Cubic Grid Tutorial for Iso-Surface Visualization #205
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I really like these examples. Unless anyone says otherwise, I am going to merge this notebook with the already cubic_grid notebook. The first example of visualization can fall under the Tensor1DGrid. Then the second example of dual descriptor can fall under the Uniform Grid Section |
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Thanks @Ali-Tehrani. Let me know when you are done, and I will do one last review of the notebook. |
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Okay, it is ready to be reviewed. I merged the two notebooks while fixing up the section/typos/wording, and removed the original notebook. Also made sure that it looked good in the website by doing a local build. |
Ali-Tehrani
approved these changes
Jan 3, 2024
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BeckeRTransform of certain OneDGrids with points at 1.0 (like Trapezoidal) resulted in RuntimeWarning: divide by zero encountered in deriv and deriv2 methods. To avoid printing a warning message, the zero devision was disabled.
To simply tutorials and make it easier to keep track of the name of 1-dimensional grids, name was added as a class attribute.
- Add relative error for [0, infty) integration - Added log plot to one of the plots
updates: - [github.com/psf/black: 23.12.0 → 23.12.1](psf/black@23.12.0...23.12.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.8...v0.1.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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- Fix some typos - Fix the headings for the website
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1. The explanation on the angular integration was improved 2. The maxima of the radial electron density distribution were found using scipy.
This API change is described in theochem/gbasis#140
This commit refines the 'Angular_grid' notebook by: 1. Adding examples of grid creation for symmetric spherical grids. 2. Improving the output formatting of select cells for readability. 3. Introducing test statements to validate cell results.
updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](astral-sh/ruff-pre-commit@v0.1.9...v0.1.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](astral-sh/ruff-pre-commit@v0.1.11...v0.1.13)
* Move jupyter notebooks to examples folder in main * Update year in conf * Add nbsphinx-link to conf.py to link notebooks - Needed to link website to notebooks outside of the doc folder * Construct nblink for every externel jup notebook * Add toc link to jupyter notebook via nbsphinx-link * Add nbsphinx-link to requirements.txt * Fix weird typo introduced in onedgrid examples * Rename table of contents title * Remove unused Becke reference - Removes warning message in sphinx - Updated to current api for .from_* methods * Update documentation to remove some sphinx errors * Add talbe link to oned juypter notebooks * Update hyperlinks and title in atom_grid_construct * Change get_rgrid_size to private - So it doesn't show up in the documentation * Fix wrong solution to Poisson example - The error is incredibly small after fix * Fix spacing in equation so it fits into page - The equations go out of page in the webstie * Fix so that bullet points show up - Docutils need to be version 0.16 - Extensions need to have the theme - stackoverflow: 67542699/readthedocs-sphinx-not-rendering-bullet-list-from-rst-file * Fix table to show angular grids link correctly * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add instructions on how to build the website * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix ruff linters on cubic and test_cubic * Update citations * Update atom grid notebook to match new api * Add jupyter notebook * Update jupyter github action workflow * Remove .png from gitignore for jup notebooks - Jupyter notebooks create .png files and so we need them for the website * Try website github actions push * Try again * Try again but with artifacts removed * Remove pip install with editable mode on * Try upgrading pip because installation UNKNOWN * Try again forgot html keyword * Add new extensions to pyproject.toml * Try again: Add pandoc installation fix * Try again: Add pandoc installation fix 2 * Try again: add explicit pandoc installation * Try again: add github token * Try again: add github token2 * Try again: add permission to github token * Try again: add permission to github token2 * Try again: add permission to github token3 * Try again: add permission to github token4 * Try again:update website * Try again: create gh-page branch * Update multipole moment notebook * Update JCP paper to match paper * Update hoe website is automatically updated * Update pre-commit to exclude certain directories * Update juypter notebook * Update molecular grid to include iodata/gbasis * Decreaes accuracy of certain test --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Thanks @marco-2023, I'm going ahead and merging this notebook so that it is included in the website upon release. |
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This is from Quickstart.ipynb notebook from #202. See: 908178c