nomad-simulation-apps 0.1.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nomad_simulation_apps/__init__.py +0 -0
- nomad_simulation_apps/apps/__init__.py +9 -0
- nomad_simulation_apps/apps/alexandria_app.py +193 -0
- nomad_simulation_apps/apps/alexandria_dashboard.yaml +340 -0
- nomad_simulation_apps-0.1.1.dist-info/LICENSE +202 -0
- nomad_simulation_apps-0.1.1.dist-info/METADATA +407 -0
- nomad_simulation_apps-0.1.1.dist-info/RECORD +10 -0
- nomad_simulation_apps-0.1.1.dist-info/WHEEL +5 -0
- nomad_simulation_apps-0.1.1.dist-info/entry_points.txt +2 -0
- nomad_simulation_apps-0.1.1.dist-info/top_level.txt +1 -0
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from nomad.config.models.plugins import AppEntryPoint
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from nomad_simulation_apps.apps.alexandria_app import alexandria_app
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alexandria_entry_point = AppEntryPoint(
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name='Alexandria',
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description='Explore the data of the Alexandria database within NOMAD.',
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app=alexandria_app
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)
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import os
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import yaml
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from nomad.config.models.ui import (
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App,
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Column,
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Dashboard,
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Menu,
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MenuItemHistogram,
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MenuItemOptimade,
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MenuItemPeriodicTable,
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MenuItemTerms,
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MenuSizeEnum,
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)
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try:
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with open(os.path.join(os.path.dirname(__file__),
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'alexandria_dashboard.yaml')) as widget_file:
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widgets = yaml.safe_load(widget_file)
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except Exception as e:
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raise RuntimeError(f'Failed to load widgets from YAML file: {e}')
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alexandria_app = App(
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label='Alexandria',
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path='alexandria',
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category='Theory',
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description='Search the Alexandria database',
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readme='''This page presents the data of the [Alexandria database](https://alexandria.icams.rub.de/). The search results at the bottom of this page contain only the final relaxed geometries. The results of the structure relaxation can be found by clicking on the VASP mainfiles in the "FILES" tab of each entry.
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**Please note** that the upload of the data is currently ongoing and therefore not all data are available. ''', # noqa: E501
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columns=[
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Column(
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label='Formula',
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quantity='results.material.chemical_formula_hill',
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selected=True
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),
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Column(
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label='Space group',
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quantity='results.material.symmetry.space_group_number',
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selected=True
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),
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Column(
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label='XC functional',
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quantity='results.method.simulation.dft.xc_functional_names',
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selected=True
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),
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Column(
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label='Band gap',
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quantity='min(results.properties.electronic.band_gap[*].value)', #jmes path
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selected=True
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)
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],
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filters_locked = {
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"datasets.dataset_name": [
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"Alexandria PBE",
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"Alexandria PBEsol"
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],
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"entry_type": [
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"VASP DFT SinglePoint"
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]
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},
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menu=Menu(
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items=[
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Menu(
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size=MenuSizeEnum.XXL,
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title='Elements / Formula',
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items=[
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MenuItemPeriodicTable(
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search_quantity='results.material.elements',
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),
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MenuItemTerms(
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search_quantity='results.material.chemical_formula_hill',
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width=6,
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.chemical_formula_iupac',
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width=6,
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.chemical_formula_reduced',
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width=6,
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.chemical_formula_anonymous',
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width=6,
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options=0,
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),
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MenuItemHistogram(
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x='results.material.n_elements',
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),
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]
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),
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Menu(
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title = 'Structure / Symmetry',
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items=[
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MenuItemTerms(
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search_quantity='results.material.symmetry.bravais_lattice',
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n_columns=2,
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show_input=False,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.crystal_system',
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n_columns=2,
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show_input=False,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.space_group_symbol',
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.structure_name',
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options=5,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.strukturbericht_designation',
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.point_group',
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.hall_symbol',
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.symmetry.prototype_aflow_id',
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options=0,
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),
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]
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),
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Menu(
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title = 'Method',
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items=[
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MenuItemTerms(
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search_quantity='results.method.simulation.program_version',
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options=5,
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show_input=False,
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),
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MenuItemHistogram(
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x='results.method.simulation.precision.k_line_density',
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),
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MenuItemTerms(
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search_quantity='results.method.simulation.precision.native_tier',
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options=2,
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),
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MenuItemTerms(
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search_quantity='results.method.simulation.dft.xc_functional_type',
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show_input=False,
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),
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MenuItemTerms(
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search_quantity='results.method.simulation.dft.xc_functional_names',
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),
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MenuItemHistogram(
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x='results.method.simulation.dft.hubbard_kanamori_model.u_effective',
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),
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]
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),
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Menu(
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title='Band gap',
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items=[
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MenuItemHistogram(
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x='results.properties.electronic.band_gap.value',
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scale='log',
