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nomad-lab
parser-openkim
Commits
5dadf385
Commit
5dadf385
authored
Sep 25, 2018
by
Berk Onat
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Initial commit of OpenKIM parser in nomad-lab
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LICENSE
LICENSE
+21
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README.md
README.md
+35
-0
parser/parser-openkim/openkim_tool.py
parser/parser-openkim/openkim_tool.py
+139
-0
parser/parser-openkim/parser_openkim.py
parser/parser-openkim/parser_openkim.py
+350
-0
parser/parser-openkim/setup_paths.py
parser/parser-openkim/setup_paths.py
+12
-0
src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala
src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala
+43
-0
src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala
src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala
+14
-0
test/examples/README.md
test/examples/README.md
+6
-0
test/examples/data.json
test/examples/data.json
+0
-0
No files found.
LICENSE
0 → 100644
View file @
5dadf385
MIT License
Copyright (c) 2018 Berk Onat
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
README.md
0 → 100644
View file @
5dadf385
# OpenKIM Parser
[
NOMAD Laboratory CoE
](
http://nomad-coe.eu
)
parser for
[
OpenKIM
](
https://openkim.org
)
## Version 0.0.1
This is the parser for OpenKIM queries at
[
OpenKIM
](
https://openkim.org
)
.
The official version lives at:
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-openkim.git
You can browse it at:
https://gitlab.rzg.mpg.de/nomad-lab/parser-openkim
It relies on having the nomad-meta-info and the python-common repositories one level higher.
The simplest way to have this is to check out nomad-lab-base recursively:
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
This parser will be in the directory parsers/openkim of this repository.
## Running and Testing the Parser
### Requirements
The required python packages can be installed with (see
[
python-common
](
https://gitlab.rzg.mpg.de/nomad-lab/python-common
)
):
pip install -r nomad-lab-base/python-common/requirements.txt
### Usage
The query output of OpenKIM simulation results can be parsed with:
python parser-openkim.py test_nomad_id openkim_query_data.json
### Test Files
Example log output files of OpenKIM query can be found in the directory test/examples.
More details about the calculations and files are explained in README file of test/examples.
parser/parser-openkim/openkim_tool.py
0 → 100644
View file @
5dadf385
import
requests
from
requests.exceptions
import
Timeout
,
TooManyRedirects
,
RequestException
,
HTTPError
from
datetime
import
datetime
import
re
import
sys
import
numpy
as
np
import
json
from
tinydb
import
TinyDB
,
Query
dbasefile
=
"openkim_query_database.json"
kimdb
=
TinyDB
(
dbasefile
)
atomlabel
=
'Al'
structure
=
'fcc'
#nomad_space_group_map={
# 'sc' : '221',
# "fcc" : '225',
# 'bcc' : '229',
# 'diamond': '227'
#}
def
secondsFromEpoch
(
date
):
epoch
=
datetime
(
1970
,
1
,
1
)
ts
=
date
-
epoch
return
ts
.
seconds
+
ts
.
microseconds
/
1000.0
def
get_timestep
(
kim_date
):
pdate
=
None
if
kim_date
:
pdate
=
datetime
.
strptime
(
kim_date
.
strip
(),
"%Y-%m-%d %H:%M:%S.%f"
)
if
pdate
:
pdate
=
secondsFromEpoch
(
pdate
)
return
pdate
def
OPENKIM_query
(
atomlabel
,
structure
,
properties
=
None
):
"""
atomlabel:
----------
string : element symbol
structure:
----------
string : fcc, bcc, sc, diamond
properties:
-----------
string : lattice_energy, elastic_constants
returns:
--------
dictionary of OpenKIM entry
"""
openkim_query
=
None
try
:
query
=
requests
.
post
(
url
=
"https://query.openkim.org/api"
,
data
=
{
'flat'
:
'on'
,
'database'
:
'data'
,
'limit'
:
'0'
,
'fields'
:
json
.
dumps
({
#"a.si-value": "1",
#"cohesive-potential-energy.si-value" : "1",
#"meta.subject.kimcode": "1"
}),
'query'
:
json
.
