CrystOD 0.3.6__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.
- crystod/CIR_data.txt.gz +0 -0
- crystod/__init__.py +98 -0
- crystod/__main__.py +5 -0
- crystod/_api.py +69 -0
- crystod/atomic_levels.py +134 -0
- crystod/band_pyscf.py +446 -0
- crystod/basis_function.py +1105 -0
- crystod/brillouin_zone.py +436 -0
- crystod/bz.py +32 -0
- crystod/bz_supercell.py +259 -0
- crystod/cli/__init__.py +21 -0
- crystod/cli/bz.py +192 -0
- crystod/cli/common.py +87 -0
- crystod/cli/group.py +566 -0
- crystod/cli/mag.py +128 -0
- crystod/cli/main.py +971 -0
- crystod/cli/md.py +202 -0
- crystod/cli/mol.py +290 -0
- crystod/cli/phonon.py +499 -0
- crystod/coset.py +252 -0
- crystod/crystal_orbital_diagram.py +1704 -0
- crystod/crystal_orbital_pyscf.py +2166 -0
- crystod/crystal_orbital_spgrep.py +1123 -0
- crystod/decompose_irrep.py +124 -0
- crystod/direct_product.py +180 -0
- crystod/dirpro_line_names.py +199 -0
- crystod/dos_pyscf.py +334 -0
- crystod/generate_basis_function.py +135 -0
- crystod/group.py +69 -0
- crystod/irreptables_compat.py +183 -0
- crystod/isoir.py +823 -0
- crystod/isotropy_subgroup.py +1237 -0
- crystod/ligand_field.py +136 -0
- crystod/mag.py +24 -0
- crystod/md.py +25 -0
- crystod/md_summary.py +111 -0
- crystod/mo_diagram.py +2067 -0
- crystod/mo_diagram_fragment.py +702 -0
- crystod/mo_diagram_pyscf.py +1111 -0
- crystod/modulation.py +1516 -0
- crystod/mol.py +40 -0
- crystod/molecular_salc.py +642 -0
- crystod/multiplet.py +562 -0
- crystod/multiplet_energy.py +1017 -0
- crystod/multiplet_visualize.py +709 -0
- crystod/operations.py +310 -0
- crystod/orbital_hybridization_spgrep.py +786 -0
- crystod/phonon.py +54 -0
- crystod/phonon_fatband.py +400 -0
- crystod/phonon_irreps.py +418 -0
- crystod/phonon_lt.py +209 -0
- crystod/phonon_subgroups.py +868 -0
- crystod/phonon_vector.py +1045 -0
- crystod/point_charge_field.py +319 -0
- crystod/poscar2cif.py +389 -0
- crystod/runtime_compat.py +161 -0
- crystod/salc.py +41 -0
- crystod/show_kpoints.py +105 -0
- crystod/spacegroup_product.py +882 -0
- crystod/spglib_compat.py +28 -0
- crystod/spin_basis.py +751 -0
- crystod/star_of_k.py +198 -0
- crystod/symmetry_mode.py +1067 -0
- crystod/vesta_element_rgb.json +127 -0
- crystod/vibration_modes.py +645 -0
- crystod/vibration_viewer.py +147 -0
- crystod/visualize_basis.py +1439 -0
- crystod/visualize_eht.py +447 -0
- crystod/visualize_pyscf.py +507 -0
- crystod/xdatcar_adp.py +537 -0
- crystod-0.3.6.dist-info/METADATA +191 -0
- crystod-0.3.6.dist-info/RECORD +76 -0
- crystod-0.3.6.dist-info/WHEEL +5 -0
- crystod-0.3.6.dist-info/entry_points.txt +8 -0
- crystod-0.3.6.dist-info/licenses/LICENSE +30 -0
- crystod-0.3.6.dist-info/top_level.txt +1 -0
crystod/CIR_data.txt.gz
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crystod/__init__.py
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"""crystod package.
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Command-line tools (``crystod``, ``crystod-group``, ``crystod-bz``,
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``crystod-phonon``, ``crystod-mag``, ``crystod-md``, ``crystod-mol``) live
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in ``crystod.cli``; the Python API mirrors the same domains:
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import crystod
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crystod.salc # crystal-orbital SALC analysis (the main command)
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crystod.group # irrep algebra, isotropy subgroups, symmetry modes
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crystod.phonon # phonon irreps, eigenvectors, modulation, subgroups
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crystod.bz # Brillouin-zone plots and special k points
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crystod.mag # symmetry-adapted spin bases
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crystod.md # MD-trajectory analyses (ADPs)
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crystod.mol # molecular SALCs and MO diagrams
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The most common entry points are also importable from the top level::
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from crystod import isotropy_subgroups, label_phonon_modes
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Domain modules and the symbols below resolve lazily (PEP 562), so plain
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``import crystod`` stays light; the implementation modules
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(``crystod.phonon_irreps``, ``crystod.isotropy_subgroup``, ...) remain
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importable directly, exactly as before.
