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nomad-lab
nomad-FAIR
Commits
3329918a
Commit
3329918a
authored
Apr 04, 2022
by
Joseph Rudzinski
Browse files
new metainfo for rdf/msd
parent
d69eafdc
Pipeline
#128560
passed with stages
in 30 minutes and 53 seconds
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2
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Subproject commit
19b39e214ee17112cbc0537e38184e8056b20b32
nomad/datamodel/metainfo/workflow.py
View file @
3329918a
...
...
@@ -1331,12 +1331,51 @@ class MolecularDynamics(MSection):
Indicates if calculation contains thermodynamic data.
'''
)
ensemble_propertie
s
=
SubSection
(
sub_section
=
SectionProxy
(
'
EnsembleProperties
'
),
repeats
=
Fals
e
)
radial_distribution_function
s
=
SubSection
(
sub_section
=
SectionProxy
(
'
Rdf
'
),
repeats
=
Tru
e
)
mean_squared_displacements
=
SubSection
(
sub_section
=
SectionProxy
(
'Msd'
),
repeats
=
True
)
class
EnsembleProperties
(
MSection
):
class
EnsemblePropertyValues
(
MSection
):
'''
Describes any observable calculated from an ensemble average.
Generic section containing information regarding the values of an ensemble property.
'''
m_def
=
Section
(
validate
=
False
)
type
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Describes the atoms or molecule types involved in determining this property.
'''
)
bins
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Distances along which the rdf was calculated.
'''
)
value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Values of the rdf.
'''
)
error_value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Error bars associated with the determination of the ensemble property.
'''
)
class
EnsembleProperty
(
MSection
):
'''
Generic section containing information about a calculation of any static observable
from a trajectory (i.e., from an ensemble average).
'''
m_def
=
Section
(
validate
=
False
)
...
...
@@ -1348,11 +1387,19 @@ class EnsembleProperties(MSection):
Label of the observable.
'''
)
types
=
Quantity
(
type
=
np
.
dtype
(
str
)
,
n_smooth
=
Quantity
(
type
=
int
,
shape
=
[],
description
=
'''
List of types for multi-component functions.
Number of bins over which the running average was computed for
the observable `values'.
'''
)
error_type
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Describes the type of error reported for this observable.
'''
)
variables_name
=
Quantity
(
...
...
@@ -1362,27 +1409,145 @@ class EnsembleProperties(MSection):
Name/description of the independent variables along which the observable is defined.
'''
)
class
RdfValues
(
EnsemblePropertyValues
):
'''
Section containing information regarding the values of
radial distribution functions (rdfs).
'''
m_def
=
Section
(
validate
=
False
)
bins
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
units
=
'angstrom'
,
description
=
'''
Distances along which the rdf was calculated.
'''
)
class
Rdf
(
EnsembleProperty
):
'''
Section containing information about the calculation of
radial distribution functions (rdfs).
'''
m_def
=
Section
(
validate
=
False
)
rdf_values
=
SubSection
(
sub_section
=
RdfValues
.
m_def
,
repeats
=
True
)
class
CorrelationFunctionValues
(
MSection
):
'''
Generic section containing information regarding the values of a correlation function.
'''
m_def
=
Section
(
validate
=
False
)
type
=
Quantity
(
type
=
np
.
dtype
(
str
),
shape
=
[],
description
=
'''
List of types for multi-component functions.
'''
)
times
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Bins along which the observable is calculated (i.e., values of the variables).
'''
)
value
s
=
Quantity
(
value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Values of the observables.
'''
)
n_smooth
=
Quantity
(
type
=
int
,
class
CorrelationFunction
(
MSection
):
'''
Generic section containing information about a calculation of any time correlation
function from a trajectory.
'''
m_def
=
Section
(
validate
=
False
)
label
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Label of the observable.
'''
)
class
DiffusionConstantValues
(
EnsemblePropertyValues
):
'''
Section containing information regarding the diffusion constants.
'''
m_def
=
Section
(
validate
=
False
)
value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
units
=
'nanometer^2/picosecond'
,
description
=
'''
Values of the diffusion constants.
'''
)
error_type
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Describes the type of error reported for this observable.
'''
)
error_value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
units
=
'nanometer^2/picosecond'
,
description
=
'''
Error bars associated with the determination of the diffusion constant.
'''
)
class
MsdValues
(
MSection
):
'''
Section containing information regarding the values of a mean squared displacements (msds).
'''
m_def
=
Section
(
validate
=
False
)
times
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
units
=
'picosecond'
,
description
=
'''
Time windows used for the calculation of the msds.
'''
)
value
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Number of bins over which the running average was computed for `
values
'
.
Msd
values.
'''
)
diffusion_constant
=
SubSection
(
sub_section
=
DiffusionConstantValues
.
m_def
,
repeats
=
False
)
class
Msd
(
CorrelationFunction
):
'''
Section containing information about a calculation of any mean squared displacements (msds).
'''
m_def
=
Section
(
validate
=
False
)
msd_values
=
SubSection
(
sub_section
=
MsdValues
.
m_def
,
repeats
=
True
)
class
SinglePoint
(
MSection
):
'''
...
...
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