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Yang M, Sissay A, Chen M, Lopata K. Intruder Peak-Free Transient Inner-Shell Spectra Using Real-Time Simulations. J Chem Theory Comput 2022; 18:992-1002. [PMID: 35025498 DOI: 10.1021/acs.jctc.1c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Real-time methods are convenient for simulating core-level absorption spectra but suffer from nonphysical intruder peaks when using atom-centered basis sets. In transient absorption spectra, these peaks exhibit highly nonphysical time-dependent modulations in their energies and oscillator strengths. In this paper, we address the origins of these intruder peaks and propose a straightforward and effective solution based on a filtered dipole operator. In combination with real-time time-dependent density functional theory (RT-TDDFT), we demonstrate how to compute intruder-free attosecond transient X-ray absorption spectra for the aminophenol (C6H7NO) oxygen and nitrogen K-edges and the α-quartz (SiO2) silicon L-edge. Without filtering, the computed spectra are qualitatively wrong. This procedure is suitable for both static and transient inner-shell spectroscopy studies and can easily be implemented in a range of real-time methodologies.
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Affiliation(s)
- Mengqi Yang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Adonay Sissay
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Min Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kenneth Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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2
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Li J, Duan Y, Li T, Li H. Extreme electron transport suppression in siloxane ring-based molecular devices. Phys Chem Chem Phys 2018; 20:23352-23362. [DOI: 10.1039/c8cp03616k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Siloxane ring-based molecular devices possess excessive transport suppression and size-dependent transport decay, based on an analysis of electronic coupling.
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Affiliation(s)
- Jie Li
- Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials
- Ministry of Education
- Shandong University
- Jinan 250061
- People's Republic of China
| | - Yunrui Duan
- Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials
- Ministry of Education
- Shandong University
- Jinan 250061
- People's Republic of China
| | - Tao Li
- Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials
- Ministry of Education
- Shandong University
- Jinan 250061
- People's Republic of China
| | - Hui Li
- Key Laboratory for Liquid–Solid Structural Evolution and Processing of Materials
- Ministry of Education
- Shandong University
- Jinan 250061
- People's Republic of China
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3
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Li H, Garner MH, Su TA, Jensen A, Inkpen MS, Steigerwald ML, Venkataraman L, Solomon GC, Nuckolls C. Extreme Conductance Suppression in Molecular Siloxanes. J Am Chem Soc 2017; 139:10212-10215. [DOI: 10.1021/jacs.7b05599] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Haixing Li
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Marc H. Garner
- Nano-Science
Center and Department of Chemistry, University of Copenhagen, Universitetsparken
5, 2100 Copenhagen
Ø, Denmark
| | - Timothy A. Su
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Anders Jensen
- Nano-Science
Center and Department of Chemistry, University of Copenhagen, Universitetsparken
5, 2100 Copenhagen
Ø, Denmark
| | - Michael S. Inkpen
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | | | - Latha Venkataraman
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Gemma C. Solomon
- Nano-Science
Center and Department of Chemistry, University of Copenhagen, Universitetsparken
5, 2100 Copenhagen
Ø, Denmark
| | - Colin Nuckolls
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
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Malyi OI, Boström M, Kulish VV, Thiyam P, Parsons DF, Persson C. Volume dependence of the dielectric properties of amorphous SiO2. Phys Chem Chem Phys 2016; 18:7483-9. [DOI: 10.1039/c5cp06775h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dielectric properties of amorphous SiO2 and other SiO2 polymorphs are linked by simple volume dependence.
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Affiliation(s)
- Oleksandr I. Malyi
- Centre for Materials Science and Nanotechnology
- University of Oslo
- NO-0316 Oslo
- Norway
| | - Mathias Boström
- Centre for Materials Science and Nanotechnology
- University of Oslo
- NO-0316 Oslo
- Norway
| | - Vadym V. Kulish
- Department of Mechanical Engineering
- National University of Singapore
- Singapore 117576
- Singapore
| | - Priyadarshini Thiyam
- Department of Materials Science and Engineering
- Royal Institute of Technology
- SE-100 44 Stockholm
- Sweden
| | - Drew F. Parsons
- School of Engineering and Information Technology
- Murdoch University
- Murdoch
- Australia
| | - Clas Persson
- Centre for Materials Science and Nanotechnology
- University of Oslo
- NO-0316 Oslo
- Norway
- Department of Materials Science and Engineering
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Fernando RG, Balhoff MC, Lopata K. X-ray Absorption in Insulators with Non-Hermitian Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2015; 11:646-54. [DOI: 10.1021/ct500943m] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ranelka G. Fernando
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Mary C. Balhoff
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kenneth Lopata
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Malyi OI, Kulish VV, Persson C. In search of new reconstructions of (001) α-quartz surface: a first principles study. RSC Adv 2014. [DOI: 10.1039/c4ra10726h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Using Born–Oppenheimer molecular dynamics simulations and “static” density functional theory calculations, reconstructions of the (001) α-quartz surface are studied in detail.
