Genetic algorithm optimization of defect clusters in crystalline materials

Kaczmarowski, Amy; Yang, Shujiang; Szlufarska, Izabela; Morgan, Dane

doi:10.1016/j.commatsci.2014.10.062

Title: Genetic algorithm optimization of defect clusters in crystalline materials

Journal Article · Sun Feb 01 00:00:00 EST 2015 · Computational Materials Science

DOI:https://doi.org/10.1016/j.commatsci.2014.10.062· OSTI ID:1250288

Kaczmarowski, Amy; Yang, Shujiang; Szlufarska, Izabela; Morgan, Dane

View Accepted Manuscript (Publisher)

Cite

Export

Save

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI ID:: 1250288

Journal Information:: Computational Materials Science, Journal Name: Computational Materials Science Vol. 98 Journal Issue: C; ISSN 0927-0256

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

Citation Metrics:

Cited by: 22 works

Citation information provided by
Web of Science

References (80)

Structure of large gold clusters obtained by global optimization using the minima hopping method Bao, Kuo; Goedecker, Stefan; Koga, Kenji Physical Review B, Vol. 79, Issue 4 https://doi.org/10.1103/PhysRevB.79.041405	journal	January 2009
Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems Goedecker, Stefan The Journal of Chemical Physics, Vol. 120, Issue 21 https://doi.org/10.1063/1.1724816	journal	June 2004
Dimensionality of interstitial cluster motion in bcc-Fe Terentyev, D. A.; Malerba, L.; Hou, M. Physical Review B, Vol. 75, Issue 10 https://doi.org/10.1103/PhysRevB.75.104108	journal	March 2007
Energy landscape of small clusters of self-interstitial dumbbells in iron Marinica, M. -C.; Willaime, F.; Mousseau, N. Physical Review B, Vol. 83, Issue 9 https://doi.org/10.1103/PhysRevB.83.094119	journal	March 2011
Basin hopping simulations for all-atom protein folding Verma, A.; Schug, A.; Lee, K. H. The Journal of Chemical Physics, Vol. 124, Issue 4 https://doi.org/10.1063/1.2138030	journal	January 2006
Crystal structure prediction from first principles Woodley, Scott M.; Catlow, Richard Nature Materials, Vol. 7, Issue 12 https://doi.org/10.1038/nmat2321	journal	December 2008
Stability and mobility of self-interstitials and small interstitial clusters in α-iron: ab initio and empirical potential calculations Willaime, F.; Fu, C. C.; Marinica, M. C. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 228, Issue 1-4 https://doi.org/10.1016/j.nimb.2004.10.028	journal	January 2005
Genetic algorithm–Monte Carlo hybrid geometry optimization method for atomic clusters Dugan, Nazım; Erkoç, Şakir Computational Materials Science, Vol. 45, Issue 1 https://doi.org/10.1016/j.commatsci.2008.03.045	journal	March 2009
Primary damage formation in bcc iron Stoller, R. E.; Odette, G. R.; Wirth, B. D. Journal of Nuclear Materials, Vol. 251 https://doi.org/10.1016/S0022-3115(97)00256-0	journal	November 1997
Evolutionary techniques in atomistic simulation: thin films and nanoparticles Sayle, Dean C.; Johnston, Roy L. Current Opinion in Solid State and Materials Science, Vol. 7, Issue 1 https://doi.org/10.1016/S1359-0286(02)00138-9	journal	February 2003
Synergy between theory and experiment in structure resolution of low-dimensional oxides Sierka, Marek Progress in Surface Science, Vol. 85, Issue 9-12 https://doi.org/10.1016/j.progsurf.2010.07.004	journal	September 2010
Efficient basin hopping in the protein energy surface Olson, Brian; Shehu, Amarda 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) https://doi.org/10.1109/BIBM.2012.6392655	conference	October 2012
Atomistic modeling of mechanical behavior Li, Ju; Ngan, Alfonso H. W.; Gumbsch, Peter Acta Materialia, Vol. 51, Issue 19 https://doi.org/10.1016/j.actamat.2003.08.002	journal	November 2003
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Ab initio study of the annealing of vacancies and interstitials in cubic SiC: Vacancy-interstitial recombination and aggregation of carbon interstitials Bockstedte, Michel; Mattausch, Alexander; Pankratov, Oleg Physical Review B, Vol. 69, Issue 23 https://doi.org/10.1103/PhysRevB.69.235202	journal	June 2004
