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Lu Y, Farrow MR, Fayon P, Logsdail AJ, Sokol AA, Catlow CRA, Sherwood P, Keal TW. Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment. J Chem Theory Comput 2019; 15:1317-1328. [PMID: 30511845 DOI: 10.1021/acs.jctc.8b01036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.
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Affiliation(s)
- You Lu
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Matthew R Farrow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Pierre Fayon
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Andrew J Logsdail
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom.,UK Catalysis Hub, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Oxon OX11 0QX , United Kingdom
| | - Paul Sherwood
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Thomas W Keal
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
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Buckeridge J, Catlow CRA, Scanlon DO, Keal TW, Sherwood P, Miskufova M, Walsh A, Woodley SM, Sokol AA. Determination of the nitrogen vacancy as a shallow compensating center in GaN doped with divalent metals. PHYSICAL REVIEW LETTERS 2015; 114:016405. [PMID: 25615487 DOI: 10.1103/physrevlett.114.016405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Indexed: 05/25/2023]
Abstract
We report accurate energetics of defects introduced in GaN on doping with divalent metals, focusing on the technologically important case of Mg doping, using a model that takes into consideration both the effect of hole localization and dipolar polarization of the host material, and includes a well-defined reference level. Defect formation and ionization energies show that divalent dopants are counterbalanced in GaN by nitrogen vacancies and not by holes, which explains both the difficulty in achieving p-type conductivity in GaN and the associated major spectroscopic features, including the ubiquitous 3.46 eV photoluminescence line, a characteristic of all lightly divalent-metal-doped GaN materials that has also been shown to occur in pure GaN samples. Our results give a comprehensive explanation for the observed behavior of GaN doped with low concentrations of divalent metals in good agreement with relevant experiment.
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Affiliation(s)
- J Buckeridge
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - C R A Catlow
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - D O Scanlon
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom and Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - T W Keal
- Scientific Computing Department, STFC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, United Kingdom
| | - P Sherwood
- Scientific Computing Department, STFC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, United Kingdom
| | - M Miskufova
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - A Walsh
- Centre for Sustainable Chemical Technologies and Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - S M Woodley
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - A A Sokol
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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