xtb-step 2026.5.12__py2.py3-none-any.whl

xtb_step/__init__.py

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+# -*- coding: utf-8 -*-
+
+"""
+xtb_step
+A SEAMM plug-in for xTB
+"""
+
+# Bring up the classes so that they appear to be directly in
+# the xtb_step package.
+
+from .xtb import xTB  # noqa: F401, E501
+from .xtb_step import xTBStep  # noqa: F401, E501
+from .tk_xtb import TkxTB  # noqa: F401, E501
+
+from .metadata import metadata  # noqa: F401
+
+from .energy_step import EnergyStep  # noqa: F401
+from .energy import Energy  # noqa: F401
+from .energy_parameters import EnergyParameters  # noqa: F401
+from .tk_energy import TkEnergy  # noqa: F401
+
+from .optimization_step import OptimizationStep  # noqa: F401
+from .optimization import Optimization  # noqa: F401
+from .optimization_parameters import OptimizationParameters  # noqa: F401
+from .tk_optimization import TkOptimization  # noqa: F401
+
+from .frequencies_step import FrequenciesStep  # noqa: F401
+from .frequencies import Frequencies  # noqa: F401
+from .frequencies_parameters import FrequenciesParameters  # noqa: F401
+from .tk_frequencies import TkFrequencies  # noqa: F401
+
+# Handle versioneer
+from ._version import get_versions
+
+__author__ = "Paul Saxe"
+__email__ = "psaxe@molssi.org"
+versions = get_versions()
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
+del get_versions, versions

xtb_step/__main__.py

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+# !/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Handle the installation of the xTB step."""
+
+from .installer import Installer
+
+
+def run():
+    """Handle the extra installation needed.
+
+    * Find and/or install the xtb executable.
+    * Add or update information in the SEAMM xtb.ini file for xTB.
+    """
+
+    # Create an installer object
+    installer = Installer()
+    installer.run()
+
+
+if __name__ == "__main__":
+    run()

xtb_step/_version.py

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+
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2026-05-12T11:03:57-0400",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "69d83a79020d663ae50dd59da590488f68d82516",
+ "version": "2026.5.12"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

xtb_step/data/properties.csv

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+Property,Type,Units,Description,URL
+total energy#xTB#{model},float,E_h,"The {model} total energy.",
+electronic energy#xTB#{model},float,E_h,"The {model} electronic energy (excluding nuclear repulsion).",
+HOMO energy#xTB#{model},float,eV,"The {model} energy of the highest occupied molecular orbital (HOMO).",https://en.wikipedia.org/wiki/HOMO_and_LUMO
+LUMO energy#xTB#{model},float,eV,"The {model} energy of the lowest unoccupied molecular orbital (LUMO).",https://en.wikipedia.org/wiki/HOMO_and_LUMO
+band gap#xTB#{model},float,eV,"The {model} HOMO-LUMO gap.",https://en.wikipedia.org/wiki/Band_gap
+dipole moment#xTB#{model},float,debye,"The {model} electric dipole moment, magnitude of the dipole vector.",https://en.wikipedia.org/wiki/Electric_dipole_moment
+gradients#xTB#{model},json,E_h/Å,The {model} gradients of the energy with respect to the atomic coordinates.,
+force constants#xTB#{model},json,E_h/Å^2,The {model} mass-weighted Hessian / force constants.,
+enthalpy of formation#xTB#{model},float,kJ/mol,"The {model} enthalpy of formation.",https://en.wikipedia.org/wiki/Standard_enthalpy_of_formation
+zero point energy#xTB#{model},float,kJ/mol,"The {model} zero-point vibrational energy.",
+entropy#xTB#{model},float,J/mol/K,"The {model} standard entropy at the chosen temperature and pressure.",https://en.wikipedia.org/wiki/Entropy
+constant pressure heat capacity#xTB#{model},float,J/mol/K,"The {model} constant-pressure heat capacity, Cp.",https://en.wikipedia.org/wiki/Heat_capacity
+Gibbs free energy#xTB#{model},float,kJ/mol,"The {model} Gibbs free energy at the chosen temperature and pressure.",

