EOn: Difference between revisions
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'''eOn''' (styled '''eOn2''' during its time on the [[wikipedia:Berkeley Open Infrastructure for Network Computing|BOINC]] platform) was a completed [[wikipedia:volunteer computing|volunteer computing]] project of the Henkelman Research Group at the [[wikipedia:University of Texas at Austin|University of Texas at Austin]], run out of the university's [[wikipedia:Institute for Computational Engineering and Sciences|Institute for Computational Engineering and Sciences]] (ICES).<ref name="wiki-eon">Chill, Samuel T., Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson, Graeme Henkelman. [https://iopscience.iop.org/article/10.1088/0965-0393/22/5/055002 EON: software for long time simulations of atomic scale systems]. ''Modelling and Simulation in Materials Science and Engineering'' 22(5), 055002 (2014). {{DOI|10.1088/0965-0393/22/5/055002}}.</ref> The project applied [[wikipedia:theoretical chemistry|theoretical chemistry]] methods, chiefly [[wikipedia:transition state theory|transition state theory]] combined with [[wikipedia:kinetic Monte Carlo|kinetic Monte Carlo]], to model the evolution of atomic scale systems over timescales far longer than those reachable with conventional [[wikipedia:molecular dynamics|molecular dynamics]]. Its name is drawn from ''[[wikipedia:aeon|eon]]'', a reference to the immeasurably long timescales the software was built to reach.<ref name="bcteam">[https://www.bc-team.org/viewtopic.php?t=595 eOn]. BOINC Confederation forum. Posted 1 September 2010.</ref> | '''[https://web.archive.org/http://eon.ices.utexas.edu/eon2/ eOn]''' (styled '''eOn2''' during its time on the [[wikipedia:Berkeley Open Infrastructure for Network Computing|BOINC]] platform) was a completed [[wikipedia:volunteer computing|volunteer computing]] project of the Henkelman Research Group at the [[wikipedia:University of Texas at Austin|University of Texas at Austin]], run out of the university's [[wikipedia:Institute for Computational Engineering and Sciences|Institute for Computational Engineering and Sciences]] (ICES).<ref name="wiki-eon">Chill, Samuel T., Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson, Graeme Henkelman. [https://iopscience.iop.org/article/10.1088/0965-0393/22/5/055002 EON: software for long time simulations of atomic scale systems]. ''Modelling and Simulation in Materials Science and Engineering'' 22(5), 055002 (2014). {{DOI|10.1088/0965-0393/22/5/055002}}.</ref> The project applied [[wikipedia:theoretical chemistry|theoretical chemistry]] methods, chiefly [[wikipedia:transition state theory|transition state theory]] combined with [[wikipedia:kinetic Monte Carlo|kinetic Monte Carlo]], to model the evolution of atomic scale systems over timescales far longer than those reachable with conventional [[wikipedia:molecular dynamics|molecular dynamics]]. Its name is drawn from ''[[wikipedia:aeon|eon]]'', a reference to the immeasurably long timescales the software was built to reach.<ref name="bcteam">[https://www.bc-team.org/viewtopic.php?t=595 eOn]. BOINC Confederation forum. Posted 1 September 2010.</ref> | ||
eOn joined the BOINC network in September 2010 and ran until it was retired in May 2014. The underlying EON research code, distinct from the retired volunteer computing project, continues to be developed and used within the [[wikipedia:computational chemistry|computational chemistry]] community. | eOn joined the BOINC network in September 2010 and ran until it was retired in May 2014. The underlying EON research code, distinct from the retired volunteer computing project, continues to be developed and used within the [[wikipedia:computational chemistry|computational chemistry]] community. | ||
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Early participants reported a bumpy rollout, including client crashes on Mac OS X and complaints about long-running, unchecked work units, alongside genuine enthusiasm from teams that had followed the Henkelman group's earlier, non-BOINC eOn effort.<ref name="boinc-launch" /><ref name="eonclient400">eOn Client 4.00. UT theoretical chemistry code forum. Posted February 2012.</ref> | Early participants reported a bumpy rollout, including client crashes on Mac OS X and complaints about long-running, unchecked work units, alongside genuine enthusiasm from teams that had followed the Henkelman group's earlier, non-BOINC eOn effort.<ref name="boinc-launch" /><ref name="eonclient400">eOn Client 4.00. UT theoretical chemistry code forum. Posted February 2012.</ref> | ||
[[File:UT Tower, University of Texas in Austin.jpg|thumb|The University of Texas at Austin, home to the Institute for Computational Engineering and Sciences, where eOn was developed and hosted.]] | [[File:UT Tower, University of Texas in Austin.jpg|thumb|The University of Texas at Austin, home to the Institute for Computational Engineering and Sciences, where eOn was developed and hosted.|658x658px]] | ||
== Scientific method == | == Scientific method == | ||
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The dimer is rotated to align with this minimum mode and then walked uphill along it until it converges on a saddle point.<ref name="dimer1999" /> Besides aKMC, the EON software also implemented [[wikipedia:parallel replica dynamics|parallel replica dynamics]], [[wikipedia:hyperdynamics|hyperdynamics]], and global optimization methods including [[wikipedia:simulated annealing|simulated annealing]], [[wikipedia:basin hopping|basin hopping]], and minima hopping.<ref name="wiki-eon" /> | The dimer is rotated to align with this minimum mode and then walked uphill along it until it converges on a saddle point.<ref name="dimer1999" /> Besides aKMC, the EON software also implemented [[wikipedia:parallel replica dynamics|parallel replica dynamics]], [[wikipedia:hyperdynamics|hyperdynamics]], and global optimization methods including [[wikipedia:simulated annealing|simulated annealing]], [[wikipedia:basin hopping|basin hopping]], and minima hopping.<ref name="wiki-eon" /> | ||
