xtb-step 2026.5.12__tar.gz

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  1. xtb_step-2026.5.12/AUTHORS.rst +5 -0
  2. xtb_step-2026.5.12/CONTRIBUTING.rst +113 -0
  3. xtb_step-2026.5.12/HISTORY.rst +10 -0
  4. xtb_step-2026.5.12/LICENSE +31 -0
  5. xtb_step-2026.5.12/MANIFEST.in +14 -0
  6. xtb_step-2026.5.12/PKG-INFO +158 -0
  7. xtb_step-2026.5.12/README.rst +104 -0
  8. xtb_step-2026.5.12/docs/Makefile +177 -0
  9. xtb_step-2026.5.12/docs/_static/SEAMM Inverted 288x181.png +0 -0
  10. xtb_step-2026.5.12/docs/_static/SEAMM logo.png +0 -0
  11. xtb_step-2026.5.12/docs/_static/molssi_main_logo.png +0 -0
  12. xtb_step-2026.5.12/docs/_static/molssi_main_logo_inverted_white.png +0 -0
  13. xtb_step-2026.5.12/docs/_static/molssi_square.png +0 -0
  14. xtb_step-2026.5.12/docs/_static/nsf.png +0 -0
  15. xtb_step-2026.5.12/docs/api/index.rst +17 -0
  16. xtb_step-2026.5.12/docs/authors.rst +1 -0
  17. xtb_step-2026.5.12/docs/conf.py +306 -0
  18. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_A.rst +133 -0
  19. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_B.rst +217 -0
  20. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_C.rst +108 -0
  21. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_D.rst +198 -0
  22. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_E.rst +124 -0
  23. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_F.rst +159 -0
  24. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_G.rst +139 -0
  25. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_H.rst +172 -0
  26. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_I.rst +187 -0
  27. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/NOTES_Installer.rst +106 -0
  28. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/index.rst +18 -0
  29. xtb_step-2026.5.12/docs/developer_guide/campaigns/2026-05-02/xtb_step_v1_scope.rst +330 -0
  30. xtb_step-2026.5.12/docs/developer_guide/campaigns/index.rst +11 -0
  31. xtb_step-2026.5.12/docs/developer_guide/contributing.rst +1 -0
  32. xtb_step-2026.5.12/docs/developer_guide/index.rst +28 -0
  33. xtb_step-2026.5.12/docs/developer_guide/installation.rst +54 -0
  34. xtb_step-2026.5.12/docs/developer_guide/usage.rst +7 -0
  35. xtb_step-2026.5.12/docs/getting_started/index.rst +83 -0
  36. xtb_step-2026.5.12/docs/history.rst +1 -0
  37. xtb_step-2026.5.12/docs/index.rst +76 -0
  38. xtb_step-2026.5.12/docs/make.bat +242 -0
  39. xtb_step-2026.5.12/docs/user_guide/energy.rst +69 -0
  40. xtb_step-2026.5.12/docs/user_guide/frequencies.rst +102 -0
  41. xtb_step-2026.5.12/docs/user_guide/index.rst +71 -0
  42. xtb_step-2026.5.12/docs/user_guide/methods.rst +108 -0
  43. xtb_step-2026.5.12/docs/user_guide/optimization.rst +68 -0
  44. xtb_step-2026.5.12/docs/user_guide/results.rst +106 -0
  45. xtb_step-2026.5.12/docs/user_guide/solvation.rst +95 -0
  46. xtb_step-2026.5.12/requirements.txt +3 -0
  47. xtb_step-2026.5.12/requirements_dev.txt +10 -0
  48. xtb_step-2026.5.12/requirements_install.txt +4 -0
  49. xtb_step-2026.5.12/setup.cfg +27 -0
  50. xtb_step-2026.5.12/setup.py +100 -0
  51. xtb_step-2026.5.12/tests/__init__.py +3 -0
  52. xtb_step-2026.5.12/tests/test_xtb_step.py +13 -0
  53. xtb_step-2026.5.12/versioneer.py +1822 -0
  54. xtb_step-2026.5.12/xtb_step/__init__.py +40 -0
  55. xtb_step-2026.5.12/xtb_step/__main__.py +22 -0
  56. xtb_step-2026.5.12/xtb_step/_version.py +21 -0
  57. xtb_step-2026.5.12/xtb_step/data/properties.csv +14 -0
  58. xtb_step-2026.5.12/xtb_step/data/references.bib +195 -0
  59. xtb_step-2026.5.12/xtb_step/data/seamm-xtb.yml +6 -0
  60. xtb_step-2026.5.12/xtb_step/data/xtb.ini +71 -0
  61. xtb_step-2026.5.12/xtb_step/energy.py +493 -0
  62. xtb_step-2026.5.12/xtb_step/energy_parameters.py +136 -0
  63. xtb_step-2026.5.12/xtb_step/energy_step.py +95 -0
  64. xtb_step-2026.5.12/xtb_step/frequencies.py +349 -0
  65. xtb_step-2026.5.12/xtb_step/frequencies_parameters.py +82 -0
  66. xtb_step-2026.5.12/xtb_step/frequencies_step.py +95 -0
  67. xtb_step-2026.5.12/xtb_step/installer.py +131 -0
  68. xtb_step-2026.5.12/xtb_step/metadata.py +253 -0
  69. xtb_step-2026.5.12/xtb_step/optimization.py +183 -0
