From dddddaa0f933d5a38b479ffdd90a95654e9df133 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Thu, 19 Mar 2020 12:23:10 +0100
Subject: [PATCH] Added metainfo python code.
---
elasticparser/metainfo/__init__.py | 13 ++
elasticparser/metainfo/elastic.py | 339 +++++++++++++++++++++++++++++
2 files changed, 352 insertions(+)
create mode 100644 elasticparser/metainfo/__init__.py
create mode 100644 elasticparser/metainfo/elastic.py
diff --git a/elasticparser/metainfo/__init__.py b/elasticparser/metainfo/__init__.py
new file mode 100644
index 0000000..98688be
--- /dev/null
+++ b/elasticparser/metainfo/__init__.py
@@ -0,0 +1,13 @@
+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import elasticparser.metainfo.elastic
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['elasticparser.metainfo.elastic'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package) # type: ignore
diff --git a/elasticparser/metainfo/elastic.py b/elasticparser/metainfo/elastic.py
new file mode 100644
index 0000000..1928e0c
--- /dev/null
+++ b/elasticparser/metainfo/elastic.py
@@ -0,0 +1,339 @@
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+ name='elastic_nomadmetainfo_json',
+ description='None',
+ a_legacy=LegacyDefinition(name='elastic.nomadmetainfo.json'))
+
+
+class x_elastic_section_strain_diagrams(MSection):
+ '''
+ section collecting the data of the strain diagrams
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_elastic_section_strain_diagrams'))
+
+ x_elastic_strain_diagram_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['x_elastic_number_of_deformations', 'x_elastic_strain_diagram_number_of_eta'],
+ description='''
+ Values of the energy(units:J)/d2E(units:Pa)/cross-validation (depending on the
+ value of x_elastic_strain_diagram_type)
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_values'))
+
+ x_elastic_strain_diagram_eta_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['x_elastic_number_of_deformations', 'x_elastic_strain_diagram_number_of_eta'],
+ description='''
+ eta values used the strain diagrams
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_eta_values'))
+
+ x_elastic_strain_diagram_number_of_eta = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of strain values used in the strain diagram
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_number_of_eta'))
+
+ x_elastic_strain_diagram_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of strain diagram. Possible values are: energy; cross-validation (cross-
+ validation error); d2E (second derivative of the energy wrt the strain)
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_type'))
+
+ x_elastic_strain_diagram_polynomial_fit_order = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Order of the polynomial fit
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_polynomial_fit_order'))
+
+
+class x_elastic_section_fitting_parameters(MSection):
+ '''
+ section collecting the fitting parameters used to calculate the elastic constants
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_elastic_section_fitting_parameters'))
+
+ x_elastic_fitting_parameters_eta = Quantity(
+ type=np.dtype(np.float64),
+ shape=['x_elastic_number_of_deformations'],
+ description='''
+ eta values used to calculate the elastic constants
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_fitting_parameters_eta'))
+
+ x_elastic_fitting_parameters_polynomial_order = Quantity(
+ type=np.dtype(np.int32),
+ shape=['x_elastic_number_of_deformations'],
+ description='''
+ polynomial order used to fit the Energy vs. volume curve and to calculate the
+ elastic constants
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_fitting_parameters_polynomial_order'))
+
+
+class section_method(public.section_method):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+ x_elastic_elastic_constant_order = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Order of the elastic constant
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_elastic_constant_order'))
+
+ x_elastic_number_of_deformations = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ number of deformed structures equally spaced in strain, which are generated
+ between the maximum negative strain and the maximum positive one
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_number_of_deformations'))
+
+ x_elastic_deformation_types = Quantity(
+ type=np.dtype('U'),
+ shape=['x_elastic_number_of_deformations', 6],
+ description='''
+ deformation types
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_deformation_types'))
+
+ x_elastic_calculation_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Method of calculation
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_calculation_method'))
+
+ x_elastic_code = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Code used for the calculation of the elastic constants
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_code'))
+
+ x_elastic_max_lagrangian_strain = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Maximum lagrangian strain used to calculate the elastic constants
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_max_lagrangian_strain'))
+
+ x_elastic_number_of_distorted_structures = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Number of distorted structures used to calculate the elastic constants
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_number_of_distorted_structures'))
+
+ x_elastic_section_fitting_parameters = SubSection(
+ sub_section=SectionProxy('x_elastic_section_fitting_parameters'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_elastic_section_fitting_parameters'))
+
+
+class section_single_configuration_calculation(public.section_single_configuration_calculation):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ x_elastic_2nd_order_constants_notation_matrix = Quantity(
+ type=np.dtype('U'),
+ shape=[6, 6],
+ description='''
+ Symmetry of the second-order elastic constant matrix in Voigt notation
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_2nd_order_constants_notation_matrix'))
+
+ x_elastic_2nd_order_constants_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=[6, 6],
+ unit='pascal',
+ description='''
+ 2nd order elastic constant (stiffness) matrix in GPa
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_2nd_order_constants_matrix'))
+
+ x_elastic_3rd_order_constants_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=[6, 6, 6],
+ unit='pascal',
+ description='''
+ 3rd order elastic constant (stiffness) matrix in GPa
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_3rd_order_constants_matrix'))
+
+ x_elastic_2nd_order_constants_compliance_matrix = Quantity(
+ type=np.dtype(np.float64),
+ shape=[6, 6],
+ unit='1 / pascal',
+ description='''
+ Elastic compliance matrix in 1/GPa
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_2nd_order_constants_compliance_matrix'))
+
+ x_elastic_Voigt_bulk_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Voigt bulk modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Voigt_bulk_modulus'))
+
+ x_elastic_Voigt_shear_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Voigt shear modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Voigt_shear_modulus'))
+
+ x_elastic_Reuss_bulk_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Reuss bulk modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Reuss_bulk_modulus'))
+
+ x_elastic_Reuss_shear_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Reuss shear modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Reuss_shear_modulus'))
+
+ x_elastic_Hill_bulk_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Hill bulk modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Hill_bulk_modulus'))
+
+ x_elastic_Hill_shear_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Hill shear modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Hill_shear_modulus'))
+
+ x_elastic_Voigt_Young_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Voigt Young modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Voigt_Young_modulus'))
+
+ x_elastic_Voigt_Poisson_ratio = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Voigt Poisson ratio
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Voigt_Poisson_ratio'))
+
+ x_elastic_Reuss_Young_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Reuss Young modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Reuss_Young_modulus'))
+
+ x_elastic_Reuss_Poisson_ratio = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Reuss Poisson ratio
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Reuss_Poisson_ratio'))
+
+ x_elastic_Hill_Young_modulus = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='pascal',
+ description='''
+ Hill Young modulus
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Hill_Young_modulus'))
+
+ x_elastic_Hill_Poisson_ratio = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Hill Poisson ratio
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_Hill_Poisson_ratio'))
+
+ x_elastic_eigenvalues = Quantity(
+ type=np.dtype(np.float64),
+ shape=[6],
+ unit='pascal',
+ description='''
+ Eigemvalues of the stiffness matrix
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_eigenvalues'))
+
+ x_elastic_section_strain_diagrams = SubSection(
+ sub_section=SectionProxy('x_elastic_section_strain_diagrams'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_elastic_section_strain_diagrams'))
+
+
+class section_system(public.section_system):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
+
+ x_elastic_space_group_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Space-group number of the system
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_space_group_number'))
+
+ x_elastic_unit_cell_volume = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Volume of the equilibrium unit cell
+ ''',
+ a_legacy=LegacyDefinition(name='x_elastic_unit_cell_volume'))
+
+
+m_package.__init_metainfo__()
--
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