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Acsf fix #143

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merged 18 commits into from
May 28, 2024
Merged

Acsf fix #143

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ef297bc
Updated ACSF interface and logic.
lauri-codes Apr 16, 2024
bd7456e
Fixed linting.
lauri-codes Apr 23, 2024
7456f4d
Fixed issue with ACSF G5 calculation, added test.
lauri-codes Apr 23, 2024
b5c9357
Moved pymatgen imports.
lauri-codes May 13, 2024
397a69b
Re-added black as dependency.
lauri-codes May 13, 2024
9d53126
Removed species check from coulomb matrix.
lauri-codes May 13, 2024
3008a5f
Updated docs.
lauri-codes May 13, 2024
7f02522
Updated actions.
lauri-codes May 13, 2024
40d2a28
Updated docs.
lauri-codes May 13, 2024
0311d94
Updated wheel action.
lauri-codes May 13, 2024
ee90b80
Building wheels.
lauri-codes May 13, 2024
5c75db9
Building wheels.
lauri-codes May 13, 2024
4dea12b
Building wheels.
lauri-codes May 13, 2024
ab23272
Updated wheel build command.
lauri-codes May 14, 2024
236f6e0
Migrated to pyproject.toml and ruff.
lauri-codes May 28, 2024
46a7132
Updated pymargen dev dependency.
lauri-codes May 28, 2024
fd56a5e
Updated pymargen dev dependency.
lauri-codes May 28, 2024
a1cf125
Updated docs.
lauri-codes May 28, 2024
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15 changes: 8 additions & 7 deletions .github/workflows/actions.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,25 @@ jobs:
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: dependencies
- name: install
if: always()
run: |
cd ${GITHUB_WORKSPACE}/scripts && ./dependencies.sh
- name: lint
cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
- name: format
if: always()
run: |
cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
- name: install
cd ${GITHUB_WORKSPACE}/scripts && ./format.sh
- name: lint
if: always()
run: |
cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
- name: test
if: always()
run: |
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19 changes: 6 additions & 13 deletions .github/workflows/wheels.yml
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Expand Up @@ -11,25 +11,18 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-20.04]
# macos-13 is an intel runner, macos-14 is apple silicon
os: [ubuntu-latest, windows-latest, macos-13, macos-14]

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

# Used to host cibuildwheel
- uses: actions/setup-python@v3

- name: Install cibuildwheel
run: python -m pip install cibuildwheel==2.13.1

- name: Build wheels
run: python -m cibuildwheel --output-dir wheelhouse
# to supply options, put them in 'env', like:
# env:
# CIBW_SOME_OPTION: value
uses: pypa/[email protected]

- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
path: ./wheelhouse/*.whl
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -2,7 +2,7 @@

![Build status](https://github.com/SINGROUP/dscribe/actions/workflows/actions.yml/badge.svg)
[![Coverage Status](https://coveralls.io/repos/github/SINGROUP/dscribe/badge.svg?branch=master)](https://coveralls.io/github/SINGROUP/dscribe?branch=master)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

DScribe is a Python package for transforming atomic structures into fixed-size
numerical fingerprints. These fingerprints are often called "descriptors" and
Expand Down
9 changes: 0 additions & 9 deletions devrequirements.txt
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This file was deleted.

2 changes: 1 addition & 1 deletion docs/2.1.x/.buildinfo
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@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 979ed1add00f32f4bc116afafadc8e3c
config: d2b1800fed63e4715a5ada69f6a537e2
tags: 645f666f9bcd5a90fca523b33c5a78b7
45 changes: 30 additions & 15 deletions docs/2.1.x/_modules/dscribe/core/lattice.html
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@@ -1,22 +1,24 @@
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>dscribe.core.lattice &mdash; DScribe 2.1.x documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/style.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/style.css?v=7d1ac55c" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->

<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/doctools.js"></script>
<script src="../../../_static/sphinx_highlight.js"></script>
<script defer="defer" src="../../../_static/js/versions.js"></script>
<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="../../../_static/documentation_options.js?v=c41997dc"></script>
<script src="../../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script defer="defer" src="../../../_static/js/versions.js?v=413e22da"></script>
<script src="../../../_static/js/theme.js"></script>
<link rel="author" title="About these documents" href="../../../about.html" />
<link rel="index" title="Index" href="../../../genindex.html" />
Expand Down Expand Up @@ -97,10 +99,13 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="sd">See the License for the specific language governing permissions and</span>
<span class="sd">limitations under the License.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>


<div class="viewcode-block" id="Lattice"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a><span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<div class="viewcode-block" id="Lattice">
<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a>
<span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A lattice object. Essentially a matrix with conversion matrices. In</span>
<span class="sd"> general, it is assumed that length units are in Angstroms and angles are in</span>
Expand Down Expand Up @@ -144,7 +149,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">inv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span>

<div class="viewcode-block" id="Lattice.get_cartesian_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a> <span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
<div class="viewcode-block" id="Lattice.get_cartesian_coords">
<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a>
<span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the cartesian coordinates given fractional coordinates.</span>

Expand All @@ -156,7 +163,10 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">fractional_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span></div>

<div class="viewcode-block" id="Lattice.get_fractional_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a> <span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>

<div class="viewcode-block" id="Lattice.get_fractional_coords">
<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a>
<span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the fractional coordinates given cartesian coordinates.</span>

Expand All @@ -168,6 +178,7 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">cart_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">inv_matrix</span><span class="p">)</span></div>


<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">lengths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lengths</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
Expand Down Expand Up @@ -206,7 +217,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">Lattice</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reciprocal_lattice</span><span class="o">.</span><span class="n">matrix</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">))</span>

<div class="viewcode-block" id="Lattice.get_points_in_sphere"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a> <span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<div class="viewcode-block" id="Lattice.get_points_in_sphere">
<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a>
<span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Find all points within a sphere from the point taking into account</span>
<span class="sd"> periodic boundary conditions. This includes sites in other periodic</span>
Expand Down Expand Up @@ -282,7 +295,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
<span class="n">shifted_coords</span><span class="p">[</span><span class="n">within_r</span><span class="p">],</span>
<span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">d_2</span><span class="p">[</span><span class="n">within_r</span><span class="p">]),</span>
<span class="n">indices</span><span class="p">[</span><span class="n">within_r</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
<span class="p">)</span></div></div>
<span class="p">)</span></div>
</div>

</pre></div>

</div>
Expand Down
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