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<!DOCTYPE html>
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<meta name="description" content="Resources: extensions available for Avogadro develoepd by the Zurek group: Randomdock, Nanotube builder, etc.">
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<h1>Resources</h1>
<hr>
<p class="lead">
Useful toolsets, articles, and more!
</p>
</div>
<a class="anchor" id="ORS">
<br><br>
</a>
<div class="jumbotron" id="ORS">
<h2>ORS</h2>
<hr>
<b>ORS</b> (Open Research Scripts), developed and maintained by <b>Xiaoyu Wang</b>, is a growing toolbox of
research utilities for electronic structure calculations, tight-binding modeling, and orbital-resolved analysis.
It provides a unified set of Python modules and command-line tools designed for clarity, reproducibility,
and extension in materials modeling workflows. The toolset is published under the MIT license and can be obtained
from its GitHub repository.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://github.com/lilithean/scripts">ORS</a>
<br><br>
</div>
<a class="anchor" id="SSCHA-MLIP">
<br><br>
</a>
<div class="jumbotron" id="SSCHA-MLIP">
<h2>SSCHA-MLIP</h2>
<hr>
<b>SSCHA-MLIP</b> is a set of libraries, scripts and workflows for the implementation of
Moment Tensor Potential for the Stochastic Self-Consistent Harmonic approximation
as described <a target='_blank' href="https://www.nature.com/articles/s41524-025-01553-1">here</a>.
The toolset is developed by <b>Francesco Belli</b>, published under the GPL-3.0 license,
and can be obtained from its GitHub repository.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://github.com/FlemkMeserath/SSCHA-MLIP">SSCHA-MLIP</a>
<br><br>
</div>
<a class="anchor" id="QuantumObservable">
<br><br>
</a>
<div class="jumbotron" id="QuantumObservable">
<h2>QuantumObservable</h2>
<hr>
<b>QuantumObservable</b> is a toolkit developed by <b>Francesco Belli</b> that determines the
<a target='_blank' href="https://arxiv.org/abs/2501.14420">symmetry index</a>
of a chemical compound in the descriptors for predicting the quantum nuclear and anharmonic effects.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://github.com/FlemkMeserath/QuantumObservable">QuantumObservable</a>
<br><br>
</div>
<a class="anchor" id="PRAPs">
<br><br>
</a>
<div class="jumbotron" id="PRAPs">
<h2>PRAPs</h2>
<hr>
<b>PRAPs</b> (The Plan for Robust and Accurate Potentials) is a package containing both an automated
workflow for training moment tensor potentials with the MLIP software and a Python library to interface
and provide utilities for the MLIP software. It is developed by <b>Josiah Roberts</b> and is
available under the BSD license via GitHub.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://github.com/Dryctarth/PRAPs">PRAPs</a>
<br><br>
</div>
<a class="anchor" id="pycxl">
<br><br>
</a>
<div class="jumbotron" id="pycxl">
<h2>Pycxl</h2>
<hr>
<b>Pycxl</b> is an open-source Python wrapper developed by <b>Samad Hajinazar</b>. It computes the
convex hull and calculates the "distance above hull" for datapoints of an N-ary system.
Pycxl is published under the "NEW" BSD license, and the code and its documentation can be
obtained from its GitHub repository.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://github.com/hajinazar/pycxl">Pycxl</a>
<br><br>
</div>
<a class="anchor" id="randspg">
<br><br>
</a>
<div class="jumbotron" id="randspg">
<h2>RandSpg</h2>
<hr>
<b>RandSpg</b> is an algorithm developed by <b>Patrick Avery</b>.
RandSpg generates random crystals of specific spacegroups and allows the user to specify
a lot of information such as minimum interatomic distances, volume constraints, etc.
