nomad-parser-plugins-workflow 1.0__py3-none-any.whl

workflowparsers/fhivibes/metainfo/fhi_vibes.py

@@ -0,0 +1,898 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+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,
+    JSON,
+)
+
+import runschema.run  # pylint: disable=unused-import
+import runschema.calculation  # pylint: disable=unused-import
+import runschema.method  # pylint: disable=unused-import
+import runschema.system  # pylint: disable=unused-import
+
+
+m_package = Package()
+
+
+class x_fhi_vibes_method(MCategory):
+    """
+    Parameters from vibes metadata belonging to section method.
+    """
+
+    m_def = Category()
+
+
+class x_fhi_vibes_section_calculator_parameters(MSection):
+    """
+    Calculator parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_calculator_parameters_xc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_k_grid = Quantity(
+        type=np.int32,
+        shape=[3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_sc_accuracy_rho = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_relativistic = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_compensate_multipole_errors = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_output_level = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_compute_forces = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_compute_heat_flux = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_use_pimd_wrapper = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_calculator_parameters_species_dir = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_calculator(MSection):
+    """
+    Calculator parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_calculator = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_section_calculator_parameters = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_calculator_parameters'),
+        repeats=True,
+    )
+
+
+class x_fhi_vibes_section_atoms(MSection):
+    """
+    Calculator parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_atoms_kind = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_natoms = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_pbc = Quantity(
+        type=bool,
+        shape=[3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_cell = Quantity(
+        type=np.float64,
+        unit='meter',
+        shape=[3, 3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_positions = Quantity(
+        type=np.float64,
+        unit='meter',
+        shape=['x_fhi_vibes_atoms_natoms', 3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_velocities = Quantity(
+        type=np.float64,
+        unit='meter / second',
+        shape=['x_fhi_vibes_atoms_natoms', 3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_symbols = Quantity(
+        type=str,
+        shape=['x_fhi_vibes_atoms_natoms'],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_masses = Quantity(
+        type=np.float64,
+        unit='kilogram',
+        shape=['x_fhi_vibes_atoms_natoms'],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atoms_info = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_MD(MSection):
+    """
+    Molecular dynamics parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_MD_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_md_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_friction = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_fix_cm = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_fs = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_kB = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_dt = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_kg = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_relaxation_kwargs(MSection):
+    """
+    Relaxation kwargs
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_relaxation_kwargs_maxstep = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_kwargs_restart = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_relaxation(MSection):
+    """
+    Relaxation parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_relaxation_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_optimizer = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_maxstep = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_driver = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_fmax = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_unit_cell = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_fix_symmetry = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_hydrostatic_strain = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_constant_volume = Quantity(
+        type=bool,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_scalar_pressure = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_decimals = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_symprec = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_relaxation_workdir = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_section_relaxation_kwargs = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_relaxation_kwargs'), repeats=True
+    )
+
+
+class x_fhi_vibes_section_phonopy(MSection):
+    """
+    Phonony parameters
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_phonopy_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_phonopy_supercell_matrix = Quantity(
+        type=np.int32,
+        shape=[3, 3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_phonopy_symprec = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_phonopy_displacement_dataset = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_section_phonopy_primitive = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_atoms'), repeats=True
+    )
+
+
+class x_fhi_vibes_section_vibes(MSection):
+    """
+    Vibes specifications
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_settings(MSection):
+    """
+    Metadata settings
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_settings_common = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_setttings_machine = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_settings_calculator = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_settings_files = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+
+class x_fhi_vibes_section_metadata(MSection):
+    """
+    Metadata
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_section_metadata_calculator = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_calculator'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_MD = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_MD'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_relaxation = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_relaxation'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_phonopy = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_phonopy'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_atoms = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_atoms'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_settings = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_settings'), repeats=True
+    )
+
+    x_fhi_vibes_section_metadata_vibes = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_vibes'), repeats=True
+    )
+
+
+class x_fhi_vibes_section_attributes(MSection):
+    """
+    Dataset attributes
+    """
+
+    m_def = Section(validate=False)
+
+    x_fhi_vibes_attributes_name = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_system_name = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_natoms = Quantity(
+        type=np.int32,
+        shape=[3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_time_unit = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_timestep = Quantity(
+        type=np.float64,
+        unit='second',
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_nsteps = Quantity(
+        type=np.int32,
+        shape=[3],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_symbols = Quantity(
+        type=str,
+        shape=['x_fhi_vibes_attributes_system_natoms'],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_masses = Quantity(
+        type=np.float64,
+        unit='kilogram',
+        shape=['x_fhi_vibes_attributes_system_natoms'],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_hash = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_hash_raw = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_volume = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_sigma = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_st_size = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_number_of_atoms_primitive = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_number_of_atoms_supercell = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_attributes_force_constants_remapped_size = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_section_attributes_atoms = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_atoms'), repeats=True
+    )
+
+    x_fhi_vibes_section_attributes_metadata = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_metadata'), repeats=True
+    )
+
+
+class Method(runschema.method.Method):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_fhi_vibes_section_attributes = SubSection(
+        sub_section=SectionProxy('x_fhi_vibes_section_attributes'), repeats=True
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_fhi_vibes_volume = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='meter**3',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_displacements = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3, 3],
+        unit='meter',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_momenta = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3, 3],
+        unit='kilogram * meter / second',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_force_constants = Quantity(
+        type=np.float64,
+        shape=[
+            'x_fhi_vibes_attributes_number_of_atoms_primitive',
+            'x_fhi_vibes_attributes_number_of_atoms_primitive',
+            3,
+            3,
+        ],
+        unit='newton / meter',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_force_constants_remapped = Quantity(
+        type=np.float64,
+        shape=[
+            'x_fhi_vibes_attributes_force_constants_remapped_size',
+            'x_fhi_vibes_attributes_force_constants_remapped_size',
+        ],
+        unit='newton / meter',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_atom_forces_harmonic = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3],
+        unit='newton',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_energy_potential_harmonic = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='joule',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_heat_flux = Quantity(
+        type=np.float64,
+        shape=[3],
+        unit='kilogram / second**3',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_heat_flux_harmonic = Quantity(
+        type=np.float64,
+        shape=[3],
+        unit='kilogram / second**3',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_heat_flux_0_harmonic = Quantity(
+        type=np.float64,
+        shape=[3],
+        unit='kilogram / second**3',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_sigma_per_sample = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_pressure_kinetic = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='pascal',
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_pressure_potential = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='pascal',
+        description="""
+        -
+        """,
+    )
+
+    # TODO in fhi aims this is raw id, however in vibes, where each calculation corresponds
+    # to an scc, we get a list of these ids, it does not make sense to put these in sec_run
+    x_fhi_vibes_aims_uuid = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        -
+        """,
+    )
+
+    x_fhi_vibes_MD_time = Quantity(
+        type=np.float64,
+        unit='second',
+        shape=[],
+        description="""
+        -
+        """,
+    )