Bump pymatgen from 2024.5.1 to 2024.5.31 (#2196)

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from
2024.5.1 to 2024.5.31.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/materialsproject/pymatgen/releases">pymatgen's
releases</a>.</em></p>
<blockquote>
<h2>v2024.5.31</h2>
<!-- raw HTML omitted -->
<h2>What's Changed</h2>
<h3>🐛 Bug Fixes</h3>
<ul>
<li>Make <code>Beautifulsoup</code> optional by <a
href="https://github.com/ab5424"><code>@​ab5424</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3774">materialsproject/pymatgen#3774</a></li>
<li>Fix overlayed subplots in
<code>BSPlotterProjected.get_projected_plots_dots()</code> by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3798">materialsproject/pymatgen#3798</a></li>
<li>Fix <code>_get_dipole_info</code> for DDEC6
<code>ChargemolAnalysis</code> and add test case by <a
href="https://github.com/JonathanSchmidt1"><code>@​JonathanSchmidt1</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3801">materialsproject/pymatgen#3801</a></li>
<li><code>Cp2kOutput.parse_initial_structure()</code> use regex for line
matching to allow arbitrary white space between Atom/Kind/Element/... by
<a href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3810">materialsproject/pymatgen#3810</a></li>
<li>Fix the minor document error in <code>POTCAR Setup</code>. by <a
href="https://github.com/hongyi-zhao"><code>@​hongyi-zhao</code></a> in
<a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3834">materialsproject/pymatgen#3834</a></li>
<li>Use <code>isclose</code> over <code>==</code> for overlap position
check in <code>SlabGenerator.get_slabs</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3825">materialsproject/pymatgen#3825</a></li>
<li>[Deprecation] Replace <code>Element</code> property
<code>is_rare_earth_metal</code> with <code>is_rare_earth</code> to
include Y and Sc by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3817">materialsproject/pymatgen#3817</a></li>
</ul>
<h3>🛠 Enhancements</h3>
<ul>
<li>Add <code>is_radioactive</code> property to Element class by <a
href="https://github.com/AntObi"><code>@​AntObi</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3804">materialsproject/pymatgen#3804</a></li>
<li>Add a <code>from_ase_atoms()</code> method to <code>Structure</code>
by <a
href="https://github.com/Andrew-S-Rosen"><code>@​Andrew-S-Rosen</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3812">materialsproject/pymatgen#3812</a></li>
<li>Adapt to the latest version of PWmat output file by <a
href="https://github.com/lhycms"><code>@​lhycms</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3823">materialsproject/pymatgen#3823</a></li>
<li>Update VASP sets to transition atomate2 to use pymatgen input sets
exclusively by <a
href="https://github.com/esoteric-ephemera"><code>@​esoteric-ephemera</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3835">materialsproject/pymatgen#3835</a></li>
</ul>
<h3>📖 Documentation</h3>
<ul>
<li>Imperative <code>get_...</code> method and <code>@Property</code>
doc strings by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3802">materialsproject/pymatgen#3802</a></li>
<li>Doc string standardization by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3805">materialsproject/pymatgen#3805</a></li>
</ul>
<h3>🧹 House-Keeping</h3>
<ul>
<li>Add types for
<code>core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc)</code>
by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3829">materialsproject/pymatgen#3829</a></li>
<li>Move test structures out of <code>util</code> directory by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3831">materialsproject/pymatgen#3831</a></li>
</ul>
<h3>🧪 Tests</h3>
<ul>
<li>Improve type annotations for <code>core.(trajectory/units)</code> by
<a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3832">materialsproject/pymatgen#3832</a></li>
</ul>
<h3>🏷️ Type Hints</h3>
<ul>
<li>More type annotations by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3800">materialsproject/pymatgen#3800</a></li>
<li>Add types for
<code>core.periodic_table/bonds/composition/ion/lattice/libxcfunc</code>,
new type <code>MillerIndex</code> and fix Lattice hash by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3814">materialsproject/pymatgen#3814</a></li>
<li>Guard <code>TYPE_CHECKING</code> only imports by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3827">materialsproject/pymatgen#3827</a></li>
<li>Improve type annotations and comments for <code>io.cif</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3820">materialsproject/pymatgen#3820</a></li>
<li>Improve type annotations for <code>core.structure</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3837">materialsproject/pymatgen#3837</a></li>
<li>Add type annotations for <code>io.vasp.outputs</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3776">materialsproject/pymatgen#3776</a></li>
</ul>
<h3>🤷‍♂️ Other Changes</h3>
<ul>
<li>mixing scheme: change default for verbose by <a
href="https://github.com/tschaume"><code>@​tschaume</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3806">materialsproject/pymatgen#3806</a></li>
<li><code>ruff</code> 0.4.3 auto-fixes by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3808">materialsproject/pymatgen#3808</a></li>
<li>Re-enable some useful <code>ruff</code> rules by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3813">materialsproject/pymatgen#3813</a></li>
<li><code>pandas.read_csv</code>: replace deprecated
<code>delim_whitespace=True</code> with <code>sep=&quot;\s+&quot;</code>
by <a href="https://github.com/ab5424"><code>@​ab5424</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3846">materialsproject/pymatgen#3846</a></li>
<li>Improve unphysical (greater than 1) occupancy handling in
<code>CifParser</code> and add missing site label <code>if not
check_occu</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3819">materialsproject/pymatgen#3819</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31">https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31</a></p>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md">pymatgen's
changelog</a>.</em></p>
<blockquote>
<h2>2024.5.31</h2>
<h3>🐛 Bug Fixes</h3>
<ul>
<li>Make <code>Beautifulsoup</code> optional by <a
href="https://github.com/ab5424"><code>@​ab5424</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3774">materialsproject/pymatgen#3774</a></li>
<li>Fix overlayed subplots in
<code>BSPlotterProjected.get_projected_plots_dots()</code> by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3798">materialsproject/pymatgen#3798</a></li>
<li>Fix <code>_get_dipole_info</code> for DDEC6
<code>ChargemolAnalysis</code> and add test case by <a
href="https://github.com/JonathanSchmidt1"><code>@​JonathanSchmidt1</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3801">materialsproject/pymatgen#3801</a></li>
<li><code>Cp2kOutput.parse_initial_structure()</code> use regex for line
