Bayesian optimization structure search

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Title: Bayesian optimization structure search
Author: Paulamäki, Henri
Other contributor: Helsingin yliopisto, Matemaattis-luonnontieteellinen tiedekunta
University of Helsinki, Faculty of Science
Helsingfors universitet, Matematisk-naturvetenskapliga fakulteten
Publisher: Helsingin yliopisto
Date: 2019
Language: eng
Thesis level: master's thesis
Degree program: Materiaalitutkimuksen maisteriohjelma
Master's Programme in Materials Research
Magisterprogrammet i materialforskning
Specialisation: ei opintosuuntaa
no specialization
ingen studieinriktning
Discipline: none
Abstract: Tailoring a hybrid surface or any complex material to have functional properties that meet the needs of an advanced device or drug requires knowledge and control of the atomic level structure of the material. The atomistic configuration can often be the decisive factor in whether the device works as intended, because the materials' macroscopic properties - such as electrical and thermal conductivity - stem from the atomic level. However, such systems are difficult to study experimentally and have so far been infeasible to study computationally due to costly simulations. I describe the theory and practical implementation of a 'building block'-based Bayesian Optimization Structure Search (BOSS) method to efficiently address heterogeneous interface optimization problems. This machine learning method is based on accelerating the identification of a material's energy landscape with respect to the number of quantum mechanical (QM) simulations executed. The acceleration is realized by applying likelihood-free Bayesian inference scheme to evolve a Gaussian process (GP) surrogate model of the target landscape. During this active learning, various atomic configurations are iteratively sampled by running static QM simulations. An approximation of using chemical building blocks reduces the search phase space to manageable dimensions. This way the most favored structures can be located with as little computation as possible. Thus it is feasible to do structure search with large simulation cells, while still maintaining high chemical accuracy. The BOSS method was implemented as a python code called aalto-boss between 2016-2019, where I was the main author in co-operation with Milica Todorović and Patrick Rinke. I conducted a dimensional scaling study using analytic functions, which quantified the scaling of BOSS efficiency for fundamentally different functions when dimension increases. The results revealed the target function's derivative's important role to the optimization efficiency. The outcome will help people with choosing the simulation variables so that they are efficient to optimize, as well as help them estimate roughly how many BOSS iterations are potentially needed until convergence. The predictive efficiency and accuracy of BOSS was showcased in the conformer search of the alanine dipeptide molecule. The two most stable conformers and the characteristic 2D potential energy map was found with greatly reduced effort compared to alternative methods. The value of BOSS in novel materials research was showcased in the surface adsorption study of bifenyldicarboxylic acid on CoO thin film using DFT simulations. We found two adsorption configurations which had a lower energy than previous calculations and approximately supported the experimental data on the system. The three applications showed that BOSS can significantly reduce the computational load of atomistic structure search while maintaining predictive accuracy. It allows material scientists to study novel materials more efficiently, and thus help tailor the materials' properties to better suit the needs of modern devices.

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