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nomad-lab
parser-cp2k
Commits
dd17d5a3
Commit
dd17d5a3
authored
Jul 07, 2016
by
Lauri Himanen
Browse files
Fixed unit conversion error in scf onvergence criteria, + some refactoring.
parent
1794d649
Changes
6
Hide whitespace changes
Inline
Side-by-side
parser/parser-cp2k/cp2kparser/versions/cp2k262/common
match
er.py
→
parser/parser-cp2k/cp2kparser/versions/cp2k262/common
pars
er.py
View file @
dd17d5a3
...
@@ -6,20 +6,20 @@ import logging
...
@@ -6,20 +6,20 @@ import logging
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.simple_parser
import
SimpleMatcher
as
SM
from
nomadcore.caching_backend
import
CachingLevel
from
nomadcore.caching_backend
import
CachingLevel
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
from
nomadcore.unit_conversion.unit_conversion
import
convert_unit
from
nomadcore.baseclasses
import
Common
Match
er
from
nomadcore.baseclasses
import
Common
Pars
er
from
.inputparser
import
CP2KInputParser
from
.inputparser
import
CP2KInputParser
logger
=
logging
.
getLogger
(
"nomad"
)
logger
=
logging
.
getLogger
(
"nomad"
)
#===============================================================================
#===============================================================================
class
CP2KCommon
Match
er
(
Common
Match
er
):
class
CP2KCommon
Pars
er
(
Common
Pars
er
):
"""
"""
This class is used to store and instantiate common parts of the
This class is used to store and instantiate common parts of the
hierarchical SimpleMatcher structure used in the parsing of a CP2K
hierarchical SimpleMatcher structure used in the parsing of a CP2K
output file.
output file.
"""
"""
def
__init__
(
self
,
parser_context
):
def
__init__
(
self
,
parser_context
):
super
(
CP2KCommon
Match
er
,
self
).
__init__
(
parser_context
)
super
(
CP2KCommon
Pars
er
,
self
).
__init__
(
parser_context
)
self
.
section_method_index
=
None
self
.
section_method_index
=
None
self
.
section_system_index
=
None
self
.
section_system_index
=
None
self
.
test_electronic_structure_method
=
"DFT"
self
.
test_electronic_structure_method
=
"DFT"
...
@@ -285,7 +285,7 @@ class CP2KCommonMatcher(CommonMatcher):
...
@@ -285,7 +285,7 @@ class CP2KCommonMatcher(CommonMatcher):
SM
(
" max_scf:\s+(?P<scf_max_iteration>{})"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" max_scf:\s+(?P<scf_max_iteration>{})"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" max_scf_history:\s+{}"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" max_scf_history:\s+{}"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" max_diis:\s+{}"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" max_diis:\s+{}"
.
format
(
self
.
regexs
.
regex_i
)),
SM
(
" eps_scf:\s+(?P<scf_threshold_energy_change>{})"
.
format
(
self
.
regexs
.
regex_f
)),
SM
(
" eps_scf:\s+(?P<scf_threshold_energy_change
__hartree
>{})"
.
format
(
self
.
regexs
.
regex_f
)),
]
]
),
),
SM
(
" MP2\|"
,
SM
(
" MP2\|"
,
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
View file @
dd17d5a3
...
@@ -4,7 +4,7 @@ from builtins import next
...
@@ -4,7 +4,7 @@ from builtins import next
from
builtins
import
range
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
.common
match
er
import
CP2KCommon
Match
er
from
.common
pars
er
import
CP2KCommon
Pars
er
import
cp2kparser.generic.configurationreading
import
cp2kparser.generic.configurationreading
import
cp2kparser.generic.csvparsing
import
cp2kparser.generic.csvparsing
from
nomadcore.caching_backend
import
CachingLevel
from
nomadcore.caching_backend
import
CachingLevel
...
@@ -21,7 +21,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
...
@@ -21,7 +21,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
"""
"""
"""
"""
super
(
CP2KGeoOptParser
,
self
).
__init__
(
file_path
,
parser_context
)
super
(
CP2KGeoOptParser
,
self
).
__init__
(
file_path
,
parser_context
)
self
.
setup_common_matcher
(
CP2KCommon
Match
er
(
parser_context
))
self
.
setup_common_matcher
(
CP2KCommon
Pars
er
(
parser_context
))
self
.
traj_iterator
=
None
self
.
traj_iterator
=
None
self
.
energy_reeval_quickstep
=
None
self
.
energy_reeval_quickstep
=
None
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @
dd17d5a3
...