== Software architecture == | == Software architecture == | ||
EON used a client/server design: computationally intensive force and energy evaluations ran on volunteer client machines, while a central server managed the overall state-to-state evolution of the simulation, for example driving the kinetic Monte Carlo bookkeeping in aKMC runs. The server was written in [[wikipedia:Python (programming language)|Python]] and the client in [[wikipedia:C++|C++]], the latter chosen so that a self-contained compiled executable could be distributed easily to volunteers.<ref name="wiki-eon" /> Beyond BOINC, the same codebase could also run on a single workstation, on cluster queuing systems, and on large parallel machines via [[wikipedia:Message Passing Interface|MPI]].<ref name="ltd-docs" /> The code was released under version 3 of the [[wikipedia:GNU General Public License|GNU General Public License]].<ref name="wiki-eon" /> | [[File:Potential Energy Surface and Corresponding Reaction Coordinate Diagram.png|thumb|A potential energy surface with a saddle point separating two minima, the kind of feature EON's dimer method searches for.|left|344x344px]]EON used a client/server design: computationally intensive force and energy evaluations ran on volunteer client machines, while a central server managed the overall state-to-state evolution of the simulation, for example driving the kinetic Monte Carlo bookkeeping in aKMC runs. The server was written in [[wikipedia:Python (programming language)|Python]] and the client in [[wikipedia:C++|C++]], the latter chosen so that a self-contained compiled executable could be distributed easily to volunteers.<ref name="wiki-eon" /> Beyond BOINC, the same codebase could also run on a single workstation, on cluster queuing systems, and on large parallel machines via [[wikipedia:Message Passing Interface|MPI]].<ref name="ltd-docs" /> The code was released under version 3 of the [[wikipedia:GNU General Public License|GNU General Public License]].<ref name="wiki-eon" /> | ||
== Discontinuation == | == Discontinuation == | ||
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== Publications == | == Publications == | ||
The Berkeley BOINC project maintains a list of [https://boinc.berkeley.edu/pubs.php#EOn publications with results arising from BOINC-based computing], including work that made use of the eOn volunteer computing project:<ref name="pubs-boinc">Publications by BOINC Projects. boinc.berkeley.edu/pubs.php. Maintained by Alex Piskun.</ref> | [[File:TiltAndTwistBoundaries remade.JPG|thumb|Illustration of tilt and twist grain boundaries, the kind of defect studied in the 2009 EON simulation of a copper grain boundary.|439x439px]]The Berkeley BOINC project maintains a list of [https://boinc.berkeley.edu/pubs.php#EOn publications with results arising from BOINC-based computing], including work that made use of the eOn volunteer computing project:<ref name="pubs-boinc">Publications by BOINC Projects. boinc.berkeley.edu/pubs.php. Maintained by Alex Piskun.</ref> | ||
# Chill, Samuel T., Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson, Graeme Henkelman. [https://iopscience.iop.org/article/10.1088/0965-0393/22/5/055002 EON: software for long time simulations of atomic scale systems]. ''Modelling and Simulation in Materials Science and Engineering'' 22(5), 055002 (2014). {{DOI|10.1088/0965-0393/22/5/055002}}. | # Chill, Samuel T., Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson, Graeme Henkelman. [https://iopscience.iop.org/article/10.1088/0965-0393/22/5/055002 EON: software for long time simulations of atomic scale systems]. ''Modelling and Simulation in Materials Science and Engineering'' 22(5), 055002 (2014). {{DOI|10.1088/0965-0393/22/5/055002}}. | ||
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# Xu, Lijun, Graeme Henkelman. [http://aip.scitation.org/doi/10.1063/1.2976010 Adaptive kinetic Monte Carlo for first-principles accelerated dynamics]. ''The Journal of Chemical Physics'' (2008). {{DOI|10.1063/1.2976010}}. | # Xu, Lijun, Graeme Henkelman. [http://aip.scitation.org/doi/10.1063/1.2976010 Adaptive kinetic Monte Carlo for first-principles accelerated dynamics]. ''The Journal of Chemical Physics'' (2008). {{DOI|10.1063/1.2976010}}. | ||
# Henkelman, Graeme, Hannes Jónsson. [https://link.aps.org/doi/10.1103/PhysRevLett.90.116101 Multiple Time Scale Simulations of Metal Crystal Growth Reveal the Importance of Multiatom Surface Processes]. ''Physical Review Letters'' (2003). {{DOI|10.1103/PhysRevLett.90.116101}}. | # Henkelman, Graeme, Hannes Jónsson. [https://link.aps.org/doi/10.1103/PhysRevLett.90.116101 Multiple Time Scale Simulations of Metal Crystal Growth Reveal the Importance of Multiatom Surface Processes]. ''Physical Review Letters'' (2003). {{DOI|10.1103/PhysRevLett.90.116101}}. | ||
No additional eOn-specific publications beyond these six were found in the BOINC publications registry at the time of writing. | No additional eOn-specific publications beyond these six were found in the BOINC publications registry at the time of writing. | ||