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

workflowparsers/lobster/metainfo/lobster.py

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+#
+# 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
+
+from nomad.metainfo import (
+    Section,
+    Quantity,
+    MSection,
+    SubSection,
+    SectionProxy,
+    Package,
+)
+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 Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_lobster_abs_total_spilling = Quantity(
+        type=float,
+        shape=['number_of_spin_channels'],
+        description="""
+        Absolute total spilling (in all levels)
+        when projecting from the original wave functions into the local basis.
+        """,
+    )
+
+    x_lobster_abs_charge_spilling = Quantity(
+        type=float,
+        shape=['number_of_spin_channels'],
+        description="""
+        Absolute total spilling of density (in occupied levels)
+        when projecting from the original wave functions into the local basis.
+        """,
+    )
+
+    x_lobster_section_cohp = SubSection(
+        sub_section=SectionProxy('x_lobster_section_cohp')
+    )
+
+    x_lobster_section_coop = SubSection(
+        sub_section=SectionProxy('x_lobster_section_coop')
+    )
+
+    x_lobster_section_atom_projected_dos = SubSection(
+        sub_section=SectionProxy('x_lobster_section_atom_projected_dos'), repeats=True
+    )
+
+
+class Method(runschema.method.Method):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_lobster_code = Quantity(
+        type=str,
+        description="""
+        Used PAW program
+        """,
+    )
+
+
+class x_lobster_section_cohp(MSection):
+    """
+    This is a section containing the crystal orbital hamilton population (COHP)
+    and integrated COHP (iCOHP) values.
+    """
+
+    m_def = Section(validate=False)
+
+    x_lobster_number_of_cohp_pairs = Quantity(
+        type=int,
+        description="""
+        Number of atom pairs for which are the COHPs and iCOHPs calculated.
+        """,
+    )
+
+    x_lobster_cohp_atom1_labels = Quantity(
+        type=str,
+        shape=['x_lobster_number_of_cohp_pairs'],
+        description="""
+        Species and indices of the first atom for which is the specific COHP/iCOHP calculated
+        """,
+    )
+
+    x_lobster_cohp_atom2_labels = Quantity(
+        type=str,
+        shape=['x_lobster_number_of_cohp_pairs'],
+        description="""
+        Species and indices of the second atom for which is the specific COHP/iCOHP calculated
+        """,
+    )
+
+    x_lobster_cohp_distances = Quantity(
+        type=np.float64,
+        unit='meter',
+        shape=['x_lobster_number_of_cohp_pairs'],
+        description="""
+        Distance between atoms of the pair for which is the specific COHP/iCOHP calculated.
+        """,
+    )
+
+    x_lobster_cohp_translations = Quantity(
+        type=np.int32,
+        shape=['x_lobster_number_of_cohp_pairs', 3],
+        description="""
+        Vector connecting the unit-cell of the first atom with the one of the second atom
+
+        This is only used with LOBSTER versions 3.0.0 and above, older versions use
+        x_lobster_cohp_number_of_bonds instead.
+        """,
+    )
+
+    x_lobster_integrated_cohp_at_fermi_level = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['number_of_spin_channels', 'x_lobster_number_of_cohp_pairs'],
+        description="""
+        Calculated iCOHP values ingregrated up to the Fermi level.
+        """,
+    )
+
+    x_lobster_number_of_cohp_values = Quantity(
+        type=int,
+        description="""
+        Number of energy values for the COHP and iCOHP.
+        """,
+    )
+
+    x_lobster_cohp_energies = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['x_lobster_number_of_cohp_values'],
+        description="""
+        Array containing the set of discrete energy values for COHP and iCOHP.
+        """,
+    )
+
+    x_lobster_cohp_values = Quantity(
+        type=np.float32,
+        shape=[
+            'x_lobster_number_of_cohp_pairs',
+            'number_of_spin_channels',
+            'x_lobster_number_of_cohp_values',
+        ],
+        description="""
+        Calculated COHP values.
+        """,
+    )
+
+    x_lobster_integrated_cohp_values = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=[
+            'x_lobster_number_of_cohp_pairs',
+            'number_of_spin_channels',
+            'x_lobster_number_of_cohp_values',
+        ],
+        description="""
+        Calculated iCOHP values.