matching to allow arbitrary white space between Atom/Kind/Element/... by
<a href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3810">materialsproject/pymatgen#3810</a></li>
<li>Fix the minor document error in <code>POTCAR Setup</code>. by <a
href="https://github.com/hongyi-zhao"><code>@​hongyi-zhao</code></a> in
<a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3834">materialsproject/pymatgen#3834</a></li>
<li>Use <code>isclose</code> over <code>==</code> for overlap position
check in <code>SlabGenerator.get_slabs</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3825">materialsproject/pymatgen#3825</a></li>
<li>[Deprecation] Replace <code>Element</code> property
<code>is_rare_earth_metal</code> with <code>is_rare_earth</code> to
include Y and Sc by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3817">materialsproject/pymatgen#3817</a></li>
</ul>
<h3>🛠 Enhancements</h3>
<ul>
<li>Add <code>is_radioactive</code> property to Element class by <a
href="https://github.com/AntObi"><code>@​AntObi</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3804">materialsproject/pymatgen#3804</a></li>
<li>Add a <code>from_ase_atoms()</code> method to <code>Structure</code>
by <a
href="https://github.com/Andrew-S-Rosen"><code>@​Andrew-S-Rosen</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3812">materialsproject/pymatgen#3812</a></li>
<li>Adapt to the latest version of PWmat output file by <a
href="https://github.com/lhycms"><code>@​lhycms</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3823">materialsproject/pymatgen#3823</a></li>
<li>Update VASP sets to transition atomate2 to use pymatgen input sets
exclusively by <a
href="https://github.com/esoteric-ephemera"><code>@​esoteric-ephemera</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3835">materialsproject/pymatgen#3835</a></li>
</ul>
<h3>📖 Documentation</h3>
<ul>
<li>Imperative <code>get_...</code> method and <code>@Property</code>
doc strings by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3802">materialsproject/pymatgen#3802</a></li>
<li>Doc string standardization by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3805">materialsproject/pymatgen#3805</a></li>
</ul>
<h3>🧹 House-Keeping</h3>
<ul>
<li>Add types for
<code>core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc)</code>
by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3829">materialsproject/pymatgen#3829</a></li>
<li>Move test structures out of <code>util</code> directory by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3831">materialsproject/pymatgen#3831</a></li>
</ul>
<h3>🧪 Tests</h3>
<ul>
<li>Improve type annotations for <code>core.(trajectory/units)</code> by
<a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3832">materialsproject/pymatgen#3832</a></li>
</ul>
<h3>🏷️ Type Hints</h3>
<ul>
<li>More type annotations by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3800">materialsproject/pymatgen#3800</a></li>
<li>Add types for
<code>core.periodic_table/bonds/composition/ion/lattice/libxcfunc</code>,
new type <code>MillerIndex</code> and fix Lattice hash by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3814">materialsproject/pymatgen#3814</a></li>
<li>Guard <code>TYPE_CHECKING</code> only imports by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3827">materialsproject/pymatgen#3827</a></li>
<li>Improve type annotations and comments for <code>io.cif</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3820">materialsproject/pymatgen#3820</a></li>
<li>Improve type annotations for <code>core.structure</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3837">materialsproject/pymatgen#3837</a></li>
</ul>
<h3>🤷‍♂️ Other Changes</h3>
<ul>
<li>mixing scheme: change default for verbose by <a
href="https://github.com/tschaume"><code>@​tschaume</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3806">materialsproject/pymatgen#3806</a></li>
<li><code>ruff</code> 0.4.3 auto-fixes by <a
href="https://github.com/janosh"><code>@​janosh</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3808">materialsproject/pymatgen#3808</a></li>
<li>Re-enable some useful <code>ruff</code> rules by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3813">materialsproject/pymatgen#3813</a></li>
<li><code>pandas.read_csv</code>: replace deprecated
<code>delim_whitespace=True</code> with <code>sep=&quot;\s+&quot;</code>
by <a href="https://github.com/ab5424"><code>@​ab5424</code></a> in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3846">materialsproject/pymatgen#3846</a></li>
<li>Improve unphysical (greater than 1) occupancy handling in
<code>CifParser</code> and add missing site label <code>if not
check_occu</code> by <a
href="https://github.com/DanielYang59"><code>@​DanielYang59</code></a>
in <a
href="https://redirect.github.com/materialsproject/pymatgen/pull/3819">materialsproject/pymatgen#3819</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31">https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31</a></p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/2982968a44d0ff65392057488aee4871210bc847"><code>2982968</code></a>
v2024.5.31</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/c70e5b8a152c0186ec83dd1f34b59a89ede3be28"><code>c70e5b8</code></a>
Add type annotations for <code>io.vasp.outputs</code> (<a
href="https://redirect.github.com/materialsproject/pymatgen/issues/3776">#3776</a>)</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/cd8846b3f07cda923edc8c7e480e1de123a3a90b"><code>cd8846b</code></a>
Update reqs.</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/cec7d35b5c65ad5d2837190293b3255bf1ca5eaf"><code>cec7d35</code></a>
Update reqs.</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/f214a5cfd82437d6214a1d60b0d195e75818bb60"><code>f214a5c</code></a>
[Deprecation] Replace <code>Element</code> property
<code>is_rare_earth_metal</code> with `is_rare_...</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/a772ddb0881be253097d1d2c0495df647595d718"><code>a772ddb</code></a>
Improve unphysical (greater than 1) occupancy handling in
<code>CifParser</code> and add...</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/0c9ff40135607040a021083048cb45ab5aed7ad7"><code>0c9ff40</code></a>
Use <code>isclose</code> over <code>==</code> for overlap position check
in `SlabGenerator.get_slab...</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/8c853cf3c2b4cf6a696f2521116dec4dc644fc00"><code>8c853cf</code></a>
--- (<a
href="https://redirect.github.com/materialsproject/pymatgen/issues/3842">#3842</a>)</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/541b58b2a62c2c5d86170b149fb4731cd5ac4277"><code>541b58b</code></a>
Fix regression.</li>
<li><a
href="https://github.com/materialsproject/pymatgen/commit/594f189d69110432a5201cfcdba56d52131ac67e"><code>594f189</code></a>
Add unittests for NotImplementedError.</li>
<li>Additional commits viewable in <a
href="https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31">compare
view</a></li>
</ul>
</details>
<br />


