Automated calculation and convergence of defect transport tensors
Source abstract
Abstract
Abstract Defect diffusion is a key process in materials science and catalysis, but as migration mechanisms are often too complex to enumerate a priori, calculation of transport tensors typically have no measure of convergence and require significant end-user intervention. These two bottlenecks prevent high-throughput implementations essential to propagate model-form uncertainty from interatomic interactions to predictive simulations. In order to address these issues, we extend a massively parallel accelerated sampling scheme, autonomously controlled by Bayesian estimators of statewide sampling completeness, to build atomistic kinetic Monte Carlo models on a state-space irreducible under exchange and space group symmetries. Focusing on isolated defects, we derive analytic expressions for drift and diffusion coefficients, providing a convergence metric by calculating the Kullback–Leibler divergence across the ensemble of diffusion processes consistent with the sampling uncertainty. The autonomy and efficacy of the method is demonstrated on surface trimers in tungsten and Hexa-interstitials in magnesium oxide, both of which exhibit complex, correlated migration mechanisms.
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Research context
OpenAlex topics: Machine Learning in Materials Science · Nuclear reactor physics and engineering · Nuclear Materials and Properties
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References (51)
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1. Fu, C.-C., Dalla Torre, J., Willaime, F., Bocquet, J.-L. & Barbu, A. Multiscale modelling of defect kinetics in irradiated iron. Nat. Mater. 4, 68–74 (2005).10.1038/nmat1286 ↗
2. Osetsky, Y. N., Beland, L. K., Barashev, A. V. & Zhang, Y. On the existence and origin of sluggish diffusion in chemically disordered concentrated alloys. Curr. Opin. Solid State Mater. Sci. 22, 65–74 (2018).10.1016/j.cossms.2018.05.003 ↗
3. Sefta, F., Hammond, K. D., Juslin, N. & Wirth, B. D. Tungsten surface evolution by helium bubble nucleation, growth and rupture. Nucl. Fusion 53, 073015 (2013).10.1088/0029-5515/53/7/073015 ↗
4. Nørskov, J. K., Bligaard, T., Rossmeisl, J. & Christensen, C. H. Towards the computational design of solid catalysts. Nat. Chem. 1, 37 (2009).10.1038/nchem.121 ↗
5. Böller, B., Durner, K. M. & Wintterlin, J. The active sites of a working Fischer–Tropsch catalyst revealed by operando scanning tunnelling microscopy. Nat. Catal. 2, 1027–1034 (2019).10.1038/s41929-019-0360-1 ↗
6. Sorensen, M. R., Mishin, Y. & Voter, A. F. Diffusion mechanisms in Cu grain boundaries. Phys. Rev. B 62, 3658–3673 (2000).10.1103/PhysRevB.62.3658 ↗
7. Uberuaga, B. et al. Structure and mobility of defects formed from collision cascades in MgO. Phys. Rev. Lett. 92, 115505 (2004).10.1103/PhysRevLett.92.115505 ↗
8. Uberuaga, B. et al. Exploring long-time response to radiation damage in MgO. Nucl. Instrum. Methods Phys. Res. Sect. B 228, 260–273 (2005).10.1016/j.nimb.2004.10.055 ↗
9. Uberuaga, B., Hoagland, R., Voter, A. & Valone, S. Direct transformation of vacancy voids to stacking fault tetrahedra. Phys. Rev. Lett. 99, 135501 (2007).10.1103/PhysRevLett.99.135501 ↗
10. Perez, D., Uberuaga, B. P., Shim, Y., Amar, J. G. & Voter, A. F. Accelerated molecular dynamics methods: introduction and recent developments. Annu. Rep. Comput. Chem. 5, 79–98 (2009).10.1016/S1574-1400(09)00504-0 ↗
11. Béland, L. K., Brommer, P., El-Mellouhi, F., Joly, J.-F. & Mousseau, N. Kinetic activation-relaxation technique. Phys. Rev. E 84, 046704 (2011).10.1103/PhysRevE.84.046704 ↗
