lineshape_tools 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

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Files changed (7) hide show
  1. lineshape_tools/__init__.py +1 -1
  2. lineshape_tools/cli.py +7 -0
  3. {lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/METADATA +1 -1
  4. {lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/RECORD +7 -7
  5. {lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/WHEEL +1 -1
  6. {lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/entry_points.txt +0 -0
  7. {lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/licenses/LICENSE +0 -0
lineshape_tools/__init__.py CHANGED
@@ -2,6 +2,6 @@
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  __author__ = "Mark E. Turiansky"
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  __email__ = "mark.e.turiansky.ctr@us.navy.mil"
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- __version__ = "0.1.1"
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+ __version__ = "0.1.2"
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  __copyright__ = "Copyright (c) 2025 Mark E. Turiansky"
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  __license__ = "MIT"
lineshape_tools/cli.py CHANGED
@@ -37,6 +37,7 @@ def collect(
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  rtol: float = 1e-5,
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  config_weight: float = 1.0,
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  force_weighting: bool = False,
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+ allow_constraint: bool = False,
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  ) -> None:
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  """Collect and process data for fine-tuning.
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@@ -66,6 +67,8 @@ def collect(
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  force_weighting (bool): store a config_weight that's inversely proportional to the max
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  force that any atom feels in the configuration [min(0.02 / max_fpa, 1)]. Overwrites
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  the value specified by config_weight.
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+ allow_constraint (bool): allow constraints on atoms (e.g. selective dynamics) to modify the
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+ forces. This is typically not desirable.
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  """
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  if strategy.lower() not in ("none", "qr", "dx"):
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  raise ValueError("invalid strategy choice")
@@ -79,6 +82,10 @@ def collect(
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  read_atoms = ase.io.read(fname, read_index)
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  total_read += len(read_atoms)
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  for atoms in tqdm(read_atoms, desc="[*] processing atoms", disable=len(read_atoms) < 10):
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+ if len(atoms.constraints) > 0 and not allow_constraint:
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+ logger.debug("atoms are constrained, removing prior to extracting forces")
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+ atoms.set_constraint(None)
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+
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  forces = atoms.get_forces()
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  if min_force < np.linalg.norm(forces, axis=1).max() < max_force:
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  atoms.info["REF_energy"] = atoms.get_potential_energy()
{lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: lineshape_tools
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Software to evaluate the optical lineshape function of a defect.
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  Keywords: defect,luminescence,absorption,electron-phonon coupling,density functional theory
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  Author-Email: "Mark E. Turiansky" <mark.e.turiansky.ctr@us.navy.mil>
{lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/RECORD RENAMED
@@ -1,8 +1,8 @@
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- lineshape_tools-0.1.1.dist-info/METADATA,sha256=hW9TR8b4pzQr0SjsgKF1GhNgHLsik697AazwVaSXanA,3677
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- lineshape_tools-0.1.1.dist-info/WHEEL,sha256=9P2ygRxDrTJz3gsagc0Z96ukrxjr-LFBGOgv3AuKlCA,90
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- lineshape_tools-0.1.1.dist-info/entry_points.txt,sha256=UXygiyrvvwic-jiUrHINzx3lUR27qjyd1BJRY6S1Mdg,86
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- lineshape_tools-0.1.1.dist-info/licenses/LICENSE,sha256=2AJLb-6XbTVThSycPkXkvDVAf697F5rbWWY8SicUdf4,1074
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- lineshape_tools/__init__.py,sha256=4EslhkZ8XtRc1m5zxW-VfC4rAsoMt4Kj5yUnHna8vuo,213
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+ lineshape_tools-0.1.2.dist-info/METADATA,sha256=BXG4V2PE1x4bPk2pa7fWRbO7wFYFM0vxrgytGqlznVU,3677
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+ lineshape_tools-0.1.2.dist-info/WHEEL,sha256=Wb0ASbVj8JvWHpOiIpPi7ucfIgJeCi__PzivviEAQFc,90
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+ lineshape_tools-0.1.2.dist-info/entry_points.txt,sha256=UXygiyrvvwic-jiUrHINzx3lUR27qjyd1BJRY6S1Mdg,86
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+ lineshape_tools-0.1.2.dist-info/licenses/LICENSE,sha256=2AJLb-6XbTVThSycPkXkvDVAf697F5rbWWY8SicUdf4,1074
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+ lineshape_tools/__init__.py,sha256=aQaLQQHq0Nyf1_4NNTGKXls23J9qpETklvJXyN6GRpw,213
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  lineshape_tools/__main__.py,sha256=X3QJ708vxRsHQhZkYDIDZlwQC0HuBO2bzZmN41KXutM,1250
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  lineshape_tools/__pycache__/lineshape._do_compute_phonon_spec_func-128.py311.1.nbc,sha256=_3BI5pjGXDDN1HAB8ZaShO60thkupbe5qfuKJTRXFZM,258854
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  lineshape_tools/__pycache__/lineshape._do_compute_phonon_spec_func-128.py311.nbi,sha256=999q880zQH3rZcqOToQ94g1sevjIIQrXRniHGcG88Ck,1752
@@ -12,9 +12,9 @@ lineshape_tools/__pycache__/lineshape.gaussian-26.py311.1.nbc,sha256=mKBwgnhBXFR
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  lineshape_tools/__pycache__/lineshape.gaussian-26.py311.nbi,sha256=4i8Jmz968WrJshLUQGQFU0CMn2biEQoxXvsmgGnvN1M,1317
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  lineshape_tools/__pycache__/lineshape.lorentzian-32.py311.1.nbc,sha256=PHMHumjybDinzvEgW_045EFobJRldbJhvSbBzZNexfI,28028
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  lineshape_tools/__pycache__/lineshape.lorentzian-32.py311.nbi,sha256=VDnI92WrDEOuhT_9dlqIahDhdDOKpAnweuiPHWko8UI,1319
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- lineshape_tools/cli.py,sha256=aMO9D2hfKPSCJCHYNg5y4h2XtfS3p6LLOHBoNQlUw1A,38826
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+ lineshape_tools/cli.py,sha256=342cwe19_7Aa3nYvU20OHH-LlIAlcjsZFoDBsvXdZjU,39218
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  lineshape_tools/constants.py,sha256=fNcTHWHajyIYbTnEM4sHHygL7MqEuULjZl_Pf2ojrE0,122
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  lineshape_tools/lineshape.py,sha256=bkdOi2pt_EiKVkpoMdWvVlYLfvp1AgWOFRVQyR2lBUY,9704
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  lineshape_tools/phonon.py,sha256=Lk8zVB_02Vzr-rvrVxqn3Bpj2PhxZSwThWuNSFCfl0c,2350
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  lineshape_tools/plot.py,sha256=YEeLWjQSSvid9BCcj0jfl654WGQn0FdNUDY9smCHI3Q,9932
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- lineshape_tools-0.1.1.dist-info/RECORD,,
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+ lineshape_tools-0.1.2.dist-info/RECORD,,
{lineshape_tools-0.1.1.dist-info → lineshape_tools-0.1.2.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: pdm-backend (2.4.5)
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+ Generator: pdm-backend (2.4.7)
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  Root-Is-Purelib: true
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  Tag: py3-none-any