dumps
({
"meta.type"
:
"tr"
,
#"property-id" : {
# "$regex" : ":property/structure-cubic-crystal-npt"
#},
#"meta.runner.kimcode" : {
# "$regex" : "^LatticeConstantCubicEnergy"
#},
#"species.source-value": {
# "$all" : [atomlabel],
# "$not" : {
# "$elemMatch" : {
# "$nin" : [atomlabel]
# }
# }
# },
"short-name.source-value"
:
structure
})
}
)
query
.
raise_for_status
()
openkim_query
=
query
.
json
()
except
(
ConnectionError
,
HTTPError
,
Timeout
,
TooManyRedirects
,
RequestException
):
print
(
"OpenKIM request exception: %s"
%
sys
.
exc_info
()[
1
])
return
openkim_query
openkim_data
=
OPENKIM_query
(
atomlabel
,
structure
)
if
openkim_data
:
now
=
datetime
.
today
().
strftime
(
"%Y-%m-%d %H:%M:%S.%f"
)
updated_data
=
[]
kim_item
=
Query
()
for
item
in
openkim_data
:
kim_instance_id
=
item
[
"instance-id"
]
kim_unique_code
=
item
[
"meta._id"
]
kim_result_code
=
item
[
"meta.test-result-id"
]
kim_unique_code
=
kim_unique_code
+
'-'
+
str
(
kim_instance_id
)
kim_result_code
=
kim_result_code
+
'-'
+
str
(
kim_instance_id
)
kim_create_date
=
get_timestep
(
item
[
"meta.created_on"
])
kim_insert_date
=
get_timestep
(
item
[
"inserted_on"
])
db_entry
=
kimdb
.
search
((
kim_item
.
unique_id
==
kim_unique_code
and
kim_item
.
result_id
==
kim_result_code
))
if
db_entry
:
if
db_entry
[
0
][
"insert_timestep"
]
<
kim_insert_date
:
kimdb
.
update
({
'insert_timestep'
:
kim_insert_date
,
},
(
kim_item
.
unique_id
==
kim_unique_code
and
kim_item
.
result_id
==
kim_result_code
))
updated_data
.
append
(
item
)
else
:
kimdb
.
insert
({
'unique_id'
:
kim_unique_code
,
'result_id'
:
kim_unique_code
,
'insert_timestep'
:
kim_insert_date
,
})
updated_data
.
append
(
item
)
if
updated_data
:
openkim_query
=
{}
openkim_query
[
'OPENKIM_QUERY_OUTPUT'
]
=
'OPENKIM_QUERY_OUTPUT'
openkim_query
[
'QUERY'
]
=
updated_data
with
open
(
'data.json'
,
'w'
)
as
outfile
:
json
.
dump
(
openkim_query
,
outfile
,
sort_keys
=
True
,
indent
=
4
,
ensure_ascii
=
True
)
with
open
(
'data.json'
,
'r'
)
as
databfile
:
qdata
=
json
.
load
(
databfile
)
parser/parser-openkim/parser_openkim.py
0 → 100644
View file @
5dadf385
# coding=utf-8
from
__future__
import
division
from
builtins
import
map
from
builtins
import
range
from
builtins
import
object
import
logging
,
sys
,
bisect
import
setup_paths
from
datetime
import
datetime
import
os
,
logging
,
re
,
traceback
from
nomadcore.parser_backend
import
JsonParseEventsWriterBackend
from
nomadcore.local_meta_info
import
loadJsonFile
,
InfoKindEl
import
numpy
as
np
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit_function
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
import
ase.geometry
import
ase.data
import
ase.build
import
json
from
ase
import
Atoms
from
ase.data
import
atomic_numbers
,
chemical_symbols
from
math
import
pi
from
contextlib
import
contextmanager
@
contextmanager
def
open_section
(
parser
,
backend
,
name
):
parser
.
gidSections
[
name
]
=
backend
.
openSection
(
name
)
yield
parser
.
gidSections
[
name
]
backend
.
closeSection
(
name
,
parser
.
gidSections
[
name
])
def
metaNameConverter
(
keyName
):
newName
=
keyName
.
lower
().
replace
(
" "
,
""
).
replace
(
"-"
,
""
)
newName
=
newName
.
replace
(
"("
,
""
).
replace
(
")"
,
""
)
newName
=
newName
.
replace
(
"["
,
""
).
replace
(
"]"
,
""
)
newName
=
newName
.
replace
(
","
,
""
).
replace
(
"."
