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Add example config files (#558)
* Add example config files * Update config examples link
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‎README.md‎

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> [!NOTE]
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> `properties` must be passed as a Yaml list, as above, not as a string.
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Example configurations for all commands can be found in [janus-tutorials](https://github.com/stfc/janus-tutorials/tree/main/configs)
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Minimal and full example configuration files for all calculations can be found
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[here](https://stfc.github.io/janus-core/examples/index.html).
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## Development

‎docs/source/examples/descriptors.rst‎

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===========
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Descriptors
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===========
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A minimal example configuration file for ``janus descriptors`` is:
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.. literalinclude:: minimal/descriptors.yml
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An example configuration file with all parameters set for ``janus descriptors`` is:
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.. literalinclude:: full/descriptors.yml

‎docs/source/examples/eos.rst‎

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=================
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Equation of State
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=================
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A minimal example configuration file for ``janus eos`` is:
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.. literalinclude:: minimal/eos.yml
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An example configuration file with all parameters set for ``janus eos`` is:
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.. literalinclude:: full/eos.yml

‎docs/source/examples/full/descriptors.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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struct: "tests/data/NaCl.cif"
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invariants_only: True
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calc_per_element: False
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calc_per_atom: True
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out: NaCl-descriptors.extxyz
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file_prefix: NaCl
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read_kwargs:
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index: ":"
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write_kwargs:
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invalidate_calc: False
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log: descriptors-log.yml
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summary: descriptors-summary.yml
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tracker: False
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progress_bar: True

‎docs/source/examples/full/eos.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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struct: "tests/data/NaCl.cif"
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min_volume: 0.9
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max_volume: 1.1
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n_volumes: 10
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eos_type: birchmurnaghan
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minimize: True
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minimize_all: True
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fmax: 0.01
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minimize_kwargs:
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filter_kwargs:
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constant_volume: True
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write_structures: True
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plot_to_file: True
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: eos-log.yml
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summary: eos-summary.yml
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tracker: False

‎docs/source/examples/full/geomopt.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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struct: "tests/data/NaCl.cif"
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optimizer: FIRE
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fmax: 0.0005
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steps: 100
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opt_cell_lengths: False
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opt_cell_fully: True
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filter_class: UnitCellFilter
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pressure: 0.0001
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symmetrize: True
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symmetry_tolerance: 0.001
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out: NaCl-opt.extxyz
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write_traj: True
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minimize_kwargs:
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filter_kwargs:
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constant_volume: True
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traj_kwargs:
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invalidate_calc: True
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opt_kwargs:
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maxstep: 0.1
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: geomopt-log.yml
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summary: geomopt-summary.yml
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tracker: False

‎docs/source/examples/full/neb.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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init-struct: "tests/data/LiFePO4_start.cif"
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final-struct: "tests/data/LiFePO4_end.cif"
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neb-structs: null
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neb-class: NEB
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n-images: 10
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write-band: True
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neb-kwargs:
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dynamic_relaxation: False
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interpolator: pymatgen
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interpolator-kwargs:
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autosort_tol: 0.0
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optimizer: FIRE
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fmax: 1
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steps: 1000
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optimizer-kwargs:
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a: 0.01
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plot-band: True
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minimize: True
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minimize_kwargs:
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opt_kwargs:
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maxstep: 0.1
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: neb-log.yml
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summary: neb-summary.yml
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tracker: False