  70. xtb_step-2026.5.12/xtb_step/optimization_parameters.py +97 -0
  71. xtb_step-2026.5.12/xtb_step/optimization_step.py +95 -0
  72. xtb_step-2026.5.12/xtb_step/substep.py +563 -0
  73. xtb_step-2026.5.12/xtb_step/tk_energy.py +185 -0
  74. xtb_step-2026.5.12/xtb_step/tk_frequencies.py +108 -0
  75. xtb_step-2026.5.12/xtb_step/tk_optimization.py +94 -0
  76. xtb_step-2026.5.12/xtb_step/tk_xtb.py +151 -0
  77. xtb_step-2026.5.12/xtb_step/xtb.py +223 -0
  78. xtb_step-2026.5.12/xtb_step/xtb_step.py +95 -0
  79. xtb_step-2026.5.12/xtb_step.egg-info/PKG-INFO +158 -0
  80. xtb_step-2026.5.12/xtb_step.egg-info/SOURCES.txt +84 -0
  81. xtb_step-2026.5.12/xtb_step.egg-info/dependency_links.txt +1 -0
  82. xtb_step-2026.5.12/xtb_step.egg-info/entry_points.txt +18 -0
  83. xtb_step-2026.5.12/xtb_step.egg-info/requires.txt +3 -0
  84. xtb_step-2026.5.12/xtb_step.egg-info/top_level.txt +1 -0
  85. xtb_step-2026.5.12/xtb_step.egg-info/zip-safe +1 -0
@@ -0,0 +1,5 @@
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+ Development Team
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+ ----------------
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+
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+ * Paul Saxe <psaxe@molssi.org> (Lead)
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+ * Why don't you join the team? Become a contributor!
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+ .. highlight:: shell
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+
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+ ============
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+ Contributing
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+ ============
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+
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+ Contributions are welcome, and they are greatly appreciated! Every
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+ little bit helps, and credit will always be given.
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+
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+ You can contribute in many ways:
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+
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+ Types of Contributions
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+ ----------------------
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+
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+ Report Bugs
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+ ~~~~~~~~~~~
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+
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+ Report bugs at https://github.com/molssi-seamm/xtb_step/issues.
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+
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+ If you are reporting a bug, please include:
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+
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+ * Your operating system name and version.
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+ * Any details about your local setup that might be helpful in troubleshooting.
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+ * Detailed steps to reproduce the bug.
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+
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+ Fix Bugs
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+ ~~~~~~~~
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+
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+ Look through the GitHub issues for bugs. Anything tagged with "bug"
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+ and "help wanted" is open to whoever wants to implement it.
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+
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+ Implement Features
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+ ~~~~~~~~~~~~~~~~~~
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+
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+ Look through the GitHub issues for features. Anything tagged with "enhancement"
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+ and "help wanted" is open to whoever wants to implement it.