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"""
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from .operations import (
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characterize_rotation,
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complex_to_real_transform,
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complex_to_real_transform_orbital,
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get_seitz_symbol,
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rotation_matrix_to_euler_zyz,
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wigner_D_matrix,
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wigner_D_real,
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)
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__all__ = [
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"__version__",
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"characterize_rotation",
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"complex_to_real_transform",
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"complex_to_real_transform_orbital",
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"get_seitz_symbol",
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"rotation_matrix_to_euler_zyz",
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"wigner_D_matrix",
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"wigner_D_real",
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# API domains (lazy)
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"salc",
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"group",
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"phonon",
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"bz",
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"mag",
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"md",
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"mol",
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# flagship API symbols (lazy)
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"isotropy_subgroups",
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"IsotropySubgroup",
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"label_phonon_modes",
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"imaginary_mode_subgroups",
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"scan_imaginary_modes",
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"PhononMode",
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"ImaginaryModeResult",
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"IsotropyAnalyzer",
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"SpaceGroupIrrepAlgebra",
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]
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__version__ = "0.3.6"
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_API_DOMAINS = ("salc", "group", "phonon", "bz", "mag", "md", "mol")
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_LAZY_SYMBOLS = {
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"isotropy_subgroups": ("phonon_subgroups", "isotropy_subgroups"),
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"IsotropySubgroup": ("phonon_subgroups", "IsotropySubgroup"),
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"label_phonon_modes": ("phonon_subgroups", "label_phonon_modes"),
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"imaginary_mode_subgroups": ("phonon_subgroups", "imaginary_mode_subgroups"),
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"scan_imaginary_modes": ("phonon_subgroups", "scan_imaginary_modes"),
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"PhononMode": ("phonon_subgroups", "PhononMode"),
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"ImaginaryModeResult": ("phonon_subgroups", "ImaginaryModeResult"),
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"IsotropyAnalyzer": ("isotropy_subgroup", "IsotropyAnalyzer"),
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"SpaceGroupIrrepAlgebra": ("spacegroup_product", "SpaceGroupIrrepAlgebra"),
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}
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def __getattr__(name):
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import importlib
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if name in _API_DOMAINS:
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return importlib.import_module(f".{name}", __name__)
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if name in _LAZY_SYMBOLS:
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module_name, attribute = _LAZY_SYMBOLS[name]
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module = importlib.import_module(f".{module_name}", __name__)
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value = getattr(module, attribute)
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globals()[name] = value
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return value
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raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
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def __dir__():
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return sorted(set(globals()) | set(__all__))
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crystod/__main__.py
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crystod/_api.py
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"""Lazy attribute machinery for the public API namespaces.
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The domain API modules (``crystod.salc``, ``crystod.phonon``,
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``crystod.group``, ``crystod.bz``, ``crystod.md``, ``crystod.mag``,
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``crystod.mol``) are thin, curated views over the implementation modules.
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Because many implementation modules import phonopy/spgrep (and patch
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spglib compatibility) at import time, the views resolve their attributes
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lazily via PEP 562: ``import crystod.phonon`` is instant, and the heavy
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machinery is only pulled in when an attribute is first used.
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"""
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from __future__ import annotations
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import functools
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import importlib
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import inspect
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def _library_errors(function):
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"""Report bad input as ``ValueError`` instead of exiting the process.
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The implementation modules double as command-line entry points and
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report bad input the way a command line wants it, by raising
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``SystemExit``. That is right for a command and wrong for a library:
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``SystemExit`` derives from ``BaseException``, so a caller's
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``except Exception`` does not catch it and the whole program dies.
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The API namespaces translate it at their boundary.
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"""
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@functools.wraps(function)
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def wrapper(*args, **kwargs):
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try:
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return function(*args, **kwargs)
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except SystemExit as exc:
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message = " ".join(str(exc).split())
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raise ValueError(
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message.removeprefix("ERROR: ") or "invalid input"
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) from None
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return wrapper
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def lazy_namespace(module_globals: dict, exports: dict):
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"""Build ``__getattr__``, ``__dir__``, and ``__all__`` for an API module.
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``exports`` maps each public name to ``(implementation_module, attribute)``
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with the implementation module given relative to the ``crystod`` package.