+        """,
+    )
+
+    x_lobster_average_cohp_values = Quantity(
+        type=np.float32,
+        shape=['number_of_spin_channels', 'x_lobster_number_of_cohp_values'],
+        description="""
+        Calculated COHP values averaged over all pairs.
+        """,
+    )
+
+    x_lobster_average_integrated_cohp_values = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['number_of_spin_channels', 'x_lobster_number_of_cohp_values'],
+        description="""
+        Calculated iCOHP values averaged over all pairs.
+        """,
+    )
+
+    x_lobster_cohp_number_of_bonds = Quantity(
+        type=int,
+        shape=['x_lobster_number_of_cohp_pairs'],
+        description="""
+        Number of bonds between first atom and the second atom (including
+        the periodic images).
+
+        This is only used in older LOBSTER versions, new versions print one line
+        for every neighbor, so a pair which had x_lobster_icohp_number_of_bonds = 4
+        in the old version would actually show as 4 lines in the ICOHPLIST or 4 columns
+        in the COPHCAR in the new format.
+        """,
+    )
+
+
+class x_lobster_section_coop(MSection):
+    """
+    This is a section containing the crystal orbital hamilton population (COOP)
+    and integrated coop (iCOOP) values.
+    """
+
+    m_def = Section(validate=False)
+
+    x_lobster_number_of_coop_pairs = Quantity(
+        type=int,
+        description="""
+        Number of atom pairs for which are the COOPs and iCOOPs calculated.
+        """,
+    )
+
+    x_lobster_coop_atom1_labels = Quantity(
+        type=str,
+        shape=['x_lobster_number_of_coop_pairs'],
+        description="""
+        Species and indices of the first atom for which is the specific COOP/iCOOP calculated
+        """,
+    )
+
+    x_lobster_coop_atom2_labels = Quantity(
+        type=str,
+        shape=['x_lobster_number_of_coop_pairs'],
+        description="""
+        Species and indices of the second atom for which is the specific COOP/iCOOP calculated
+        """,
+    )
+
+    x_lobster_coop_distances = Quantity(
+        type=np.float64,
+        unit='meter',
+        shape=['x_lobster_number_of_coop_pairs'],
+        description="""
+        Distance between atoms of the pair for which is the specific COOP/iCOOP calculated.
+        """,
+    )
+
+    x_lobster_coop_translations = Quantity(
+        type=np.int32,
+        shape=['x_lobster_number_of_coop_pairs', 3],
+        description="""
+        Vector connecting the unit-cell of the first atom with the one of the second atom
+
+        This is only used with LOBSTER versions 3.0.0 and above, older versions use
+        x_lobster_coop_number_of_bonds instead.
+        """,
+    )
+
+    x_lobster_integrated_coop_at_fermi_level = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['number_of_spin_channels', 'x_lobster_number_of_coop_pairs'],
+        description="""
+        Calculated iCOOP values ingregrated up to the Fermi level.
+        """,
+    )
+
+    x_lobster_number_of_coop_values = Quantity(
+        type=int,
+        description="""
+        Number of energy values for the COOP and iCOOP.
+        """,
+    )
+
+    x_lobster_coop_energies = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['x_lobster_number_of_coop_values'],
+        description="""
+        Array containing the set of discrete energy values for COOP and iCOOP.
+        """,
+    )
+
+    x_lobster_coop_values = Quantity(
+        type=np.float32,
+        shape=[
+            'x_lobster_number_of_coop_pairs',
+            'number_of_spin_channels',
+            'x_lobster_number_of_coop_values',
+        ],
+        description="""
+        Calculated COOP values.
+        """,
+    )
+
+    x_lobster_integrated_coop_values = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=[
+            'x_lobster_number_of_coop_pairs',
+            'number_of_spin_channels',
+            'x_lobster_number_of_coop_values',
+        ],
+        description="""
+        Calculated iCOOP values.
+        """,
+    )
+
+    x_lobster_average_coop_values = Quantity(
+        type=np.float32,
+        shape=['number_of_spin_channels', 'x_lobster_number_of_coop_values'],
+        description="""
+        Calculated COOP values averaged over all pairs.
+        """,
+    )
+
+    x_lobster_average_integrated_coop_values = Quantity(
+        type=np.float32,
+        unit='joule',
+        shape=['number_of_spin_channels', 'x_lobster_number_of_coop_values'],
+        description="""
+        Calculated iCOOP values averaged over all pairs.
