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1. Unraveling the interlayer and intralayer coupling in two-dimensional layered MoS$_2$ by X-ray absorption spectroscopy and ab initio molecular dynamics simulations

Author

Pudza, Inga, Bocharov, Dmitry, Anspoks, Andris, Krack, Matthias, Kalinko, Aleksandr, Welter, Edmund, and Kuzmin, Alexei

Subjects
Condensed Matter - Materials Science
Abstract

Understanding interlayer and intralayer coupling in two-dimensional layered materials (2DLMs) has fundamental and technological importance for their large-scale production, engineering heterostructures, and development of flexible and transparent electronics. At the same time, the quantification of weak interlayer interactions in 2DMLs is a challenging task, especially, from the experimental point of view. Herein, we demonstrate that the use of X-ray absorption spectroscopy in combination with reverse Monte Carlo (RMC) and ab initio molecular dynamics (AIMD) simulations can provide useful information on both interlayer and intralayer coupling in 2DLM 2H$_c$-MoS$_2$. The analysis of the low-temperature (10-300 K) Mo K-edge extended X-ray absorption fine structure (EXAFS) using RMC simulations allows for obtaining information on the means-squared relative displacements $\sigma^2$ for nearest and distant Mo-S and Mo-Mo atom pairs. This information allowed us further to determine the strength of the interlayer and intralayer interactions in terms of the characteristic Einstein frequencies $\omega_E$ and the effective force constants $\kappa$ for the nearest ten coordination shells around molybdenum. The studied temperature range was extended up to 1200 K employing AIMD simulations which were validated at 300 K using the EXAFS data. Both RMC and AIMD results provide evidence of the reduction of correlation in thermal motion between distant atoms and suggest strong anisotropy of atom thermal vibrations within the plane of the layers and in the orthogonal direction.

Published
2023
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2. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

Author

Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Blügel, Stefan, Bröder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, Garcia, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan P., Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kühne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K. H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Müller, Tiziano M. A., Petretto, Guido, Pickard, Chris J., Poncé, Samuel, Rignanese, Gian-Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E. P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, and Pizzi, Giovanni

Subjects
Condensed Matter - Materials Science, Physics - Computational Physics
Abstract

In the past decades many density-functional theory methods and codes adopting periodic boundary conditions have been developed and are now extensively used in condensed matter physics and materials science research. Only in 2016, however, their precision (i.e., to which extent properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. We discuss here general recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z=1 to 96 and characterizing 10 prototypical cubic compounds for each element: 4 unaries and 6 oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Such effort is facilitated by deploying AiiDA common workflows that perform automatic input parameter selection, provide identical input/output interfaces across codes, and ensure full reproducibility. Finally, we discuss the extent to which the current results for total energies can be reused for different goals (e.g., obtaining formation energies)., Comment: Main text: 23 pages, 4 figures. Supplementary: 68 pages. Nature Review Physics 2023

Published
2023
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3. CP2K: An Electronic Structure and Molecular Dynamics Software Package -- Quickstep: Efficient and Accurate Electronic Structure Calculations

Author

Kühne, Thomas D., Iannuzzi, Marcella, Del Ben, Mauro, Rybkin, Vladimir V., Seewald, Patrick, Stein, Frederick, Laino, Teodoro, Khaliullin, Rustam Z., Schütt, Ole, Schiffmann, Florian, Golze, Dorothea, Wilhelm, Jan, Chulkov, Sergey, Bani-Hashemian, Mohammad Hossein, Weber, Valéry, Borstnik, Urban, Taillefumier, Mathieu, Jakobovits, Alice Shoshana, Lazzaro, Alfio, Pabst, Hans, Müller, Tiziano, Schade, Robert, Guidon, Manuel, Andermatt, Samuel, Holmberg, Nico, Schenter, Gregory K., Hehn, Anna, Bussy, Augustin, Belleflamme, Fabian, Tabacchi, Gloria, Glöß, Andreas, Lass, Michael, Bethune, Iain, Mundy, Christopher J., Plessl, Christian, Watkins, Matt, VandeVondele, Joost, Krack, Matthias, and Hutter, Jürg

