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

atomisticparsers/amber/metainfo/amber.py

@@ -0,0 +1,495 @@
+#
+# 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,
+)
+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_amber_mdin_method(MCategory):
+    """
+    Parameters of mdin belonging to section method.
+    """
+
+    m_def = Category()
+
+
+class x_amber_mdout_single_configuration_calculation(MCategory):
+    """
+    Parameters of mdout belonging to section_single_configuration_calculation.
+    """
+
+    m_def = Category()
+
+
+class x_amber_mdout_method(MCategory):
+    """
+    Parameters of mdin belonging to section method.
+    """
+
+    m_def = Category()
+
+
+class x_amber_mdout_run(MCategory):
+    """
+    Parameters of mdin belonging to settings run.
+    """
+
+    m_def = Category()
+
+
+class x_amber_mdin_run(MCategory):
+    """
+    Parameters of mdin belonging to settings run.
+    """
+
+    m_def = Category()
+
+
+class x_amber_section_input_output_files(MSection):
+    """
+    Temperory variable to store input and output file keywords
+    """
+
+    m_def = Section(validate=False)
+
+
+class x_amber_section_single_configuration_calculation(MSection):
+    """
+    section for gathering values for MD steps
+    """
+
+    m_def = Section(validate=False)
+
+
+class System(runschema.system.System):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_atom_positions_image_index = Quantity(
+        type=np.int32,
+        shape=['number_of_atoms', 3],
+        unit='dimensionless',
+        description="""
+        PBC image flag index.
+        """,
+    )
+
+    x_amber_atom_positions_scaled = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3],
+        unit='dimensionless',
+        description="""
+        Position of the atoms in a scaled format [0, 1].
+        """,
+    )
+
+    x_amber_atom_positions_wrapped = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3],
+        unit='meter',
+        description="""
+        Position of the atoms wrapped back to the periodic box.
+        """,
+    )
+
+    x_amber_dummy = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        dummy
+        """,
+    )
+
+    x_amber_mdin_finline = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        finline in mdin
+        """,
+    )
+
+    x_amber_traj_timestep_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_traj_number_of_atoms_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_traj_box_bound_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_traj_box_bounds_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_traj_variables_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_traj_atoms_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_barostat_target_pressure = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='pascal',
+        description="""
+        MD barostat target pressure.
+        """,
+    )
+
+    x_amber_barostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD barostat relaxation time.
+        """,
+    )
+
+    x_amber_barostat_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD barostat type, valid values are defined in the barostat_type wiki page.
+        """,
+    )
+
+    x_amber_integrator_dt = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD integration time step.
+        """,
+    )
+
+    x_amber_integrator_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD integrator type, valid values are defined in the integrator_type wiki page.
+        """,
+    )
+
+    x_amber_periodicity_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Periodic boundary condition type in the sampling (non-PBC or PBC).
+        """,
+    )
+
+    x_amber_langevin_gamma = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        Langevin thermostat damping factor.
+        """,
+    )
+
+    x_amber_number_of_steps_requested = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Number of requested MD integration time steps.
+        """,
+    )
+
+    x_amber_thermostat_level = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD thermostat level (see wiki: single, multiple, regional).
+        """,
+    )
+
+    x_amber_thermostat_target_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='kelvin',
+        description="""
+        MD thermostat target temperature.
+        """,
+    )
+
+    x_amber_thermostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD thermostat relaxation time.
+        """,
+    )
+
+    x_amber_thermostat_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD thermostat type, valid values are defined in the thermostat_type wiki page.
+        """,
+    )
+
+
+class AtomParameters(runschema.method.AtomParameters):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_atom_type_element = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Element symbol of an atom type.
+        """,
+    )
+
+    x_amber_atom_type_radius = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        van der Waals radius of an atom type.
+        """,
+    )
+
+
+class Interaction(runschema.method.Interaction):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_interaction_atom_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=['number_of_atoms_per_interaction'],
+        description="""
+        Reference to the atom type of each interaction atoms.
+        """,
+    )
+
+    x_amber_number_of_defined_pair_interactions = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Number of defined pair interactions (L-J pairs).
+        """,
+    )
+
+    x_amber_pair_interaction_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=[
+            'x_amber_number_of_defined_pair_interactions',
+            'number_of_atoms_per_interaction',
+        ],
+        description="""
+        Reference to the atom type for pair interactions.
+        """,
+    )
+
+    x_amber_pair_interaction_parameters = Quantity(
+        type=np.float64,
+        shape=['x_amber_number_of_defined_pair_interactions', 2],
+        description="""
+        Pair interactions parameters.
+        """,
+    )
+
+    x_amber_molecule_interaction_atom_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=['number_of_atoms_per_interaction'],
+        description="""
+        Reference to the atom type of each molecule interaction atoms.
+        """,
+    )
+
+    x_amber_number_of_defined_molecule_pair_interactions = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Number of defined pair interactions within a molecule (L-J pairs).
+        """,
+    )
+
+    x_amber_pair_molecule_interaction_parameters = Quantity(
+        type=np.float64,
+        shape=['number_of_defined_molecule_pair_interactions', 2],
+        description="""
+        Molecule pair interactions parameters.
+        """,
+    )
+
+    x_amber_pair_molecule_interaction_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=[
+            'x_amber_number_of_defined_pair_interactions',
+            'number_of_atoms_per_interaction',
+        ],
+        description="""
+        Reference to the atom type for pair interactions within a molecule.
+        """,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_program_version_date = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Program version date.
+        """,
+    )
+
+    x_amber_xlo_xhi = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        test
+        """,
+    )
+
+    x_amber_data_file_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Filename of data file
+        """,
+    )
+
+    x_amber_program_working_path = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_program_execution_host = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_program_execution_path = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_program_module = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_program_execution_date = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_program_execution_time = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_mdin_header = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_mdin_wt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_amber_section_input_output_files = SubSection(
+        sub_section=SectionProxy('x_amber_section_input_output_files'), repeats=False
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_amber_section_single_configuration_calculation = SubSection(
+        sub_section=SectionProxy('x_amber_section_single_configuration_calculation'),
+        repeats=True,
+    )