Overview of materials research for fusion reactors Muroga, T.; Gasparotto, M.; Zinkle, S. J. Fusion Engineering and Design, Vol. 61-62 https://doi.org/10.1016/S0920-3796(02)00219-3	journal	November 2002
Simulated annealing algorithm : technical improvements Delamarre, D.; Virot, B. RAIRO - Operations Research, Vol. 32, Issue 1 https://doi.org/10.1051/ro/1998320100431	journal	January 1998
Molecular dynamics determination of defect energetics in beta -SiC using three representative empirical potentials Huang, Hanchen; Ghoniem, N. M.; Wong, J. K. Modelling and Simulation in Materials Science and Engineering, Vol. 3, Issue 5 https://doi.org/10.1088/0965-0393/3/5/003	journal	September 1995
A genetic algorithm for predicting the structures of interfaces in multicomponent systems Chua, Alvin L. -S.; Benedek, Nicole A.; Chen, Lin Nature Materials, Vol. 9, Issue 5 https://doi.org/10.1038/nmat2712	journal	February 2010
Model reconstructions for the Si(337) orientation Chuang, Feng-Chuan; Ciobanu, Cristian V.; Wang, Cai-Zhuang Journal of Applied Physics, Vol. 98, Issue 7 https://doi.org/10.1063/1.2064309	journal	October 2005
Global space-group optimization problem: Finding the stablest crystal structure without constraints Trimarchi, Giancarlo; Zunger, Alex Physical Review B, Vol. 75, Issue 10 https://doi.org/10.1103/PhysRevB.75.104113	journal	March 2007
Ab initio and empirical-potential studies of defect properties in $3 C - SiC$ Gao, Fei; Bylaska, Eric J.; Weber, William J. Physical Review B, Vol. 64, Issue 24 https://doi.org/10.1103/PhysRevB.64.245208	journal	December 2001
Embrittlement of nuclear reactor pressure vessels Odette, G. R.; Lucas, G. E. JOM, Vol. 53, Issue 7 https://doi.org/10.1007/s11837-001-0081-0	journal	July 2001
Structures and electronic properties of Cu20, Ag20, and Au20 clusters with density functional method Wang, Jinlan; Wang, Guanghou; Zhao, Jijun Chemical Physics Letters, Vol. 380, Issue 5-6 https://doi.org/10.1016/j.cplett.2003.09.062	journal	October 2003
Finding the reconstructions of semiconductor surfaces via a genetic algorithm Chuang, F. C.; Ciobanu, C. V.; Shenoy, V. B. Surface Science, Vol. 573, Issue 2 https://doi.org/10.1016/j.susc.2004.09.041	journal	December 2004
Benchmarking FeCr empirical potentials against density functional theory data Klaver, T. P. C.; Bonny, G.; Olsson, P. Modelling and Simulation in Materials Science and Engineering, Vol. 18, Issue 7 https://doi.org/10.1088/0965-0393/18/7/075004	journal	August 2010
Formation energy of vacancies in FeCr alloys: Dependence on Cr concentration del Rio, Emma; Sampedro, Jesús M.; Dogo, Harun Journal of Nuclear Materials, Vol. 408, Issue 1 https://doi.org/10.1016/j.jnucmat.2010.10.021	journal	January 2011
Efficient implementation of the concentration-dependent embedded atom method for molecular-dynamics and Monte-Carlo simulations Stukowski, Alexander; Sadigh, Babak; Erhart, Paul Modelling and Simulation in Materials Science and Engineering, Vol. 17, Issue 7 https://doi.org/10.1088/0965-0393/17/7/075005	journal	July 2009
Role of defects in tailoring structural, electrical and optical properties of ZnO Dutta, Sreetama; Chattopadhyay, S.; Sarkar, A. Progress in Materials Science, Vol. 54, Issue 1 https://doi.org/10.1016/j.pmatsci.2008.07.002	journal	January 2009
Structures at high pressure from random searching Pickard, C. J.; Needs, R. J. physica status solidi (b), Vol. 246, Issue 3 https://doi.org/10.1002/pssb.200880546	journal	March 2009
Prediction of crystal structures from crystal chemistry rules by simulated annealing Pannetier, J.; Bassas-Alsina, J.; Rodriguez-Carvajal, J. Nature, Vol. 346, Issue 6282 https://doi.org/10.1038/346343a0	journal	July 1990
USPEX—Evolutionary crystal structure prediction Glass, Colin W.; Oganov, Artem R.; Hansen, Nikolaus Computer Physics Communications, Vol. 175, Issue 11-12 https://doi.org/10.1016/j.cpc.2006.07.020	journal	December 2006
