Add external plugins and helper scripts

Author: bbye98

README.md

@@ -1 +1,74 @@
-# mdcraft
+<img src="https://raw.githubusercontent.com/bbye98/mdcraft/main/assets/logo.png" align="right" width="256"/>
+
+# MDCraft
+
+[![continuous-integration](https://github.com/bbye98/mdcraft/actions/workflows/ci.yml/badge.svg)](https://github.com/bbye98/mdcraft/actions/workflows/ci.yml)
+
+MDCraft is a toolkit of analysis modules and helper functions for
+molecular dynamics (MD) simulations.
+
+* **Documentation**: https://bbye98.github.io/mdcraft/
+* **Conda**: https://anaconda.org/bbye98/mdcraft
+* **Python Package Index (PyPI)**: https://pypi.org/project/mdcraft/
+
+Note that MDCraft is currently an *experimental* library that has
+only been tested on Linux and may contain bugs and issues. If you come
+across one or would like to request new features, please
+[submit a new issue](https://github.com/bbye98/mdcraft/issues/new).
+
+## Features
+
+* [`algorithm`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/algorithm):
+Efficient NumPy and SciPy algorithms for data wrangling and evaluating
+structural and dynamical properties.
+* [`analysis`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/analysis):
+Serial and parallel data analysis tools built on top of the MDAnalysis
+framework.
+* [`fit`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/fit):
+Two-dimensional curve fitting models for use with SciPy.
+* [`lammps`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/lammps):
+Helper functions for setting up LAMMPS simulations.
+* [`openmm`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/openmm):
+Extensions to the high-performance OpenMM toolkit, such as custom
+bond/pair potentials, support for NetCDF trajectories, and much more.
+* [`plot`](https://github.com/bbye98/mdcraft/tree/main/src/mdcraft/plot):
+Settings and additional functionality for Matplotlib figures.
+
+## Installation
+
+MDCraft requires Python 3.9 or later.
+
+For the most up-to-date version of MDCraft, clone the repository and
+install the package using pip:
+
+    git clone https://github.com/bbye98/mdcraft.git
+    cd mdcraft
+    python -m pip install -e .
+
+MDCraft is also available on Conda and PyPI:
+
+    conda install -c bbye98 mdcraft
+    python -m pip install mdcraft
+
+### Prerequisites
+
+If you use pip to manage your Python packages and plan on using the
+OpenMM simulation toolkit, you must compile and install OpenMM manually
+since OpenMM is not available in PyPI. See the
+["Compiling OpenMM from Source Code"](
+http://docs.openmm.org/latest/userguide/library/02_compiling.html)
+section of the OpenMM User Guide for more information.
+
+If you use Conda, it is recommended that you use the conda-forge
+channel to install dependencies. To make conda-forge the default
+channel, use
+
+    conda config --add channels conda-forge
+
+### Postrequisites
+
+To use the image of method charges
+(`mdcraft.openmm.system.add_image_charges()`) in your OpenMM
+simulations, you must compile and install [`constvplugin`](
+https://github.com/scychon/openmm_constV) or [`openmm-ic-plugin`](
+https://github.com/bbye98/mdcraft/tree/main/lib/openmm-ic-plugin).

docs/.buildinfo

@@ -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: e234653b78e30dc08ca3e09893d75a29
+config: 6503ead5ed52dbc60acff3a27651489a
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docs/.doctrees/environment.pickle

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>Overview: module code - MDCraft documentation</title>
+        <title>Overview: module code - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -557,7 +557,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
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docs/_modules/index.html

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '',
+    VERSION: '1.0.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_static/documentation_options.js

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     <link rel="shortcut icon" href="_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>&lt;no title&gt; - MDCraft documentation</title>
+        <title>&lt;no title&gt; - MDCraft 1.0.0 documentation</title>
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@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
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     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="_static/documentation_options.js?v=8d563738"></script>
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docs/api.html

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     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>cosine_sum_1d - MDCraft documentation</title>
+        <title>cosine_sum_1d - MDCraft 1.0.0 documentation</title>
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     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
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@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -595,7 +595,7 @@ <h1>cosine_sum_1d<a class="headerlink" href="#cosine-sum-1d" title="Link to this
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
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docs/api/mdcraft.algorithm.accelerated.cosine_sum_1d.html

@@ -6,7 +6,7 @@
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     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>cosine_sum_2d - MDCraft documentation</title>
+        <title>cosine_sum_2d - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
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@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -596,7 +596,7 @@ <h1>cosine_sum_2d<a class="headerlink" href="#cosine-sum-2d" title="Link to this
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
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docs/api/mdcraft.algorithm.accelerated.cosine_sum_2d.html

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     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>cosine_sum_inplace_2d - MDCraft documentation</title>
+        <title>cosine_sum_inplace_2d - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -592,7 +592,7 @@ <h1>cosine_sum_inplace_2d<a class="headerlink" href="#cosine-sum-inplace-2d" tit
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/api/mdcraft.algorithm.accelerated.cosine_sum_inplace_2d.html

@@ -6,7 +6,7 @@
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     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>cosine_sum_inplace_parallel_2d - MDCraft documentation</title>
+        <title>cosine_sum_inplace_parallel_2d - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
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     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -592,7 +592,7 @@ <h1>cosine_sum_inplace_parallel_2d<a class="headerlink" href="#cosine-sum-inplac
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
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docs/api/mdcraft.algorithm.accelerated.cosine_sum_inplace_parallel_2d.html

@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="delta_fourier_transform_1d_1d" href="mdcraft.algorithm.accelerated.delta_fourier_transform_1d_1d.html" /><link rel="prev" title="cosine_sum_inplace_parallel_2d" href="mdcraft.algorithm.accelerated.cosine_sum_inplace_parallel_2d.html" />
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>cosine_sum_parallel_2d - MDCraft documentation</title>
+        <title>cosine_sum_parallel_2d - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -596,7 +596,7 @@ <h1>cosine_sum_parallel_2d<a class="headerlink" href="#cosine-sum-parallel-2d" t
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/api/mdcraft.algorithm.accelerated.cosine_sum_parallel_2d.html

@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="delta_fourier_transform_sum_2d_2d" href="mdcraft.algorithm.accelerated.delta_fourier_transform_sum_2d_2d.html" /><link rel="prev" title="cosine_sum_parallel_2d" href="mdcraft.algorithm.accelerated.cosine_sum_parallel_2d.html" />
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>delta_fourier_transform_1d_1d - MDCraft documentation</title>
+        <title>delta_fourier_transform_1d_1d - MDCraft 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
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     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -601,7 +601,7 @@ <h1>delta_fourier_transform_1d_1d<a class="headerlink" href="#delta-fourier-tran
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
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     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/api/mdcraft.algorithm.accelerated.delta_fourier_transform_1d_1d.html

@@ -6,7 +6,7 @@
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     <link rel="shortcut icon" href="../_static/favicon.ico"/><!-- Generated with Sphinx 7.3.7 and Furo 2024.05.06 -->
-        <title>delta_fourier_transform_sum_2d_2d - MDCraft documentation</title>
+        <title>delta_fourier_transform_sum_2d_2d - MDCraft 1.0.0 documentation</title>
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     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MDCraft  documentation</div></a>
+      <a href="../index.html"><div class="brand">MDCraft 1.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -603,7 +603,7 @@ <h1>delta_fourier_transform_sum_2d_2d<a class="headerlink" href="#delta-fourier-
 
     </aside>
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-</div><script src="../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../_static/documentation_options.js?v=8d563738"></script>
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