scholarly journals Common workflows for computing material properties using different quantum engines

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sebastiaan P. Huber ◽  
Emanuele Bosoni ◽  
Marnik Bercx ◽  
Jens Bröder ◽  
Augustin Degomme ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Open Source ◽  
Material Properties ◽  
Density Functional ◽  
Steady Increase ◽  
Functional Theory ◽  
Design Rules ◽  
Simulation Parameters ◽  
Workflow Logic

AbstractThe prediction of material properties based on density-functional theory has become routinely common, thanks, in part, to the steady increase in the number and robustness of available simulation packages. This plurality of codes and methods is both a boon and a burden. While providing great opportunities for cross-verification, these packages adopt different methods, algorithms, and paradigms, making it challenging to choose, master, and efficiently use them. We demonstrate how developing common interfaces for workflows that automatically compute material properties greatly simplifies interoperability and cross-verification. We introduce design rules for reusable, code-agnostic, workflow interfaces to compute well-defined material properties, which we implement for eleven quantum engines and use to compute various material properties. Each implementation encodes carefully selected simulation parameters and workflow logic, making the implementer’s expertise of the quantum engine directly available to non-experts. All workflows are made available as open-source and full reproducibility of the workflows is guaranteed through the use of the AiiDA infrastructure.

Ab initio investigation of the elastic properties of CaxSn1-x alloys for use as battery anodes

2021 ◽  
pp. 1-19
Author(s):  
Michael Woodcox ◽  
Manuel Smeu
Keyword(s):  
Thermal Conductivity ◽  
Density Functional Theory ◽  
Material Properties ◽  
Density Functional ◽  
Elastic Moduli ◽  
Steady Increase ◽  
Similar Material ◽  
Bulk Materials ◽  
Functional Theory ◽  
Peak Value

Abstract Density functional theory has been used to investigate 19 CaxSn1-x structures (6 bulk materials and 13 alloys) as potential battery anodes. Of the alloys, we have found 4 stable phases (x = 0.25, 0.5, 0.625 and 0.75) and 3 metastable phases (two at x = 0.5 and one at x = 0.75). For the (meta)stable phases, we compare quantities such as the elastic moduli (bulk (K), shear (G), and Young's (E)), Poisson's ratio (v) and the Pugh ratio (γ), the latter two being metrics for ductility. Nearly all of the alloys exhibit a steady increase in G (from 21.62 GPa to 25.31 GPa) and E (56.12 GPa to 59.12 GPa). K ranges from 25.72 GPa to 46.31 GPa across the same concentration window. For bulk Sn, the n and G values are close to the ductile/brittle boundary, followed by an increase in ductility to the peak value at x = 0.25 (v = 0.298 and γ = 2.14), beyond which both quantities decrease, reaching a minimum value at x = 0.75 (γ = 0.168 and γ = 1.17). The Debye temperature (θD) and minimum thermal conductivity (kmin) of each compound were also calculated, following a trend that is identical to the shear modulus. We have found that for stable/metastable compositions of CaxSn1-x, those sharing the same chemical composition (stoichiometry) also share remarkably similar material properties, indicating that such materials would be advantageous for uses in battery anodes.

Interface and heterostructure design in polyelemental nanoparticles

Science ◽  
2019 ◽  
Vol 363 (6430) ◽  
pp. 959-964 ◽  
Author(s):  
Peng-Cheng Chen ◽  
Mohan Liu ◽  
Jingshan S. Du ◽  
Brian Meckes ◽  
Shunzhi Wang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Experimental Work ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Mixed Composition ◽  
Functional Theory ◽  
Design Rules ◽  
Tin Alloys ◽  
Interfacial Energies

Nanomaterials that form as heterostructures have applications in catalysis, plasmonics, and electronics. Multielement nanoparticles can now be synthesized through a variety of routes, but how thermodynamic phases form in such structures and how specific interfaces between them can be designed and synthesized are still poorly understood. We explored how palladium-tin alloys form mixed-composition phases with metals with known but complex miscibilities. Nanoparticles with up to seven elements were synthesized, and many form triphase heterostructures consisting of either three-interface or two-interface architectures. Density functional theory calculations and experimental work were used to determine the balance between the surface and interfacial energies of the observed phases. From these observations, design rules have been established for making polyelemental systems with specific heterostructures, including tetraphase nanoparticles with as many as six junctions.

Editorial for PCCP themed issue “Developments in Density Functional Theory”

2016 ◽  
Vol 18 (31) ◽  
pp. 20864-20867
Author(s):  
Robert van Leeuwen ◽  
Johannes Neugebauer ◽  
Lucas Visscher ◽  
F. Matthias Bickelhaupt
Keyword(s):  
Density Functional Theory ◽  
Chemical Bonding ◽  
Material Properties ◽  
Density Functional ◽  
State Of The Art ◽  
The State ◽  
Functional Theory ◽  
Bonding Theory

This issue provides an overview of the state-of-the-art of DFT, ranging from mathematical and software developments, via topics in chemical bonding theory, to all kinds of molecular and material properties. Through this issue, we also celebrate the enormous contributions that Evert Jan Baerends has made to this field.

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

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