+        """,
+    )
+
+    x_lobster_coop_number_of_bonds = Quantity(
+        type=int,
+        shape=['x_lobster_number_of_coop_pairs'],
+        description="""
+        Number of bonds between first atom and the second atom (including
+        the periodic images).
+
+        This is only used in older LOBSTER versions, new versions print one line
+        for every neighbor, so a pair which had x_lobster_icoop_number_of_bonds = 4
+        in the old version would actually show as 4 lines in the ICOOPLIST or 4 columns
+        in the COOPCAR in the new format.
+        """,
+    )
+
+
+class x_lobster_section_atom_projected_dos(MSection):
+    """
+    Section collecting the information on an atom projected density of states (DOS)
+    evaluation.
+    FIXME: this should ultimatelly go into some common section but that is not possible
+    right now, see: https://matsci.org/t/section-atom-projected-dos/36008
+    """
+
+    m_def = Section(validate=False)
+
+    x_lobster_atom_projected_dos_energies = Quantity(
+        type=np.float64,
+        shape=['x_lobster_number_of_atom_projected_dos_values'],
+        unit='joule',
+        description="""
+        Array containing the set of discrete energy values for the atom-projected density
+        (electronic-energy) of states (DOS).
+        """,
+    )
+
+    x_lobster_atom_projected_dos_lm = Quantity(
+        type=np.int32,
+        shape=['x_lobster_number_of_lm_atom_projected_dos', 2],
+        description="""
+        Tuples of $l$ and $m$ values for which x_lobster_atom_projected_dos_values_lm are given.
+        For the quantum number $l$ the conventional meaning of azimuthal quantum number is
+        always adopted. For the integer number $m$, besides the conventional use as
+        magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
+        different conventions is accepted (see the [m_kind wiki
+        page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+        The adopted convention is specified by atom_projected_dos_m_kind.
+        """,
+    )
+
+    x_lobster_atom_projected_dos_m_kind = Quantity(
+        type=str,
+        description="""
+        String describing what the integer numbers of $m$ in atom_projected_dos_lm mean.
+        The allowed values are listed in the [m_kind wiki
+        page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+        """,
+    )
+
+    x_lobster_atom_projected_dos_values_lm = Quantity(
+        type=np.float64,
+        shape=[
+            'x_lobster_number_of_lm_atom_projected_dos',
+            'number_of_spin_channels',
+            'x_lobster_number_of_atom_projected_dos_values',
+        ],
+        description="""
+        Values correspond to the number of states for a given energy (the set of discrete
+        energy values is given in atom_projected_dos_energies) divided into contributions
+        from each $l,m$ channel for the atom-projected density (electronic-energy) of
+        states for atom specified in atom_projected_dos_atom_index.
+        """,
+    )
+
+    x_lobster_atom_projected_dos_values_total = Quantity(
+        type=np.float64,
+        shape=[
+            'number_of_spin_channels',
+            'x_lobster_number_of_atom_projected_dos_values',
+        ],
+        description="""
+        Values correspond to the number of states for a given energy (the set of discrete
+        energy values is given in atom_projected_dos_energies) divided into contributions
+        summed up over all $l$ channels for the atom-projected density (electronic-energy)
+        of states (DOS) for atom specified in atom_projected_dos_atom_index.
+        """,
+    )
+
+    x_lobster_number_of_atom_projected_dos_values = Quantity(
+        type=int,
+        description="""
+        Gives the number of energy values for the atom-projected density of states (DOS)
+        based on x_lobster_atom_projected_dos_values_lm and
+        x_lobster_atom_projected_dos_values_total.
+        """,
+    )
+
+    x_lobster_number_of_lm_atom_projected_dos = Quantity(
+        type=int,
+        description="""
+        Gives the number of $l$, $m$ combinations for the atom projected density of states
+        (DOS) defined in x_lobster_section_atom_projected_dos.
+        """,
+    )
+
+    x_lobster_atom_projected_dos_atom_index = Quantity(
+        type=int,
+        description="""
+        Index of atom for which is the x_lobster_atom_projected_dos provided.
+        """,
+    )
+
+
+m_package.__init_metainfo__()