xtb_step/data/references.bib

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+This is an initial library of BibTex references for the xtb_step plug-in for SEAMM,
+generated automatically by the cookiecutter. You may wish to edit the first entry to correct some
+of the information.
+
+Add other references to the end of the file and add code in the plug-in to cite the references as
+appropriate. This is done with code like this:
+
+        self.references.cite(
+            raw=self._bibliography['doi:10.1002/jcc.21224'],
+            alias='packmol',
+            module='packmol_step',
+            level=1,
+            note='The principle PACKMOL citation.'
+        )
+
+which is typically in the run() method of the plug-in.
+
+The base node class in SEAMM automatically reads this list of references into a dictionary in
+self._bibliography with the key being the key of the BibTex entry -- usually the name on the
+first line of the entry after the 'article' or 'misc' (for software) keyword.
+
+See the documentation for the Reference Handler for the other arguments to cite().
+
+# End of initial comments #
+
+# This is the citation for this plug-in, generated and used automatically.
+# You might need to edit the author, address, etc. The month, year and version fields
+# are automatically filled in with information about current version of the plug-in.
+# This is handled in seamm/nody.py, the run() method.
+
+@Misc{xtb_step,
+	author = {Paul Saxe},
+	title = {xTB plug-in for SEAMM},
+	month = {$month},
+	year = {$year},
+	organization = {The Molecular Sciences Software Institute (MolSSI)},
+	url = {https://github.com/molssi-seamm/xtb_step},
+	address = {Virginia Tech, Blacksburg, VA, USA},
+	version = {$version}
+}
+
+# ----------------------------------------------------------------------
+# References for xTB itself and the GFN method family
+# ----------------------------------------------------------------------
+
+# The general xTB review. Cited at level 1 whenever any GFN-x-TB or GFN-FF
+# method is used.
+@article{Bannwarth2021,
+	author = {Bannwarth, Christoph and Caldeweyher, Eike and Ehlert, Sebastian and
+	          Hansen, Andreas and Pracht, Philipp and Seibert, Jakob and
+	          Spicher, Sebastian and Grimme, Stefan},
+	title = {Extended tight-binding quantum chemistry methods},
+	journal = {WIREs Computational Molecular Science},
+	volume = {11},
+	number = {2},
+	pages = {e1493},
+	year = {2021},
+	doi = {10.1002/wcms.1493},
+	url = {https://doi.org/10.1002/wcms.1493}
+}
+
+# GFN2-xTB primary citation.
+@article{Bannwarth2019,
+	author = {Bannwarth, Christoph and Ehlert, Sebastian and Grimme, Stefan},
+	title = {{GFN2}-{xTB}---{An} Accurate and Broadly Parametrized Self-Consistent
+	         Tight-Binding Quantum Chemical Method with Multipole Electrostatics
+	         and Density-Dependent Dispersion Contributions},
+	journal = {Journal of Chemical Theory and Computation},
+	volume = {15},
+	number = {3},
+	pages = {1652--1671},
+	year = {2019},
+	doi = {10.1021/acs.jctc.8b01176},
+	url = {https://doi.org/10.1021/acs.jctc.8b01176}
+}
+
+# GFN1-xTB primary citation.
+@article{Grimme2017,
+	author = {Grimme, Stefan and Bannwarth, Christoph and Shushkov, Philip},
+	title = {A Robust and Accurate Tight-Binding Quantum Chemical Method for
+	         Structures, Vibrational Frequencies, and Noncovalent Interactions of
+	         Large Molecular Systems Parametrized for All spd-Block Elements
+	         ({Z} = 1--86)},
+	journal = {Journal of Chemical Theory and Computation},
+	volume = {13},
+	number = {5},
+	pages = {1989--2009},
+	year = {2017},
+	doi = {10.1021/acs.jctc.7b00118},
+	url = {https://doi.org/10.1021/acs.jctc.7b00118}
+}
+
+# GFN0-xTB. As of last check, this method has only a ChemRxiv preprint, not a
+# peer-reviewed journal paper. Update if/when a journal version appears.
+@misc{Pracht2019,
+	author = {Pracht, Philipp and Caldeweyher, Eike and Ehlert, Sebastian and
+	          Grimme, Stefan},
+	title = {A Robust Non-Self-Consistent Tight-Binding Quantum Chemistry Method
+	         for Large Molecules},
+	howpublished = {ChemRxiv preprint},
+	year = {2019},
+	doi = {10.26434/chemrxiv.8326202.v1},
+	url = {https://doi.org/10.26434/chemrxiv.8326202.v1},
+	note = {Preprint; no peer-reviewed journal paper as of plug-in v1 release.}
+}
+
+# GFN-FF: a generic force field automatically parameterized via xTB.
+@article{Spicher2020,
+	author = {Spicher, Sebastian and Grimme, Stefan},
+	title = {Robust Atomistic Modeling of Materials, Organometallic, and
+	         Biochemical Systems},
+	journal = {Angewandte Chemie International Edition},
+	volume = {59},
+	number = {36},
+	pages = {15665--15673},
+	year = {2020},
+	doi = {10.1002/anie.202004239},
+	url = {https://doi.org/10.1002/anie.202004239}
+}
+
+# Implicit solvation: ALPB and the related GBSA implementation in xTB.
+@article{Ehlert2021,
+	author = {Ehlert, Sebastian and Stahn, Marcel and Spicher, Sebastian and
+	          Grimme, Stefan},
+	title = {Robust and Efficient Implicit Solvation Model for Fast
+	         Semiempirical Methods},
+	journal = {Journal of Chemical Theory and Computation},
+	volume = {17},
+	number = {7},
+	pages = {4250--4261},
+	year = {2021},
+	doi = {10.1021/acs.jctc.1c00471},
+	url = {https://doi.org/10.1021/acs.jctc.1c00471}
+}
+
+# CPCM-X solvation model. Cited at level 1 when CPCM-X is selected.
+@article{Stahn2023,
+	author = {Stahn, Marcel and Ehlert, Sebastian and Grimme, Stefan},
+	title = {Extended Conductor-like Polarizable Continuum Solvation Model
+	         ({CPCM-X}) for Semiempirical Methods},
+	journal = {The Journal of Physical Chemistry A},
+	volume = {127},
+	number = {33},
+	pages = {7036--7043},
+	year = {2023},
+	doi = {10.1021/acs.jpca.3c04382},
+	url = {https://doi.org/10.1021/acs.jpca.3c04382}
+}
+
+# ----------------------------------------------------------------------
+# Component citations -- secondary (level 2)
+# ----------------------------------------------------------------------
+
+# DFT-D4 dispersion correction. Cited at level 2 whenever a method that
+# uses D4-style dispersion is invoked (GFN2-xTB in v1).
+@article{Caldeweyher2017,
+	author = {Caldeweyher, Eike and Bannwarth, Christoph and Grimme, Stefan},
+	title = {Extension of the {D3} Dispersion Coefficient Model},
+	journal = {The Journal of Chemical Physics},
+	volume = {147},
+	number = {3},
+	pages = {034112},
+	year = {2017},
+	doi = {10.1063/1.4993215},
+	url = {https://doi.org/10.1063/1.4993215}
+}
+
+@article{Caldeweyher2019,
+	author = {Caldeweyher, Eike and Ehlert, Sebastian and Hansen, Andreas and
+	          Neugebauer, Hagen and Spicher, Sebastian and Bannwarth, Christoph
+	          and Grimme, Stefan},
+	title = {A Generally Applicable Atomic-Charge Dependent {London} Dispersion
+	         Correction},
+	journal = {The Journal of Chemical Physics},
+	volume = {150},
+	number = {15},
+	pages = {154122},
+	year = {2019},
+	doi = {10.1063/1.5090222},
+	url = {https://doi.org/10.1063/1.5090222}
+}
+
+@article{Caldeweyher2020,
+	author = {Caldeweyher, Eike and Mewes, Jan-Michael and Ehlert, Sebastian
+	          and Grimme, Stefan},
+	title = {Extension and Evaluation of the {D4} London-Dispersion Model
+	         for Periodic Systems},
+	journal = {Physical Chemistry Chemical Physics},
+	volume = {22},
+	number = {16},
+	pages = {8499--8512},
+	year = {2020},
+	doi = {10.1039/D0CP00502A},
+	url = {https://doi.org/10.1039/D0CP00502A}
+}