<br><br>
The source code is available under the <a target='_blank' href="https://opensource.org/licenses/BSD-3-Clause">"New" BSD open source license</a>
and may be viewed at its <a target='_blank' href="https://github.com/psavery/randSpg">GitHub repository</a>.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="http://xtalopt.openmolecules.net/randSpg/randSpg.html">RandSpg</a>
<br><br>
If you encounter any bugs, please email <a href='mailto:psavery@buffalo.edu'>psavery@buffalo.edu</a>
</div>
<a class="anchor" id="xtalcomp">
<br><br>
</a>
<div class="jumbotron" id="xtalcomp">
<h2>XtalComp</h2>
<hr>
<b>XtalComp</b> is an open-source code to check the similarity between two structures. It is published under the <a target='_blank' href="https://opensource.org/licenses/BSD-3-Clause">"New" BSD open source license</a> and can be downloaded from its <a target='_blank' href="https://github.com/allisonvacanti/XtalComp">GitHub repository</a>.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html">XtalComp</a>
<br><br>
</div>
<a class="anchor" id="related">
<br><br>
</a>
<div class="jumbotron" id="related">
<h2>Articles</h2>
<hr>
<ul align="left" style="text-align:-moz-left">
<li>Marcus D. Hanwell, Donald Ephraim Curtis, David C. Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R. Hutchison, <b>Avogadro: An advanced semantic chemical editor, visualization, and analysis platform</b>, J. Cheminformatics 4.1 (2012) pp. 17 <a class="ext-link" target="_blank" href="http://www.jcheminf.com/content/4/1/17"><span class="icon"> </span>[open access</a><a class="ext-link" target="_blank" href="http://www.biomedcentral.com/content/pdf/1758-2946-4-17.pdf"><span class="icon"></span>, pdf]</a></li>
<li>Noel M. O'Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, Geoffrey R. Hutchison, <b>Open Babel: An open chemical toolbox</b>, J Cheminf 3 (2011) pp. 33 <a class="ext-link" target="_blank" href="http://www.jcheminf.com/content/3/1/33"><span class="icon"> </span>[open access</a><a class="ext-link" target="_blank" href="http://www.biomedcentral.com/content/pdf/1758-2946-3-33.pdf"><span class="icon"></span>, pdf]</a></li>
<li>O'Boyle NM, Guha R, Willighagen EL, et al., <b>Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on</b>, Journal of Cheminformatics (2011) 3(1):37 <a class="ext-link" target="_blank" href="http://www.jcheminf.com/content/3/1/37"><span class="icon"> </span>[open access</a><a class="ext-link" target="_blank" href="http://www.jcheminf.com/content/pdf/1758-2946-3-37.pdf"><span class="icon"></span>, pdf]</a></li>
</ul>
</div>
<a class="anchor" id="yaehmop">
<br><br>
</a>
<div class="jumbotron" id="yaehmop">
<h2>Avogadro1 + Yaehmop</h2>
<hr>
<details>
<summary></summary>
<a class="ext-link" target="_blank" href="https://github.com/greglandrum/yaehmop"><span class="icon"> </span>YAeHMOP</a> is an extended Hückel package which is interfaced to the open-source molecular editor <a class="ext-link" target="_blank" href="https://avogadro.cc/"><span class="icon"> </span>Avogadro</a>.
<br><br>
<a class="btn btn-large btn-basic" target="_blank" href="https://avogadro-yaehmop.github.io">Website</a>
<br><br>
</details>
</div>
<a class="anchor" id="nanotube">
<br><br>
</a>
<div class="jumbotron">
<h2>Avogadro1: Nanotube Builder</h2>
<hr>
<details>
<summary></summary>
<div class="row-fluid">
<div class="span4">
<br>
<p align="left" style="text-align:-moz-left">
Avogadro contains a nanotube builder extension (shown on the right). The extension generates a single-wall carbon nanotube from an (n,m) specification. More info can be found <a class="ext-link" href="http://davidlonie.blogspot.com/2011/10/nanotube-builder-for-avogadro.html">here</a>.
</p>
<img src="dist/img/resources/avogadro-nanotube-menu.png" alt="avogadro-nanotube-menu.png">
<br><br>
</div>
<div class="span8">
<img src="dist/img/resources/avogadro-nanotube.png" alt="avogadro-nanotube.png">
A 20 angstrom, hydrogen capped (6,6) nanotube.