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Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Andrew S. Rosen <[email protected]>

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "psutil", # for getting compute architecture details
     "pydantic>=2.0.1", # for settings management
     "pydantic-settings>=2.2.0", # for settings management
-    "pymatgen>=2024.4.13", # for structure manipulation
+    "pymatgen>=2024.5.31", # for structure manipulation
     "ruamel.yaml>=0.17.40", # for YAML
     "typer>=0.12.1", # for the CLI
 ]

src/quacc/calculators/vasp/params.py

@@ -425,7 +425,7 @@ def convert_dict_set(self, dict_set: DictSet) -> dict:
         )
         self.incar_dict = vasp_input["INCAR"]
         self.pmg_kpts = vasp_input.get("KPOINTS")
-        self.potcar_symbols = vasp_input["POTCAR"]
+        self.potcar_symbols = vasp_input["POTCAR.spec"].split("\n")
         self.potcar_functional = input_set.potcar_functional
         self.poscar = vasp_input["POSCAR"]
         return self._convert()

tests/requirements.txt

@@ -8,6 +8,6 @@ numpy==1.26.4
 psutil==5.9.8
 pydantic==2.7.3
 pydantic-settings==2.3.1
-pymatgen==2024.5.1
+pymatgen==2024.5.31
 ruamel.yaml==0.18.6
 typer==0.12.3