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+
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+ Write Documentation
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+ ~~~~~~~~~~~~~~~~~~~
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+
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+ xTB Step could always use more documentation, whether as part of the
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+ official xTB Step docs, in docstrings, or even on the web in blog posts,
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+ articles, and such.
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+
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+ Submit Feedback
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+ ~~~~~~~~~~~~~~~
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+
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+ The best way to send feedback is to file an issue at https://github.com/molssi-seamm/xtb_step/issues.
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+
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+ If you are proposing a feature:
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+
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+ * Explain in detail how it would work.
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+ * Keep the scope as narrow as possible, to make it easier to implement.
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+ * Remember that this is a volunteer-driven project, and that contributions
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+ are welcome :)
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+
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+ Get Started!
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+ ------------
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+
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+ Ready to contribute? Here's how to set up `xtb_step` for local development.
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+
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+ 1. Fork the `xtb_step` repo on GitHub.
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+ 2. Clone your fork locally::
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+
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+ $ git clone git@github.com:your_name_here/xtb_step.git
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+
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+ 3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
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+
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+ $ mkvirtualenv xtb_step
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+ $ cd xtb_step/
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+ $ python setup.py develop
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+
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+ 4. Create a branch for local development::
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+
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+ $ git checkout -b name-of-your-bugfix-or-feature
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+
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+ Now you can make your changes locally.
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+
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+ 5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
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+
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+ $ flake8 xtb_step tests
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+ $ python setup.py test or py.test
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+ $ tox
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+
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+ To get flake8 and tox, just pip install them into your virtualenv.
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+
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+ 6. Commit your changes and push your branch to GitHub::
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+
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+ $ git add .
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+ $ git commit -m "Your detailed description of your changes."
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+ $ git push origin name-of-your-bugfix-or-feature
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+
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+ 7. Submit a pull request through the GitHub website.
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+
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+ Pull Request Guidelines
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+ -----------------------
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+
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+ Before you submit a pull request, check that it meets these guidelines:
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+
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+ 1. The pull request should include tests.
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+ 2. If the pull request adds functionality, the docs should be updated. Put
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+ your new functionality into a function with a docstring, and add the
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+ feature to the list in README.rst.
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+ 3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
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+ https://travis-ci.org/molssi-seamm/xtb_step/pull_requests
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+ and make sure that the tests pass for all supported Python versions.
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+
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+ Tips
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+ ----
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+
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+ To run a subset of tests::
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+
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+ $ py.test tests.test_xtb_step
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+ =======
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+ History
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+ =======
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+
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+ 2026.5.2: Plug-in created using the SEAMM plug-in cookiecutter.
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+
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+ 2026.5.12: Initial working version
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+ * Support for Energy, Optimization, and Frequencies
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+ * GFN0-xTB, GFN1-xTB, GFN2-xTB (the default), and GFN-FF supported
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+ * ALPB, GBSA, or CPCM-X implicit solvation
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+
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+ BSD 3-Clause License
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+
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+ Copyright (c) 2026, Paul Saxe
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+ All rights reserved.
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are met:
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+
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+ 1. Redistributions of source code must retain the above copyright notice, this
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+ list of conditions and the following disclaimer.
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+
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+ 2. Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
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+ and/or other materials provided with the distribution.