Subjects
Physics - Chemical Physics, Condensed Matter - Materials Science, Physics - Computational Physics
Abstract

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2k to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension., Comment: 51 pages, 5 figures

Published
2020
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6. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

Author

Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Bluegel, Stefan, Broeder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, Garcia, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan Philippe, Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kuehne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K. H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Mueller, Tiziano M. A., Petretto, Guido, Pickard, Chris J., Ponce, Samuel, Rignanese, Gian-Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E. P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, Pizzi, Giovanni, Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Bluegel, Stefan, Broeder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, Garcia, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan Philippe, Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kuehne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K. H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Mueller, Tiziano M. A., Petretto, Guido, Pickard, Chris J., Ponce, Samuel, Rignanese, Gian-Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E. P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, and Pizzi, Giovanni

Abstract

Density-functional theory methods and codes adopting periodic boundary conditions are extensively used in condensed matter physics and materials science research. In 2016, their precision (how well properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. In this Expert Recommendation, we discuss recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z = 1 to 96 and characterizing 10 prototypical cubic compounds for each element: four unaries and six oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Finally, we discuss the extent to which the current results for total energies can be reused for different goals.|Verification efforts of density-functional theory (DFT) calculations are of crucial importance to evaluate the reliability of simulation results. In this Expert Recommendation, we suggest metrics for DFT verification, illustrating them with an all-electron reference dataset of 960 equations of state covering the whole periodic table (hydrogen to curium) and discuss the importance of improving pseudopotential codes.|Verification efforts are critical to assess the reliability of density-functional theory (DFT) simulations and provide results with properly quantified uncertainties.Developing standard computation protocols to perform verification studies and publishing curated and FAIR reference datasets can greatly aid their use to improve codes and computational approaches.The use of fully automated workflows with c

Published
2024
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7. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