atomisticparsers/amber/parser.py

@@ -0,0 +1,42 @@
+#
+# 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.
+#
+
+from nomad.units import ureg
+from simulationparsers.utils import BasicParser
+
+
+class AmberParser:
+    def __init__(self):
+        re_f = r'\-*\d+\.\d+E*\-*\+*\d*'
+        self._parser = BasicParser(
+            'Amber',
+            units_mapping=dict(length=ureg.angstrom, energy=ureg.eV),
+            program_version=r'Amber\s*(\d+)\s*(\w+)\s*(\d+)',
+            # will only read initial coordinates
+            auxilliary_files=r'(\S+\.inpcrd|\S+\.prmtop)',
+            atom_positions=(
+                rf'\d+\s+({re_f} +{re_f} +{re_f} +{re_f} +{re_f} +{re_f}[\s\S]+)',
+                lambda x: x.strip().split(),
+            ),
+            atom_atom_number=r'\%FLAG ATOMIC_NUMBER\s*\%FORMAT\(.+\)\s*([\d\s]+)',
+            energy_total=rf'NSTEP\s*ENERGY.+\s*\d+\s*({re_f})',
+        )
+
+    def parse(self, mainfile, archive, logger=None):
+        self._parser.parse(mainfile, archive, logger=None)

atomisticparsers/asap/__init__.py

@@ -0,0 +1,19 @@
+#
+# 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.
+#
+from .parser import AsapParser

atomisticparsers/asap/__main__.py

@@ -0,0 +1,31 @@
+#
+# 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 sys
+import json
+import logging
+
+from nomad.utils import configure_logging
+from nomad.datamodel import EntryArchive
+from atomisticparsers.asap import AsapParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    AsapParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

atomisticparsers/asap/metainfo/__init__.py

@@ -0,0 +1,19 @@
+#
+# 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.
+#
+from . import asap

atomisticparsers/asap/metainfo/asap.py

@@ -0,0 +1,75 @@
+#
+# 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,
+)
+import simulationworkflowschema
+
+
+m_package = Package()
+
+
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_asap_langevin_friction = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Friction coeffient used in Langevin dynamics
+        """,
+    )
+
+    x_asap_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Temperature used in molecular-dynamics
+        """,
+    )
+
+    x_asap_timestep = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Timestep in molecular dynamics
+        """,
+    )
+
+
+class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_asap_maxstep = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Maxstep in Angstrom for geometry optimization
+        """,
+    )