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+
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+ 3. Neither the name of the copyright holder nor the names of its
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+ contributors may be used to endorse or promote products derived from
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+ this software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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+
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+ include AUTHORS.rst
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+ include CONTRIBUTING.rst
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+ include HISTORY.rst
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+ include LICENSE
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+ include README.rst
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+ include requirements*
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+ include versioneer.py
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+
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+ recursive-include xtb_step/data *
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+ recursive-include tests *
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+ recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
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+
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+ recursive-exclude * __pycache__
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+ recursive-exclude * *.py[co]
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+ Metadata-Version: 2.4
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+ Name: xtb_step
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+ Version: 2026.5.12
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+ Summary: A SEAMM plug-in for xTB
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+ Home-page: https://github.com/molssi-seamm/xtb_step
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+ Author: Paul Saxe
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+ Author-email: psaxe@molssi.org
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+ License: BSD-3-Clause
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+ Keywords: SEAMM,SEAMMplugin,flowchart
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+ Platform: Linux
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+ Platform: Mac OS-X
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+ Platform: Unix
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+ Platform: Windows
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+ Classifier: Environment :: Plugins
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+ Classifier: Development Status :: 2 - Pre-Alpha
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Topic :: Scientific/Engineering :: Chemistry
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+ Classifier: Topic :: Scientific/Engineering :: Physics
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+ Classifier: License :: OSI Approved :: BSD License
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+ Classifier: Natural Language :: English
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+ Classifier: Programming Language :: Python :: 3 :: Only
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Description-Content-Type: text/x-rst
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+ License-File: LICENSE
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+ License-File: AUTHORS.rst
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+ Requires-Dist: seamm
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+ Requires-Dist: seamm-util
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+ Requires-Dist: seamm-widgets
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: keywords
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+ Dynamic: license
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+ Dynamic: license-file
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+ Dynamic: platform
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+ Dynamic: requires-dist
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+ Dynamic: summary
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+
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+ =================
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+ SEAMM xTB Plug-in
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+ =================
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+
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+ .. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/xtb_step
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+ :target: https://github.com/molssi-seamm/xtb_step/pulls
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+ :alt: GitHub pull requests
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/CI/badge.svg
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+ :target: https://github.com/molssi-seamm/xtb_step/actions
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+ :alt: Build Status
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+
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+ .. image:: https://codecov.io/gh/molssi-seamm/xtb_step/branch/master/graph/badge.svg
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+ :target: https://codecov.io/gh/molssi-seamm/xtb_step
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+ :alt: Code Coverage
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/CodeQL/badge.svg
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+ :target: https://github.com/molssi-seamm/xtb_step/security/code-scanning
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+ :alt: Code Quality
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/Release/badge.svg
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+ :target: https://molssi-seamm.github.io/xtb_step/index.html
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+ :alt: Documentation Status
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+
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+ .. image:: https://img.shields.io/pypi/v/xtb_step.svg
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+ :target: https://pypi.python.org/pypi/xtb_step
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+ :alt: PyPi VERSION
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+
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+ A SEAMM plug-in for the `xTB <https://github.com/grimme-lab/xtb>`_ family
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+ of extended tight-binding methods from the Grimme group.
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+
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+ * Free software: BSD-3-Clause
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+ * Documentation: https://molssi-seamm.github.io/xtb_step/index.html
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+ * Code: https://github.com/molssi-seamm/xtb_step
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+
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+ Features
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+ --------
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+
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+ * Single-point energies, geometry optimizations, and harmonic
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+ vibrational frequencies for molecular (non-periodic) systems.
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+ * The full set of xTB Hamiltonians and the GFN-FF force field:
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+
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+ - **GFN2-xTB** (default) -- self-consistent, multipole electrostatics,
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+ density-dependent dispersion. Recommended for general use.
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+ - **GFN1-xTB** -- earlier self-consistent method.
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+ - **GFN0-xTB** -- non-self-consistent, useful for robust screening.
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+ - **GFN-FF** -- generic force field, automatically parameterized.
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+
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+ * Implicit solvation with all three xTB-supported models:
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+
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+ - **ALPB** -- analytical linearized Poisson-Boltzmann
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+ (Ehlert et al., *J. Chem. Theory Comput.* **2021**, *17*, 4250).
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+ - **GBSA** -- generalized-Born model.
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+ - **CPCM-X** -- conductor-like polarizable continuum
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+ (Stahn et al., *J. Phys. Chem. A* **2023**, *127*, 7036).
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+
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+ with the standard xTB solvent list (water, methanol, DMSO,
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+ acetonitrile, etc.).
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+
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+ * Net charge and spin multiplicity are read from the configuration,
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+ so the same flowchart works unchanged across O\ :sub:`2`,
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+ triplet O\ :sub:`2`, and O\ :sub:`2`\ :sup:`+` -- a single loop
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+ can scan a list of systems with different charge/spin states.
