High-throughput analysis of crystalline porous materials By Maciej Haranczyk, Chris H Rycroft, Richard L Martin, Thomas F Willems
This repository contains a fork of the original zeo++ code (version 0.3.0) with bug fixes and improvements, maintained by the Laboratory of Molecular Simulation at EPFL. For a list of changes, see the CHANGELOG.md.
Email: mharanczyk@lbl.gov (Zeo++) and chr@alum.mit.edu (Voro++)
Zeo++ is a software package for high-throughput analysis of structure and topology of crystalline porous materials. For a given material's structure, the code calculates the geometrical parameters describing pores. The tool is based on the Voronoi decomposition, which for a given arrangement of atoms in a periodic domain provides a graph representation of the void space. The resulting Voronoi network is analyzed to obtain the diameter of the largest included sphere and the largest free sphere, which are two geometrical parameters that are frequently used to describe pore geometry. Accessibility of nodes in the network is also determined for a given guest molecule and the resulting information is later used to retrieve dimensionality of channel systems as well as in Monte Carlo sampling of accessible surfaces, volumes and pore size distributions. The code also offers some aids with structure analysis, e.g. MOF open metal site detection, and simluations, e.g. generation of blocking spheres.
The easiest way to install zeo++ is through the conda package manager:
conda install -c conda-forge zeopp-lsmo
The code is written in ANSI C++, and compiles on many system architectures. The package contains the C++ source code of Zeo++ as well as Voro++ library. On Linux, Mac OS, and Windows (using Cygwin), the compilation and installed can be carried out using GNU Make.
Clone the git repository
git clone https://github.com/lsmo-epfl/zeopp-lsmo
cd zeopp-lsmo
Download Eigen library v3.2.7 (if not already installed)
wget https://gitlab.com/libeigen/eigen/-/archive/3.2.7/eigen-3.2.7.tar.bz2
tar xf eigen-3.2.7.tar.bz2
Compile Voro++ library (you may need first to review config.mk file in voro++/ directory; please check Voro++ documentation or read voro++/README):
cd voro++
make
Compile Zeo++ code:
cd ../zeo++
make
This will create network binary, the main Zeo++ binary.
Please view the Zeo++ website for instructions, review documentation/README or contact the authors to inquire about otherwise undocumented or custom features.
No external dependencies are required to compile and run the code (except for the Voro++ library provided with the code), but several programs may be useful for analyzing the output:
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VMD - molecular visualization package can be used to visualize some of characteristics calculated by Zeo++, for example, Voronoi networks, Monte Carlo-sampled surface areas and volumes etc. Zeo++ can be called from within VMD vis TCl ZeoVis interface (not yet documented, if interested, please contact me at mharanczyk@lbl.gov)
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The freeware raytracer POV-Ray (available at www.povray.org) can be used for high-quality renderings of the Zeo++/VMD outputs.
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VisIt - powerful visualization package; https://wci.llnl.gov/codes/visit/
Zeo++ is released as free software through the Lawrence Berkeley National Laboratory - a detailed copyright notice is provided below, and the complete terms of the license can be found in the LICENSE file.
I am very interested to hear from users of Zeo++, so if you find this useful, please email me at mharanczyk@lbl.gov. Also, if you plan to publish an academic paper using this software, please consider citing the following publications:
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Thomas F. Willems, Chris H. Rycroft, Michael Kazi, Juan C. Meza, and Maciej Haranczyk, "Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials", Microporous and Mesoporous Materials 149 (2012) 134-141
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Richard L. Martin, Berend Smit, Maciej Haranczyk, "Addressing challenges of identifying geometrically diverse sets of crystalline porous materials", Journal of Chemical Information and Modeling, DOI: 10.1021/ci200386x
The first reference is the main Zeo++ reference describing the idea of using Voronoi networks in analysis of porous materials. The second reference describes extensions allowing sampling of structures from a database of porous materials using divrsity-based selelction.
Before making changes to the code, please install the pre-commit hooks for automatic code formatting and linting:
pip install pre-commit
pre-commit install
Zeo++, Copyright (c) 2011, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov.
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
This work was supported by the U.S. Department of Energy under contract DE-AC02-05CH11231 and through SciDAC project #CSNEW918 entitled “Knowledge guided screening tools for identification of porous materials for CO2 separations”.