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nomad-lab
parser-gpaw
Commits
f5be159e
Commit
f5be159e
authored
Mar 14, 2019
by
Daniel Speckhard
Browse files
Made two parsers for diff gpaw files.
parent
cbd073af
Changes
3
Hide whitespace changes
Inline
Side-by-side
gpawparser/__init__.py
View file @
f5be159e
from
gpawparser.parser
import
GpawParserWrapper
from
gpawparser.parser
import
GPAWParserWrapper
from
gpawparser.parser2
import
GPAWParser2Wrapper
gpawparser/parser.py
View file @
f5be159e
...
@@ -41,13 +41,6 @@ def c(value, unit=None):
...
@@ -41,13 +41,6 @@ def c(value, unit=None):
parser_info
=
{
"name"
:
"parser_gpaw"
,
"version"
:
"1.0"
}
parser_info
=
{
"name"
:
"parser_gpaw"
,
"version"
:
"1.0"
}
path
=
'../../../../nomad-meta-info/meta_info/nomad_meta_info/'
+
\
path
=
'../../../../nomad-meta-info/meta_info/nomad_meta_info/'
+
\
'gpaw.nomadmetainfo.json'
'gpaw.nomadmetainfo.json'
# metaInfoPath = os.path.normpath(
# os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
# metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
# dependencyLoader=None,
# extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
# uri=None)
import
nomad_meta_info
import
nomad_meta_info
metaInfoPath
=
os
.
path
.
normpath
(
metaInfoPath
=
os
.
path
.
normpath
(
...
@@ -57,14 +50,14 @@ metaInfoEnv, warnings = loadJsonFile(
...
@@ -57,14 +50,14 @@ metaInfoEnv, warnings = loadJsonFile(
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
class
G
paw
ParserWrapper
():
class
G
PAW
ParserWrapper
():
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
def
__init__
(
self
,
backend
,
**
kwargs
):
def
__init__
(
self
,
backend
,
**
kwargs
):
self
.
backend_factory
=
backend
self
.
backend_factory
=
backend
def
parse
(
self
,
mainfile
):
def
parse
(
self
,
mainfile
):
from
unittest.mock
import
patch
from
unittest.mock
import
patch
logging
.
info
(
'
lib-atoms
parser started'
)
logging
.
info
(
'
GPAW
parser started'
)
logging
.
getLogger
(
'nomadcore'
).
setLevel
(
logging
.
WARNING
)
logging
.
getLogger
(
'nomadcore'
).
setLevel
(
logging
.
WARNING
)
backend
=
self
.
backend_factory
(
metaInfoEnv
)
backend
=
self
.
backend_factory
(
metaInfoEnv
)
backend
=
parse_without_class
(
mainfile
,
backend
)
backend
=
parse_without_class
(
mainfile
,
backend
)
...
...
gpawparser/parser2.py
View file @
f5be159e
...
@@ -16,6 +16,7 @@ from __future__ import division
...
@@ -16,6 +16,7 @@ from __future__ import division
import
os
import
os
from
contextlib
import
contextmanager
from
contextlib
import
contextmanager
import
numpy
as
np
import
numpy
as
np
import
logging
from
ase
import
units
from
ase
import
units
from
ase.data
import
chemical_symbols
from
ase.data
import
chemical_symbols
from
ase.io.ulm
import
ulmopen
from
ase.io.ulm
import
ulmopen
...
@@ -23,12 +24,11 @@ from ase.utils import basestring
...
@@ -23,12 +24,11 @@ from ase.utils import basestring
#from ase.io.trajectory import read_atoms
#from ase.io.trajectory import read_atoms
from
ase.data
import
atomic_masses
from
ase.data
import
atomic_masses
from
ase.units
import
Rydberg
from
ase.units
import
Rydberg
import
setup_paths
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
as
cu
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
as
cu
from
nomadcore.local_meta_info
import
loadJsonFile
,
InfoKindEl
from
nomadcore.local_meta_info
import
loadJsonFile
,
InfoKindEl
from
nomadcore.parser_backend
import
JsonParseEventsWriterBackend
from
nomadcore.parser_backend
import
JsonParseEventsWriterBackend
from
libxc_names
import
get_libxc_name
from
gpawparser.
libxc_names
import
get_libxc_name
from
default_parameters
import
parameters
as
parms
from
gpawparser.
default_parameters
import
parameters
as
parms
@
contextmanager
@
contextmanager
...
@@ -46,13 +46,7 @@ def c(value, unit=None):
...
@@ -46,13 +46,7 @@ def c(value, unit=None):
parser_info
=
{
"name"
:
"parser2_gpaw"
,
"version"
:
"1.0"
}
parser_info
=
{
"name"
:
"parser2_gpaw"
,
"version"
:
"1.0"
}
path
=
'../../../../nomad-meta-info/meta_info/nomad_meta_info/'
+
\
path
=
'../../../../nomad-meta-info/meta_info/nomad_meta_info/'
+
\
'gpaw.nomadmetainfo.json'
'gpaw.nomadmetainfo.json'
# metaInfoPath = os.path.normpath(
# os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
# metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
# dependencyLoader=None,
# extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
# uri=None)
import
nomad_meta_info
import
nomad_meta_info
metaInfoPath
=
os
.
path
.
normpath
(
metaInfoPath
=
os
.
path
.
normpath
(
os
.
path
.
join
(
os
.
path
.
dirname
(
os
.
path
.
abspath
(
nomad_meta_info
.
__file__
)),
os
.
path
.
join
(
os
.
path
.
dirname
(
os
.
path
.
abspath
(
nomad_meta_info
.
__file__
)),
...
@@ -61,8 +55,23 @@ metaInfoEnv, warnings = loadJsonFile(
...
@@ -61,8 +55,23 @@ metaInfoEnv, warnings = loadJsonFile(
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
def
parse
(
filename
):
class
GPAWParser2Wrapper
():
p
=
JsonParseEventsWriterBackend
(
metaInfoEnv
)
""" A proper class envolop for running this parser using Noamd-FAIRD infra. """
def
__init__
(
self
,
backend
,
**
kwargs
):
self
.
backend_factory
=
backend
def
parse
(
self
,
mainfile
):
from
unittest.mock
import
patch
logging
.
info
(
'GPAW parser 2 (note the 2) started'
)
logging
.
getLogger
(
'nomadcore'
).
setLevel
(
logging
.
WARNING
)
backend
=
self
.
backend_factory
(
metaInfoEnv
)
backend
=
parse_without_class
(
mainfile
,
backend
)
return
backend
def
parse_without_class
(
filename
,
backend
):
p
=
backend
# p = JsonParseEventsWriterBackend(metaInfoEnv)
o
=
open_section
o
=
open_section
r
=
ulmopen
(
filename
)
# Reader(filename)
r
=
ulmopen
(
filename
)
# Reader(filename)
p
.
startedParsingSession
(
filename
,
parser_info
)
p
.
startedParsingSession
(
filename
,
parser_info
)
...
@@ -225,6 +234,7 @@ def parse(filename):
...
@@ -225,6 +234,7 @@ def parse(filename):
p
.
finishedParsingSession
(
"ParseSuccess"
,
None
)
p
.
finishedParsingSession
(
"ParseSuccess"
,
None
)
return
p
if
__name__
==
'__main__'
:
if
__name__
==
'__main__'
:
import
sys
import
sys
...
...
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