GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction

Journal of Chemical Theory and Computation
Farren CurtisNoa Marom

Abstract

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functio...Continue Reading

References

Feb 15, 1985·Physical Review. B, Condensed Matter·J Harris
Jul 10, 1995·Physical Review Letters·D M Deaven, K M Ho
Oct 28, 1996·Physical Review Letters·J P PerdewM Ernzerhof
Aug 6, 2000·Acta Crystallographica. Section B, Structural Science·A J BlakeC C Sommerville
Aug 16, 2000·Acta Crystallographica. Section B, Structural Science·J P LommerseD E Williams
Jul 5, 2002·Physical Review Letters·G H JóhannessonJ K Nørskov
Aug 1, 2002·Acta Crystallographica. Section B, Structural Science·W D Sam MotherwellDonald E Williams
Dec 24, 2003·Acta Crystallographica. Section A, Foundations of Crystallography·R W Grosse-KunstleveP D Adams
Jul 13, 2004·Physical Review Letters·M DionB I Lundqvist
Jul 30, 2005·The Journal of Chemical Physics·Erin R Johnson, Axel D Becke
Sep 28, 2005·Acta Crystallographica. Section B, Structural Science·G M DayP Verwer
Jul 11, 2006·The Journal of Chemical Physics·Artem R Oganov, Colin W Glass
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Jan 16, 2007·Science·Brendan J Frey, Delbert Dueck
Mar 31, 2007·Physical Chemistry Chemical Physics : PCCP·G M DayW Jones
Oct 24, 2007·The Journal of Chemical Physics·Axel D Becke, Erin R Johnson
Jul 23, 2008·The Journal of Physical Chemistry. B·Marcus A Neumann
Mar 5, 2009·Physical Review Letters·Alexandre Tkatchenko, Matthias Scheffler
Mar 21, 2009·Acta Crystallographica. Section B, Structural Science·Graeme M DayBernd Schweizer
Feb 1, 2007·Journal of Applied Crystallography·N PaninaG Deroover
Oct 2, 2009·Physical Review Letters·Oleg A Vydrov, Troy Van Voorhis
Dec 3, 2009·The Journal of Physical Chemistry. B·Aldi AsmadiFrank J J Leusen
Jan 13, 2010·Physical Chemistry Chemical Physics : PCCP·C Richard A CatlowScott M Woodley
Mar 2, 2010·Nature Materials·Alvin L-S ChuaAdrian P Sutton
Jul 16, 2010·Acta Crystallographica. Section B, Structural Science·Christophe M L Vande VeldeSergey Sergeyev
Aug 18, 2010·Physical Chemistry Chemical Physics : PCCP·Min JiKai-Ming Ho
Jan 5, 2011·The Journal of Chemical Physics·Oleg A Vydrov, Troy Van Voorhis
Feb 2, 2011·The Journal of Chemical Physics·Stephan N Steinmann, Clemence Corminboeuf
Mar 17, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Chris J Pickard, R J Needs
Jul 30, 2011·Physical Review Letters·Tang-Qing Yu, Mark E Tuckerman
Oct 14, 2011·Physical Chemistry Chemical Physics : PCCP·H C Stephen ChanFrank J J Leusen
Nov 22, 2011·Acta Crystallographica. Section B, Structural Science·David A BardwellIlia K Zhitkov
Mar 7, 2012·The Journal of Physical Chemistry. B·Doris E BraunUlrich J Griesser
May 16, 2012·The Journal of Chemical Physics·A Otero-de-la-Roza, Erin R Johnson
May 23, 2012·Acta Crystallographica. Section B, Structural Science·Qiang ZhuHarold T Stokes
Aug 17, 2012·The Journal of Chemical Physics·A Otero-de-la-Roza, Erin R Johnson
Aug 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Robert A DiStasioAlexandre Tkatchenko
Sep 26, 2012·Physical Review Letters·Alexandre TkatchenkoMatthias Scheffler
Nov 28, 2012·Nature Materials·Bryce Meredig, C Wolverton
Apr 6, 2013·Journal of the American Chemical Society·Jianguo MeiZhenan Bao
May 18, 2013·Angewandte Chemie·Noa MaromAlexandre Tkatchenko
Jul 23, 2013·Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials·Sarah L Price

❮ Previous
Next ❯

Citations

Apr 22, 2019·The Journal of Chemical Physics·Michele Ceriotti
Jan 8, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Linyuan WangChunyan Chen
Dec 21, 2018·Chemical Science·Enrico BerardoKim E Jelfs
Oct 27, 2020·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Scott M WoodleyR Catlow
Feb 3, 2021·Journal of Chemical Theory and Computation·Shiyue Yang, Graeme M Day
Mar 18, 2021·ACS Nano·Andreas JeindlOliver T Hofmann
Apr 3, 2021·Journal of Chemical Theory and Computation·Samet Demir, Adem Tekin
Apr 22, 2021·The Journal of Physical Chemistry. a·Atreyee BanerjeeDavid J Wales
Mar 27, 2021·Annual Review of Chemical and Biomolecular Engineering·David H BowskillConstantinos C Pantelides
Jul 10, 2021·The Journal of Chemical Physics·Julia WestermayrReinhard J Maurer
Jul 27, 2021·Chemical Reviews·Felix MusilMichele Ceriotti
May 13, 2020·Journal of the American Chemical Society·John Carpenter, Michael Gruenwald
Oct 21, 2020·The Journal of Physical Chemistry. a·B Christopher Rinderspacher
Dec 11, 2020·The Journal of Physical Chemistry. a·Jianjun HuEdirisuriya M Dilanga Siriwardane
Sep 4, 2020·The Journal of Physical Chemistry. a·Olga EgorovaGraeme M Day
Mar 17, 2020·The Journal of Physical Chemistry. a·Evan PrettiNathan A Mahynski
Aug 14, 2021·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Wenhui YangJianjun Hu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials
Farren CurtisNoa Marom
Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials
Jan Gerit Brandenburg, Stefan Grimme
Genes & Genetic Systems
Fatemeh Zare-MirakabadBahram Goliaei
Physical Chemistry Chemical Physics : PCCP
Scott M WoodleyC Richard A Catlow
© 2022 Meta ULC. All rights reserved