=========================
SEAMM Energy Scan Plug-in
=========================
.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/energy_scan_step
:target: https://github.com/molssi-seamm/energy_scan_step/pulls
:alt: GitHub pull requests
.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/CI/badge.svg
:target: https://github.com/molssi-seamm/energy_scan_step/actions
:alt: Build Status
.. image:: https://codecov.io/gh/molssi-seamm/energy_scan_step/branch/master/graph/badge.svg
:target: https://codecov.io/gh/molssi-seamm/energy_scan_step
:alt: Code Coverage
.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/CodeQL/badge.svg
:target: https://github.com/molssi-seamm/energy_scan_step/security/code-scanning
:alt: Code Quality
.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/Release/badge.svg
:target: https://molssi-seamm.github.io/energy_scan_step/index.html
:alt: Documentation Status
.. image:: https://img.shields.io/pypi/v/energy_scan_step.svg
:target: https://pypi.python.org/pypi/energy_scan_step
:alt: PyPi VERSION
A SEAMM plug-in for calculating energy profiles along coordinates
* Free software: BSD-3-Clause
* Documentation: https://molssi-seamm.github.io/energy_scan_step/index.html
* Code: https://github.com/molssi-seamm/energy_scan_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
=======
2025.8.20 -- Improved the graphs and added spins to them if available.
* Added the ability to output graphs to one or more of the following formats: html,
png, webp, svg, or pdf.
* Capture the spin values, S**2 and the projected S**2, if captured by the quantum
code, and add them to the graphs.
* Fixed an issue if the two atoms in a bond scan were not actually bonded.
2025.8.6 -- Allows the values defining the scans to be variables.
* This enhancement allows the variables defining the scan or frozen coordinate to be
variables as well as static values.
2025.8.5 -- Bugfix: not correctly naming the configurations in the scan
* The code did not correctly name the configurations generated during a scan, so
their names were None.
2025.5.7 -- Enhancement to continue if minimization does not converge
* Continue even if the minimization does not fully converge, as sometimes seems to be
the case.
2025.4.11 -- Enhancements to allow repeated points
* Allows the path to have repeated points, which is useful to e.g. go forwards and
backawards to see the hysteresis.
2025.4.1 -- Bugfix: Error handling the coordinates in some cases
* There was an error in handling the coordinates created by changes in the RDKit module
in molsystem. This fixes it.
* The incorrect logger was used for debugging.
* Small format updates to due to changes in the code formatting rules in black.
2024.12.14 -- Cleanup! Reasonable working version.
2024.5.23 -- Initial working version
* Can handle scans, freezing coordinates. Is not optimized yet.
* Produces a graph of 1- and 2-D scans
* Creates an SDF file with the optmized points along scans, which can be viewed in
the Dashboard.
2024.4.3 (2024-04-03)
---------------------
* Plug-in created using the SEAMM plug-in cookiecutter.
Raw data
{
"_id": null,
"home_page": "https://github.com/molssi-seamm/energy_scan_step",
"name": "energy-scan-step",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "SEAMM, SEAMMplugin, flowchart",
"author": "Paul Saxe",
"author_email": "psaxe@molssi.org",
"download_url": "https://files.pythonhosted.org/packages/7e/55/4b0484d3bcb99ec4314c08b33dab2cac76730945b83348440c3f330ae3e8/energy_scan_step-2025.8.20.tar.gz",
"platform": "Linux",
"description": "=========================\nSEAMM Energy Scan Plug-in\n=========================\n\n.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/energy_scan_step\n :target: https://github.com/molssi-seamm/energy_scan_step/pulls\n :alt: GitHub pull requests\n\n.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/CI/badge.svg\n :target: https://github.com/molssi-seamm/energy_scan_step/actions\n :alt: Build Status\n\n.. image:: https://codecov.io/gh/molssi-seamm/energy_scan_step/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/molssi-seamm/energy_scan_step\n :alt: Code Coverage\n\n.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/CodeQL/badge.svg\n :target: https://github.com/molssi-seamm/energy_scan_step/security/code-scanning\n :alt: Code Quality\n\n.. image:: https://github.com/molssi-seamm/energy_scan_step/workflows/Release/badge.svg\n :target: https://molssi-seamm.github.io/energy_scan_step/index.html\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/pypi/v/energy_scan_step.svg\n :target: https://pypi.python.org/pypi/energy_scan_step\n :alt: PyPi VERSION\n\nA SEAMM plug-in for calculating energy profiles along coordinates\n\n* Free software: BSD-3-Clause\n* Documentation: https://molssi-seamm.github.io/energy_scan_step/index.html\n* Code: https://github.com/molssi-seamm/energy_scan_step\n\nFeatures\n--------\n\n* Please edit this section!