Author

European Commission, Swiss National Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Vienna University of Technology, Jülich Research Centre, Helmholtz Platform for Research Software Engineering, Commissariat à l'Ènergie Atomique et aux Ènergies Alternatives (France), Fonds de La Recherche Scientifique (Belgique), Fédération Wallonie-Bruxelles, Villum Fonden, Technical University of Denmark, Ghent University, Research Foundation - Flanders, Flemish Government, Bosoni, Emanuele [0000-0003-4585-5478], Blaha, Peter [0000-0001-5849-5788], Blügel, Stefan [0000-0001-9987-4733], Bröder, Jens [0000-0001-7939-226X], Cottenier, Stefaan [0000-0003-2541-8043], Eimre, Kristjan [0000-0002-3444-3286], Fornari, Marco [0000-0001-6527-8511], García Arribas, Alberto [0000-0001-5138-9579], Giantomassi, Matteo [0000-0002-7007-9813], Huber, Sebastiaan P. [0000-0001-5845-8880], Janssen, Henning [0000-0003-3558-9487], Kastlunger, Georg [0000-0002-3767-8734], Krack, Matthias [0000-0002-2082-7027], Kresse, Georg [0000-0001-9102-4259], Kühne, Thomas D. [0000-0001-5471-2407], Lejaeghere, Kurt [0000-0002-4462-8209], Marzari, Nicola [0000-0002-9764-0199], Michalicek, Gregor [0000-0003-4719-188X], Müller, Tiziano M.A. [0000-0002-1387-5717], Pickard, Chris J. [0000-0002-9684-5432], Rignanese, Gian Marco [0000-0002-1422-1205], Ruh, Thomas [0000-0001-7577-0198], Vanpoucke, Danny E.P. [0000-0001-5919-7336], Wolloch, Michael [0000-0002-3419-5526], Wortmann, Daniel [0000-0002-2248-1904], Yu, Jusong [0000-0001-9246-6067], Zhu, Bonan [0000-0001-5601-6130], Pizzi, Giovanni [0000-0002-3583-4377], Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Blügel, Stefan, Bröder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, García Arribas, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan P., Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kühne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K.H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Müller, Tiziano M.A., Petretto, Guido, Pickard, Chris J., Poncé, Samuel, Rignanese, Gian Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E.P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, Pizzi, Giovanni, European Commission, Swiss National Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Vienna University of Technology, Jülich Research Centre, Helmholtz Platform for Research Software Engineering, Commissariat à l'Ènergie Atomique et aux Ènergies Alternatives (France), Fonds de La Recherche Scientifique (Belgique), Fédération Wallonie-Bruxelles, Villum Fonden, Technical University of Denmark, Ghent University, Research Foundation - Flanders, Flemish Government, Bosoni, Emanuele [0000-0003-4585-5478], Blaha, Peter [0000-0001-5849-5788], Blügel, Stefan [0000-0001-9987-4733], Bröder, Jens [0000-0001-7939-226X], Cottenier, Stefaan [0000-0003-2541-8043], Eimre, Kristjan [0000-0002-3444-3286], Fornari, Marco [0000-0001-6527-8511], García Arribas, Alberto [0000-0001-5138-9579], Giantomassi, Matteo [0000-0002-7007-9813], Huber, Sebastiaan P. [0000-0001-5845-8880], Janssen, Henning [0000-0003-3558-9487], Kastlunger, Georg [0000-0002-3767-8734], Krack, Matthias [0000-0002-2082-7027], Kresse, Georg [0000-0001-9102-4259], Kühne, Thomas D. [0000-0001-5471-2407], Lejaeghere, Kurt [0000-0002-4462-8209], Marzari, Nicola [0000-0002-9764-0199], Michalicek, Gregor [0000-0003-4719-188X], Müller, Tiziano M.A. [0000-0002-1387-5717], Pickard, Chris J. [0000-0002-9684-5432], Rignanese, Gian Marco [0000-0002-1422-1205], Ruh, Thomas [0000-0001-7577-0198], Vanpoucke, Danny E.P. [0000-0001-5919-7336], Wolloch, Michael [0000-0002-3419-5526], Wortmann, Daniel [0000-0002-2248-1904], Yu, Jusong [0000-0001-9246-6067], Zhu, Bonan [0000-0001-5601-6130], Pizzi, Giovanni [0000-0002-3583-4377], Bosoni, Emanuele, Beal, Louis, Bercx, Marnik, Blaha, Peter, Blügel, Stefan, Bröder, Jens, Callsen, Martin, Cottenier, Stefaan, Degomme, Augustin, Dikan, Vladimir, Eimre, Kristjan, Flage-Larsen, Espen, Fornari, Marco, García Arribas, Alberto, Genovese, Luigi, Giantomassi, Matteo, Huber, Sebastiaan P., Janssen, Henning, Kastlunger, Georg, Krack, Matthias, Kresse, Georg, Kühne, Thomas D., Lejaeghere, Kurt, Madsen, Georg K.H., Marsman, Martijn, Marzari, Nicola, Michalicek, Gregor, Mirhosseini, Hossein, Müller, Tiziano M.A., Petretto, Guido, Pickard, Chris J., Poncé, Samuel, Rignanese, Gian Marco, Rubel, Oleg, Ruh, Thomas, Sluydts, Michael, Vanpoucke, Danny E.P., Vijay, Sudarshan, Wolloch, Michael, Wortmann, Daniel, Yakutovich, Aliaksandr V., Yu, Jusong, Zadoks, Austin, Zhu, Bonan, and Pizzi, Giovanni

Abstract

Density-functional theory methods and codes adopting periodic boundary conditions are extensively used in condensed matter physics and materials science research. In 2016, their precision (how well properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. In this Expert Recommendation, we discuss recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z = 1 to 96 and characterizing 10 prototypical cubic compounds for each element: four unaries and six oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Finally, we discuss the extent to which the current results for total energies can be reused for different goals.