,
""
)
newName
=
newName
.
replace
(
"
\\
"
,
""
).
replace
(
"/"
,
""
)
newName
=
newName
.
replace
(
"'"
,
""
).
replace
(
":"
,
""
)
return
newName
def
metaNameConverter_UnderscoreAll
(
keyName
):
newName
=
keyName
.
lower
()
newName
=
' '
.
join
(
newName
.
split
())
newName
=
newName
.
replace
(
" "
,
"_"
).
replace
(
"-"
,
"_"
).
replace
(
"."
,
"_"
)
newName
=
metaNameConverter
(
newName
)
return
newName
def
metaNameConverter_OpenKIM
(
keyName
):
newName
=
metaNameConverter_UnderscoreAll
(
keyName
)
newName
=
'x_openkim_'
+
newName
return
newName
def
secondsFromEpoch
(
date
):
epoch
=
datetime
(
1970
,
1
,
1
)
ts
=
date
-
epoch
return
ts
.
seconds
+
ts
.
microseconds
/
1000.0
def
KIMQueryReader
(
jsonfile
):
with
open
(
jsonfile
,
'r'
)
as
dbfile
:
data
=
json
.
load
(
dbfile
)
return
data
[
'QUERY'
]
class
OpenkimContext
(
object
):
def
__init__
(
self
):
self
.
parser
=
None
self
.
weights
=
None
self
.
lastSystemDescription
=
None
self
.
labels
=
None
self
.
singleConfCalcs
=
[]
self
.
KIM_TE
=
0
self
.
KIM_TD
=
None
self
.
KIM_MO
=
None
self
.
KIM_MD
=
None
self
.
cell
=
None
self
.
temperature
=
[]
self
.
cohesivepot
=
[]
self
.
cohesiveeng
=
[]
def
reset
(
self
):
self
.
lastSystemDescription
=
None
self
.
labels
=
None
self
.
singleConfCalcs
=
[]
self
.
KIM_TE
=
0
self
.
KIM_TD
=
None
self
.
KIM_MO
=
None
self
.
KIM_MD
=
None
self
.
cell
=
None
self
.
temperature
=
[]
self
.
cohesivepot
=
[]
self
.
cohesiveeng
=
[]
def
startedParsing
(
self
,
parser
):
self
.
parser
=
parser
def
onEnd_program
(
self
,
parser
,
querydict
):
backend
=
parser
.
backend
backend
.
addValue
(
"program_name"
,
"OpenKIM"
)
backend
.
addValue
(
"program_version"
,
g
(
querydict
,
"meta.runner.short-id"
,
""
))
date
=
g
(
querydict
,
"meta.created_on"
)
pdate
=
None
if
date
:
pdate
=
datetime
.
strptime
(
date
.
strip
(),
"%Y-%m-%d %H:%M:%S.%f"
)
if
pdate
:
backend
.
addValue
(
"program_compilation_datetime"
,
secondsFromEpoch
(
pdate
))
def
onEnd_openkim_data
(
self
,
parser
,
kimquery
):
for
k
,
v
in
kimquery
.
items
():
nomad_k
=
metaNameConverter_OpenKIM
(
k
)
if
isinstance
(
v
,
(
list
,
tuple
)):
dictInList
=
False
if
len
(
v
)
>
0
:
if
isinstance
(
v
[
0
],
dict
):
dictInList
=
True
if
dictInList
:
for
it
,
item
in
enumerate
(
v
):
if
isinstance
(
item
,
dict
):
#keyFooter = '_' + str(it+1)
for
key
,
val
in
item
.
items
():
#key = nomad_k + '_' + key + keyFooter
key
=
nomad_k
+
'_'
+
key
if
isinstance
(
val
,
list
):
backend
.
addArrayValues
(
key
,
np
.
asarray
(
val
))
else
:
backend
.
addValue
(
key
,
val
)
else
:
backend
.
addArrayValues
(
nomad_k
,
np
.
asarray
(
v
))
elif
isinstance
(
v
,
dict
):
for
key
,
val
in
item
.
items
():
key
=
nomad_k
+
'_'
+
key
if
isinstance
(
val
,
list
):
backend
.
addArrayValues
(
key
,
np
.
asarray
(
val
))
else
:
backend
.
addValue
(
key
,
val
)
else
:
backend
.
