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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
numpy
as
np
import
logging
import
logging
from
collections
import
defaultdict
from
collections
import
defaultdict
...
...
parser/parser-cp2k/cp2kparser/parser.py
View file @
3582b096
from
builtins
import
next
from
builtins
import
range
import
os
import
os
import
re
import
re
import
logging
import
logging
...
@@ -31,7 +33,7 @@ class CP2KParser(ParserInterface):
...
@@ -31,7 +33,7 @@ class CP2KParser(ParserInterface):
version_id
=
None
version_id
=
None
run_type
=
None
run_type
=
None
with
open
(
self
.
parser_context
.
main_file
,
'r'
)
as
outputfile
:
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
)
line
=
next
(
outputfile
)
result_version
=
regex_version
.
match
(
line
)
result_version
=
regex_version
.
match
(
line
)
result_run_type
=
regex_run_type
.
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
...
@@ -13,11 +13,13 @@ the object can be queried for the results, or the default values defined by the
cp2k_input.xml.
cp2k_input.xml.
"""
"""
from
__future__
import
print_function
from
__future__
import
print_function
from
future
import
standard_library
standard_library
.
install_aliases
()
import
xml.etree.cElementTree
as
ET
import
xml.etree.cElementTree
as
ET
import
logging
import
logging
import
json
import
json
import
cPickle
as
pickle
import
pickle
from
cp2kparser.generic.inputparsing
import
*
from
cp2kparser.generic.inputparsing
import
*
logger
=
logging
logger
=
logging
...
@@ -217,9 +219,9 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
...
@@ -217,9 +219,9 @@ def generate_metainfo_recursively(obj, parent, container, name_stack):
if
isinstance
(
obj
,
Section
):
if
isinstance
(
obj
,
Section
):
name_stack
.
append
(
obj
.
name
)
name_stack
.
append
(
obj
.
name
)
json
=
generate_section_metainfo_json
(
obj
,
parent
,
name_stack
)
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
)
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
)
generate_metainfo_recursively
(
child
[
0
],
obj
,
container
,
name_stack
)
if
obj
.
section_parameter
is
not
None
:
if
obj
.
section_parameter
is
not
None
:
generate_metainfo_recursively
(
obj
.
section_parameter
,
obj
,
container
,
name_stack
)
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
__future__
import
absolute_import
from
builtins
import
str
from
builtins
import
object
import
re
import
re
import
numpy
as
np
import
numpy
as
np
import
logging
import
logging
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
View file @
3582b096
from
__future__
import
print_function
from
__future__
import
print_function
from
__future__
import
absolute_import
from
__future__
import
absolute_import
from
builtins
import
next
from
builtins
import
range
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.baseclasses
import
MainHierarchicalParser
from
nomadcore.baseclasses
import
MainHierarchicalParser
from
.commonmatcher
import
CommonMatcher
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
os
import
re
import
re
import
logging
import
logging
import
cPickle
as
pickle
import
pickle
import
numpy
as
np
import
numpy
as
np
from
nomadcore.baseclasses
import
BasicParser
from
nomadcore.baseclasses
import
BasicParser
from
cp2kparser.generic.inputparsing
import
*
from
cp2kparser.generic.inputparsing
import
*
...
@@ -435,7 +438,7 @@ class CP2KInputParser(BasicParser):
...
@@ -435,7 +438,7 @@ class CP2KInputParser(BasicParser):
self
.
backend
.
addValue
(
name
,
default_keyword
.
value
)
self
.
backend
.
addValue
(
name
,
default_keyword
.
value
)
# Subsections
# Subsections
for
name
,
subsections
in
section
.
sections
.
iter
items
():
for
name
,
subsections
in
section
.
sections
.
items
():
for
subsection
in
subsections
:
for
subsection
in
subsections
:
self
.
fill_metadata_recursively
(
subsection
,
name_stack
)
self
.
fill_metadata_recursively
(
subsection
,
name_stack
)
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @
3582b096
from
__future__
import
absolute_import
from
__future__
import
absolute_import
from
builtins
import
next
from
builtins
import
range
import
numpy
as
np
import
numpy
as
np
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.baseclasses
import
MainHierarchicalParser
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):
...
@@ -672,7 +672,7 @@ class TestGeoOptTrajectory(unittest.TestCase):
systems
=
results
[
"section_system"
]
systems
=
results
[
"section_system"
]
i_conf
=
0
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_index
=
calc
[
"single_configuration_calculation_to_system_ref"
][
0
]
system
=
systems
[
system_index
]
system
=
systems
[
system_index
]
pos
=
system
[
"atom_positions"
]
pos
=
system
[
"atom_positions"
]
...
...
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