Evolutionary Crystal Structure Prediction as a Method for the Discovery of Minerals and Materials Oganov, A. R.; Ma, Y.; Lyakhov, A. O. Reviews in Mineralogy and Geochemistry, Vol. 71, Issue 1 https://doi.org/10.2138/rmg.2010.71.13	journal	January 2010
Interstitials in FeCr alloys studied by density functional theory Klaver, T. P. C.; Olsson, P.; Finnis, M. W. Physical Review B, Vol. 76, Issue 21 https://doi.org/10.1103/PhysRevB.76.214110	journal	December 2007
Bell-Evans-Polanyi principle for molecular dynamics trajectories and its implications for global optimization Roy, Shantanu; Goedecker, Stefan; Hellmann, Vladimir Physical Review E, Vol. 77, Issue 5 https://doi.org/10.1103/PhysRevE.77.056707	journal	May 2008
An object-oriented scripting interface to a legacy electronic structure code Bahn, S. R.; Jacobsen, K. W. Computing in Science & Engineering, Vol. 4, Issue 3 https://doi.org/10.1109/5992.998641	journal	January 2002
Composition dependence of formation energy of self-interstitial atom clusters in β-SiC: Molecular dynamics and molecular statics calculations Watanabe, Yoshiyuki; Morishita, Kazunori; Kohyama, Akira Journal of Nuclear Materials, Vol. 417, Issue 1-3 https://doi.org/10.1016/j.jnucmat.2010.12.087	journal	October 2011
Key differences in the fabrication, irradiation and high temperature accident testing of US and German TRISO-coated particle fuel, and their implications on fuel performance Petti, D. A.; Buongiorno, J.; Maki, J. T. Nuclear Engineering and Design, Vol. 222, Issue 2-3 https://doi.org/10.1016/S0029-5493(03)00033-5	journal	June 2003
Atomistic aspects of the deformation of NiAl Gumbsch, Peter; Schroll, Ralph Intermetallics, Vol. 7, Issue 3-4 https://doi.org/10.1016/S0966-9795(98)00096-X	journal	March 1999
The performance of minima hopping and evolutionary algorithms for cluster structure prediction Schönborn, Sandro E.; Goedecker, Stefan; Roy, Shantanu The Journal of Chemical Physics, Vol. 130, Issue 14 https://doi.org/10.1063/1.3097197	journal	April 2009
Hopping in a supercooled Lennard-Jones liquid: Metabasins, waiting time distribution, and diffusion Doliwa, B.; Heuer, A. Physical Review E, Vol. 67, Issue 3 https://doi.org/10.1103/PhysRevE.67.030501	journal	March 2003
Defect energetics in Fe–Cr alloys from empirical interatomic potentials Sampedro, Jesús M.; del Rio, Emma; Caturla, María J. Journal of Nuclear Materials, Vol. 417, Issue 1-3 https://doi.org/10.1016/j.jnucmat.2010.12.249	journal	October 2011
Evolutionary approach for finding the atomic structure of steps on stable crystal surfaces Briggs, Ryan M.; Ciobanu, Cristian V. Physical Review B, Vol. 75, Issue 19 https://doi.org/10.1103/PhysRevB.75.195415	journal	May 2007
Combined Electronic Structure and Evolutionary Search Approach to Materials Design Jóhannesson, G. H.; Bligaard, T.; Ruban, A. V. Physical Review Letters, Vol. 88, Issue 25 https://doi.org/10.1103/PhysRevLett.88.255506	journal	June 2002
An investigation of two approaches to basin hopping minimization for atomic and molecular clusters White, Ronald P.; Mayne, Howard R. Chemical Physics Letters, Vol. 289, Issue 5-6 https://doi.org/10.1016/S0009-2614(98)00431-X	journal	June 1998
Determination of Structure Candidates of Simple CrystallineAB2Systems Wevers, M. A. C.; Schön, J. C.; Jansen, M. Journal of Solid State Chemistry, Vol. 136, Issue 2 https://doi.org/10.1006/jssc.1997.7688	journal	March 1998
New algorithm in the basin hopping Monte Carlo to find the global minimum structure of unary and binary metallic nanoclusters Kim, Hyoung Gyu; Choi, Si Kyung; Lee, Hyuck Mo The Journal of Chemical Physics, Vol. 128, Issue 14 https://doi.org/10.1063/1.2900644	journal	April 2008
Properties and evolution of sessile interstitial clusters produced by displacement cascades in α-iron Gao, F.; Bacon, D. J.; Osetsky, Yu. N. Journal of Nuclear Materials, Vol. 276, Issue 1-3 https://doi.org/10.1016/S0022-3115(99)00180-4	journal	January 2000