‎docs/source/examples/full/nph.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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ensemble: nph
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struct: "tests/data/NaCl.cif"
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steps: 100
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timestep: 0.1
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temp: 100
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equil_steps: 100
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minimize: True
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minimize_every: 50
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minimize_kwargs:
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filter_class: null
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rescale_velocities: True
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remove_rot: True
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rescale_every: 50
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post_process_kwargs:
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rdf_compute: True
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correlation_kwargs:
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vaf:
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a: Velocity
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points: 250
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saf:
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a: Stress
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a_kwargs: {'components': ['xy', 'yz', 'zx']}
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points: 250
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plumed_input: null
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plumed_log: null
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barostat_time: 75
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bulk_modulus: 1
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pressure: 1
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ensemble_kwargs:
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mask: [0, 1, 0]
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restart: False
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restart_auto: True
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restart_stem: nph-restart
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restart_every: 1000
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rotate_restart: True
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restarts_to_keep: 2
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final_file: nph-final.extxyz
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stats_file: nph-stats.dat
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stats_every: 100
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traj_file: nph-traj.extxyz
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traj_append: False
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traj_start: 10
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traj_every: 100
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: nph-log.yml
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summary: nph-summary.yml
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tracker: False
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progress_bar: True
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update_progress_every: 10

‎docs/source/examples/full/npt-mtk.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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ensemble: npt-mtk
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struct: "tests/data/NaCl.cif"
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steps: 100
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timestep: 0.1
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temp: 100
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equil_steps: 100
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minimize: True
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minimize_every: 50
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minimize_kwargs:
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opt_kwargs:
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maxstep: 0.1
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rescale_velocities: True
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remove_rot: True
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rescale_every: 50
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post_process_kwargs:
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rdf_compute: True
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correlation_kwargs:
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vaf:
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a: Velocity
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points: 250
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saf:
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a: Stress
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a_kwargs: {'components': ['xy', 'yz', 'zx']}
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points: 250
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plumed_input: null
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plumed_log: null
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pressure: 1
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thermostat_time: 100
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barostat_time: 1000
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thermostat_chain: 3
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barostat_chain: 3
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thermostat_substeps: 1
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barostat_substeps: 1
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temp_start: 0
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temp_end: 100
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temp_step: 10
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temp_time: 1
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restart: False
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restart_auto: True
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restart_stem: npt-mtk-restart
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restart_every: 1000
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rotate_restart: True
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restarts_to_keep: 2
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final_file: npt-mtk-final.extxyz
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stats_file: npt-mtk-stats.dat
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stats_every: 100
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traj_file: npt-mtk-traj.extxyz
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traj_append: False
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traj_start: 10
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traj_every: 100
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: npt-mtk-log.yml
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summary: npt-mtk-summary.yml
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tracker: False
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progress_bar: True
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update_progress_every: 10

‎docs/source/examples/full/npt.yml‎

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arch: mace_mp
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device: cpu
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model: "tests/models/mace_mp_small.model"
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calc_kwargs:
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dispersion: True
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ensemble: npt
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struct: "tests/data/NaCl.cif"
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steps: 100
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timestep: 0.1
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temp: 100
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equil_steps: 100
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minimize: True
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minimize_every: 50
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minimize_kwargs:
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filter_class: null
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rescale_velocities: True
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remove_rot: True
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rescale_every: 50
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post_process_kwargs:
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rdf_compute: True
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correlation_kwargs:
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vaf:
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a: Velocity
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points: 250
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saf:
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a: Stress
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a_kwargs: {'components': ['xy', 'yz', 'zx']}
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points: 250
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plumed_input: null
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plumed_log: null
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thermostat_time: 50
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barostat_time: 75
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bulk_modulus: 1
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pressure: 1
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ensemble_kwargs:
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mask: [0, 1, 0]
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temp_start: 0
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temp_end: 100
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temp_step: 10
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temp_time: 1
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restart: False
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restart_auto: True
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restart_stem: npt-restart
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restart_every: 1000
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rotate_restart: True
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restarts_to_keep: 2
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final_file: npt-final.extxyz
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stats_file: npt-stats.dat
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stats_every: 100
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traj_file: npt-traj.extxyz
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traj_append: False
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traj_start: 10
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traj_every: 100
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file_prefix: NaCl
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read_kwargs:
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index: "0"
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write_kwargs:
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invalidate_calc: True
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log: npt-log.yml
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summary: npt-summary.yml
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tracker: False
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progress_bar: True
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update_progress_every: 10

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