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autorange=True,
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n_bins=30,
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show_input=True
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),
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]
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),
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Menu(
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title = 'IDs',
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items=[
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MenuItemTerms(
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search_quantity='entry_id',
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options=0,
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),
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MenuItemTerms(
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search_quantity='results.material.material_id',
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options=0,
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),
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]
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),
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Menu(
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title = 'Optimade',
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items=[MenuItemOptimade()]
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),
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]
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),
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dashboard=Dashboard.parse_obj(widgets),
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)
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widgets:
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- type: periodictable
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scale: linear
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search_quantity: results.material.elements
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layout:
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xxl:
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minH: 3
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minW: 3
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h: 11
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w: 18
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y: 0
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x: 0
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xl:
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minH: 3
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minW: 3
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h: 12
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w: 20
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y: 0
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x: 0
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lg:
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minH: 3
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minW: 3
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h: 10
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w: 19
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y: 0
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x: 0
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md:
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minH: 3
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minW: 3
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h: 8
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y: 0
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x: 0
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sm:
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minH: 3
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minW: 3
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h: 8
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y: 0
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x: 0
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- type: terms
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show_input: true
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scale: linear
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search_quantity: results.material.symmetry.space_group_symbol
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layout:
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xxl:
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minH: 3
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minW: 3
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h: 6
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y: 5
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x: 18
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minH: 3
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minW: 3
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h: 6
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minH: 3
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minW: 3
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h: 6
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y: 10
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x: 14
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md:
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minH: 3
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minW: 3
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h: 8
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w: 4
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y: 5
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x: 14
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sm:
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minH: 3
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minW: 3
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h: 4
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w: 3
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y: 8
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x: 6
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- type: terms
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show_input: true
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scale: linear
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search_quantity: results.material.structural_type
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layout:
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xxl:
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minH: 3
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minW: 3
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h: 5
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w: 5
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y: 0
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x: 23
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xl:
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minH: 3
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minW: 3
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h: 6
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w: 5
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y: 0
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x: 25
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lg:
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minH: 3
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minW: 3
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h: 5
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w: 5
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y: 5
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x: 19
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md:
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minH: 3
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minW: 3
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h: 5
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w: 4
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y: 8
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x: 0
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sm:
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minH: 3
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minW: 3
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h: 4
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w: 3
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y: 8
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x: 3
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- type: terms
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show_input: true
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scale: linear
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search_quantity: results.method.simulation.dft.xc_functional_names
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layout:
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xxl:
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minH: 3
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minW: 3
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h: 5
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w: 5
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y: 0
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x: 18
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xl:
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minH: 3
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minW: 3
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h: 6
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w: 5
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y: 0
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x: 20
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lg:
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minH: 3
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minW: 3
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h: 5
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w: 5
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y: 0
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x: 19
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md:
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minH: 3
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minW: 3
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h: 5
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w: 4
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y: 0
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x: 14
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sm:
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Metadata-Version: 2.2
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Name: nomad-simulation-apps
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Version: 0.1.1
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Summary: A repository for housing NOMAD's collection of simulation app plugins.
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Author-email: Martin Kuban <kuban@physik.hu-berlin.de>
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Project-URL: Repository, https://github.com/FAIRmat-NFDI/nomad-simulation-apps
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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# nomad-simulation-apps
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A repository for housing NOMAD's collection of simulation app plugins.