Published
2023

8. Cobalt-free layered perovskites RBaCuFeO5+δ (R = 4f lanthanide) as electrocatalysts for the oxygen evolution reaction

Author

Marelli, Elena, primary, Lyu, Jike, additional, Morin, Mickaël, additional, Leménager, Maxime, additional, Shang, Tian, additional, Yüzbasi, N. Sena, additional, Aegerter, Dino, additional, Huang, Jinzhen, additional, Daffé, Niéli D., additional, Clark, Adam H., additional, Sheptyakov, Denis, additional, Graule, Thomas, additional, Nachtegaal, Maarten, additional, Pomjakushina, Ekaterina, additional, Schmidt, Thomas J., additional, Krack, Matthias, additional, Fabbri, Emiliana, additional, and Medarde, Marisa, additional

Published
2024
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10. Comparative classical and ab initio Molecular Dynamics study of molten and glassy germanium dioxide

Author

Hawlitzky, Michael, Horbach, Juergen, Ispas, Simona, Krack, Matthias, and Binder, Kurt

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Materials Science
Abstract

A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE) [Oeffner R D and Elliott S R 1998, Phys. Rev. B, 58, 14791]. We compare our results to experiments and previous simulations. In addition, an ab initio method, the so-called Car-Parrinello Molecular Dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO2, the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO2, for high temperatures the dynamics of molten GeO2 is compatible with a description in terms of mode coupling theory., Comment: 27 pages, 16 figures

Published
2008
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11. An Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics

Author

Kühne, Thomas D., Krack, Matthias, Mohamed, Fawzi R., and Parrinello, Michele

Subjects
Condensed Matter - Materials Science, Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics, Physics - Computational Physics
Abstract

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of magnitude has been observed, which allows ab-initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab-initio simulations., Comment: 4 pages, 3 figures; Accepted by Phys. Rev. Lett. for publication

Published
2006
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12. How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

Author

Bosoni, Emanuele, primary, Beal, Louis, additional, Bercx, Marnik, additional, Blaha, Peter, additional, Blügel, Stefan, additional, Bröder, Jens, additional, Callsen, Martin, additional, Cottenier, Stefaan, additional, Degomme, Augustin, additional, Dikan, Vladimir, additional, Eimre, Kristjan, additional, Flage-Larsen, Espen, additional, Fornari, Marco, additional, Garcia, Alberto, additional, Genovese, Luigi, additional, Giantomassi, Matteo, additional, Huber, Sebastiaan P., additional, Janssen, Henning, additional, Kastlunger, Georg, additional, Krack, Matthias, additional, Kresse, Georg, additional, Kühne, Thomas D., additional, Lejaeghere, Kurt, additional, Madsen, Georg K. H., additional, Marsman, Martijn, additional, Marzari, Nicola, additional, Michalicek, Gregor, additional, Mirhosseini, Hossein, additional, Müller, Tiziano M. A., additional, Petretto, Guido, additional, Pickard, Chris J., additional, Poncé, Samuel, additional, Rignanese, Gian-Marco, additional, Rubel, Oleg, additional, Ruh, Thomas, additional, Sluydts, Michael, additional, Vanpoucke, Danny E. P., additional, Vijay, Sudarshan, additional, Wolloch, Michael, additional, Wortmann, Daniel, additional, Yakutovich, Aliaksandr V., additional, Yu, Jusong, additional, Zadoks, Austin, additional, Zhu, Bonan, additional, and Pizzi, Giovanni, additional

Published
2023
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18. Linking atomic and mesoscopic scales for the modelling of the transport properties of uranium dioxide under irradiation

Author

Bertolus, Marjorie, Freyss, Michel, Dorado, Boris, Martin, Guillaume, Hoang, Kiet, Maillard, Serge, Skorek, Richard, Garcia, Philippe, Valot, Carole, Chartier, Alain, Van Brutzel, Laurent, Fossati, Paul, Grimes, Robin W., Parfitt, David C., Bishop, Clare L., Murphy, Samuel T., Rushton, Michael J.D., Staicu, Dragos, Yakub, Eugen, Nichenko, Sergii, Krack, Matthias, Devynck, Fabien, Ngayam-Happy, Raoul, Govers, Kevin, Deo, Chaitanya S., and Behera, Rakesh K.