12. Martínez, E. & Uberuaga, B. P. Mobility and coalescence of stacking fault tetrahedra in Cu. Sci. Rep. 5, 1–5 (2015).
13. Dezerald, L., Proville, L., Ventelon, L., Willaime, F. & Rodney, D. First-principles prediction of kink-pair activation enthalpy on screw dislocations in bcc transition metals: V, nb, ta, mo, w, and fe. Phys. Rev. B 91, 094105 (2015).10.1103/PhysRevB.91.094105 ↗
14. Swinburne, T. D. et al. Fast, vacancy-free climb of prismatic dislocation loops in bcc metals. Sci. Rep. 6, 30596–30604 (2016).10.1038/srep30596 ↗
15. Alexander, R. et al. Ab initio scaling laws for the formation energy of nanosized interstitial defect clusters in iron, tungsten, and vanadium. Phys. Rev. B 94, 024103 (2016).10.1103/PhysRevB.94.024103 ↗
16. Voter, A. F. Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys. Rev. Lett. 78, 3908 (1997).10.1103/PhysRevLett.78.3908 ↗
17. Voter, A. F. Parallel replica method for dynamics of infrequent events. Phys. Rev. B 57, R13985 (1998).10.1103/PhysRevB.57.R13985 ↗
18. Sorensen, M. & Voter, A. Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 112, 9599–9606 (2000).10.1063/1.481576 ↗
19. Chatterjee, A. & Bhattacharya, S. Uncertainty in a Markov state model with missing states and rates: application to a room temperature kinetic model obtained using high temperature molecular dynamics. J. Chem. Phys. 143, 114109 (2015).10.1063/1.4930976 ↗
20. Chill, S. T. & Henkelman, G. Molecular dynamics saddle search adaptive kinetic Monte Carlo. J. Chem. Phys. 140, 214110 (2014).10.1063/1.4880721 ↗
21. Henkelman, G. & Jónsson, H. A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. J. Chem. Phys. 111, 7010–7022 (1999).10.1063/1.480097 ↗
22. Wales, D. J. Discrete path sampling. Mol. Phys. 100, 3285–3305 (2002).10.1080/00268970210162691 ↗
23. Wales, D. J. Energy Landscapes (Cambridge, 2003).
24. Le Bris, C., Lelievre, T., Luskin, M. & Perez, D. A mathematical formalization of the parallel replica dynamics. Monte Carlo Methods Appl. 18, 119–146 (2012).10.1515/mcma-2012-0003 ↗
25. Lelièvre, T. Mathematical Foundations of Accelerated Molecular Dynamics Methods, 1–32 (Springer International Publishing, Cham, 2018). https://doi.org/10.1007/978-3-319-42913-7_27-1.10.1007/978-3-319-42913-7_27-1 ↗
26. Henkelman, G. Atomistic simulations of activated processes in materials. Annu. Rev. Mater. Res. 47, 199–216 (2017).10.1146/annurev-matsci-071312-121616 ↗
27. Aristoff, D., Chill, S. & Simpson, G. Analysis of estimators for adaptive kinetic Monte Carlo. Commun. Appl. Math. Comput. Sci. 11, 171–186 (2016).10.2140/camcos.2016.11.171 ↗
28. Swinburne, T. D. & Perez, D. Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification. Phys. Rev. Mater. 2, 053802 (2018).10.1103/PhysRevMaterials.2.053802 ↗
29. Bartók, A. P. et al. Machine learning unifies the modeling of materials and molecules. Sci. Adv. 3, e1701816 (2017).10.1126/sciadv.1701816 ↗
30. Marinica, M. Towards better efficiency of interatomic linear machine learning potentials. Comput. Mater. Sci. 166, 200–209 (2019).10.1016/j.commatsci.2019.04.043 ↗
31. Shapeev, A. V. Moment tensor potentials: a class of systematically improvable interatomic potentials. Multiscale Model. Simul. 14, 1153–1173 (2016).10.1137/15M1054183 ↗
32. Boulougouris, G. C. & Frenkel, D. Monte Carlo sampling of a Markov web. J. Chem. Theory Comput. 1, 389–393 (2005).10.1021/ct049900m ↗
33. Bhoutekar, A., Ghosh, S., Bhattacharya, S. & Chatterjee, A. A new class of enhanced kinetic sampling methods for building Markov state models. J. Chem. Phys. 147, 152702 (2017).10.1063/1.4984932 ↗
34. Perez, D., Cubuk, E. D., Waterland, A., Kaxiras, E. & Voter, A. F. Long-time dynamics through parallel trajectory splicing. J. Chem. Theory Comput. 12, 18–28 (2015).10.1021/acs.jctc.5b00916 ↗
35. McKay, B. D. & Piperno, A. Practical graph isomorphism, II. J. Symb. Comput. 60, 94–112 (2014).10.1016/j.jsc.2013.09.003 ↗
