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lmp2xyz.py
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Created
Wed, Oct 16, 13:24
Size
3 KB
Mime Type
text/x-python
Expires
Fri, Oct 18, 13:24 (1 d, 23 h)
Engine
blob
Format
Raw Data
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21567050
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rLAMMPS lammps
lmp2xyz.py
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=
"""
Module name: lmp2xyz.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@caltech.edu
Project: pEFF
Version: August 2009
Extracts the xyz from a lammps trajectory dump of style custom:
dump 1 all custom period dump_file id type x y z spin radius ...
Usage: python lmp2xyz.py lammps_dump_filename xyz_filename
"""
import
os
,
sys
from
math
import
log10
,
floor
from
numpy
import
zeros
masses
=
{
"1.00794"
:
"H"
,
"4.002602"
:
"He"
,
"6.941"
:
"Li"
,
"9.012182"
:
"Be"
,
"10.811"
:
"B"
,
"12.0107"
:
"C"
,
"1.00"
:
"Au"
,
"0.0005486"
:
"Au"
}
mass_floor
=
{
1
:
"H"
,
4
:
"He"
,
6
:
"Li"
,
9
:
"Be"
,
10
:
"B"
,
12
:
"C"
,
0
:
"Au"
,
28
:
"Si"
}
def
lmp2xyz
(
lammps
,
xyz
,
xpos
):
print
"
\n
Generating
%s
file"
%
(
xyz
)
fin
=
open
(
lammps
,
'r'
)
fout
=
open
(
xyz
,
'w'
)
data
=
raw_input
(
"Do you have a corresponding data file? please enter filename or 'n': "
)
count
=
1
if
data
!=
'n'
:
dataf
=
open
(
data
,
'r'
)
datafile
=
dataf
.
readlines
()
dataf
.
close
()
for
line
in
datafile
:
if
line
.
find
(
"atom types"
)
>=
0
:
numtypes
=
int
(
line
.
split
()[
0
])
mass
=
zeros
(
numtypes
,
dtype
=
float
)
elif
line
.
find
(
"Masses"
)
>=
0
:
count
+=
1
+
datafile
.
index
(
line
)
elif
line
.
find
(
"Atoms"
)
>=
0
:
break
for
i
in
range
(
numtypes
):
mass
[
i
]
=
float
(
datafile
[
count
]
.
split
()[
1
])
count
+=
1
else
:
print
"
\n
Will continue without a data file specification"
header
=
9
lines
=
fin
.
readlines
()
numatoms
=
lines
[
3
]
.
split
()[
0
]
fsize
=
os
.
system
(
"wc -l
%s
> lines"
%
(
lammps
))
tmp
=
open
(
'lines'
,
'r'
)
tlines
=
tmp
.
readline
()
tmp
.
close
()
os
.
system
(
"rm lines"
)
flines
=
int
(
tlines
.
split
()[
0
])
snaps
=
flines
/
(
int
(
numatoms
)
+
header
)
countsnap
=
1
if
data
!=
'n'
:
coords
=
{}
else
:
coords
=
zeros
((
int
(
numatoms
),
4
),
dtype
=
float
)
# sys.stdout.write("Writing %d snapshots\n"%(snaps))
# sys.stdout.flush()
read_atoms
=
0
types
=
{}
for
line
in
lines
:
if
line
.
find
(
'ITEM: TIMESTEP'
)
==
0
:
read_atom_flag
=
False
# sys.stdout.write("%d "%(countsnap))
# sys.stdout.flush()
fout
.
writelines
(
"
%s
\n
Atoms
\n
"
%
(
numatoms
))
countsnap
+=
1
continue
if
line
.
find
(
'ITEM: ATOMS'
)
==
0
:
read_atom_flag
=
True
continue
if
read_atom_flag
==
True
:
read_atoms
+=
1
parse
=
line
.
split
()
if
parse
[
0
]
!=
""
:
if
data
!=
'n'
:
if
parse
[
1
]
not
in
types
.
keys
():
type
=
raw_input
(
"Atom name for type
%s
: "
%
parse
[
1
])
types
[
parse
[
1
]]
=
type
coords
[
int
(
parse
[
0
])
-
1
]
=
[
types
[
parse
[
1
]],
float
(
parse
[
xpos
-
1
]),
float
(
parse
[
xpos
]),
float
(
parse
[
xpos
+
1
])]
else
:
coords
[
int
(
parse
[
0
])
-
1
][
0
]
=
int
(
parse
[
1
])
coords
[
int
(
parse
[
0
])
-
1
][
1
]
=
float
(
parse
[
xpos
-
1
])
coords
[
int
(
parse
[
0
])
-
1
][
2
]
=
float
(
parse
[
xpos
])
coords
[
int
(
parse
[
0
])
-
1
][
3
]
=
float
(
parse
[
xpos
+
1
])
if
read_atoms
==
int
(
numatoms
):
read_atoms
=
0
for
i
in
range
(
int
(
numatoms
)):
if
data
!=
'n'
:
fout
.
writelines
(
"
%s
%2.4f
%2.4f
%2.4f
\n
"
%
(
coords
[
i
][
0
],
coords
[
i
][
1
],
coords
[
i
][
2
],
coords
[
i
][
3
]))
else
:
fout
.
writelines
(
"
%d
%2.4f
%2.4f
%2.4f
\n
"
%
(
coords
[
i
][
0
],
coords
[
i
][
1
],
coords
[
i
][
2
],
coords
[
i
][
3
]))
print
"
\n
Done converting to xyz!!
\n
"
fin
.
close
()
fout
.
close
()
return
if
__name__
==
'__main__'
:
# if no input, print help and exit
if
len
(
sys
.
argv
)
<
2
:
print
Info
()
sys
.
exit
(
1
)
inputfile
=
sys
.
argv
[
1
]
outfile
=
sys
.
argv
[
2
]
if
len
(
sys
.
argv
)
==
4
:
xpos
=
sys
.
arv
[
3
]
-
1
else
:
xpos
=
5
lmp2xyz
(
inputfile
,
outfile
.
split
()[
0
],
xpos
)
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