Commit 5027c943 authored by Joseph Rudzinski's avatar Joseph Rudzinski
Browse files

fixes after Alvin's comments

parent 248373c2
Pipeline #128844 passed with stages
in 40 minutes and 54 seconds
Subproject commit 7636f7f192c347870c5587a72c819cf56dca1325
Subproject commit ef6209c60f3a4a92b5411f9bdef1dd7a326ed32c
......@@ -1331,9 +1331,9 @@ class MolecularDynamics(MSection):
Indicates if calculation contains thermodynamic data.
''')
radial_distribution_functions = SubSection(sub_section=SectionProxy('Rdf'), repeats=True)
radial_distribution_functions = SubSection(sub_section=SectionProxy('RadialDistributionFunction'), repeats=True)
mean_squared_displacements = SubSection(sub_section=SectionProxy('Msd'), repeats=True)
mean_squared_displacements = SubSection(sub_section=SectionProxy('MeanSquaredDisplacement'), repeats=True)
class EnsemblePropertyValues(MSection):
......@@ -1343,34 +1343,13 @@ class EnsemblePropertyValues(MSection):
m_def = Section(validate=False)
type = Quantity(
label = Quantity(
type=str,
shape=[],
description='''
Describes the atoms or molecule types involved in determining the property.
''')
bins = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Values of the variable/s along which the property was calculated.
''')
value = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Values of the property.
''')
error_value = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Error bars associated with the determination of the property.
''')
class EnsembleProperty(MSection):
'''
......@@ -1380,11 +1359,11 @@ class EnsembleProperty(MSection):
m_def = Section(validate=False)
label = Quantity(
type=str,
type = Quantity(
type=MEnum('Molecular', 'Atomic'),
shape=[],
description='''
Label of the observable.
Describes if the observable is calculated at the molecular or atomic level.
''')
n_smooth = Quantity(
......@@ -1402,15 +1381,22 @@ class EnsembleProperty(MSection):
Describes the type of error reported for this observable.
''')
n_variables = Quantity(
type=int,
shape=[],
description='''
Number of variables along which the property is determined.
''')
variables_name = Quantity(
type=np.dtype(str),
shape=[],
shape=['n_variables'],
description='''
Name/description of the independent variables along which the observable is defined.
''')
class RdfValues(EnsemblePropertyValues):
class RadialDistributionFunctionValues(EnsemblePropertyValues):
'''
Section containing information regarding the values of
radial distribution functions (rdfs).
......@@ -1418,16 +1404,30 @@ class RdfValues(EnsemblePropertyValues):
m_def = Section(validate=False)
n_bins = Quantity(
type=int,
shape=[],
description='''
Number of bins.
''')
bins = Quantity(
type=np.dtype(np.float64),
shape=[],
shape=['n_bins'],
unit='m',
description='''
Distances along which the rdf was calculated.
''')
value = Quantity(
type=np.dtype(np.float64),
shape=['n_bins'],
description='''
Values of the property.
''')
class Rdf(EnsembleProperty):
class RadialDistributionFunction(EnsembleProperty):
'''
Section containing information about the calculation of
radial distribution functions (rdfs).
......@@ -1435,7 +1435,7 @@ class Rdf(EnsembleProperty):
m_def = Section(validate=False)
rdf_values = SubSection(sub_section=RdfValues.m_def, repeats=True)
radial_distribution_function_values = SubSection(sub_section=RadialDistributionFunctionValues.m_def, repeats=True)
class CorrelationFunctionValues(MSection):
......@@ -1445,25 +1445,18 @@ class CorrelationFunctionValues(MSection):
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),
label = Quantity(
type=str,
shape=[],
description='''
Time windows used for the calculation of the correlation function.
Describes the atoms or molecule types involved in determining the property.
''')
value = Quantity(
type=np.dtype(np.float64),
n_times = Quantity(
type=int,
shape=[],
description='''
Values of the correlation function.
Number of times windows for the calculation of the correlation function.
''')
......@@ -1475,15 +1468,29 @@ class CorrelationFunction(MSection):
m_def = Section(validate=False)
label = Quantity(
type = Quantity(
type=MEnum('Molecular', 'Atomic'),
shape=[],
description='''
Describes if the correlation function is calculated at the molecular or atomic level.
''')
direction = Quantity(
type=MEnum('x', 'y', 'z', 'xy', 'yz', 'xz', 'xyz'),
shape=[],
description='''
Describes the direction in which the correlation function was calculated.
''')
error_type = Quantity(
type=str,
shape=[],
description='''
Label of the correlation function.
Describes the type of error reported for this correlation function.
''')
class DiffusionConstantValues(EnsemblePropertyValues):
class DiffusionConstantValues(MSection):
'''
Section containing information regarding the diffusion constants.
'''
......@@ -1505,16 +1512,15 @@ class DiffusionConstantValues(EnsemblePropertyValues):
Describes the type of error reported for this observable.
''')
error_value = Quantity(
errors = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='m^2/s',
shape=['*'],
description='''
Error associated with the determination of the diffusion constant.
''')
class MsdValues(CorrelationFunctionValues):
class MeanSquaredDisplacementValues(CorrelationFunctionValues):
'''
Section containing information regarding the values of a mean squared displacements (msds).
'''
......@@ -1523,7 +1529,7 @@ class MsdValues(CorrelationFunctionValues):
times = Quantity(
type=np.dtype(np.float64),
shape=[],
shape=['n_times'],
unit='s',
description='''
Time windows used for the calculation of the msds.
......@@ -1531,7 +1537,7 @@ class MsdValues(CorrelationFunctionValues):
value = Quantity(
type=np.dtype(np.float64),
shape=[],
shape=['n_times'],
unit='m^2',
description='''
Msd values.
......@@ -1540,14 +1546,14 @@ class MsdValues(CorrelationFunctionValues):
diffusion_constant = SubSection(sub_section=DiffusionConstantValues.m_def, repeats=False)
class Msd(CorrelationFunction):
class MeanSquaredDisplacement(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)
mean_squared_displacement_values = SubSection(sub_section=MeanSquaredDisplacementValues.m_def, repeats=True)
class SinglePoint(MSection):
......
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