36. Scott, W. R. Group Theory (Courier Corporation, 2012).
37. Bortz, A. B., Kalos, M. H. & Lebowitz, J. L. A new algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 17, 10–18 (1975).10.1016/0021-9991(75)90060-1 ↗
38. Trinkle, D. R. Variational principle for mass transport. Phys. Rev. Lett. 121, 235901 (2018).10.1103/PhysRevLett.121.235901 ↗
39. Landman, U. & Shlesinger, M. F. Stochastic theory of multistate diffusion in perfect and defective systems. I. Mathematical formalism. Phys. Rev. B 19, 6207 (1979).10.1103/PhysRevB.19.6207 ↗
40. We note that the calculated transition rates presently employ harmonic transition state theory, which can be in error at high temperatures [50]. However, as the present method is generally applicable for any employed rate theory we do not consider such errors.
41. Cover, T. M. & Thomas, J. A. Elements of Information Theory (John Wiley & Sons, 2012).
42. Marinica, M.-C., Willaime, F. & Crocombette, J.-P. Irradiation-induced formation of nanocrystallites with c15 laves phase structure in bcc iron. Phys. Rev. Lett. 108, 025501 (2012).10.1103/PhysRevLett.108.025501 ↗
43. Yang, L., Wirth, B., Perez, D. & Voter, A. F. Mobility of tungsten clusters on tungsten surfaces. Nucl. Instrum. Methods Phys. Res. Sect. B 453, 61–66 (2019).10.1016/j.nimb.2019.05.078 ↗
44. Marinica, M. C. et al. Interatomic potentials for modelling radiation defects and dislocations in tungsten. J. Phys. 25, 395502 (2013).
45. Dijkstra, E. W. A note on two problems in connexion with graphs. Numer. Math. 1, 269–271 (1959).10.1007/BF01386390 ↗
46. Juslin, N. & Wirth, B. D. Interatomic potentials for simulation of the bubble formation in W. J. Nucl. Mater. 432, 61–66 (2013).10.1016/j.jnucmat.2012.07.023 ↗
47. Henkelman, G., Uberuaga, B. P. & Jonsson, H. A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J. Chem. Phys. 113, 9901–9904 (2000).10.1063/1.1329672 ↗
48. Hänggi, P., Talkner, P. & Borkovec, M. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251–342 (1990).10.1103/RevModPhys.62.251 ↗
49. Cordella, L. P., Foggia, P., Sansone, C. & Vento, M. An improved algorithm for matching large graphs. in Proc. 3rd IAPR-TC15 workshop on graph-based representations in pattern recognition, 149–159 (2001).
50. Swinburne, T. D. & Marinica, M.-C. Unsupervised calculation of free energy barriers in large crystalline systems. Phys. Rev. Lett. 120, 135503 (2018).10.1103/PhysRevLett.120.135503 ↗
51. Stukowski, A. Visualization and analysis of atomistic simulation data with OVITO—the open visualization tool. Model. Simul. Mater. Sci. Eng. 18, 015012 (2010).10.1088/0965-0393/18/1/015012 ↗