Commit 3329918a authored by Joseph Rudzinski's avatar Joseph Rudzinski
Browse files

new metainfo for rdf/msd

parent d69eafdc
Pipeline #128560 passed with stages
in 30 minutes and 53 seconds
Subproject commit 7be55968fbf45e8e49377b58e745548c55c06788 Subproject commit 19b39e214ee17112cbc0537e38184e8056b20b32
...@@ -1331,12 +1331,51 @@ class MolecularDynamics(MSection): ...@@ -1331,12 +1331,51 @@ class MolecularDynamics(MSection):
Indicates if calculation contains thermodynamic data. Indicates if calculation contains thermodynamic data.
''') ''')
ensemble_properties = SubSection(sub_section=SectionProxy('EnsembleProperties'), repeats=False) radial_distribution_functions = SubSection(sub_section=SectionProxy('Rdf'), repeats=True)
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) m_def = Section(validate=False)
...@@ -1348,11 +1387,19 @@ class EnsembleProperties(MSection): ...@@ -1348,11 +1387,19 @@ class EnsembleProperties(MSection):
Label of the observable. Label of the observable.
''') ''')
types = Quantity( n_smooth = Quantity(
type=np.dtype(str), type=int,
shape=[], shape=[],
description=''' 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( variables_name = Quantity(
...@@ -1362,27 +1409,145 @@ class EnsembleProperties(MSection): ...@@ -1362,27 +1409,145 @@ class EnsembleProperties(MSection):
Name/description of the independent variables along which the observable is defined. 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( 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), type=np.dtype(np.float64),
shape=[], shape=[],
description=''' description='''
Bins along which the observable is calculated (i.e., values of the variables). Bins along which the observable is calculated (i.e., values of the variables).
''') ''')
values = Quantity( value = Quantity(
type=np.dtype(np.float64), type=np.dtype(np.float64),
shape=[], shape=[],
description=''' description='''
Values of the observables. 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=[], shape=[],
description=''' 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): class SinglePoint(MSection):
''' '''
......
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