Nucleation and growth of self-interstitial atom clusters in β-SiC during irradiation: Kinetic Monte-Carlo modeling Watanabe, Yoshiyuki; Morishita, Kazunori; Yamamoto, Yasunori Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 269, Issue 14 https://doi.org/10.1016/j.nimb.2011.01.132	journal	July 2011
Energetics of formation and migration of self-interstitials and self-interstitial clusters in α-iron Wirth, B. D.; Odette, G. R.; Maroudas, D. Journal of Nuclear Materials, Vol. 244, Issue 3 https://doi.org/10.1016/S0022-3115(96)00736-2	journal	April 1997
Elemental vacancy diffusion database from high-throughput first-principles calculations for fcc and hcp structures Angsten, Thomas; Mayeshiba, Tam; Wu, Henry New Journal of Physics, Vol. 16, Issue 1 https://doi.org/10.1088/1367-2630/16/1/015018	journal	January 2014
Ab initio study of Cr interactions with point defects in bcc Fe Olsson, Pär; Domain, Christophe; Wallenius, Janne Physical Review B, Vol. 75, Issue 1 https://doi.org/10.1103/PhysRevB.75.014110	journal	January 2007
Structure prediction based on ab initio simulated annealing for boron nitride Doll, K.; Schön, J. C.; Jansen, M. Physical Review B, Vol. 78, Issue 14 https://doi.org/10.1103/PhysRevB.78.144110	journal	October 2008
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms Wales, David J.; Doye, Jonathan P. K. The Journal of Physical Chemistry A, Vol. 101, Issue 28 https://doi.org/10.1021/jp970984n	journal	July 1997
Assessing the efficiency of first-principles basin-hopping sampling Gehrke, Ralf; Reuter, Karsten Physical Review B, Vol. 79, Issue 8 https://doi.org/10.1103/PhysRevB.79.085412	journal	February 2009
Molecular Geometry Optimization with a Genetic Algorithm Deaven, D. M.; Ho, K. M. Physical Review Letters, Vol. 75, Issue 2 https://doi.org/10.1103/PhysRevLett.75.288	journal	July 1995
Determination of candidate structures for Lennard-Jones-crystals through cell optimisation Schön, J. C.; Jansen, M. Berichte der Bunsengesellschaft für physikalische Chemie, Vol. 98, Issue 12 https://doi.org/10.1002/bbpc.19940981207	journal	December 1994
Structures and stabilities of small carbon interstitial clusters in cubic silicon carbide Jiang, Chao; Morgan, Dane; Szlufarska, Izabela Acta Materialia, Vol. 62 https://doi.org/10.1016/j.actamat.2013.09.044	journal	January 2014
Carbon tri-interstitial defect: A model for the D $_{II}$ center Jiang, Chao; Morgan, Dane; Szlufarska, Izabela Physical Review B, Vol. 86, Issue 14 https://doi.org/10.1103/PhysRevB.86.144118	journal	October 2012
Recent developments in the theory of protein folding: searching for the global energy minimum Scheraga, Harold A. Biophysical Chemistry, Vol. 59, Issue 3 https://doi.org/10.1016/0301-4622(95)00126-3	journal	April 1996
Combined method for ab initio structure solution from powder diffraction data Putz, H.; Schön, J. C.; Jansen, M. Journal of Applied Crystallography, Vol. 32, Issue 5 https://doi.org/10.1107/S0021889899006615	journal	October 1999
Finding the low-energy structures of Si[001] symmetric tilted grain boundaries with a genetic algorithm Zhang, Jian; Wang, Cai-Zhuang; Ho, Kai-Ming Physical Review B, Vol. 80, Issue 17 https://doi.org/10.1103/PhysRevB.80.174102	journal	November 2009
Comparison of empirical interatomic potentials for iron applied to radiation damage studies Malerba, L.; Marinica, M. C.; Anento, N. Journal of Nuclear Materials, Vol. 406, Issue 1 https://doi.org/10.1016/j.jnucmat.2010.05.017	journal	November 2010
Ab initio calculations and interatomic potentials for iron and iron alloys: Achievements within the Perfect Project Malerba, L.; Ackland, G. J.; Becquart, C. S. Journal of Nuclear Materials, Vol. 406, Issue 1 https://doi.org/10.1016/j.jnucmat.2010.05.016	journal	November 2010
On the migration and trapping of single self-interstitial atoms in dilute and concentrated Fe–Cr alloys: Atomistic study and comparison with resistivity recovery experiments Terentyev, D.; Olsson, P.; Klaver, T. P. C. Computational Materials Science, Vol. 43, Issue 4 https://doi.org/10.1016/j.commatsci.2008.03.013	journal	October 2008
