arg
[
0
])
+
1
;
id
=
new
char
[
n
];
strcpy
(
id
,
arg
[
0
]);
for
(
int
i
=
0
;
i
<
n
-
1
;
i
++
)
if
(
!
isalnum
(
id
[
i
])
&&
id
[
i
]
!=
'_'
)
error
->
all
(
FLERR
,
"Compute ID must be alphanumeric or underscore characters"
);
igroup
=
group
->
find
(
arg
[
1
]);
if
(
igroup
==
-
1
)
error
->
all
(
FLERR
,
"Could not find compute group ID"
);
groupbit
=
group
->
bitmask
[
igroup
];
n
=
strlen
(
arg
[
2
])
+
1
;
style
=
new
char
[
n
];
strcpy
(
style
,
arg
[
2
]);
// set child class defaults
scalar_flag
=
vector_flag
=
array_flag
=
0
;
peratom_flag
=
local_flag
=
0
;
tempflag
=
pressflag
=
peflag
=
0
;
pressatomflag
=
peatomflag
=
0
;
tempbias
=
0
;
timeflag
=
0
;
comm_forward
=
comm_reverse
=
0
;
cudable
=
0
;
invoked_scalar
=
invoked_vector
=
invoked_array
=
-
1
;
invoked_peratom
=
invoked_local
=
-
1
;
// set modify defaults
extra_dof
=
domain
->
dimension
;
dynamic
=
0
;
// setup list of timesteps
ntime
=
maxtime
=
0
;
tlist
=
NULL
;
// setup map for molecule IDs
molmap
=
NULL
;
}
/* ---------------------------------------------------------------------- */
Compute
::~
Compute
()
{
delete
[]
id
;
delete
[]
style
;
memory
->
destroy
(
tlist
);
memory
->
destroy
(
molmap
);
}
/* ---------------------------------------------------------------------- */
void
Compute
::
modify_params
(
int
narg
,
char
**
arg
)
{
if
(
narg
==
0
)
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"extra"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
extra_dof
=
atoi
(
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"dynamic"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
dynamic
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
dynamic
=
1
;
else
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"thermo"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
thermoflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
thermoflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal compute_modify command"
);
}
}
/* ----------------------------------------------------------------------
reset extra_dof to its default value
------------------------------------------------------------------------- */
void
Compute
::
reset_extra_dof
()
{
extra_dof
=
domain
->
dimension
;
}
/* ---------------------------------------------------------------------- */
void
Compute
::
reset_extra_compute_fix
(
const
char
*
)
{
error
->
all
(
FLERR
,
"Compute does not allow an extra compute or fix to be reset"
);
}
/* ----------------------------------------------------------------------
add ntimestep to list of timesteps the compute will be called on
do not add if already in list
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
void
Compute
::
addstep
(
bigint
ntimestep
)
{
// i = location in list to insert ntimestep
int
i
;
for
(
i
=
ntime
-
1
;
i
>=
0
;
i
--
)
{
if
(
ntimestep
==
tlist
[
i
])
return
;
if
(
ntimestep
<
tlist
[
i
])
break
;
}
i
++
;
// extend list as needed
if
(
ntime
==
maxtime
)
{
maxtime
+=
DELTA
;
memory
->
grow
(
tlist
,
maxtime
,
"compute:tlist"
);
}
// move remainder of list upward and insert ntimestep
for
(
int
j
=
ntime
-
1
;
j
>=
i
;
j
--
)
tlist
[
j
+
1
]
=
tlist
[
j
];
tlist
[
i
]
=
ntimestep
;
ntime
++
;
}
/* ----------------------------------------------------------------------
return 1/0 if ntimestep is or is not in list of calling timesteps
if value(s) on top of list are less than ntimestep, delete them
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
int
Compute
::
matchstep
(
bigint
ntimestep
)
{
for
(
int
i
=
ntime
-
1
;
i
>=
0
;
i
--
)
{
if
(
ntimestep
<
tlist
[
i
])
return
0
;
if
(
ntimestep
==
tlist
[
i
])
return
1
;
if
(
ntimestep
>
tlist
[
i
])
ntime
--
;
}
return
0
;
}
/* ----------------------------------------------------------------------
clean out list of timesteps to call the compute on
------------------------------------------------------------------------- */
void
Compute
::
clearstep
()
{
ntime
=
0
;
}
/* ----------------------------------------------------------------------
identify molecule IDs with atoms in group
warn if any atom in group has molecule ID = 0
warn if any molecule has only some atoms in group
return Ncount = # of molecules with atoms in group
set molmap to NULL if molecule IDs include all in range from 1 to Ncount
else: molecule IDs range from idlo to idhi
set molmap to vector of length idhi-idlo+1
molmap[id-idlo] = index from 0 to Ncount-1
return idlo and idhi
------------------------------------------------------------------------- */
int
Compute
::
molecules_in_group
(
int
&
idlo
,
int
&
idhi
)
{
int
i
;
memory
->
destroy
(
molmap
);
molmap
=
NULL
;
// find lo/hi molecule ID for any atom in group
// warn if atom in group has ID = 0
int
*
molecule
=
atom
->
molecule
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
lo
=
BIG
;
int
hi
=
-
BIG
;
int
flag
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
molecule
[
i
]
==
0
)
flag
=
1
;
lo
=
MIN
(
lo
,
molecule
[
i
]);
hi
=
MAX
(
hi
,
molecule
[
i
]);
}
int
flagall
;
MPI_Allreduce
(
&
flag
,
&
flagall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flagall
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Atom with molecule ID = 0 included in "
"compute molecule group"
);
MPI_Allreduce
(
&
lo
,
&
idlo
,
1
,
MPI_INT
,
MPI_MIN
,
world
);
MPI_Allreduce
(
&
hi
,
&
idhi
,
1
,
MPI_INT
,
MPI_MAX
,
world
);
if
(
idlo
==
BIG
)
return
0
;
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
int
nlen
=
idhi
-
idlo
+
1
;
memory
->
create
(
molmap
,
nlen
,
"compute:molmap"
);
for
(
i
=
0
;
i
<
nlen
;
i
++
)
molmap
[
i
]
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
molmap
[
molecule
[
i
]
-
idlo
]
=
1
;
int
*
molmapall
;
memory
->
create
(
molmapall
,
nlen
,
"compute:molmapall"
);
MPI_Allreduce
(
molmap
,
molmapall
,
nlen
,
MPI_INT
,
MPI_MAX
,
world
);
// nmolecules = # of non-zero IDs in molmap
// molmap[i] = index of molecule, skipping molecules not in group with -1
int
nmolecules
=
0
;
for
(
i
=
0
;
i
<
nlen
;
i
++
)
if
(
molmapall
[
i
])
molmap
[
i
]
=
nmolecules
++
;
else
molmap
[
i
]
=
-
1
;
memory
->
destroy
(
molmapall
);
// warn if any molecule has some atoms in group and some not in group
flag
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
continue
;
if
(
molecule
[
i
]
<
idlo
||
molecule
[
i
]
>
idhi
)
continue
;
if
(
molmap
[
molecule
[
i
]
-
idlo
]
>=
0
)
flag
=
1
;
}
MPI_Allreduce
(
&
flag
,
&
flagall
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
flagall
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"One or more compute molecules has atoms not in group"
);
// if molmap simply stores 1 to Nmolecules, then free it
if
(
idlo
==
1
&&
idhi
==
nmolecules
&&
nlen
==
nmolecules
)
{
memory
->
destroy
(
molmap
);
molmap
=
NULL
;
}
return
nmolecules
;
}
Event Timeline
Log In to Comment