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+
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+ * Optimization with all eight xTB convergence levels (crude through
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+ extreme) and flexible structure handling: overwrite the current
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+ configuration in place, store the optimized structure as a new
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+ configuration, store it in a new system, or discard.
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+
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+ * Vibrational analysis using xTB's analytic Hessian, with the
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+ optimize-then-Hessian (``--ohess``) workflow recommended by xTB
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+ (or ``--hess`` alone if the geometry is already at a stationary
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+ point). Thermochemistry quantities (ZPE, H(T), T*S, S, G(T),
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+ total free energy) are reported in chemist-friendly units of
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+ kJ/mol and J/mol/K, not E\ :sub:`h`.
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+
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+ * Tabulated results in the local ``step.out`` and storage in the
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+ SEAMM property database using the standard ``<name>#xTB#{model}``
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+ property-naming convention, so downstream plug-ins
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+ (Thermochemistry, Reaction Path, ...) can pick up the values.
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+
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+ * Automatic citation tracking. The principal xTB program reference,
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+ the active GFN method reference, the DFT-D4 dispersion references
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+ (for GFN2-xTB), and the implicit-solvation reference are all added
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+ to the run's reference list automatically.
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+
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+ * Automatic installation of the xtb executable into a dedicated
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+ ``seamm-xtb`` conda environment via the standard SEAMM Installer.
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+
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+ Acknowledgements
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+ ----------------
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+
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+ This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
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+ is based on the excellent Cookiecutter_.
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+
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+ .. _Cookiecutter: https://github.com/audreyr/cookiecutter
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+ .. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
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+
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+ Developed by the Molecular Sciences Software Institute (MolSSI_),
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+ which receives funding from the `National Science Foundation`_ under
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+ award CHE-2136142.
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+
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+ .. _MolSSI: https://molssi.org
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+ .. _`National Science Foundation`: https://www.nsf.gov
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+
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+
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+ =======
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+ History
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+ =======
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+
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+ 2026.5.2: Plug-in created using the SEAMM plug-in cookiecutter.
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+
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+ 2026.5.12: Initial working version
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+ * Support for Energy, Optimization, and Frequencies
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+ * GFN0-xTB, GFN1-xTB, GFN2-xTB (the default), and GFN-FF supported
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+ * ALPB, GBSA, or CPCM-X implicit solvation
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+ =================
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+ SEAMM xTB Plug-in
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+ =================
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+
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+ .. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/xtb_step
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+ :target: https://github.com/molssi-seamm/xtb_step/pulls
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+ :alt: GitHub pull requests
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/CI/badge.svg
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+ :target: https://github.com/molssi-seamm/xtb_step/actions
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+ :alt: Build Status
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+
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+ .. image:: https://codecov.io/gh/molssi-seamm/xtb_step/branch/master/graph/badge.svg
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+ :target: https://codecov.io/gh/molssi-seamm/xtb_step
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+ :alt: Code Coverage
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/CodeQL/badge.svg
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+ :target: https://github.com/molssi-seamm/xtb_step/security/code-scanning
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+ :alt: Code Quality
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+
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+ .. image:: https://github.com/molssi-seamm/xtb_step/workflows/Release/badge.svg
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+ :target: https://molssi-seamm.github.io/xtb_step/index.html
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+ :alt: Documentation Status
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+
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+ .. image:: https://img.shields.io/pypi/v/xtb_step.svg
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+ :target: https://pypi.python.org/pypi/xtb_step
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+ :alt: PyPi VERSION
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+
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+ A SEAMM plug-in for the `xTB <https://github.com/grimme-lab/xtb>`_ family
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+ of extended tight-binding methods from the Grimme group.
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+
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+ * Free software: BSD-3-Clause
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+ * Documentation: https://molssi-seamm.github.io/xtb_step/index.html
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+ * Code: https://github.com/molssi-seamm/xtb_step
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+
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+ Features
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+ --------
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+
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+ * Single-point energies, geometry optimizations, and harmonic
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+ vibrational frequencies for molecular (non-periodic) systems.
