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

atomisticparsers/dlpoly/metainfo/dl_poly.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  # 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
+import simulationworkflowschema
+
+
+m_package = Package()
+
+
+class x_dl_poly_section_md_molecule_type(MSection):
+    """
+    Section to store molecule type information
+    """
+
+    m_def = Section(validate=False)
+
+    x_dl_poly_md_molecule_type_id = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Molecule type id
+        """,
+    )
+
+    x_dl_poly_md_molecule_type_name = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Molecule type name
+        """,
+    )
+
+
+class x_dl_poly_section_md_topology(MSection):
+    """
+    Section modelling the MD topology
+    """
+
+    m_def = Section(validate=False)
+
+    x_dl_poly_md_molecular_types = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Number of molecular types in topology
+        """,
+    )
+
+    x_dl_poly_section_md_molecule_type = SubSection(
+        sub_section=SectionProxy('x_dl_poly_section_md_molecule_type'), repeats=True
+    )
+
+
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_barostat_target_pressure = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='pascal',
+        description="""
+        MD barostat target pressure.
+        """,
+    )
+
+    x_dl_poly_barostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD barostat relaxation time.
+        """,
+    )
+
+    x_dl_poly_integrator_dt = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD integration time step.
+        """,
+    )
+
+    x_dl_poly_integrator_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD integrator type, valid values are defined in the integrator_type wiki page.
+        """,
+    )
+
+    x_dl_poly_number_of_steps_requested = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Number of requested MD integration time steps.
+        """,
+    )
+
+    x_dl_poly_thermostat_target_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='kelvin',
+        description="""
+        MD thermostat target temperature.
+        """,
+    )
+
+    x_dl_poly_thermostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD thermostat relaxation time.
+        """,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_program_version_date = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Program version date
+        """,
+    )
+
+    x_dl_poly_system_description = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Simulation run title
+        """,
+    )
+
+
+class System(runschema.system.System):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_section_md_topology = SubSection(
+        sub_section=SectionProxy('x_dl_poly_section_md_topology'), repeats=True
+    )
+
+
+class Method(runschema.method.Method):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_step_number_equilibration = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        MD equilibration step number
+        """,
+    )
+
+    x_dl_poly_step_number = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        MD total step number
+        """,
+    )
+
+    x_dl_poly_thermostat_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Thermostat coupling temperature
+        """,
+    )
+
+    x_dl_poly_control_parameters = Quantity(
+        type=JSON,
+        shape=[],
+        description="""
+        """,
+    )
+
+
+class AtomParameters(runschema.method.AtomParameters):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_nrept = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_ifrz = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_igrp = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_dl_poly_virial_configurational = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_short_range = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_coulomb = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_bond = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_angle = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_constraint = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_tethering = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_volume = Quantity(
+        type=np.float64,
+        unit='m ** 3',
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_core_shell = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_dl_poly_virial_potential_mean_force = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        """,
+    )