</div>
</div>
</details>
</div>
<a class="anchor" id="crystal">
<br><br>
</a>
<div class="jumbotron">
<h2>Avogadro1: Crystallography Extension</h2>
<hr>
<details>
<summary></summary>
<p align="left" style="text-align:-moz-left">
While Avogadro has provided basic crystallography tools through its existing Unit Cell and Super Cell extensions (which enabled users to modify unit cell parameters and build supercells, respectively), advanced tasks such as space group detection and primitive cell reduction have required closed source (and often expensive!) tools such as Materials Studio or ISOTROPY/FINDSYM.
</p>
<img src="dist/img/resources/avogadro-crystal.png" alt="avogadro-crystal.png" width=70%>
<p style="font-size:11px">
Screenshot of Avogadro visualizing a MgTiO<sub>3</sub> cell and displaying the crystallographic properties.
</p>
<br>
<div class="row-fluid">
<div class="span3">
<center>
<img src="dist/img/resources/avogadro-crystal-edit.png" alt="avogadro-crystal-edit.png" style="max-width:70%;border:2px solid grey;border-radius:10px">
<p style="font-size:11px">
The docking editors.
The Cell Matrix editor shows the on-the-fly input checking.
As soon as an invalid character is entered (note the extra 0's in the final row), the text turns red.
</p>
</center>
</div>
<div class="span9">
<p align="left" style="text-align:-moz-left">
So what new functionality does the extension add?
The short answer: Everything I could think of.
The long answer?
Well, that needs a list or two:
</p>
<p align="left" style="text-align:-moz-left">
<ul align="left" style="text-align:-moz-left">
<li>Customizable docking editors allow direct editing of:</li>
<ul align="left" style="text-align:-moz-left">
<li>Cell parameters a, b, c, alpha, beta, and gamma</li>
<li>The cell matrix, as either row or column vectors</li>
<li>The atomic coordinates, in either cartesian or fractional units</li>
<li>Customizable unit display:</li>
<li>All lengths (parameters, cell matrix, cartesian coordinates) can be displayed in Angstrom, Bohr, nanometer, or picometer</li>
<li>All angles can be displayed in degree or radian</li>
<li>Immediate feedback on invalid entry: Text turns red when an invalid entry is made</li>
<li>Plain text entry -- perfect for copy/pasting to/from input/output files.</li>
</ul>
</ul>
</p>
</div>
</div>
<div class="row-fluid">
<div class="span3">
<center>
<img src="dist/img/resources/avogadro-crystal-menu.png" alt="avogadro-crystal-menu.png">
<p style="font-size:11px">
Some of the new tools in the Crystallography menu
</p>
</center>
</div>
<div class="span9">
<p align="left" style="text-align:-moz-left">
<ul align="left" style="text-align:-moz-left">
<li>Some of the new tools in the Crystallography menu:</li>
<ul align="left" style="text-align:-moz-left">
<li>Add / Remove unit cell Symmetry tools:</li>
<ul align="left" style="text-align:-moz-left">
<li>Detect spacegroup</li>
<li>Manually set spacegroup</li>
<li>Symmetrize cell and coordinates to detected space group</li>
</ul>
<li>Fill unit cell using a few atoms and the current space group's symmetry operations</li>
<li>Structure reductions:</li>
<ul align="left" style="text-align:-moz-left">
<li>Reduce to primitive cell</li>
<li>Reduce to Niggli cell</li>
</ul>
<li>Option to preserve either cartesian or fractional coordinates when the cell is modified</li>
<li>Display fractionalization matrix</li>
<li>Import POSCAR style data from clipboard (more formats to come)</li>
<li>Copy POSCAR to clipboard</li>
<li>Translate ("wrap") atoms to lie inside unit cell</li>
<li>Rotate to standard orientation (i.e. A along x, B in x,y plane)</li>
<li>Scale cell to a specified volume (isotropic scaling)</li>
</ul>
<li>On-screen display of crystallographic properties:</li>
<ul align="left" style="text-align:-moz-left">
<li>Lattice type</li>
<li>Space group</li>
<li>Cell Volume</li>
</ul>
</ul>
</p>
</div>
<p align="left" style="text-align:-moz-left">
Many of these great features would not have been possible without the contributions of other open-source programmers, namely Atsushi Togo for spglib, a BSD-licensed library which provides the awesome symmetry tools, and Jean Bréfort for contributing the space group transform database and unit cell implementation and tools in Open Babel.