xtb_step/data/seamm-xtb.yml

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+name: seamm-xtb
+channels:
+  - conda-forge
+dependencies:
+  - python
+  - xtb

xtb_step/data/xtb.ini

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+# Configuration options for how to run xTB
+
+[docker]
+# The code to use. This may be more than just the name of the code, and variables in
+# braces {} will be expanded. For example:
+#   code = mpiexec -np {NTASKS} xtb
+# would expand {NTASKS} to the number of tasks and run the command
+
+code = xtb
+
+# The name and location of the Docker container to use, optionally with the version
+
+container = ghcr.io/molssi-seamm/seamm-xtb:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# apple silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64
+
+[local]
+# The type of local installation to use. Options are:
+#     conda: Use a conda environment
+#   modules: Use the modules system
+#     local: Use a local installation
+#    docker: Use a Docker container
+# By default SEAMM installs xTB using conda from conda-forge.
+
+installation = conda
+
+# The command line to use, which should start with the executable followed by any options.
+# Variables in braces {} will be expanded. For example:
+#
+#   code = mpiexec -np {NTASKS} xtb
+#
+# would expand {NTASKS} to the number of tasks and run the command.
+# For a 'local' installation, the command line should include the full path to the
+# executable or it should be in the path.
+
+code = xtb
+
+######################### conda section ############################
+# The full path to the conda executable:
+
+# conda =
+
+# The Conda environment to use. This is either the name or full path.
+
+# conda-environment = seamm-xtb
+
+######################### modules section ############################
+# The modules to load to run xTB, as a list of strings.
+# For example:
+#   modules = xtb
+
+# modules =
+
+######################### local section ############################
+# The full path to the xTB executable should be in the 'code' option.
+
+######################### docker section ############################
+# The name and location of the Docker container to use, optionally with the version.
+# {version} will be expanded to the version of the plug-in.
+
+# container = ghcr.io/molssi-seamm/seamm-xtb:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# apple silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64