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This `nomad` plugin was generated with `Cookiecutter` along with `@nomad`'s [`cookiecutter-nomad-plugin`](https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin) template.
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## Usage
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```sh
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```
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## Development
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If you want to develop locally this plugin, clone the project and in the plugin folder, create a virtual environment (you can use Python 3.9, 3.10, or 3.11):
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```sh
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```sh
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pip install --upgrade pip
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```
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```sh
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pip install uv
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```
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Install the `nomad-lab` package:
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```sh
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uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
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```
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**Note!**
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Until we have an official pypi NOMAD release with the plugins functionality make
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sure to include NOMAD's internal package registry (via `--index-url` in the above command).
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The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag):
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```sh
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uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
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```
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### Run the tests
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You can run locally the tests:
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```sh
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python -m pytest -sv tests
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```
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+
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where the `-s` and `-v` options toggle the output verbosity.
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+
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Our CI/CD pipeline produces a more comprehensive test report using the `pytest-cov` package. You can generate a local coverage report:
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+
```sh
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|
+
uv pip install pytest-cov
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python -m pytest --cov=src tests
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+
```
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+
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### Run linting and auto-formatting
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We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally:
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+
```sh
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|
+
ruff check .
|
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+
ruff format . --check
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|
+
```
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+
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+
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### Debugging
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For interactive debugging of the tests, use `pytest` with the `--pdb` flag. We recommend using an IDE for debugging, e.g., _VSCode_. If that is the case, add the following snippet to your `.vscode/launch.json`:
|
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|
+
```json
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|
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{
|
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|
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"configurations": [
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+
{
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"name": "<descriptive tag>",
|
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|
+
"type": "debugpy",
|
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|
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"request": "launch",
|
|
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|
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"cwd": "${workspaceFolder}",
|
|
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|
+
"program": "${workspaceFolder}/.pyenv/bin/pytest",
|
|
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|
+
"justMyCode": true,
|
|
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|
+
"env": {
|
|
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|
+
"_PYTEST_RAISE": "1"
|
|
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|
+
},
|
|
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|
+
"args": [
|
|
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|
+
"-sv",
|
|
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|
+
"--pdb",
|
|
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|
+
"<path-to-plugin-tests>",
|
|
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|
+
]
|
|
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|
+
}
|
|
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|
+
]
|
|
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|
+
}
|
|
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|
+
```
|
|
328
|
+
|
|
329
|
+
where `<path-to-plugin-tests>` must be changed to the local path to the test module to be debugged.
|
|
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|
+
|
|
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|
+
The settings configuration file `.vscode/settings.json` automatically applies the linting and formatting upon saving the modified file.
|
|
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|
+
|
|
333
|
+
|
|
334
|
+
### Documentation on Github pages
|
|
335
|
+
|
|
336
|
+
To view the documentation locally, install the related packages using:
|
|
337
|
+
```sh
|
|
338
|
+
uv pip install -r requirements_docs.txt
|
|
339
|
+
```
|
|
340
|
+
|
|
341
|
+
Run the documentation server:
|
|
342
|
+
```sh
|
|
343
|
+
mkdocs serve
|
|
344
|
+
```
|
|
345
|
+
|
|
346
|
+
|
|
347
|
+
## Adding this plugin to NOMAD
|
|
348
|
+
|
|
349
|
+
Currently, NOMAD has two distinct flavors that are relevant depending on your role as an user:
|
|
350
|
+
1. [A NOMAD Oasis](#adding-this-plugin-in-your-nomad-oasis): any user with a NOMAD Oasis instance.
|
|
351
|
+
2. [Local NOMAD installation and the source code of NOMAD](#adding-this-plugin-in-your-local-nomad-installation-and-the-source-code-of-nomad): internal developers.
|
|
352
|
+
|
|
353
|
+
### Adding this plugin in your NOMAD Oasis
|
|
354
|
+
|
|
355
|
+
Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your NOMAD instance.
