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nomad-lab
parser-cp2k
Commits
3582b096
Commit
3582b096
authored
Jun 21, 2016
by
Mohamed, Fawzi Roberto (fawzi)
Browse files
python3: futurize stage2
parent
b1ef5b11
Changes
8
Hide whitespace changes
Inline
Side-by-side
parser/parser-cp2k/cp2kparser/generic/inputparsing.py
View file @
3582b096
from
builtins
import
str
from
builtins
import
object
import
numpy
as
np
import
logging
from
collections
import
defaultdict
...
...
parser/parser-cp2k/cp2kparser/parser.py
View file @
3582b096
from
builtins
import
next
from
builtins
import
range
import
os
import
re
import
logging
...
...
@@ -31,7 +33,7 @@ class CP2KParser(ParserInterface):
version_id
=
None
run_type
=
None
with
open
(
self
.
parser_context
.
main_file
,
'r'
)
as
outputfile
:
for
i_line
in
x
range
(
n_lines
):
for
i_line
in
range
(
n_lines
):
line
=
next
(
outputfile
)
result_version
=
regex_version
.
match
(
line
)
result_run_type
=
regex_run_type
.
match
(
line
)
...
...
parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py
View file @
3582b096
...
...
@@ -13,11 +13,13 @@ the object can be queried for the results, or the default values defined by the
cp2k_input.xml.
"""
from
__future__
import
print_function
from
future
import
standard_library
standard_library
.
install_aliases
()
import
xml.etree.cElementTree
as
ET
import
logging
import
json
import
cPickle
as
pickle
import
pickle
from
cp2kparser.generic.inputparsing
import
*
logger
=
logging
...
...
@@ -217,9 +219,9 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
if
isinstance
(
obj
,
Section
):
name_stack
.
append
(
obj
.
name
)
json
=
generate_section_metainfo_json
(
obj
,
parent
,
name_stack
)
for
child
in
obj
.
sections
.
iter
values
():
for
child
in
obj
.
sections
.
values
():
generate_metainfo_recursively
(
child
[
0
],
obj
,
container
,
name_stack
)
for
child
in
obj
.
keywords
.
iter
values
():
for
child
in
obj
.
keywords
.
values
():
generate_metainfo_recursively
(
child
[
0
],
obj
,
container
,
name_stack
)
if
obj
.
section_parameter
is
not
None
:
generate_metainfo_recursively
(
obj
.
section_parameter
,
obj
,
container
,
name_stack
)
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
View file @
3582b096
from
__future__
import
absolute_import
from
builtins
import
str
from
builtins
import
object
import
re
import
numpy
as
np
import
logging
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
View file @
3582b096
from
__future__
import
print_function
from
__future__
import
absolute_import
from
builtins
import
next
from
builtins
import
range
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.baseclasses
import
MainHierarchicalParser
from
.commonmatcher
import
CommonMatcher
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
View file @
3582b096
from
future
import
standard_library
standard_library
.
install_aliases
()
from
builtins
import
object
import
os
import
re
import
logging
import
cPickle
as
pickle
import
pickle
import
numpy
as
np
from
nomadcore.baseclasses
import
BasicParser
from
cp2kparser.generic.inputparsing
import
*
...
...
@@ -435,7 +438,7 @@ class CP2KInputParser(BasicParser):
self
.
backend
.
addValue
(
name
,
default_keyword
.
value
)
# Subsections
for
name
,
subsections
in
section
.
sections
.
iter
items
():
for
name
,
subsections
in
section
.
sections
.
items
():
for
subsection
in
subsections
:
self
.
fill_metadata_recursively
(
subsection
,
name_stack
)
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @
3582b096
from
__future__
import
absolute_import
from
builtins
import
next
from
builtins
import
range
import
numpy
as
np
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.baseclasses
import
MainHierarchicalParser
...
...
test/unittests/cp2k_2.6.2/run_tests.py
View file @
3582b096
...
...
@@ -672,7 +672,7 @@ class TestGeoOptTrajectory(unittest.TestCase):
systems
=
results
[
"section_system"
]
i_conf
=
0
for
calc
in
single_conf
.
iter
values
():
for
calc
in
single_conf
.
values
():
system_index
=
calc
[
"single_configuration_calculation_to_system_ref"
][
0
]
system
=
systems
[
system_index
]
pos
=
system
[
"atom_positions"
]
...
...
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