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"""
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module_name = module_globals["__name__"]
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def __getattr__(name: str):
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try:
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target_module, attribute = exports[name]
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except KeyError:
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raise AttributeError(
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f"module {module_name!r} has no attribute {name!r}"
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) from None
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module = importlib.import_module(f".{target_module}", "crystod")
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value = getattr(module, attribute)
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if inspect.isfunction(value):
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value = _library_errors(value)
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module_globals[name] = value # cache; later access bypasses __getattr__
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return value
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def __dir__():
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dunders = {name for name in module_globals if name.startswith("__")}
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return sorted(dunders | set(exports))
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return __getattr__, __dir__, sorted(exports)
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crystod/atomic_levels.py
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"""Neutral-atom orbital energies from the archived PySCF
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calculations (reference/atomic_level_*, script
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script/generate_atomic_levels.py; Hartree-Fock, def2-svp with the
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def2 ECP beyond Kr, Stuttgart RSC 1997 for Ce-Yb and CRENBL for Lu
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-- 4f in the valence space). Energies in eV, spin- and m-averaged
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per shell; virtual shells included. AUTO-GENERATED by
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script/collect_atomic_levels.py -- do not edit by hand."""
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ATOMIC_LEVELS = {
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"H": {"electrons": 1, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -13.586, "2s": 4.944, "2p": 28.53}},
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"Li": {"electrons": 3, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -67.451, "2s": -2.418, "2p": 2.836, "3s": 2.774, "3p": 18.981}},
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"Be": {"electrons": 4, "ecp_core": 0, "method": "RHF/def2-svp",
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"levels": {"1s": -128.858, "2s": -8.311, "2p": 1.506, "3s": 5.059, "3p": 9.449}},
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"B": {"electrons": 5, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -209.324, "2s": -13.234, "2p": 0.097, "3s": 9.111, "3p": 13.445, "3d": 34.645}},
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"C": {"electrons": 6, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -308.023, "2s": -18.828, "2p": -2.204, "3s": 14.253, "3p": 19.693, "3d": 53.822}},
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"N": {"electrons": 7, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -425.05, "2s": -25.158, "2p": -5.543, "3s": 20.481, "3p": 26.877, "3d": 66.871}},
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"O": {"electrons": 8, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -562.081, "2s": -33.107, "2p": -10.307, "3s": 27.409, "3p": 31.817, "3d": 79.571}},
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"F": {"electrons": 9, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -717.492, "2s": -41.796, "2p": -16.058, "3s": 35.404, "3p": 38.333, "3d": 92.692}},
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"Na": {"electrons": 11, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -1101.352, "2s": -76.188, "2p": -41.414, "3s": -2.192, "3p": 2.171, "3d": 9.859, "4s": 3.69}},
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"Mg": {"electrons": 12, "ecp_core": 0, "method": "RHF/def2-svp",
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"levels": {"1s": -1334.333, "2s": -102.739, "2p": -62.342, "3s": -6.846, "3p": 1.464, "3d": 7.389, "4s": 3.676, "4p": 11.437}},
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"Al": {"electrons": 13, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -1590.98, "2s": -133.354, "2p": -87.383, "3s": -10.58, "3p": 0.032, "3d": 16.92, "4s": 5.629, "4p": 13.132}},
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"Si": {"electrons": 14, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -1871.456, "2s": -167.237, "2p": -115.624, "3s": -14.544, "3p": -1.841, "3d": 18.204, "4s": 7.927, "4p": 16.266}},
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"P": {"electrons": 15, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -2174.965, "2s": -204.095, "2p": -146.802, "3s": -18.723, "3p": -4.296, "3d": 21.618, "4s": 10.656, "4p": 20.933}},
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"S": {"electrons": 16, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -2502.232, "2s": -244.614, "2p": -181.592, "3s": -23.663, "3p": -7.563, "3d": 24.61, "4s": 13.587, "4p": 25.086}},
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"Cl": {"electrons": 17, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -2852.55, "2s": -288.171, "2p": -219.372, "3s": -28.847, "3p": -11.361, "3d": 27.624, "4s": 16.944, "4p": 30.137}},
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"K": {"electrons": 19, "ecp_core": 0, "method": "UHF/def2-svp",
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"levels": {"1s": -3633.406, "2s": -394.268, "2p": -313.524, "3s": -47.615, "3p": -26.011, "3d": 6.219, "4s": -1.878, "4p": 1.863, "4d": 19.746, "5s": 1.642}},
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"Ca": {"electrons": 20, "ecp_core": 0, "method": "RHF/def2-svp",
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|
+
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44
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45
|
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47
|
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48
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49
|
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50
|
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51
|
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52
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53
|
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55
|
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57
|
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59
|
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61
|
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62
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63
|
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65
|
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67
|
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69
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71
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73
|
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75
|
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77
|
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81
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83
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85
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86
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87
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89
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91
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92
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93
|
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94
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95
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96
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97
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98
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99
|
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100
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101
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102
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103
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104
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105
|
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106
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107
|
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108
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109
|
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110
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|
|
111
|
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112
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113
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114
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115
|
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116
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117
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118
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|
|
119
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120
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|
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121
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122
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|
|
123
|
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124
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|
|
125
|
+
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|
|
126
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|
|
127
|
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|
|
128
|
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|
|
129
|
+
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|
|
130
|
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|
|
131
|
+
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|
|
132
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|
|
133
|
+
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|
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134
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}
|