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nomad-lab
parser-amber
Commits
8ab0c666
Commit
8ab0c666
authored
Jul 18, 2017
by
Berk Onat
Browse files
Corrected a typo in x_amber metainfo
parent
08d245f5
Changes
1
Hide whitespace changes
Inline
Side-by-side
parser/parser-amber/AMBERParser.py
View file @
8ab0c666
...
...
@@ -326,7 +326,7 @@ class AMBERParser(AmberC.AMBERParserBase):
# self.superP.addValue('interaction_kind', bondFunctional) # functional form of the interaction
# this points to the relative section_atom_type
self
.
superP
.
addArrayValues
(
'x_
l
am
mps
_interaction_atom_to_atom_type_ref'
,
self
.
superP
.
addArrayValues
(
'x_am
ber
_interaction_atom_to_atom_type_ref'
,
np
.
asarray
(
interTypeDict
[
elm
]))
# interaction parameters for the functional
#self.superP.addValue('interaction_parameters', bondParameters)
...
...
@@ -502,6 +502,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDict
=
{
'startSection'
:
[
[
'section_topology'
]],
'muteSections'
:
[[
'section_sampling_method'
]],
#'muteSections' : [['section_method']],
'dictionary'
:
section_topology_Dict
}
...
...
@@ -545,7 +546,8 @@ class AMBERParser(AmberC.AMBERParserBase):
self
.
trajRefSingleConfigurationCalculation
=
gIndex
SloppyBackend
.
addArrayValues
(
'atom_positions'
,
np
.
transpose
(
np
.
asarray
(
self
.
atompositions
[
0
])))
if
self
.
topology
is
not
None
:
#SloppyBackend.addArrayValues('atom_labels', np.asarray(atom_labels))
atom_labels
=
self
.
topologyDict
[
"element"
]
SloppyBackend
.
addArrayValues
(
'atom_labels'
,
np
.
asarray
(
atom_labels
))
pass
# Read the next step at trajectory in advance
...
...
@@ -604,7 +606,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateFrameDict
=
{
'startSection'
:
[
[
'section_frame_sequence'
]],
'muteSections'
:
[[
'section_method'
]],
'muteSections'
:
[[
'section_
sampling_
method'
]],
'dictionary'
:
section_frameseq_Dict
}
self
.
metaStorage
.
update
(
updateFrameDict
)
...
...
@@ -612,6 +614,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDictVDW
=
{
'startSection'
:
[
[
'section_energy_van_der_Waals'
]],
'muteSections'
:
[[
'section_sampling_method'
]],
#'muteSections' : [['section_method']],
'dictionary'
:
section_singlevdw_Dict
}
...
...
@@ -625,6 +628,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDict
=
{
'startSection'
:
[
[
'section_single_configuration_calculation'
]],
'muteSections'
:
[[
'section_sampling_method'
]],
#'muteSections' : [['section_method']],
'dictionary'
:
section_singlecalc_Dict
}
...
...
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