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Affiliation(s)
- Oleksandr I. Malyi
- Centre for Materials Science and Nanotechnology
- University of Oslo
- No.-0316 Oslo, Norway
| | - Vadym V. Kulish
- Singapore University of Technology and Design
- Singapore 138682, Singapore
| | - Clas Persson
- Centre for Materials Science and Nanotechnology
- University of Oslo
- No.-0316 Oslo, Norway
- Department of Physics
- University of Oslo
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Ledyastuti M, Liang Y, Miranda CR, Matsuoka T. Comparison of thermodynamic stabilities and mechanical properties of CO2, SiO2, and GeO2 polymorphs by first-principles calculations. J Chem Phys 2012; 137:034703. [DOI: 10.1063/1.4735077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Grabowsky S, Hesse MF, Paulmann C, Luger P, Beckmann J. How to Make the Ionic Si−O Bond More Covalent and the Si−O−Si Linkage a Better Acceptor for Hydrogen Bonding. Inorg Chem 2009; 48:4384-93. [DOI: 10.1021/ic900074r] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Grabowsky
- Anorganische und Analytische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 34-36, 14195 Berlin, Germany, Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, 14195 Berlin, Germany, and Mineralogisch-Petrographisches Institut, Universität Hamburg, c/o HASYLAB/DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Maxie F. Hesse
- Anorganische und Analytische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 34-36, 14195 Berlin, Germany, Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, 14195 Berlin, Germany, and Mineralogisch-Petrographisches Institut, Universität Hamburg, c/o HASYLAB/DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Carsten Paulmann
- Anorganische und Analytische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 34-36, 14195 Berlin, Germany, Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, 14195 Berlin, Germany, and Mineralogisch-Petrographisches Institut, Universität Hamburg, c/o HASYLAB/DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Peter Luger
- Anorganische und Analytische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 34-36, 14195 Berlin, Germany, Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, 14195 Berlin, Germany, and Mineralogisch-Petrographisches Institut, Universität Hamburg, c/o HASYLAB/DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jens Beckmann
- Anorganische und Analytische Chemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 34-36, 14195 Berlin, Germany, Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstr. 36a, 14195 Berlin, Germany, and Mineralogisch-Petrographisches Institut, Universität Hamburg, c/o HASYLAB/DESY, Notkestr. 85, 22607 Hamburg, Germany
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Khyzhun OY, Strunskus T, Wöll C, Gies H, Staemmler V. Comparison of the OKα x-ray emission bands in micro- and mesoporous silica materials and in α-quartz. J Chem Phys 2008; 129:084711. [DOI: 10.1063/1.2972145] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Du J, Corrales LR. Characterization of the Structural and Electronic Properties of Crystalline Lithium Silicates. J Phys Chem B 2006; 110:22346-52. [PMID: 17091974 DOI: 10.1021/jp056879s] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT) calculations within the generalized gradient approximation (GGA) were performed to study the atomic and electronic structure of lithium silicate crystals that were fully optimized within the theory. It is found that the relative stability of two crystalline forms of lithium disilicate agrees well with experimental results. The calculated electronic density of states shows distinguishable contributions to the oxygen 2s and upper valence bands associated with bridging (BO) and nonbridging oxygen (NBO) atoms. Bond ionicity, characterized by determining the relative atomic charges, is used to distinguish BO and NBO atoms as well as the corresponding Si-BO and Si-NBO bonds. Results from this work reveal that atomic charges obtained by using population analysis methods based on electron deformation density rather than total electron density provide an accurate description of bond ionicity consistent with chemical intuition.