addValue
(
nomad_k
,
v
)
def
onEnd_structure
(
self
,
parser
,
querydict
,
step
=
0
):
backend
=
parser
.
backend
self
.
lastSystemDescription
=
parser
.
gidSections
[
"section_system"
]
self
.
cell
=
None
self
.
labels
=
None
celltype
=
None
if
(
'basis-atom-coordinates.source-value'
in
querydict
and
(
'a.si-value'
in
querydict
)
or
(
'b.si-value'
in
querydict
)
or
(
'c.si-value'
in
querydict
)
or
(
'a-host.si-value'
in
querydict
)
or
(
'b-host.si-value'
in
querydict
)
or
(
'c-host.si-value'
in
querydict
)):
basis
=
querydict
[
'basis-atom-coordinates.source-value'
]
#celltype = ase.geometry.crystal_structure_from_cell(basis)
if
not
celltype
:
kimprefix
=
g
(
querydict
,
'meta.runner.kimid-prefix'
,
None
).
split
(
'_'
)
celltype
=
kimprefix
[
1
]
if
len
(
kimprefix
)
>
1
else
None
if
not
celltype
:
kimprefix
=
g
(
querydict
,
'meta.runner.extended-id'
,
None
).
split
(
'_'
)
celltype
=
kimprefix
[
1
]
if
len
(
kimprefix
)
>
1
else
None
if
celltype
:
backend
.
addValue
(
"x_openkim_cubic_crystal_type"
,
celltype
)
if
'species.source-value'
in
querydict
:
self
.
labels
=
querydict
[
'species.source-value'
]
species_nums
=
[
atomic_numbers
[
Z
]
for
Z
in
self
.
labels
]
a_si_val
=
querydict
[
'a.si-value'
]
if
isinstance
(
a_si_val
,
list
):
lat_a
=
float
(
a_si_val
[
int
(
step
)])
else
:
lat_a
=
float
(
a_si_val
)
si_conv
=
convert_unit_function
(
"m"
,
"angstrom"
)
cellAtoms
=
Atoms
(
positions
=
basis
,
cell
=
[
si_conv
(
lat_a
),
si_conv
(
lat_a
),
si_conv
(
lat_a
)],
pbc
=
True
)
cellAtoms
.
positions
=
ase
.
geometry
.
wrap_positions
(
cellAtoms
.
positions
,
cellAtoms
.
cell
,
pbc
=
True
)
if
len
(
cellAtoms
.
numbers
)
==
len
(
species_nums
):
cellAtoms
.
numbers
=
species_nums
else
:
if
len
(
species_nums
)
<
2
and
len
(
cellAtoms
.
numbers
)
>
1
:
cellAtoms
.
numbers
=
[
species_nums
[
0
]
for
i
in
cellAtoms
.
numbers
]
if
len
(
self
.
labels
)
<
2
:
self
.
labels
=
[
self
.
labels
[
0
]
for
s
in
cellAtoms
.
positions
]
ang_conv
=
convert_unit_function
(
"angstrom"
,
"m"
)
si_cell
=
np
.
array
([[
ang_conv
(
x
)
for
x
in
i
]
for
i
in
cellAtoms
.
cell
])
si_pos
=
np
.
array
([[
ang_conv
(
x
)
for
x
in
i
]
for
i
in
cellAtoms
.
positions
])
backend
.
addArrayValues
(
"simulation_cell"
,
si_cell
)
backend
.
addArrayValues
(
"configuration_periodic_dimensions"
,
np
.
ones
(
3
,
dtype
=
bool
))
backend
.
addArrayValues
(
"atom_positions"
,
si_pos
)
if
self
.
labels
is
not
None
:
backend
.
addArrayValues
(
"atom_labels"
,
np
.
asarray
(
self
.
labels
))
def
onEnd_model
(
self
,
parser
,
kimquery
):
backend
=
parser
.
backend
with
open_section
(
parser
,
backend
,
"section_sampling_method"
):
if
self
.