Published
2015
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27. CP2K

Author

Kuehne, Thomas D., Iannuzzi, Marcella, Del Ben, Mauro, Rybkin, Vladimir V., Seewald, Patrick, Stein, Frederick, Laino, Teodoro, Khaliullin, Rustam Z., Schutt, Ole, Schiffmann, Florian, Golze, Dorothea, Wilhelm, Jan, Chulkov, Sergey, Bani-Hashemian, Mohammad Hossein, Weber, Valery, Borstnik, Urban, Taillefumier, Mathieu, Jakobovits, Alice Shoshana, Lazzaro, Alfio, Pabst, Hans, Mueller, Tiziano, Schade, Robert, Guidon, Manuel, Andermatt, Samuel, Holmberg, Nico, Schenter, Gregory K., Hehn, Anna, Bussy, Augustin, Belleflamme, Fabian, Tabacchi, Gloria, Gloss, Andreas, Lass, Michael, Bethune, Iain, Mundy, Christopher J., Plessl, Christian, Watkins, Matt, VandeVondele, Joost, Krack, Matthias, Hutter, Jurg, Department of Applied Physics, Computational Chemistry, Department of Chemistry and Materials Science, Aalto-yliopisto, and Aalto University

Subjects
DENSITY-FUNCTIONAL THEORY, CONSISTENT-FIELD THEORY, DER-WAALS INTERACTIONS, PARTICLE MESH EWALD, AB-INITIO CALCULATIONS, LOCALIZED WANNIER FUNCTIONS, PLANE-WAVES SCHEME, RANDOM-PHASE-APPROXIMATION, LONG-RANGE INTERACTIONS, NMR CHEMICAL-SHIFTS
Abstract

openaire: EC/H2020/824143/EU//MAX CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Published
2020

28. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

Author

Kühne, Thomas D., primary, Iannuzzi, Marcella, additional, Del Ben, Mauro, additional, Rybkin, Vladimir V., additional, Seewald, Patrick, additional, Stein, Frederick, additional, Laino, Teodoro, additional, Khaliullin, Rustam Z., additional, Schütt, Ole, additional, Schiffmann, Florian, additional, Golze, Dorothea, additional, Wilhelm, Jan, additional, Chulkov, Sergey, additional, Bani-Hashemian, Mohammad Hossein, additional, Weber, Valéry, additional, Borštnik, Urban, additional, Taillefumier, Mathieu, additional, Jakobovits, Alice Shoshana, additional, Lazzaro, Alfio, additional, Pabst, Hans, additional, Müller, Tiziano, additional, Schade, Robert, additional, Guidon, Manuel, additional, Andermatt, Samuel, additional, Holmberg, Nico, additional, Schenter, Gregory K., additional, Hehn, Anna, additional, Bussy, Augustin, additional, Belleflamme, Fabian, additional, Tabacchi, Gloria, additional, Glöß, Andreas, additional, Lass, Michael, additional, Bethune, Iain, additional, Mundy, Christopher J., additional, Plessl, Christian, additional, Watkins, Matt, additional, VandeVondele, Joost, additional, Krack, Matthias, additional, and Hutter, Jürg, additional

Published
2020
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36. Interfacial water: A first principles molecular dynamics study of a nanoscale water film on salt.

Author

Li-Min Liu, Krack, Matthias, and Michaelides, Angelos

Subjects
*WATER, *SALT, *THIN films, *MOLECULAR dynamics, *MOLECULES, *HYDROGEN bonding, *DENSITY functionals, *PHYSICAL & theoretical chemistry
Abstract

Density functional theory (DFT) molecular dynamics simulations of a thin (∼15 Å) water film on NaCl(001) have been performed, with the aim of understanding the structural and dynamic properties of this important interfacial water system. The interaction of the water film with the surface orders the water molecules in the immediate vicinity of the interface. This is reflected by oscillations in the planar-averaged water density distribution along the surface normal that extend to about 8 Å from the surface. The interaction with the substrate leaves many of the water molecules in the immediate vicinity with broken hydrogen bonds and as a consequence considerably reduced dipole moments. Indeed a clear correlation between the number of hydrogen bonds which a water molecule is involved in and its dipole moment for both water on NaCl and bulk water is observed. How the DFT results obtained here compare to those obtained with various empirical potentials is briefly discussed. [ABSTRACT FROM AUTHOR]

Published
2009
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37. The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water.

