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nomad-lab
parser-amber
Commits
46558b8d
Commit
46558b8d
authored
Jul 21, 2017
by
Berk Onat
Browse files
Modifications for None and numpy passes at Dictionaries and MetaInfoStorage
parent
6f5cedbd
Changes
2
Hide whitespace changes
Inline
Side-by-side
parser/parser-amber/AMBERDictionary.py
View file @
46558b8d
...
...
@@ -1013,46 +1013,46 @@ def get_updateDictionary(self, defname):
value
=
self
.
minConverged
),
'number_of_conserved_quantity_evaluations_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_conserved_quantity_frames'
:
None
}
)[
'frame_sequence_conserved_quantity_frames'
]
]
)
)[
'frame_sequence_conserved_quantity_frames'
]
[
'val'
]
)
),
'number_of_frames_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_potential_energy_frames'
:
None
}
)[
'frame_sequence_potential_energy_frames'
]
]
)
)[
'frame_sequence_potential_energy_frames'
]
[
'val'
]
)
),
'number_of_kinetic_energies_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_kinetic_energy_frames'
:
None
}
)[
'frame_sequence_kinetic_energy_frames'
]
]
)
)[
'frame_sequence_kinetic_energy_frames'
]
[
'val'
]
)
),
'number_of_potential_energies_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_potential_energy_frames'
:
None
}
)[
'frame_sequence_potential_energy_frames'
]
]
)
)[
'frame_sequence_potential_energy_frames'
]
[
'val'
]
)
),
'number_of_pressure_evaluations_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_pressure_frames'
:
None
}
)[
'frame_sequence_pressure_frames'
]
]
)
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_pressure_frames'
:
None
}
)[
'frame_sequence_pressure_frames'
]
[
'val'
]
)
),
'number_of_temperatures_in_sequence'
:
MetaInfoMap
(
startpage
,
value
=
len
([
item
for
item
in
self
.
metaStorage
.
fetchAttr
(
value
=
(
lambda
x
:
np
.
array
(
x
).
flatten
().
shape
[
0
]
if
x
is
not
None
else
None
)(
self
.
metaStorage
.
fetchAttr
(
{
'frame_sequence_temperature_frames'
:
None
}
)[
'frame_sequence_temperature_frames'
]
]
)
)[
'frame_sequence_temperature_frames'
]
[
'val'
]
)
),
#'previous_sequence_ref' : MetaInfoMap(startpage)
}
...
...
parser/parser-amber/MetaInfoStorage.py
View file @
46558b8d
...
...
@@ -16,6 +16,8 @@ PUBLIC_META_INFO_PATH = os.path.normpath(os.path.join(
os
.
path
.
dirname
(
os
.
path
.
abspath
(
__file__
)),
"../../../../nomad-meta-info/meta_info/nomad_meta_info/public.nomadmetainfo.json"
))
NOTEXCEPT
=
re
.
compile
(
r
'[^a-cf-zA-CF-Z!\.?,]'
)
class
Container
(
object
):
"""The container class for nested data storage
"""
...
...
@@ -316,6 +318,7 @@ class Container(object):
newunit
=
newunit
.
replace
(
'-'
,
'*'
).
replace
(
' '
,
'*'
).
replace
(
'^'
,
"**"
)
for
key
,
value
in
unitdict
.
items
():
newunit
=
newunit
.
replace
(
str
(
key
),
str
(
value
))
NOTEXCEPT
.
sub
(
''
,
newunit
)
return
float
(
eval
(
newunit
))
def
checkTestsDicts
(
self
,
item
,
localdict
):
...
...
@@ -393,6 +396,8 @@ class Container(object):
backend
.
addArrayValues
(
itemk
,
value
)
elif
isinstance
(
value
,
(
list
,
tuple
)):
backend
.
addArrayValues
(
itemk
,
np
.
asarray
(
value
))
elif
value
is
None
:
pass
else
:
backend
.
addValue
(
itemk
,
value
)
...
...
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