KIM_TE
==
0
:
sampling_method
=
"geometry_optimization"
else
:
sampling_method
=
"molecular_dynamics"
backend
.
addValue
(
"sampling_method"
,
sampling_method
)
with
open_section
(
parser
,
backend
,
"section_frame_sequence"
):
if
self
.
temperature
:
backend
.
addArrayValues
(
'frame_sequence_temperature_frames'
,
np
.
array
([
i
for
i
in
self
.
singleConfCalcs
]))
if
isinstance
(
self
.
temperature
,
list
):
if
len
(
self
.
temperature
)
<
2
:
backend
.
addArrayValues
(
'frame_sequence_temperature'
,
np
.
array
([
self
.
temperature
[
0
]
for
i
in
self
.
singleConfCalcs
]))
else
:
backend
.
addArrayValues
(
'frame_sequence_temperature'
,
np
.
asarray
(
self
.
temperature
))
else
:
backend
.
addArrayValues
(
'frame_sequence_temperature'
,
np
.
asarray
([
self
.
temperature
]))
if
self
.
cohesivepot
:
backend
.
addArrayValues
(
'frame_sequence_potential_energy_frames'
,
np
.
array
([
i
for
i
in
self
.
singleConfCalcs
]))
if
isinstance
(
self
.
cohesivepot
,
list
):
if
len
(
self
.
cohesivepot
)
<
2
:
backend
.
addArrayValues
(
'frame_sequence_potential_energy'
,
np
.
array
([
self
.
cohesivepot
[
0
]
for
i
in
self
.
singleConfCalcs
]))
else
:
backend
.
addArrayValues
(
'frame_sequence_potential_energy'
,
np
.
asarray
(
self
.
cohesivepot
))
else
:
backend
.
addArrayValues
(
'frame_sequence_potential_energy'
,
np
.
asarray
([
self
.
cohesivepot
]))
if
self
.
cohesiveeng
:
backend
.
addArrayValues
(
'x_openkim_frame_sequence_cohesive_energy_frames'
,
np
.
array
([
i
for
i
in
self
.
singleConfCalcs
]))
if
isinstance
(
self
.
cohesiveeng
,
list
):
if
len
(
self
.
cohesiveeng
)
<
2
:
backend
.
addArrayValues
(
'x_openkim_frame_sequence_cohesive_energy'
,
np
.
array
([
self
.
cohesiveeng
for
i
in
self
.
singleConfCalcs
]))
else
:
backend
.
addArrayValues
(
'x_openkim_frame_sequence_cohesive_energy'
,
np
.
asarray
(
self
.
cohesiveeng
))
else
:
backend
.
addArrayValues
(
'x_openkim_frame_sequence_cohesive_energy'
,
np
.
asarray
([
self
.
cohesiveeng
]))
backend
.
addArrayValues
(
'frame_sequence_time'
,
np
.
array
([
0.
for
i
in
self
.
singleConfCalcs
]))
backend
.
addValue
(
"frame_sequence_to_sampling_ref"
,
parser
.
gidSections
[
"section_sampling_method"
])
backend
.
addArrayValues
(
"frame_sequence_local_frames_ref"
,
np
.
asarray
(
self
.
singleConfCalcs
))
def
onEnd_calculation
(
self
,
parser
,
kimquery
,
step
=
0
):
backend
=
parser
.
backend
backend
.
addValue
(
"single_configuration_calculation_to_system_ref"
,
self
.
lastSystemDescription
)
zeroTemp
=
None
if
'temperature.si-value'
in
kimquery
:
self
.
temperature
=
kimquery
[
'temperature.si-value'
]
if
'cohesive-potential-energy.si-value'
in
kimquery
:
self
.
cohesivepot
=
kimquery
[
'cohesive-potential-energy.si-value'
]
if
self
.
temperature
:
if
not
isinstance
(
self
.
temperature
,
list
):
if
float
(
self
.
temperature
)
>
0
:
zeroTemp
=
False
else
:
zeroTemp
=
True
if
isinstance
(
self
.
cohesivepot
,
list
):
backend
.
addValue
(
"energy_total"
,
float
(
self
.
cohesivepot
[
int
(
step
)]))
backend
.
addValue
(
"energy_potential"
,
float
(
self
.
cohesivepot
[
int
(
step
)]))
if
zeroTemp
:
backend
.
addValue
(
"energy_total_T0"
,
float
(
self
.
cohesivepot
[
int
(
step
)]))
else
:
backend
.
addValue
(
"energy_total"
,
float
(
self
.
cohesivepot
))
backend
.
addValue
(
"energy_potential"
,
float
(
self
.
cohesivepot
))
if
zeroTemp
:
backend
.