\n\nAcknowledgements\n----------------\n\nThis package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which\nis based on the excellent Cookiecutter_.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin\n\nDeveloped by the Molecular Sciences Software Institute (MolSSI_),\nwhich receives funding from the `National Science Foundation`_ under\naward CHE-2136142.\n\n.. _MolSSI: https://molssi.org\n.. _`National Science Foundation`: https://www.nsf.gov\n\n\n=======\nHistory\n=======\n2025.8.20 -- Improved the graphs and added spins to them if available.\n * Added the ability to output graphs to one or more of the following formats: html,\n png, webp, svg, or pdf.\n * Capture the spin values, S**2 and the projected S**2, if captured by the quantum\n code, and add them to the graphs.\n * Fixed an issue if the two atoms in a bond scan were not actually bonded.\n\n2025.8.6 -- Allows the values defining the scans to be variables.\n * This enhancement allows the variables defining the scan or frozen coordinate to be\n variables as well as static values.\n\n2025.8.5 -- Bugfix: not correctly naming the configurations in the scan\n * The code did not correctly name the configurations generated during a scan, so\n their names were None.\n\n2025.5.7 -- Enhancement to continue if minimization does not converge\n * Continue even if the minimization does not fully converge, as sometimes seems to be\n the case.\n \n2025.4.11 -- Enhancements to allow repeated points\n * Allows the path to have repeated points, which is useful to e.g. go forwards and\n backawards to see the hysteresis.\n \n2025.4.1 -- Bugfix: Error handling the coordinates in some cases\n * There was an error in handling the coordinates created by changes in the RDKit module\n in molsystem. This fixes it.\n * The incorrect logger was used for debugging.\n * Small format updates to due to changes in the code formatting rules in black.\n \n2024.12.14 -- Cleanup! Reasonable working version.\n\n2024.5.23 -- Initial working version\n * Can handle scans, freezing coordinates. Is not optimized yet.\n * Produces a graph of 1- and 2-D scans\n * Creates an SDF file with the optmized points along scans, which can be viewed in\n the Dashboard.\n\n2024.4.3 (2024-04-03)\n---------------------\n\n* Plug-in created using the SEAMM plug-in cookiecutter.\n",
"bugtrack_url": null,
"license": "BSD-3-Clause",
"summary": "A SEAMM plug-in for calculating energy profiles along coordinates",
"version": "2025.8.20",
"project_urls": {
"Homepage": "https://github.com/molssi-seamm/energy_scan_step"
},
"split_keywords": [
"seamm",
" seammplugin",
" flowchart"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "d9c15fdfee3980e558426ee29b03f68881b4dbbce10678a9e0d8d09e25fc283a",
"md5": "622556e17622ff77d599301414aad00a",
"sha256": "70daf641b7ff4be2c60f0d8c6c7c89f6c4d9d3352574a8a1333e72f9a7ad6d69"
},
"downloads": -1,
"filename": "energy_scan_step-2025.8.20-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "622556e17622ff77d599301414aad00a",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 29381,
"upload_time": "2025-08-20T13:51:13",
"upload_time_iso_8601": "2025-08-20T13:51:13.398979Z",
"url": "https://files.pythonhosted.org/packages/d9/c1/5fdfee3980e558426ee29b03f68881b4dbbce10678a9e0d8d09e25fc283a/energy_scan_step-2025.8.20-py2.py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "7e554b0484d3bcb99ec4314c08b33dab2cac76730945b83348440c3f330ae3e8",
"md5": "3d30b2cd4109151732c7168ae7c26a49",
"sha256": "173b924e3e0f92fcca9a2546ca17a0960b3b16208b66a384582d031419af27f7"
},
"downloads": -1,
"filename": "energy_scan_step-2025.8.20.tar.gz",
"has_sig": false,
"md5_digest": "3d30b2cd4109151732c7168ae7c26a49",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 318414,
"upload_time": "2025-08-20T13:51:14",
"upload_time_iso_8601": "2025-08-20T13:51:14.660865Z",
"url": "https://files.pythonhosted.org/packages/7e/55/4b0484d3bcb99ec4314c08b33dab2cac76730945b83348440c3f330ae3e8/energy_scan_step-2025.8.20.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-08-20 13:51:14",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "molssi-seamm",
"github_project": "energy_scan_step",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "geometric",
"specs": []
},
{
"name": "numpy",
"specs": []
},
{
"name": "rdkit",
"specs": []
},
{
"name": "read-structure-step",
"specs": []
},
{
"name": "seamm",
"specs": []
},
{
"name": "seamm-util",
"specs": []
},
{
"name": "seamm-widgets",
"specs": []
},
{
"name": "tabulate",
"specs": []
}
],
"lcname": "energy-scan-step"
}
JSON
