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nomad-lab
parser-asap
Commits
43404684
Commit
43404684
authored
8 years ago
by
Mikkel Strange
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asap parser
parent
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parser/parser-asap/parser.py
+71
-0
71 additions, 0 deletions
parser/parser-asap/parser.py
parser/parser-asap/setup_paths.py
+6
-0
6 additions, 0 deletions
parser/parser-asap/setup_paths.py
with
77 additions
and
0 deletions
parser/parser-asap/parser.py
0 → 100644
+
71
−
0
View file @
43404684
from
__future__
import
division
import
os
from
contextlib
import
contextmanager
import
numpy
as
np
from
ase.data
import
chemical_symbols
from
ase.io.aff
import
affopen
as
Reader
import
setup_paths
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
as
cu
from
nomadcore.local_meta_info
import
loadJsonFile
,
InfoKindEl
from
nomadcore.parser_backend
import
JsonParseEventsWriterBackend
@contextmanager
def
open_section
(
p
,
name
):
gid
=
p
.
openSection
(
name
)
yield
p
.
closeSection
(
name
,
gid
)
def
c
(
value
,
unit
=
None
):
"""
Dummy function for unit conversion
"""
return
cu
(
value
,
unit
)
parser_info
=
{
"
name
"
:
"
parser_asap
"
,
"
version
"
:
"
1.0
"
}
path
=
'
../../../../nomad-meta-info/meta_info/nomad_meta_info/
'
+
\
'
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
)
def
parse
(
filename
):
p
=
JsonParseEventsWriterBackend
(
metaInfoEnv
)
o
=
open_section
r
=
Reader
(
filename
)
p
.
startedParsingSession
(
filename
,
parser_info
)
with
o
(
p
,
'
section_run
'
):
p
.
addValue
(
'
program_name
'
,
'
ASAP
'
)
p
.
addValue
(
'
program_version
'
,
'
1.0.0
'
)
with
o
(
p
,
'
section_system
'
):
p
.
addArrayValues
(
'
simulation_cell
'
,
c
(
r
.
UnitCell
,
'
bohr
'
))
symbols
=
np
.
array
([
chemical_symbols
[
z
]
for
z
in
r
.
AtomicNumbers
])
p
.
addArrayValues
(
'
atom_labels
'
,
symbols
)
p
.
addArrayValues
(
'
atom_positions
'
,
c
(
r
.
CartesianPositions
,
'
bohr
'
))
p
.
addArrayValues
(
'
configuration_periodic_dimensions
'
,
np
.
array
(
r
.
BoundaryConditions
,
bool
))
with
o
(
p
,
'
section_sampling_method
'
):
p
.
addValue
(
'
ensemble_type
'
,
'
NVE
'
)
with
o
(
p
,
'
section_frame_sequence
'
):
pass
with
o
(
p
,
'
section_single_configuration_calculation
'
):
p
.
addRealValue
(
'
energy_total
'
,
c
(
r
.
Epot
,
'
hartree
'
))
p
.
addRealValue
(
'
energy_correction_entropy
'
,
c
(
r
.
S
,
'
hartree
'
))
if
'
CartesianForces
'
in
r
:
p
.
addArrayValues
(
'
atom_forces_free
'
,
c
(
r
.
CartesianForces
,
'
bohr/hartree
'
))
with
o
(
p
,
'
section_method
'
):
pass
#p.addValue('x_asap_electronic_structure_method', 'EMT')
p
.
finishedParsingSession
(
"
ParseSuccess
"
,
None
)
if
__name__
==
'
__main__
'
:
import
sys
filename
=
sys
.
argv
[
1
]
parse
(
filename
)
This diff is collapsed.
Click to expand it.
parser/parser-asap/setup_paths.py
0 → 100644
+
6
−
0
View file @
43404684
import
sys
,
os
,
os
.
path
baseDir
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
commonDir
=
os
.
path
.
normpath
(
os
.
path
.
join
(
baseDir
,
"
../../../../python-common/common/python
"
))
if
not
commonDir
in
sys
.
path
:
sys
.
path
.
insert
(
0
,
commonDir
)
This diff is collapsed.
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