addValue
(
"energy_total_T0"
,
float
(
self
.
cohesivepot
))
if
'cauchy-stress.si-value'
in
kimquery
:
cstress
=
kimquery
[
'cauchy-stress.si-value'
]
f
=
np
.
zeros
((
3
,
3
))
f
[
0
][
0
]
=
float
(
cstress
[
0
])
f
[
1
][
1
]
=
float
(
cstress
[
1
])
f
[
2
][
2
]
=
float
(
cstress
[
2
])
f
[
1
][
2
]
=
float
(
cstress
[
3
])
f
[
0
][
2
]
=
float
(
cstress
[
4
])
f
[
0
][
1
]
=
float
(
cstress
[
5
])
backend
.
addArrayValues
(
"stress_tensor"
,
np
.
asarray
(
f
))
class
KIMParser
(
object
):
@
staticmethod
def
maybeGet
(
el
,
meta
,
default
=
None
):
if
meta
in
el
:
return
el
[
meta
]
else
:
return
default
def
__init__
(
self
,
parserInfo
,
superContext
):
self
.
fIn
=
None
self
.
parserInfo
=
parserInfo
self
.
superContext
=
superContext
self
.
gidSections
=
{}
def
parse
(
self
,
mainFileUri
,
fIn
,
backend
):
self
.
mainFileUri
=
mainFileUri
self
.
fIn
=
fIn
self
.
backend
=
backend
backend
.
startedParsingSession
(
mainFileUri
=
mainFileUri
,
parserInfo
=
self
.
parserInfo
)
self
.
superContext
.
startedParsing
(
self
)
QueryList
=
KIMQueryReader
(
self
.
fIn
)
try
:
for
qi
,
qdict
in
enumerate
(
QueryList
):
superContext
.
reset
()
with
open_section
(
self
,
backend
,
'section_run'
):
superContext
.
onEnd_program
(
self
,
qdict
)
with
open_section
(
self
,
backend
,
'x_openkim_section_metadata'
):
superContext
.
onEnd_openkim_data
(
self
,
qdict
)
if
'a.si-value'
in
qdict
or
'a-host.si-value'
in
qdict
:
if
isinstance
(
qdict
[
'a.si-value'
],
list
):
for
step
in
qdict
[
'a.si-value'
]:
with
open_section
(
self
,
backend
,
'section_single_configuration_calculation'
):
superContext
.
singleConfCalcs
.
append
(
self
.
gidSections
[
"section_single_configuration_calculation"
])
with
open_section
(
self
,
backend
,
'section_system'
):
superContext
.
onEnd_structure
(
self
,
qdict
,
step
)
superContext
.
onEnd_calculation
(
self
,
qdict
,
step
)
else
:
with
open_section
(
self
,
backend
,
'section_single_configuration_calculation'
):
superContext
.
singleConfCalcs
.
append
(
self
.
gidSections
[
"section_single_configuration_calculation"
])
with
open_section
(
self
,
backend
,
'section_system'
):
superContext
.
onEnd_structure
(
self
,
qdict
)
superContext
.
onEnd_calculation
(
self
,
qdict
)
superContext
.
onEnd_model
(
self
,
qdict
)
except
:
logging
.
exception
(
"failure when parsing %s"
,
self
.
mainFileUri
)
backend
.
finishedParsingSession
(
parserStatus
=
"ParseFailure"
,
parserErrors
=
[
"exception: %s"
%
sys
.
exc_info
()[
1
]]
)
else
:
backend
.
finishedParsingSession
(
parserStatus
=
"ParseSuccess"
,
parserErrors
=
None
)
g
=
KIMParser
.
maybeGet
parserInfo
=
{
"name"
:
"parser_openkim"
,
"version"
:
"1.0"
}
if
__name__
==
"__main__"
:
"""
This code is modified from parser-vasprun to work for OpenKIM
"""
metaInfoPath
=
os
.
path
.
normpath
(
os
.
path
.
join
(
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
)),
"../../../../nomad-meta-info/meta_info/nomad_meta_info/openkim.nomadmetainfo.json"
))
metaInfoEnv
,
warnings
=
loadJsonFile
(
filePath
=
metaInfoPath
,
dependencyLoader
=
None
,
extraArgsHandling
=
InfoKindEl
.
