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postprocess_input_script.py
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Created
Tue, Jun 11, 00:54
Size
5 KB
Mime Type
text/x-python
Expires
Thu, Jun 13, 00:54 (2 d)
Engine
blob
Format
Raw Data
Handle
18196595
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rLAMMPS lammps
postprocess_input_script.py
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#!/usr/bin/env python
"""
Reorder the integer arguments to the commands in a LAMMPS input
file if these arguments violate LAMMPS order requirements.
We have to do this because the moltemplate.sh script will automatically
assign these integers in a way which may violate these restrictions
and the user has little control over this.
Right now, the only thing this script does is swap the I and J integers in
"pair_coeff I J ..." commands. Later changes may be added.
"""
import
sys
lines_orig
=
[]
f
=
None
fname
=
None
num_lines_ignore
=
0
# Lines from files passed as arguments are read and processed silently.
# (Why? Sometimes it's necessary to read the contents of previous input scripts
# in order to be able to understand a script command which appears later.
# I'm assuming these files will be processed by lammps in the same order. So I
# must insure that moltemplate.sh passes them to this program in that order.
# I'm too lazy to read the "include" commands in input scripts correctly.)
if
len
(
sys
.
argv
)
>
1
:
for
fname
in
sys
.
argv
[
1
:]:
f
=
open
(
fname
,
'r'
)
in_stream
=
f
lines_orig
+=
in_stream
.
readlines
()
num_lines_ignore
+=
len
(
lines_orig
)
f
.
close
()
# Lines read from the standard input are read, processed, and printed to stdout
in_stream
=
sys
.
stdin
lines_orig
+=
in_stream
.
readlines
()
pair_style_list
=
[]
swap_occured
=
False
warn_wildcard
=
False
i
=
0
while
i
<
len
(
lines_orig
):
# Read the next logical line
# Any lines ending in '&' should be merged with the next line before breaking
line_orig
=
''
while
i
<
len
(
lines_orig
):
line_counter
=
1
+
i
-
num_lines_ignore
line_orig
+=
lines_orig
[
i
]
if
((
len
(
line_orig
)
<
2
)
or
(
line_orig
[
-
2
:]
!=
'&
\n
'
)):
break
i
+=
1
line
=
line_orig
.
replace
(
'&
\n
'
,
'
\n
'
)
.
rstrip
(
'
\n
'
)
comment
=
''
if
'#'
in
line_orig
:
ic
=
line
.
find
(
'#'
)
line
=
line_orig
[:
ic
]
comment
=
line_orig
[
ic
:]
# keep track of comments (put them back later)
tokens
=
line
.
strip
()
.
split
()
if
((
len
(
tokens
)
>=
2
)
and
(
tokens
[
0
]
==
'pair_style'
)):
pair_style_list
=
tokens
[
1
:]
if
((
len
(
tokens
)
>=
3
)
and
(
tokens
[
0
]
==
'pair_coeff'
)):
if
((
tokens
[
1
]
.
isdigit
()
and
(
tokens
[
2
]
.
isdigit
()))
and
(
int
(
tokens
[
1
])
>
int
(
tokens
[
2
]))):
swap_occured
=
True
tmp
=
tokens
[
2
]
tokens
[
2
]
=
tokens
[
1
]
tokens
[
1
]
=
tmp
if
i
>=
num_lines_ignore
:
# polite warning:
sys
.
stderr
.
write
(
'swapped pair_coeff order on line '
+
str
(
line_counter
))
#if (fname != None):
# sys.stderr.write(' of file \"'+fname+'\"')
sys
.
stderr
.
write
(
'
\n
'
)
# Deal with the "hbond/" pair coeffs.
#
# The hbond/dreiding pair style designates one of the two atom types
# as a donor, and the other as an acceptor (using the 'i','j' flags)
# If swapped atom types eariler, we also need to swap 'i' with 'j'.
#
# If "hbond/dreiding.." pair style is used with "hybrid" or
# "hybrid/overlay" then tokens[3] is the name of the pair style
# and tokens[5] is either 'i' or 'j'.
if
len
(
pair_style_list
)
>
0
:
if
((
pair_style_list
[
0
]
==
'hybrid'
)
or
(
pair_style_list
[
0
]
==
'hybrid/overlay'
)):
if
((
len
(
tokens
)
>
5
)
and
(
tokens
[
5
]
==
'i'
)
and
(
tokens
[
3
][
0
:
6
]
==
'hbond/'
)):
tokens
[
5
]
=
'j'
sys
.
stderr
.
write
(
' (and replaced
\"
i
\"
with
\"
j
\"
)
\n
'
)
elif
((
len
(
tokens
)
>
5
)
and
(
tokens
[
5
]
==
'j'
)
and
(
tokens
[
3
][
0
:
6
]
==
'hbond/'
)):
tokens
[
5
]
=
'i'
sys
.
stderr
.
write
(
' (and replaced
\"
j
\"
with
\"
i
\"
)
\n
'
)
elif
(
pair_style_list
[
0
][
0
:
6
]
==
'hbond/'
):
if
((
len
(
tokens
)
>
4
)
and
(
tokens
[
4
]
==
'i'
)):
tokens
[
4
]
=
'j'
sys
.
stderr
.
write
(
' (and replaced
\"
i
\"
with
\"
j
\"
)
\n
'
)
elif
((
len
(
tokens
)
>
4
)
and
(
tokens
[
4
]
==
'j'
)):
tokens
[
4
]
=
'i'
sys
.
stderr
.
write
(
' (and replaced
\"
j
\"
with
\"
i
\"
)
\n
'
)
sys
.
stdout
.
write
((
' '
.
join
(
tokens
)
+
comment
)
.
replace
(
'
\n
'
,
'&
\n
'
)
+
'
\n
'
)
else
:
if
(((
'*'
in
tokens
[
1
])
or
(
'*'
in
tokens
[
2
]))
and
(
not
((
'*'
==
tokens
[
1
])
and
(
'*'
==
tokens
[
2
])))):
warn_wildcard
=
True
if
i
>=
num_lines_ignore
:
sys
.
stdout
.
write
(
line_orig
)
else
:
if
i
>=
num_lines_ignore
:
sys
.
stdout
.
write
(
line_orig
)
i
+=
1
if
swap_occured
:
sys
.
stderr
.
write
(
'
\n
'
' WARNING: Atom order in some pair_coeff commands was swapped to pacify LAMMPS.
\n
'
' For some exotic pair_styles such as hbond/dreiding, this is not enough. If you
\n
'
' use exotic pair_styles, please verify the
\"
pair_coeff
\"
commands are correct.
\n
'
)
if
warn_wildcard
:
sys
.
stderr
.
write
(
'
\n
'
' WARNING: The use of wildcard characters (
\"
*
\"
) in your
\"
pair_coeff
\"\n
'
' commands is not recommended.
\n
'
' (It is safer to specify each interaction pair manually.
\n
'
' Check every pair_coeff command. Make sure that every atom type in
\n
'
' the first group is <= atom types in the second group.
\n
'
' Moltemplate does NOT do this when wildcards are used.)
\n
'
' If you are using a many-body pair style then ignore this warning.
\n
'
)
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