@@ -4,7 +4,7 @@ from builtins import range
...
@@ -4,7 +4,7 @@ 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
from
.common
match
er
import
CP2KCommon
Match
er
from
.common
pars
er
import
CP2KCommon
Pars
er
import
cp2kparser.generic.configurationreading
import
cp2kparser.generic.configurationreading
import
cp2kparser.generic.csvparsing
import
cp2kparser.generic.csvparsing
from
nomadcore.caching_backend
import
CachingLevel
from
nomadcore.caching_backend
import
CachingLevel
...
@@ -23,7 +23,7 @@ class CP2KMDParser(MainHierarchicalParser):
...
@@ -23,7 +23,7 @@ class CP2KMDParser(MainHierarchicalParser):
"""
"""
"""
"""
super
(
CP2KMDParser
,
self
).
__init__
(
file_path
,
parser_context
)
super
(
CP2KMDParser
,
self
).
__init__
(
file_path
,
parser_context
)
self
.
setup_common_matcher
(
CP2KCommon
Match
er
(
parser_context
))
self
.
setup_common_matcher
(
CP2KCommon
Pars
er
(
parser_context
))
self
.
traj_iterator
=
None
self
.
traj_iterator
=
None
self
.
vel_iterator
=
None
self
.
vel_iterator
=
None
self
.
energy_iterator
=
None
self
.
energy_iterator
=
None
...
...
parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
View file @
dd17d5a3
...
@@ -3,7 +3,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM
...
@@ -3,7 +3,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM
from
nomadcore.baseclasses
import
MainHierarchicalParser
from
nomadcore.baseclasses
import
MainHierarchicalParser
from
.singlepointforceparser
import
CP2KSinglePointForceParser
from
.singlepointforceparser
import
CP2KSinglePointForceParser
from
nomadcore.caching_backend
import
CachingLevel
from
nomadcore.caching_backend
import
CachingLevel
from
.common
match
er
import
CP2KCommon
Match
er
from
.common
pars
er
import
CP2KCommon
Pars
er
import
logging
import
logging
logger
=
logging
.
getLogger
(
"nomad"
)
logger
=
logging
.
getLogger
(
"nomad"
)
...
@@ -18,7 +18,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
...
@@ -18,7 +18,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
"""
"""
"""
"""
super
(
CP2KSinglePointParser
,
self
).
__init__
(
file_path
,
parser_context
)
super
(
CP2KSinglePointParser
,
self
).
__init__
(
file_path
,
parser_context
)
self
.
setup_common_matcher
(
CP2KCommon
Match
er
(
parser_context
))
self
.
setup_common_matcher
(
CP2KCommon
Pars
er
(
parser_context
))
#=======================================================================
#=======================================================================
# Cache levels
# Cache levels
...
...
src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala
View file @
dd17d5a3
...
@@ -49,7 +49,7 @@ object Cp2kParser extends SimpleExternalParserGenerator(
...
@@ -49,7 +49,7 @@ object Cp2kParser extends SimpleExternalParserGenerator(
"parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/common
match
er.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/common
pars
er.py"
,
"parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle"
,
"parser-cp2k/cp2kparser/versions/cp2k262/input_data/cp2k_input_tree.pickle"
,
"parser-cp2k/cp2kparser/scalainterface.py"
,
"parser-cp2k/cp2kparser/scalainterface.py"
,
"nomad_meta_info/public.nomadmetainfo.json"
,
"nomad_meta_info/public.nomadmetainfo.json"
,
...
...
test/unittests/cp2k_2.6.2/run_tests.py
View file @
dd17d5a3
...
@@ -295,7 +295,7 @@ class TestEnergyForce(unittest.TestCase):
...
@@ -295,7 +295,7 @@ class TestEnergyForce(unittest.TestCase):
def
test_scf_threshold_energy_change
(
self
):
def
test_scf_threshold_energy_change
(
self
):
result
=
self
.
results
[
"scf_threshold_energy_change"
]
result
=
self
.
results
[
"scf_threshold_energy_change"
]
self
.
assertEqual
(
result
,
1.00E-07
)
self
.
assertEqual
(
result
,
convert_unit
(
1.00E-07
,
"hartree"
)
)
def
test_number_of_spin_channels
(
self
):
def
test_number_of_spin_channels
(
self
):
result
=
self
.
results
[
"number_of_spin_channels"
]
result
=
self
.
results
[
"number_of_spin_channels"
]
...
...
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