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Affiliation(s)
- Jincheng Du
- Chemical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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11
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Du J, Corrales LR. Structure, dynamics, and electronic properties of lithium disilicate melt and glass. J Chem Phys 2006; 125:114702. [PMID: 16999496 DOI: 10.1063/1.2345060] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ab initio molecular dynamics simulations within the framework of density functional theory have been performed to study the structural, dynamic, and electronic properties of lithium disilicate melt and the glass derived from quenching the melt. It is found that lithium ions have a much higher diffusion coefficient and show different diffusion mechanisms than the network forming silicon and oxygen ions in the melt. The simulated lithium disilicate glass structure has 100% four coordinated silicon, close to theoretical nonbridging oxygen to bridging oxygen ratio (2:3), and Q(n) distributions of 20.8%, 58.4%, and 20.8% for n=2,3,4, respectively. In the melt there are considerable amounts (10%-15%) of silicon coordination defects; however, the average silicon coordination number remains about 4, similar to that in the glass. The lithium ion coordination number increases from 3.7 in the glass to 4.4 in the melt mainly due to the increase of bridging oxygen in the first coordination shell. The bond length and bond angle distributions, vibrational density of states, and static structure factors of the simulated glass were determined where the latter was found to be in good agreement with experimental measurement. Atomic charges were obtained based on Bader and Hirshfeld population analyses [Atoms in Molecule: A Quantum Theory (Oxford University Press, Oxford, 1990); Theor. Chim. Acta 44, 129 (1977)]. The average Bader charges found in lithium disilicate glass were -1.729, 3.419, and 0.915 for oxygen, silicon, and lithium, respectively. The corresponding Hirshfeld charges were -0.307, 0.550, and 0.229. The electronic densities of states of the melt and glass were calculated and compared with those of crystalline lithium disilicate.
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Affiliation(s)
- Jincheng Du
- Chemical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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12
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Gibbs G, Rosso K, Teter D, Boisen M, Bukowinski M. Model structures and properties of the electron density distribution for low quartz at pressure: a study of the SiO bond. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(99)00179-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jansen AP, Watson GW, Parker SC. Free-energy calculations of thermodynamic, vibrational, elastic, and structural properties of alpha -quartz at variable pressures and temperatures. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 54:826-835. [PMID: 9985348 DOI: 10.1103/physrevb.54.826] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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14
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Sarnthein J, Pasquarello A, Car R. Model of vitreous SiO2 generated by an ab initio molecular-dynamics quench from the melt. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:12690-12695. [PMID: 9980432 DOI: 10.1103/physrevb.52.12690] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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15
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Chaboy J, Benfatto M, Davoli I. Theoretical analysis of x-ray-absorption spectra at the silicon K and L2,3 edges of crystalline and amorphous SiO2. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:10014-10020. [PMID: 9980046 DOI: 10.1103/physrevb.52.10014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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16
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Fiorentini V, Baldereschi A. Dielectric scaling of the self-energy scissor operator in semiconductors and insulators. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 51:17196-17198. [PMID: 9978735 DOI: 10.1103/physrevb.51.17196] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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17
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Sarnthein J, Pasquarello A, Car R. Structural and electronic properties of liquid and amorphous SiO2: An ab initio molecular dynamics study. PHYSICAL REVIEW LETTERS 1995; 74:4682-4685. [PMID: 10058572 DOI: 10.1103/physrevlett.74.4682] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Continenza A. Electronic properties of alpha -quartz under high pressure and the transition to the amorphous phase. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:5950-5956. [PMID: 9976964 DOI: 10.1103/physrevb.50.5950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Binggeli N, Keskar NR, Chelikowsky JR. Pressure-induced amorphization, elastic instability, and soft modes in alpha -quartz. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:3075-3081. [PMID: 10011162 DOI: 10.1103/physrevb.49.3075] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Continenza A. Structural properties of alpha -quartz under high pressure and amorphization effects. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:12558-12565. [PMID: 10007623 DOI: 10.1103/physrevb.48.12558] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Huang MZ, Ching WY. Calculation of optical excitations in cubic semiconductors. I. Electronic structure and linear response. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:9449-9463. [PMID: 10005011 DOI: 10.1103/physrevb.47.9449] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Wiech G, Feldhütter H, Simunek A. Electronic structure of amorphous SiOx:H alloy films studied by x-ray emission spectroscopy: Si K, Si L, and O K emission bands. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:6981-6989. [PMID: 10004692 DOI: 10.1103/physrevb.47.6981] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Binggeli N, Chelikowsky JR. Elastic instability in alpha -quartz under pressure. PHYSICAL REVIEW LETTERS 1992; 69:2220-2223. [PMID: 10046429 DOI: 10.1103/physrevlett.69.2220] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Gonze X, Allan DC, Teter MP. Dielectric tensor, effective charges, and phonons in alpha -quartz by variational density-functional perturbation theory. PHYSICAL REVIEW LETTERS 1992; 68:3603-3606. [PMID: 10045746 DOI: 10.1103/physrevlett.68.3603] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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