Commit 21a53541 authored by Markus Scheidgen's avatar Markus Scheidgen

Added metainfo python code.

parent de6d49f8
import sys
from nomad.metainfo import Environment
from nomad.metainfo.legacy import LegacyMetainfoEnvironment
import dlpolyparser.metainfo.dl_poly
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['dlpolyparser.metainfo.dl_poly'].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
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='dl_poly_nomadmetainfo_json',
description='None',
a_legacy=LegacyDefinition(name='dl_poly.nomadmetainfo.json'))
class x_dl_poly_section_md_molecule_type(MSection):
'''
Section to store molecule type information
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_dl_poly_section_md_molecule_type'))
x_dl_poly_md_molecule_type_id = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
Molecule type id
''',
a_legacy=LegacyDefinition(name='x_dl_poly_md_molecule_type_id'))
x_dl_poly_md_molecule_type_name = Quantity(
type=str,
shape=[],
description='''
Molecule type name
''',
a_legacy=LegacyDefinition(name='x_dl_poly_md_molecule_type_name'))
class x_dl_poly_section_md_topology(MSection):
'''
Section modelling the MD topology
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_dl_poly_section_md_topology'))
x_dl_poly_md_molecular_types = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
Number of molecular types in topology
''',
a_legacy=LegacyDefinition(name='x_dl_poly_md_molecular_types'))
x_dl_poly_section_md_molecule_type = SubSection(
sub_section=SectionProxy('x_dl_poly_section_md_molecule_type'),
repeats=True,
a_legacy=LegacyDefinition(name='x_dl_poly_section_md_molecule_type'))
class section_sampling_method(public.section_sampling_method):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_sampling_method'))
x_dl_poly_barostat_target_pressure = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='pascal',
description='''
MD barostat target pressure.
''',
categories=[public.settings_molecular_dynamics, public.settings_barostat, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_barostat_target_pressure'))
x_dl_poly_barostat_tau = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='second',
description='''
MD barostat relaxation time.
''',
categories=[public.settings_molecular_dynamics, public.settings_barostat, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_barostat_tau'))
x_dl_poly_integrator_dt = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='second',
description='''
MD integration time step.
''',
categories=[public.settings_molecular_dynamics, public.settings_integrator, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_integrator_dt'))
x_dl_poly_integrator_type = Quantity(
type=str,
shape=[],
description='''
MD integrator type, valid values are defined in the integrator_type wiki page.
''',
categories=[public.settings_molecular_dynamics, public.settings_integrator, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_integrator_type'))
x_dl_poly_number_of_steps_requested = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Number of requested MD integration time steps.
''',
categories=[public.settings_molecular_dynamics, public.settings_integrator, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_number_of_steps_requested'))
x_dl_poly_thermostat_target_temperature = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='kelvin',
description='''
MD thermostat target temperature.
''',
categories=[public.settings_molecular_dynamics, public.settings_thermostat, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_thermostat_target_temperature'))
x_dl_poly_thermostat_tau = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='second',
description='''
MD thermostat relaxation time.
''',
categories=[public.settings_molecular_dynamics, public.settings_thermostat, public.settings_sampling],
a_legacy=LegacyDefinition(name='x_dl_poly_thermostat_tau'))
class section_run(public.section_run):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
x_dl_poly_program_version_date = Quantity(
type=str,
shape=[],
description='''
Program version date
''',
a_legacy=LegacyDefinition(name='x_dl_poly_program_version_date'))
x_dl_poly_system_description = Quantity(
type=str,
shape=[],
description='''
Simulation run title
''',
a_legacy=LegacyDefinition(name='x_dl_poly_system_description'))
class section_system(public.section_system):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
x_dl_poly_section_md_topology = SubSection(
sub_section=SectionProxy('x_dl_poly_section_md_topology'),
repeats=True,
a_legacy=LegacyDefinition(name='x_dl_poly_section_md_topology'))
class section_method(public.section_method):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
x_dl_poly_step_number_equilibration = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
MD equilibration step number
''',
a_legacy=LegacyDefinition(name='x_dl_poly_step_number_equilibration'))
x_dl_poly_step_number = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
MD total step number
''',
a_legacy=LegacyDefinition(name='x_dl_poly_step_number'))
x_dl_poly_thermostat_temperature = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Thermostat coupling temperature
''',
a_legacy=LegacyDefinition(name='x_dl_poly_thermostat_temperature'))
m_package.__init_metainfo__()
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