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+ * The full set of xTB Hamiltonians and the GFN-FF force field:
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+
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+ - **GFN2-xTB** (default) -- self-consistent, multipole electrostatics,
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+ density-dependent dispersion. Recommended for general use.
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+ - **GFN1-xTB** -- earlier self-consistent method.
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+ - **GFN0-xTB** -- non-self-consistent, useful for robust screening.
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+ - **GFN-FF** -- generic force field, automatically parameterized.
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+
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+ * Implicit solvation with all three xTB-supported models:
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+
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+ - **ALPB** -- analytical linearized Poisson-Boltzmann
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+ (Ehlert et al., *J. Chem. Theory Comput.* **2021**, *17*, 4250).
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+ - **GBSA** -- generalized-Born model.
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+ - **CPCM-X** -- conductor-like polarizable continuum
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+ (Stahn et al., *J. Phys. Chem. A* **2023**, *127*, 7036).
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+
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+ with the standard xTB solvent list (water, methanol, DMSO,
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+ acetonitrile, etc.).
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+
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+ * Net charge and spin multiplicity are read from the configuration,
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+ so the same flowchart works unchanged across O\ :sub:`2`,
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+ triplet O\ :sub:`2`, and O\ :sub:`2`\ :sup:`+` -- a single loop
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+ can scan a list of systems with different charge/spin states.
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+
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+ * Optimization with all eight xTB convergence levels (crude through
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+ extreme) and flexible structure handling: overwrite the current
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+ configuration in place, store the optimized structure as a new
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+ configuration, store it in a new system, or discard.
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+
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+ * Vibrational analysis using xTB's analytic Hessian, with the
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+ optimize-then-Hessian (``--ohess``) workflow recommended by xTB
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+ (or ``--hess`` alone if the geometry is already at a stationary
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+ point). Thermochemistry quantities (ZPE, H(T), T*S, S, G(T),
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+ total free energy) are reported in chemist-friendly units of
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+ kJ/mol and J/mol/K, not E\ :sub:`h`.
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+
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+ * Tabulated results in the local ``step.out`` and storage in the
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+ SEAMM property database using the standard ``<name>#xTB#{model}``
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+ property-naming convention, so downstream plug-ins
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+ (Thermochemistry, Reaction Path, ...) can pick up the values.
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+
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+ * Automatic citation tracking. The principal xTB program reference,
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+ the active GFN method reference, the DFT-D4 dispersion references
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+ (for GFN2-xTB), and the implicit-solvation reference are all added
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+ to the run's reference list automatically.
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+
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+ * Automatic installation of the xtb executable into a dedicated
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+ ``seamm-xtb`` conda environment via the standard SEAMM Installer.
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+
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+ Acknowledgements
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+ ----------------
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+
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+ This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
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+ is based on the excellent Cookiecutter_.
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+
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+ .. _Cookiecutter: https://github.com/audreyr/cookiecutter
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+ .. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
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+
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+ Developed by the Molecular Sciences Software Institute (MolSSI_),
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+ which receives funding from the `National Science Foundation`_ under
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+ award CHE-2136142.
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+
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+ .. _MolSSI: https://molssi.org
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+ .. _`National Science Foundation`: https://www.nsf.gov
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+ # Makefile for Sphinx documentation
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+ #
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+
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+ # You can set these variables from the command line.
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+ SPHINXOPTS =
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+ SPHINXBUILD = sphinx-build
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+ PAPER =
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+ BUILDDIR = _build
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+
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+ # User-friendly check for sphinx-build
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+ ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
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+ $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
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+ endif
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+
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+ # Internal variables.
