Merge branch 'main' into patch-1

Author: Andrew-S-Rosen

README.md

@@ -25,7 +25,7 @@ Calculator).
 
 ## Documentation
 
-The API documentation and tutorials are available at https://matcalc.ai.
+The API documentation and tutorials are available at http://matcalc.ai.
 
 ## Outline
 
@@ -175,6 +175,11 @@ initializing the benchmark to limit the number of calculations to do some testin
 
 Docker images with MatCalc and LAMMPS support are available at the [Materials Virtual Lab Docker Repository].
 
+## Tutorials
+
+Anubhav Jain (@computron) has created a nice [YouTube tutorial](https://youtu.be/57Elhe4IIhI?si=KbZh5s7HAyNGvmFT) on
+how to use MatCalc to quickly obtain properties of materials.
+
 ## Citing
 
 A manuscript on `matcalc` is currently in the works. In the meantime, please see [`citation.cff`](citation.cff) or the GitHub

docs/index.md

@@ -31,16 +31,17 @@ Calculator).
 
 ## Documentation
 
-The API documentation and tutorials are available at https://matcalc.ai.
+The API documentation and tutorials are available at http://matcalc.ai.
 
 ## Outline
 
 The main base class in MatCalc is `PropCalc` (property calculator). [All `PropCalc` subclasses](https://github.com/search?q=repo%3Amaterialsvirtuallab%2Fmatcalc%20%22(PropCalc)%22) should implement a
-`calc(pymatgen.Structure) -> dict` method that returns a dictionary of properties.
+`calc(pymatgen.Structure | ase.Atoms | dict) -> dict` method that returns a dictionary of properties.
 
 In general, `PropCalc` should be initialized with an ML model or [ASE] calculator, which is then used by either ASE,
 LAMMPS or some other simulation code to perform calculations of properties. The `matcalc.PESCalculator` class
-provides easy access to many universal MLIPs as well as an interface to
+provides easy access to many foundation potentials (FPs) as well as an interface to MAML for custom MLIPs
+such as MTP, NNP, GAP, etc.
 
 # Basic Usage
 
@@ -60,6 +61,12 @@ print(f"K_VRH = {props['bulk_modulus_vrh'] * 160.2176621} GPa")
 
 The calculated `K_VRH` is about 102 GPa, in reasonably good agreement with the experimental and DFT values.
 
+You can easily access a list of universal calculators (not comprehensive) using the UNIVERSAL_CALCULATORS enum.
+
+```python
+print(mtc.UNIVERSAL_CALCULATORS)
+```
+
 While we generally recommend users to specify exactly the model they would like to use, MatCalc provides useful
 (case-insensitive) aliases to our recommended models for PBE and r2SCAN predictions. These can be loaded using:
 
@@ -69,8 +76,8 @@ pbe_calculator = mtc.load_fp("pbe")
 r2scan_calculator = mtc.load_fp("r2scan")
 ```
 
-At the time of writing, these are the TensorNet-MatPES models. However, these recommendations may updated as improved
-models become available.
+At the time of writing, these are the `TensorNet-MatPES-v2025.1` models for these functionals. However, these
+recommendations may updated as improved models become available.
 
 MatCalc also supports trivial parallelization using joblib via the `calc_many` method.
 
@@ -129,7 +136,7 @@ Chaining can also be used with the `calc_many` method, with parallelization.
 
 ### CLI tool
 
-A CLI tool provides a means to use universal MLIPs to obtain properties for any structure. Example usage:
+A CLI tool provides a means to use FPs to obtain properties for any structure. Example usage:
 
 ```shell
 matcalc calc -p ElasticityCalc -s Li2O.cif
@@ -174,6 +181,11 @@ initializing the benchmark to limit the number of calculations to do some testin
 
 Docker images with MatCalc and LAMMPS support are available at the [Materials Virtual Lab Docker Repository].
 
+## Tutorials
+
+Anubhav Jain (@computron) has created a nice [YouTube tutorial](https://youtu.be/57Elhe4IIhI?si=KbZh5s7HAyNGvmFT) on
+how to use MatCalc to quickly obtain properties of materials.
+
 ## Citing
 
 A manuscript on `matcalc` is currently in the works. In the meantime, please see [`citation.cff`](citation.cff) or the GitHub

docs/matcalc._base.html

@@ -6,7 +6,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>matcalc._cli module &mdash; matcalc 0.3.3 documentation</title>
+  <title>matcalc._cli module &mdash; matcalc 0.4.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="assets/pygments.css?v=03e43079" />
       <link rel="stylesheet" type="text/css" href="assets/css/theme.css?v=e59714d7" />
       <link rel="stylesheet" type="text/css" href="assets/css/custom.css" />
@@ -15,7 +15,7 @@
     <link rel="canonical" href="http://matcalc.aimatcalc._cli.html"/>
       <script src="assets/jquery.js?v=5d32c60e"></script>
       <script src="assets/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="assets/documentation_options.js?v=d5a15cff"></script>
+      <script src="assets/documentation_options.js?v=ff822928"></script>
       <script src="assets/doctools.js?v=9bcbadda"></script>
       <script src="assets/sphinx_highlight.js?v=dc90522c"></script>
     <script src="assets/js/theme.js"></script>
@@ -46,6 +46,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="matcalc.html">matcalc package</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="matcalc.html#subpackages">Subpackages</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="matcalc.html#submodules">Submodules</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="matcalc._base.html">matcalc._base module</a></li>
 <li class="toctree-l3 current"><a class="current reference internal" href="#">matcalc._cli module</a><ul>
@@ -56,6 +57,8 @@
 </li>
 <li class="toctree-l3"><a class="reference internal" href="matcalc._elasticity.html">matcalc._elasticity module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="matcalc._eos.html">matcalc._eos module</a></li>
+<li class="toctree-l3"><a class="reference internal" href="matcalc._lammps.html">matcalc._lammps module</a></li>
+<li class="toctree-l3"><a class="reference internal" href="matcalc._md.html">matcalc._md module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="matcalc._neb.html">matcalc._neb module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="matcalc._phonon.html">matcalc._phonon module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="matcalc._phonon3.html">matcalc._phonon3 module</a></li>
@@ -103,7 +106,7 @@
 <p>Command line interface to matcalc.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="matcalc._cli.calculate_property">
-<span class="sig-name descname"><span class="pre">calculate_property</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.3.3/src/matcalc/_cli.py#L19-L38"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.calculate_property" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">calculate_property</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.4.2/src/matcalc/_cli.py#L19-L38"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.calculate_property" title="Link to this definition"></a></dt>
 <dd><p>Implements calculate property.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -117,7 +120,7 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="matcalc._cli.clear_cache">
-<span class="sig-name descname"><span class="pre">clear_cache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.3.3/src/matcalc/_cli.py#L41-L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.clear_cache" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">clear_cache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.4.2/src/matcalc/_cli.py#L41-L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.clear_cache" title="Link to this definition"></a></dt>
 <dd><p>Clear the benchmark cache.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -131,7 +134,7 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="matcalc._cli.main">
-<span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.3.3/src/matcalc/_cli.py#L51-L126"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.main" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsvirtuallab/matcalc/blob/v0.4.2/src/matcalc/_cli.py#L51-L126"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#matcalc._cli.main" title="Link to this definition"></a></dt>
 <dd><p>Handle main.</p>
 </dd></dl>