Author
Emine Kucukbenli
Other affiliations: École Polytechnique Fédérale de Lausanne, Harvard University, Boston University
Bio: Emine Kucukbenli is an academic researcher from International School for Advanced Studies. The author has contributed to research in topics: van der Waals force & Density functional theory. The author has an hindex of 13, co-authored 21 publications receiving 5273 citations. Previous affiliations of Emine Kucukbenli include École Polytechnique Fédérale de Lausanne & Harvard University.
Papers
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University of Udine1, University of Lugano2, École Polytechnique Fédérale de Lausanne3, Leipzig University4, University of Paris5, University of North Texas6, Princeton University7, National Research Council8, International School for Advanced Studies9, Cornell University10, University of Lincoln11, University of Milan12, École Polytechnique13, International Centre for Theoretical Physics14, University of Paderborn15, University of Oxford16, Jožef Stefan Institute17, University of Padua18, Sapienza University of Rome19, Vietnam Academy of Science and Technology20, University of British Columbia21, Centre national de la recherche scientifique22, University of Lorraine23, University of Zurich24, École Normale Supérieure25, Université Paris-Saclay26, Wake Forest University27, Temple University28
TL;DR: Recent extensions and improvements are described, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software
3,638 citations
University of Udine1, University of Lugano2, École Polytechnique Fédérale de Lausanne3, Leipzig University4, University of Paris5, University of North Texas6, Princeton University7, National Research Council8, International School for Advanced Studies9, Cornell University10, University of Lincoln11, University of Milan12, École Polytechnique13, International Centre for Theoretical Physics14, University of Paderborn15, University of Oxford16, Jožef Stefan Institute17, University of Padua18, Sapienza University of Rome19, Vietnam Academy of Science and Technology20, University of British Columbia21, Centre national de la recherche scientifique22, University of Lorraine23, University of Zurich24, École Normale Supérieure25, Université Paris-Saclay26, Wake Forest University27, Temple University28
TL;DR: Quantum ESPRESSO as discussed by the authors is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density functional theory, density functional perturbation theory, and many-body perturbations theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches.
Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
2,818 citations
Ghent University1, Forschungszentrum Jülich2, Aalto University3, Åbo Akademi University4, Vienna University of Technology5, Duke University6, University of Grenoble7, École Polytechnique Fédérale de Lausanne8, Durham University9, International School for Advanced Studies10, Max Planck Society11, Uppsala University12, Fritz Haber Institute of the Max Planck Society13, Humboldt University of Berlin14, Technical University of Denmark15, National Institute of Standards and Technology16, University of Udine17, Université catholique de Louvain18, University of Basel19, Harvard University20, University of California, Davis21, Rutgers University22, University of York23, Wake Forest University24, Science and Technology Facilities Council25, University of Oxford26, University of Vienna27, Dresden University of Technology28, Leibniz Institute for Neurobiology29, Radboud University Nijmegen30, University of Tokyo31, Centre national de la recherche scientifique32, University of Cambridge33, Royal Holloway, University of London34, University of California, Santa Barbara35, University of Luxembourg36, Los Alamos National Laboratory37, Harbin Institute of Technology38
TL;DR: A procedure to assess the precision of DFT methods was devised and used to demonstrate reproducibility among many of the most widely used DFT codes, demonstrating that the precisionof DFT implementations can be determined, even in the absence of one absolute reference code.
Abstract: The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
1,141 citations
TL;DR: The vdW-DF theory is extended and the corresponding stress tensor is derived in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code.
Abstract: Use of the non-local correlation functional vdW-DF (from ?van der Waals density functional?; Dion M et?al 2004 Phys.?Rev.?Lett.?92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10?GPa?with and without van der Waals interactions?and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3?GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.
87 citations
TL;DR: In this article, the authors applied the GIPAW method to compute solid state NMR parameters for aluminum oxide phases and their precursors, and found a linear correlation between chemical shifts and Born effective charges.
Abstract: The Gauge-Including Projector Augmented Wave (GIPAW) method, within the Density Functional Theory (DFT) Generalized Gradient Approximation (GGA) framework, is applied to compute solid state NMR parameters for $^{27}Al$ in the $\alpha$, $\theta$, and $\kappa$ aluminium oxide phases and their gibbsite and boehmite precursors. The results for well-established crystalline phases compare very well with available experimental data and provide confidence in the accuracy of the method. For $\gamma$-alumina, four structural models proposed in the literature are discussed in terms of their ability to reproduce the experimental spectra also reported in the literature. Among the considered models, the $Fd\bar{3}m$ structure proposed by Paglia {\it et al.} [Phys. Rev. B {\bf 71}, 224115 (2005)] shows the best agreement. We attempt to link the theoretical NMR parameters to the local geometry. Chemical shifts depend on coordination number but no further correlation is found with geometrical parameters. Instead our calculations reveal that, within a given coordination number, a linear correlation exists between chemical shifts and Born effective charges.
48 citations
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01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.
29,323 citations
University of Udine1, University of Lugano2, École Polytechnique Fédérale de Lausanne3, Leipzig University4, University of Paris5, University of North Texas6, Princeton University7, National Research Council8, International School for Advanced Studies9, Cornell University10, University of Lincoln11, University of Milan12, École Polytechnique13, International Centre for Theoretical Physics14, University of Paderborn15, University of Oxford16, Jožef Stefan Institute17, University of Padua18, Sapienza University of Rome19, Vietnam Academy of Science and Technology20, University of British Columbia21, Centre national de la recherche scientifique22, University of Lorraine23, University of Zurich24, École Normale Supérieure25, Université Paris-Saclay26, Wake Forest University27, Temple University28
TL;DR: Recent extensions and improvements are described, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software
3,638 citations
University of Udine1, École Polytechnique Fédérale de Lausanne2, University of Lugano3, Leipzig University4, University of Paris5, University of North Texas6, Princeton University7, National Research Council8, International School for Advanced Studies9, Cornell University10, University of Lincoln11, University of Milan12, École Polytechnique13, International Centre for Theoretical Physics14, University of Paderborn15, University of Oxford16, Jožef Stefan Institute17, University of Padua18, Sapienza University of Rome19, Vietnam Academy of Science and Technology20, University of British Columbia21, University of Lorraine22, Centre national de la recherche scientifique23, University of Zurich24, École Normale Supérieure25, Université Paris-Saclay26, Wake Forest University27, Temple University28
TL;DR: Quantum ESPRESSO as discussed by the authors is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density functional theory, density functional perturbation theory, and many-body perturbations theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches.
Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
2,818 citations
TL;DR: A future in which the design, synthesis, characterization and application of molecules and materials is accelerated by artificial intelligence is envisaged.
Abstract: Here we summarize recent progress in machine learning for the chemical sciences. We outline machine-learning techniques that are suitable for addressing research questions in this domain, as well as future directions for the field. We envisage a future in which the design, synthesis, characterization and application of molecules and materials is accelerated by artificial intelligence.
2,295 citations
TL;DR: Several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers, and some capabilities recently added to the code which were enabled by this flexibility are highlighted.
1,956 citations