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+ PAPEROPT_a4 = -D latex_paper_size=a4
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+ PAPEROPT_letter = -D latex_paper_size=letter
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+ ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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+ # the i18n builder cannot share the environment and doctrees with the others
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+ I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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+
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+ .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
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+
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+ help:
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+ @echo "Please use \`make <target>' where <target> is one of"
26
+ @echo " html to make standalone HTML files"
27
+ @echo " dirhtml to make HTML files named index.html in directories"
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+ @echo " singlehtml to make a single large HTML file"
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+ @echo " pickle to make pickle files"
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+ @echo " json to make JSON files"
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+ @echo " htmlhelp to make HTML files and a HTML help project"
32
+ @echo " qthelp to make HTML files and a qthelp project"
33
+ @echo " devhelp to make HTML files and a Devhelp project"
34
+ @echo " epub to make an epub"
35
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
36
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
37
+ @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
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+ @echo " text to make text files"
39
+ @echo " man to make manual pages"
40
+ @echo " texinfo to make Texinfo files"
41
+ @echo " info to make Texinfo files and run them through makeinfo"
42
+ @echo " gettext to make PO message catalogs"
43
+ @echo " changes to make an overview of all changed/added/deprecated items"
44
+ @echo " xml to make Docutils-native XML files"
45
+ @echo " pseudoxml to make pseudoxml-XML files for display purposes"
46
+ @echo " linkcheck to check all external links for integrity"
47
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
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+
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+ clean:
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+ rm -rf $(BUILDDIR)/*
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+
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+ html:
53
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
54
+ @echo
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+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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+
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+ dirhtml:
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+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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+ @echo
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+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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+
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+ singlehtml:
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+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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+ @echo
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+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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+
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+ pickle:
68
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
69
+ @echo
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+ @echo "Build finished; now you can process the pickle files."
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+
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+ json:
73
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
74
+ @echo
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+ @echo "Build finished; now you can process the JSON files."
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+
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+ htmlhelp:
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+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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+ @echo
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+ @echo "Build finished; now you can run HTML Help Workshop with the" \
81
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
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+
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+ qthelp:
84
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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+ @echo
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+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
87
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
88
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/xtb_step.qhcp"
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+ @echo "To view the help file:"
90
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/xtb_step.qhc"
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+
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+ devhelp:
93
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
94
+ @echo
95
+ @echo "Build finished."
96
+ @echo "To view the help file:"
97
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/xtb_step"
98
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/xtb_step"
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+ @echo "# devhelp"
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+
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+ epub:
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+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
103
+ @echo
104
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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+
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+ latex:
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+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
108
+ @echo
109
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
110
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
111
+ "(use \`make latexpdf' here to do that automatically)."
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+
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+ latexpdf:
114
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
115
+ @echo "Running LaTeX files through pdflatex..."
116
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
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+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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+
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+ latexpdfja:
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+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
121
+ @echo "Running LaTeX files through platex and dvipdfmx..."
122
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
123
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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+
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+ text:
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+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
127
+ @echo
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+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
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+
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+ man:
131
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
132
+ @echo
133
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
134
+
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+ texinfo:
136
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
137
+ @echo
138
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
139
+ @echo "Run \`make' in that directory to run these through makeinfo" \
140
+ "(use \`make info' here to do that automatically)."
141
+
142
+ info:
143
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
144
+ @echo "Running Texinfo files through makeinfo..."
145
+ make -C $(BUILDDIR)/texinfo info
146
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
147
+
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+ gettext:
149
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
150
+ @echo
151
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
152
+
153
+ changes:
154
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
155
+ @echo
156
+ @echo "The overview file is in $(BUILDDIR)/changes."
157
+
158
+ linkcheck:
159
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
160
+ @echo
161
+ @echo "Link check complete; look for any errors in the above output " \
162
+ "or in $(BUILDDIR)/linkcheck/output.txt."
163
+
164
+ doctest:
165
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
166
+ @echo "Testing of doctests in the sources finished, look at the " \
167
+ "results in $(BUILDDIR)/doctest/output.txt."
168
+
169
+ xml:
170
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
171
+ @echo
172
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
173
+
174
+ pseudoxml:
175
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
176
+ @echo
177
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
Binary file
@@ -0,0 +1,17 @@
1
+ API Documentation
2
+ =================
3
+
4
+ Contents:
5
+
6
+ .. toctree::
7
+ :maxdepth: 2
8
+
9
+ modules
10
+
11
+
12
+ Indices and tables
13
+ ------------------
14
+
15
+ * :ref:`genindex`
16
+ * :ref:`modindex`
17
+ * :ref:`search`
@@ -0,0 +1 @@
1
+ .. include:: ../AUTHORS.rst