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Do not use underscores for folders
* This may fixes the build warning * Also this may happen in the future: readthedocs/readthedocs.org#1776 (comment)
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docs/conf.py

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'sphinx_rtd_theme'
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]
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exclude_patterns = []
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templates_path = ['_templates']
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templates_path = ['templates']
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pygments_style = 'sphinx'
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# -- Options for HTML output -------------------------------------------------
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html_theme = 'sphinx_rtd_theme'
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html_static_path = ['_static']
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html_static_path = ['static']
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docs/introduction.rst

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Introduction
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************
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What is this?
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=============
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| The default setting for the variational mesh function is strictly bound to PySCF's grid levels (0-9) that are just lists of ten radial and angular grids for every group of elements.
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| To show how the algorithm works, a molecule with two atomic species will be used (:math:`\mathrm{H}_2\mathrm{O}`). Assuming that more grid points mean a better representation of the density (for an atomic species) and therefore results in a smaller error, we use this knowledge to generate more accurate grids. Our optimal grid for a specific threshold would be somewhere in the combination space shown in the figure below.
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.. figure:: _images/comb0.png
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.. figure:: images/comb0.png
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First, we will do a coarse grid search (seen the figure below, colored in red) where the grid levels for every atomic species are the same. Eventually, we find a match (colored in blue), i.e., a combination whose error is below our threshold. If there is no match the best possible grid will be used.
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.. figure:: _images/comb1.png
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.. figure:: images/comb1.png
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| With the found match we can eliminate further grid level pairs, shown below. It is safe to remove the upper right regime, since raising either one of the grid levels will only result in a larger grid than the found one.
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| We can also remove the bottom left part. With no match in the previous steps of the coarse grid search, it is unlikely to find a smaller grid below the threshold while reducing grid levels.
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.. figure:: _images/comb2.png
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.. figure:: images/comb2.png
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At last, we can remove every combination that would have a larger number of grid points than our match since we are only interested in the minimum. For :math:`\mathrm{H}_2\mathrm{O}` this step can be seen, again, in the figure below. Afterward, we go through the list of possible candidates sorted by growing numbers of grid points and calculate the resulting error until we eventually get a new match (colored in green). This will be referred to as the fine grid search.
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.. figure:: _images/comb3.png
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.. figure:: images/comb3.png
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Program flow
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------------
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.. figure:: _images/uml_diagram.png
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.. figure:: images/uml_diagram.png
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docs/modules.rst

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=============
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.. automodule:: var_mesh.helpers
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:members:
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docs/tutorial.rst

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>>> import var_mesh
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Minimal example
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===============
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>>> mesh.build()
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>>> plot_mesh_3d(mesh=mesh, weight=True)
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.. figure:: _images/plot_mesh_3d.png
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.. figure:: images/plot_mesh_3d.png
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>>> from var_mesh import plot_mesh_2d
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>>> plot_mesh_2d(mesh=mesh, weight=5, plane='xz')
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.. figure:: images/plot_mesh_2d.png
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The script for this example can be downloaded :download:`here </../examples/04_precise_option/04_precise_option.py>`.
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Mesh time
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=========
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>>> plt.legend()
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>>> plt.show()
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.. figure:: images/mesh_time.png
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>>> plt.legend()
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>>> plt.show()
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.. figure:: _images/calculation_time.png
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.. figure:: images/calculation_time.png
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