Crystal Structure Prediction of Energetic Materials and a Twisted Arene with Genarris and GAtor

CrystEngComm ◽  
2021 ◽  
Author(s):  
Imanuel Bier ◽  
Dana O'Connor ◽  
Yun-Ting Hsieh ◽  
Wen Wen ◽  
Anna Hiszpanski ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Energetic Materials ◽  
Structure Prediction ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Structure Generator

A crystal structure prediction (CSP) workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is applied to the energetic materials 2,4,6-trinitrobenzene-1,3,5-triamine (TATB) and 2,4,6-trinitrobenzene-1,3-diamine (DATB),...

scholarly journals Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling

2020 ◽  
Author(s):  
Shiyue Yang ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Random Sampling ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Optimization Procedure ◽  
Low Energy ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Structure Generation ◽  
Basin Hopping

We describe the implementation of a Monte Carlo basin hopping global optimization procedure for the prediction of molecular crystal structure. The basin hopping method is combined with quasi-random structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by quasi-random sequences with basin hopping's efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure quasi-random sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs.

scholarly journals Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling

2020 ◽  
Author(s):  
Shiyue Yang ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Random Sampling ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Optimization Procedure ◽  
Low Energy ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Structure Generation ◽  
Basin Hopping

We describe the implementation of a Monte Carlo basin hopping global optimization procedure for the prediction of molecular crystal structure. The basin hopping method is combined with quasi-random structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by quasi-random sequences with basin hopping's efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure quasi-random sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs.

scholarly journals An adaptive genetic algorithm for crystal structure prediction

2013 ◽  
Vol 26 (3) ◽  
pp. 035402 ◽  
Author(s):  
S Q Wu ◽  
M Ji ◽  
C Z Wang ◽  
M C Nguyen ◽  
X Zhao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Structure Prediction ◽  
Adaptive Genetic Algorithm ◽  
Crystal Structure Prediction

scholarly journals Mechanism of Polymorphic Transformations in the Chemical Elements

2014 ◽  
Vol 70 (a1) ◽  
pp. C1536-C1536
Author(s):  
Salah Eddine Boulfelfel ◽  
Daniele Selli ◽  
Stefano Leoni
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Chemical Elements ◽  
Structural Motif ◽  
Random Structure ◽  
Crystal Structure Prediction ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling ◽  
The Impact

The prediction of a crystal structure at given composition and thermodynamic coupling parameters is a major challenge. Powerful methods have boosted progress in this field, recently, and have promoted this are of research into a multidisciplinary one. The capacity of anticipating the outcome of a synthetic effort, or the search for novel materials with distinct, improved properties greatly benefit from numerical methods able to efficiently scan for novel structural motifs. Several techniques based on evolutionary algorithms, metadynamics, random structure prediction, or transition path sampling are contributing important advances in the understanding of polymorphic transformation, and are enriching the catalogue of crystalline matter by surprising novel packings [1]. One of the central aspects to fully unfold the impact of crystal structure prediction is the elucidation of transformation mechanisms, which are productive towards a particular structural motif under experiment-relavant conditions. In the recent dispute on the structural identity of the product of graphite cold compression, the true product was confirmed to be Oganov's M-Carbon by applying transition path sampling [2]. While many carbon polymorphs can exist in principle, kinetic control will typically select a particular mechanism of formation of a distinct carbon. This proves that, while the enumeration of crystal structures is invaluable in discovering novel material with improved properties, and in exploring novel compositions, it is important to associate a mechanism with the formation of a particular structure, for a realistic crystal structure prediction, one that can be turned into a real material. The talk will have a review character, and will touch upon recent results in the filed of the polymorphism of the elements and binary semiconductors [3].

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

2018 ◽  
Vol 14 (4) ◽  
pp. 2246-2264 ◽  
Author(s):  
Farren Curtis ◽  
Xiayue Li ◽  
Timothy Rose ◽  
Álvaro Vázquez-Mayagoitia ◽  
Saswata Bhattacharya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
First Principles ◽  
Structure Prediction ◽  
Molecular Crystal ◽  
Crystal Structure Prediction

scholarly journals Evolutionary niching in the GAtor genetic algorithm for molecular crystal structure prediction

2018 ◽  
Vol 211 ◽  
pp. 61-77 ◽  
Author(s):  
Farren Curtis ◽  
Timothy Rose ◽  
Noa Marom
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Structure Prediction ◽  
Molecular Crystal ◽  
Crystal Structure Prediction

The effects of evolutionary niching are investigated for the crystal structure prediction of 1,3-dibromo-2-chloro-5-fluorobenzene.

Crystal Structure Prediction via Deep Learning

2018 ◽  
Vol 140 (32) ◽  
pp. 10158-10168 ◽  
Author(s):  
Kevin Ryan ◽  
Jeff Lengyel ◽  
Michael Shatruk
Keyword(s):  
Crystal Structure ◽  
Deep Learning ◽  
Structure Prediction ◽  
Crystal Structure Prediction

scholarly journals New high-pressure phases of Fe7N3 and Fe7C3 stable at Earth's core conditions: evidences for carbon–nitrogen isomorphism in Fe-compounds

RSC Advances ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 3577-3581 ◽  
Author(s):  
Nursultan Sagatov ◽  
Pavel N. Gavryushkin ◽  
Talgat M. Inerbaev ◽  
Konstantin D. Litasov
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Ab Initio ◽  
Structure Prediction ◽  
Harmonic Approximation ◽  
Crystal Structure Prediction ◽  
Earth’S Core ◽  
Earth's Core ◽  
Core Conditions

We carried out ab initio calculations on the crystal structure prediction and determination of P–T diagrams within the quasi-harmonic approximation for Fe7N3 and Fe7C3.

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