</p>
</div>
</details>
</div>
<a class="anchor" id="randomdock">
<br><br>
</a>
<div class="jumbotron" id="randomdock">
<h2>RandomDock</h2>
<hr>
<details>
<summary></summary>
<p align="left" style="text-align:-moz-left">
<h4><b><em>Note: This functionality is not currently available in XtalOpt.</em></b></h4>
<br>
RandomDock is included with XtalOpt. The RandomDock extension is built by configuring XtalOpt with the</p>
<pre>-DENABLE_RandomDock=1</pre>
<p align="left" style="text-align:-moz-left">
flag during the cmake step of the installation. RandomDock generates a user–specified number of geometries which are sent out for relaxation by an external quantum chemical program. These are generated as follows:
</p>
<div class="row-fluid">
<div class="span9">
<ul align="left" style="text-align:-moz-left">
<li>The substrate (template) and matrix (monomer) molecules can be drawn and pre–optimized by Avogadro or imported into Avogadro from a file using one of the common chemical structure formats. The number of matrix and substrate molecules are specified in the GUI. Either isolated molecules or complexes (dimers, trimers etc.) may be employed.</li>
<br>
<li>Conformers of the substrate and/or matrix molecules are generated and pre–optimized using one of the force field implementations in the OpenBabel library. Either an exhaustive search can be performed, or a specified number of conformers may be created. The latter option does not guarantee that the most stable conformers will be found, since the conformergenerating algorithm stops once the specified number has been reached.</li>
<br>
<li>Conformers of the matrix and/or substrate molecules are chosen such that the probability \(p_i\) of selecting a given individual is calculated from its energy \(E_i\) (evaluated via the specified force field) as:
<br><br>
<center>
<p>
\(p_{i}=N\left(1-\frac{E_{i}-E_\mathrm{min}}{E_\mathrm{max}-E_\mathrm{min}}\right)\)
</p>
</center>
where \(E_\mathrm{min}\) and \(E_\mathrm{max}\) are the energies of the most stable and the least stable conformer, and \(N\) is a normalization factor ensuring that \(\Sigma p_i = 1\).</li>
</ul>
</div>
<div class="span3">
<a class="popup" target="_blank" href="dist/img/resources/rd-menu.png">
<img src="dist/img/resources/rd-menu.png" alt="rd-menu.png" style="max-width:80%">
</a>
</div>
</div>
<br>
<ul align="left" style="text-align:-moz-left">
<li>The matrix molecules are placed randomly about the substrate subject to user–specified distance constraints. A range for the interatomic distances (IAD) between all atoms in the matrix and substrate molecules may be specified. This ensures that all atoms between any templatematrix pair are separated by at least the minimum IAD (in angstroms), but at least one pair, from each matrix molecule, must be closer than the IAD maximum value.</li>
<br>
<li>An option to force the formation of hydrogen bonds ensures that each configuration has at least one short X–H–X contact between the matrix and the substrate, where X is F, O, or N.</li>
<br>
<li>The 'cluster' option changes the intermolecular distance constraint. Instead of ensuring that each matrix molecule is close to the substrate, it enforces each matrix molecule to be close to the substrate or another matrix molecule.</li>
<br>
<li>The structures are submitted for optimization by an external program. Currently, ADF, Gaussian, GAMESS and MOPAC are supported. The calculations may be performed on a remote supercomputing cluster by specifying secureshell login credentials and selecting a queuing system type, or on a local workstation. Remote calculations are automatically staged, copied, submitted, monitored, and analyzed by RandomDock, making searches fully automatic.</li>
</ul>
</details>
</div>
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