Metadata-Version: 2.4
Name: mbe_step
Version: 2026.10.6
Summary: A SEAMM plug-in for many-body expansion (MBE) corrections of periodic cells and clusters
Home-page: https://github.com/molssi-seamm/mbe_step
Author: Paul Saxe
Author-email: psaxe@molssi.org
License: BSD-3-Clause
Keywords: SEAMM,SEAMMplugin,flowchart
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Platform: Windows
Classifier: Environment :: Plugins
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: molsystem>=2026.9.20
Requires-Dist: model-chemistry-step>=2026.10.3
Requires-Dist: numpy
Requires-Dist: seamm>=2026.10.3
Requires-Dist: seamm-exec>=2026.10.3.2
Requires-Dist: seamm-bsse>=2026.8.7.1
Requires-Dist: seamm-mbe>=2026.10.6
Requires-Dist: seamm-util
Requires-Dist: seamm-widgets
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: platform
Dynamic: requires-dist
Dynamic: summary

=================
SEAMM MBE Plug-in
=================

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   :target: https://github.com/molssi-seamm/mbe_step/pulls
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A SEAMM plug-in for many-body expansion (MBE) corrections of periodic cells and clusters

* Free software: BSD-3-Clause
* Documentation: https://molssi-seamm.github.io/mbe_step/index.html
* Code: https://github.com/molssi-seamm/mbe_step

Features
--------

* Please edit this section!

Acknowledgements
----------------

This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
is based on the excellent Cookiecutter_.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award CHE-2136142.

.. _MolSSI: https://molssi.org
.. _`National Science Foundation`: https://www.nsf.gov


=======
History
=======

2026.10.6 -- A low level of their own for the triples
    * The new 'triples low level' gives the triples' increments their own molecular low
      level, e.g. r2SCAN-D4 at def2-TZVPPD with the molecular low level at def2-QZVPPD
      for the pairs. Each triple's increment is built entirely at that level, so the
      triples' monomers and pairs are computed at both levels. It is shown only when
      there are triples; by default it is the molecular low level. A triples' low level
      that is the molecular low level under another name is refused.
    * The increments file records each increment's low level.
    * The user guide explains when to use the periodic low level for the monomers only.
    * Requires seamm-mbe 2026.10.6.

2026.10.5 -- A high level of their own for the triples; the increments in a file
    * The new 'triples high level' gives the triples' increments their own high
      level, e.g. revDSD at def2-TZVPPD with the high level at def2-QZVPPD for the
      monomers and pairs. Each triple's increment is built entirely at that level, so
      the triples' monomers and pairs are computed at both levels. It is shown only
      when there are triples; by default it is the high level. A triples' level that
      is the high level under another name is refused, since every monomer and pair
      would be computed twice.
    * Each configuration's increments are written to
      increments_c<configuration id>.json in the step's directory, for later
      analysis: each fragment's molecules, images, pair distances, levels, energy and
      forces, with triples marked "chain" or "closed".
    * Requires seamm-mbe 2026.10.5.

2026.10.4.1 -- Pairwise counterpoise corrects the high level only by default
    * 'pairwise' counterpoise now corrects each pair at the high level only. The new
      choice 'pairwise, both levels' also corrects the molecular low level, as
      'pairwise' did before. In tests on Li⁺/BF₄⁻/water/EC clusters the r2SCAN-D4
      correction was tiny where it could be computed, and its ghost calculations
      sometimes ended at spurious energies, while the revDSD correction was 3–4
      kJ/mol per molecule.
    * The user guide notes that ORCA's ghost-atom gradients are unreliable for
      double hybrids such as revDSD, so counterpoise-corrected forces from them need
      caution.

2026.10.4 -- Requires seamm-exec 2026.10.3.2 for running on a cluster
    * Requires seamm-exec 2026.10.3.2: each bundle of calculations sent to a cluster's
      queue now runs on one node, a calculation runs inside the job itself only when it
      fits there, and bundles get a time limit from their calculations' estimated cost.
      Before, a VASP or ORCA calculation could be spread over several nodes and fail, or
      be cut off by the queue's default time limit.
    * Checked end to end on TinkerCliffs: the 64-water pilot frame reproduces the
      prototype's labels (energy to 0.001 meV, forces to 0.2 meV/Å RMS, pressures to
      about 1 atm).

2026.10.3 -- Initial release: many-body expansion (MBE) corrections
    * A step that estimates high-level energies, forces and, for periodic cells, the
      stress of a cell or a large cluster: a low-level calculation of the whole system
      plus [high - low] corrections computed on monomers, pairs and triples of
      molecules, using the seamm_mbe library.
    * The levels are model chemistries: the high level, a molecular low level, and
      optionally a periodic low level (e.g. VASP) for the fragments of periodic cells,
      run as batches of calculations through seamm_exec.
    * Pair and triple cutoffs, a rule for which triples to include, and a check that
      the cell is large enough for the chosen cutoffs.
    * For a periodic low level, the fragments are placed on the cell's FFT grid so that
      the grid errors cancel between the cell and its fragments.
    * Optional pairwise counterpoise correction of the basis-set superposition error.
    * Optional energy offsets per molecule type, and the results stored as properties
      and written to an extended XYZ file for training machine-learned force fields.
