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README
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Zeo++, high-throughput analysis of crystalline porous materials
By Maciej Haranczyk, Chris H Rycroft, Richard L Martin, Thomas F Willems
WWW: http://www.carboncapturematerials.org/Zeo++/
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.
Compilation - Linux / Mac OS / Windows with Cygwin
=====================================================================
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.
*** Step by step compilation ***
1) Unpack the provided Zeo++ package (the following commands will create
zeo++-0.3.0 directory containing the Zeo++ code; Voro++ library
will be placed in one of subfolders (zeo++-0.3.0/voro++)):
gunzip zeo++-0.3.0.tar.gz
tar xvf zeo++-0.3.0.tar
2) Compile Voro++ library (you may need first to review config.mk file in
zeo++-0.3.0/voro++/ directory; please check Voro++ documentation or
read zeo++-0.3.0/voro++/README):
cd zeo++-0.3.0/voro++/src
make
3) Compile Zeo++ code:
cd ../..
make
4) Step (3) will create "network" binary inside zeo++-0.3.0. This is the main
Zeo++ binary. Please view the Zeo++ website for instructions, review
zeo++-0.3.0/documentation/README or contact the authors to inquire about
otherwise undocumented or custom features.
Related programs
=====================================================================
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:
- 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)
- The freeware raytracer POV-Ray (available at www.povray.org) can be used for
high-quality renderings of the Zeo++/VMD outputs.
- VisIt - powerful visualization package; https://wci.llnl.gov/codes/visit/
Usage
=====================================================================
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:
- 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
- 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.
Copyright Notice
=====================================================================
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.
Acknowledgements
=====================================================================
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”.