Minimization by Random Search Techniques Solis, Francisco J.; Wets, Roger J. -B. Mathematics of Operations Research, Vol. 6, Issue 1 https://doi.org/10.1287/moor.6.1.19	journal	February 1981
Global exploration of the energy landscape of solids on the ab initio level Doll, K.; Schön, J. C.; Jansen, M. Physical Chemistry Chemical Physics, Vol. 9, Issue 46 https://doi.org/10.1039/b709943f	journal	January 2007
Irradiation-Induced Formation of Nanocrystallites with $C 15$ Laves Phase Structure in bcc Iron Marinica, M. -C.; Willaime, F.; Crocombette, J. -P. Physical Review Letters, Vol. 108, Issue 2 https://doi.org/10.1103/PhysRevLett.108.025501	journal	January 2012
Stability and mobility of defect clusters and dislocation loops in metals Osetsky, Yu. N.; Bacon, D. J.; Serra, A. Journal of Nuclear Materials, Vol. 276, Issue 1-3 https://doi.org/10.1016/S0022-3115(99)00170-1	journal	January 2000
Self-Trapped Interstitial-Type Defects in Iron Terentyev, D. A.; Klaver, T. P. C.; Olsson, P. Physical Review Letters, Vol. 100, Issue 14 https://doi.org/10.1103/PhysRevLett.100.145503	journal	April 2008
Potential Energy and Free Energy Landscapes Wales, David J.; Bogdan, Tetyana V. The Journal of Physical Chemistry B, Vol. 110, Issue 42 https://doi.org/10.1021/jp0680544	journal	October 2006
Evolving better nanoparticles: Genetic algorithms for optimising cluster geometries Johnston, Roy L. Dalton Transactions, Issue 22 https://doi.org/10.1039/b305686d	journal	January 2003
Energy barriers for point-defect reactions in $3 C$ -SiC Zheng, Ming-Jie; Swaminathan, Narasimhan; Morgan, Dane Physical Review B, Vol. 88, Issue 5 https://doi.org/10.1103/PhysRevB.88.054105	journal	August 2013
Evolution of energetics and bonding of compact self-interstitial clusters in Si Bongiorno, A.; Colombo, L.; Cargnoni, F. Europhysics Letters (EPL), Vol. 50, Issue 5 https://doi.org/10.1209/epl/i2000-00313-4	journal	June 2000
Crystal structure prediction using ab initio evolutionary techniques: Principles and applications Oganov, Artem R.; Glass, Colin W. The Journal of Chemical Physics, Vol. 124, Issue 24 https://doi.org/10.1063/1.2210932	journal	June 2006
Structure and vibrational spectra of carbon clusters in SiC Mattausch, Alexander; Bockstedte, Michel; Pankratov, Oleg Physical Review B, Vol. 70, Issue 23 https://doi.org/10.1103/PhysRevB.70.235211	journal	December 2004
Interstitials and Vacancies in $α$ Iron Johnson, R. A. Physical Review, Vol. 134, Issue 5A https://doi.org/10.1103/PhysRev.134.A1329	journal	June 1964
OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach Dieterich, Johannes M.; Hartke, Bernd Molecular Physics, Vol. 108, Issue 3-4 https://doi.org/10.1080/00268970903446756	journal	February 2010
Global Optimization of Clusters, Crystals, and Biomolecules Wales, D. J. Science, Vol. 285, Issue 5432 https://doi.org/10.1126/science.285.5432.1368	journal	August 1999
Predicting stable stoichiometries of compounds via evolutionary global space-group optimization Trimarchi, Giancarlo; Freeman, Arthur J.; Zunger, Alex Physical Review B, Vol. 80, Issue 9 https://doi.org/10.1103/PhysRevB.80.092101	journal	September 2009

Similar Records

Optimization of self-interstitial clusters in 3C-SiC with genetic algorithm

Journal Article · Tue Aug 01 00:00:00 EDT 2017 · Journal of Nuclear Materials · OSTI ID:1250288

Ko, Hyunseok; Kaczmarowski, Amy; Szlufarska, Izabela; +1 more

Genetic algorithm optimization of atomic clusters

Conference · Tue Dec 31 00:00:00 EST 1996 · OSTI ID:1250288

Morris, J R; Deaven, D M; Ho, K M; +4 more

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Journal Article · Tue Nov 12 00:00:00 EST 2013 · PNAS · OSTI ID:1250288

Kumar, S.; Gang, O.; Srinivasana, B.; +5 more

Title: Genetic algorithm optimization of defect clusters in crystalline materials

Citation Formats

References (80)

Similar Records

Related Subjects