ADD_EXTRA_ARGS
,
uri
=
None
)
superContext
=
OpenkimContext
()
parser
=
KIMParser
(
parserInfo
,
superContext
)
backend
=
JsonParseEventsWriterBackend
(
metaInfoEnv
,
sys
.
stdout
)
parser
.
parse
(
sys
.
argv
[
1
],
sys
.
argv
[
2
],
backend
)
parser/parser-openkim/setup_paths.py
0 → 100644
View file @
5dadf385
import
sys
import
os
import
os.path
basedir
=
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
))
commondir
=
os
.
path
.
normpath
(
os
.
path
.
join
(
basedir
,
"../../../../python-common/common/python"
))
parserdir
=
os
.
path
.
normpath
(
os
.
path
.
join
(
basedir
,
".."
))
if
commondir
not
in
sys
.
path
:
sys
.
path
.
insert
(
1
,
commondir
)
if
parserdir
not
in
sys
.
path
:
sys
.
path
.
insert
(
1
,
parserdir
)
src/main/scala/eu/nomad_lab/parsers/OpenkimParser.scala
0 → 100644
View file @
5dadf385
package
eu.nomad_lab.parsers
import
eu.nomad_lab
import
eu.nomad_lab.DefaultPythonInterpreter
import
org.
{
json4s
=>
jn
}
import
eu.
{
nomad_lab
=>
lab
}
import
scala.collection.breakOut
object
OpenkimParser
extends
SimpleExternalParserGenerator
(
name
=
"OpenkimParser"
,
parserInfo
=
jn
.
JObject
(
(
"name"
->
jn
.
JString
(
"OpenkimParser"
))
::
(
"parserId"
->
jn
.
JString
(
"OpenkimParser"
+
lab
.
OpenkimVersionInfo
.
version
))
::
(
"versionInfo"
->
jn
.
JObject
(
(
"nomadCoreVersion"
->
jn
.
JObject
(
lab
.
NomadCoreVersionInfo
.
toMap
.
map
{
case
(
k
,
v
)
=>
k
->
jn
.
JString
(
v
.
toString
)
}(
breakOut
)
:
List
[(
String
,
jn.JString
)]))
::
(
lab
.
OpenkimVersionInfo
.
toMap
.
map
{
case
(
key
,
value
)
=>
(
key
->
jn
.
JString
(
value
.
toString
))
}(
breakOut
)
:
List
[(
String
,
jn.JString
)])
))
::
Nil
),
mainFileTypes
=
Seq
(
"text/.*"
),
mainFileRe
=
"""\s*OPENKIM_QUERY_OUTPUT\s*"""
.
r
,
cmd
=
Seq
(
DefaultPythonInterpreter
.
pythonExe
(),
"${envDir}/parsers/openkim/parser/parser-openkim/parser-openkim.py"
,
"${mainFilePath}"
,
"${mainFilePath}/data.json"
),
resList
=
Seq
(
"parser-openkim/parser-openkim.py"
,
"parser-openkim/setup_paths.py"
,
"nomad_meta_info/public.nomadmetainfo.json"
,
"nomad_meta_info/common.nomadmetainfo.json"
,
"nomad_meta_info/meta_types.nomadmetainfo.json"
,
"nomad_meta_info/openkim.nomadmetainfo.json"
)
++
DefaultPythonInterpreter
.
commonFiles
(),
dirMap
=
Map
(
"parser-openkim"
->
"parsers/openkim/parser/parser-openkim"
,
"nomad_meta_info"
->
"nomad-meta-info/meta_info/nomad_meta_info"
,
"python"
->
"python-common/common/python/nomadcore"
)
++
DefaultPythonInterpreter
.
commonDirMapping
(),
metaInfoEnv
=
Some
(
lab
.
meta
.
KnownMetaInfoEnvs
.
openkim
)
)
src/test/scala/eu/nomad_lab/parsers/OpenkimParserSpec.scala
0 → 100644
View file @
5dadf385
package
eu.nomad_lab.parsers
import
org.specs2.mutable.Specification
object
OpenkimParserTests
extends
Specification
{
"OpenkimParserTest"
>>
{
"[OpenKIM Query with 3767 entries] test with json-events"
>>
{
ParserRun
.
parse
(
OpenkimParser
,
"parsers/openkim/test/examples/data.json"