|
|
356
|
+
|
|
357
|
+
### Adding this plugin in your local NOMAD installation and the source code of NOMAD
|
|
358
|
+
|
|
359
|
+
Modify the text file under `/nomad/default_plugins.txt` and add:
|
|
360
|
+
```sh
|
|
361
|
+
<other-content-in-default_plugins.txt>
|
|
362
|
+
nomad-simulation-apps==x.y.z
|
|
363
|
+
```
|
|
364
|
+
where `x.y.z` represents the released version of this plugin.
|
|
365
|
+
|
|
366
|
+
Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:
|
|
367
|
+
```sh
|
|
368
|
+
deactivate
|
|
369
|
+
cd <route-to-NOMAD-folder>/nomad
|
|
370
|
+
source .pyenv/bin/activate
|
|
371
|
+
./scripts/setup_dev_env.sh
|
|
372
|
+
```
|
|
373
|
+
|
|
374
|
+
Alternatively and only valid for your local NOMAD installation, you can modify `nomad.yaml` to include this plugin, see [NOMAD Oasis - Install plugins](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html).
|
|
375
|
+
|
|
376
|
+
|
|
377
|
+
### Build the python package
|
|
378
|
+
|
|
379
|
+
The `pyproject.toml` file contains everything that is necessary to turn the project
|
|
380
|
+
into a pip installable python package. Run the python build tool to create a package distribution:
|
|
381
|
+
|
|
382
|
+
```sh
|
|
383
|
+
pip install build
|
|
384
|
+
python -m build --sdist
|
|
385
|
+
```
|
|
386
|
+
|
|
387
|
+
You can install the package with pip:
|
|
388
|
+
|
|
389
|
+
```sh
|
|
390
|
+
pip install dist/nomad-simulation-apps-0.1.0
|
|
391
|
+
```
|
|
392
|
+
|
|
393
|
+
Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI
|
|
394
|
+
on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
|
|
395
|
+
|
|
396
|
+
|
|
397
|
+
### Template update
|
|
398
|
+
|
|
399
|
+
We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests.
|
|
400
|
+
|
|
401
|
+
To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project).
|
|
402
|
+
|
|
403
|
+
|
|
404
|
+
## Main contributors
|
|
405
|
+
| Name | E-mail |
|
|
406
|
+
|------|------------|
|
|
407
|
+
| Martin Kuban | [kuban@physik.hu-berlin.de](mailto:kuban@physik.hu-berlin.de)
|
|
@@ -0,0 +1,10 @@
|
|
|
1
|
+
nomad_simulation_apps/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
2
|
+
nomad_simulation_apps/apps/__init__.py,sha256=XB8A9j3sCgJm8X_gd1IyfIhCdVL2mf5qWEUmSUOi5b0,290
|
|
3
|
+
nomad_simulation_apps/apps/alexandria_app.py,sha256=tFwtn5_h7Eh7wI2_mUzfKZO6Av7vuDanUmZC4urYCC0,7007
|
|
4
|
+
nomad_simulation_apps/apps/alexandria_dashboard.yaml,sha256=PfDvlCUAi49vY1QQ9v1A7vDiVZnJSO1RbY7Cyjuf9P0,5192
|
|
5
|
+
nomad_simulation_apps-0.1.1.dist-info/LICENSE,sha256=CUvt2ilcBwKAfRAnoA4RNPTLcdUj3En21LPK9YkFMGg,11358
|
|
6
|
+
nomad_simulation_apps-0.1.1.dist-info/METADATA,sha256=yTOiDMdqUKqG6lPswYx9chzPhBxdd7rL86mxbgVM3Uc,19886
|
|
7
|
+
nomad_simulation_apps-0.1.1.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
|
|
8
|
+
nomad_simulation_apps-0.1.1.dist-info/entry_points.txt,sha256=SH6eDQSVUO8E3iVA6ZtLQD5_x1Me9wiGwX3JJDROtMg,82
|
|
9
|
+
nomad_simulation_apps-0.1.1.dist-info/top_level.txt,sha256=aKZJIyLT0bRVL0nxTZPHb7DoG2-R2ogG9r0SavaE_UE,22
|
|
10
|
+
nomad_simulation_apps-0.1.1.dist-info/RECORD,,
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
nomad_simulation_apps
|