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doctoral thesis

Entropy as a tool for crystal discovery

Piaggi, Pablo Miguel  
2019

The computational prediction of crystal structures has emerged as an useful alternative to expensive and often cumbersome experiments. We propose an approach to the prediction of crystal structures and polymorphism based on reproducing the crystallization process on the computer. The main hurdle faced by such an approach is that crystallization usually takes place in timescales much longer than those that can be afforded with standard molecular simulations. In order to circumvent this difficulty we construct a bias potential which is a function of one or more collective variables and whose role is to promote crystallization. This approach can only have true predictive power if the collective variable is crystal structure agnostic, that is to say, it does not include information about the geometry of any particular crystal structure. In order to achieve this goal, we take inspiration from thermodynamics and propose to use an entropy surrogate as collective variable. We use an approximation for the entropy based on the radial distribution function g(r). Using this collective variable we are able to explore polymorphism in simple metals and molecular crystals. We study the case of urea and find a new polymorph stabilized by entropic effects. We also propose a projection of the collective variable onto each atom that is useful to characterize atomic environments. Lastly, we introduce a generalized Kullback-Leibler divergence that measures the distance between two radial distribution functions. We apply this divergence to the automatic classification of the polymorphs that crystallize during the simulations.

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Type
doctoral thesis
DOI
10.5075/epfl-thesis-9148
Author(s)
Piaggi, Pablo Miguel  
Advisors
Marzari, Nicola  
•
Parrinello, Michele  
Jury

Prof. Paul Muralt (président) ; Prof. Nicola Marzari, Prof. Michele Parrinello (directeurs) ; Prof. Michele Ceriotti, Prof. Marco Mazzotti, Prof. Matteo Salvalaglio (rapporteurs)

Date Issued

2019

Publisher

EPFL

Publisher place

Lausanne

Public defense year

2019-01-25

Thesis number

9148

Total of pages

82

Subjects

molecular simulation

•

crystallization

•

crystal structure prediction

•

polymorphism

•

enhanced sampling methods

•

entropy

•

clustering

•

fingerprint

•

nucleation

•

divergence

EPFL units
THEOS  
Faculty
STI  
School
IMX  
Doctoral School
EDMX  
Award

IBM Research Award

2021
Available on Infoscience
January 17, 2019
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/153509
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