Author

VandeVondele, Joost, Mohamed, Fawzi, Krack, Matthias, Hutter, Jürg, Sprik, Michiel, and Parrinello, Michele

Subjects
LIQUIDS, DENSITY functionals, MOLECULAR dynamics, SOLUTION (Chemistry), SIMULATION methods & models, FUNCTIONAL analysis
Abstract

The performance of density functional theory methods for the modeling of condensed aqueous systems is hard to predict and validation by ab initio molecular simulation of liquid water is absolutely necessary. In order to assess the reliability of these tests, the effect of temperature on the structure and dynamics of liquid water has been characterized with 16 simulations of 20 ps in the temperature range of 280–380 K. We find a pronounced influence of temperature on the pair correlation functions and on the diffusion constant including nonergodic behavior on the time scale of the simulation in the lower temperature range (which includes ambient temperature). These observations were taken into account in a consistent comparison of a series of density functionals (BLYP, PBE, TPSS, OLYP, HCTH120, HCTH407). All simulations were carried out using an ab initio molecular dynamics approach in which wave functions are represented using Gaussians and the density is expanded in an auxiliary basis of plane waves. Whereas the first three functionals show similar behavior, it is found that the latter three functionals yield more diffusive dynamics and less structure.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Published
2005
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38. Ab initio x-ray scattering of liquid water.

Author

Krack, Matthias, Gambirasio, Alfredo, and Parrinello, Michele

Subjects
*X-ray scattering, *LIQUIDS
Abstract

A direct calculation of the coherent x-ray scattering spectrum of liquid water under ambient conditions is presented using ab initio density functional theory. The experimental data are compared with the calculated x-ray scattering spectra retrieved from the trajectories of two CarParrinello molecular dynamics runs of about 10 ps with 32 and 64 water molecules in the simulation cell, respectively. Furthermore, the x-ray spectra obtained from molecular dynamics runs of 20 ps for 128 water molecules using empirical water models are presented. All calculations were performed with the QUICKSTEP code, which includes an all-electron implementation of the Gaussian augmented plane wave method. It is shown that by this approach one can assess how well different models describe the structural properties of water. [ABSTRACT FROM AUTHOR]

Published
2002
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39. Density oscillations in a nanoscale water film on salt: insight from ab initio molecular dynamics

Author

Limin Liu, Krack, Matthias, and Michaelides, Angelos

Subjects
Density functionals -- Usage, Molecular dynamics -- Analysis, Polarization (Light) -- Analysis, Water -- Chemical properties, Water -- Optical properties, Chemistry
Abstract

First-principles approach is used within the density functional theory framework in order to study the properties of the nanoscale water film that covers NaCl(001). The water density has displayed a damped oscillatory behavior in the direction of the surface normal and the water molecules in the contact layer are polarized through their interaction with the substrate.

Published
2008

42. Liquid water from first principles: Investigation of different sampling approaches

Author

I-Feng, W. Kuo, Mundy, Christopher J., Krack, Matthias, McGrath, Matthew J., Siepmann, J. Ijja, Parinello, Michele, Vondele, Joost Vande, Sprik, Michiel, Hutter, Jurg, Bin Chen, Klien, Michael L., and Mohamed, Fawzi

Subjects
Molecular dynamics -- Research, Water chemistry -- Research, Chemicals, plastics and rubber industries
Abstract

A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to investigate the reproducibility of different sampling approaches. The computational benefits of CPMD sampling over Born-Oppenheimer sampling for structural and thermodynamic properties are appreciable for liquid water and arise from the substantial reduction time per step.

Published
2004

43. Influence of outer shell metal ligands on the structural and electronic properties of horse liver alcohol dehydrogenase zinc active site

Author

Gervasio, Francesco Luigi, Schettino, Vincenzo, Mangani, Stefano, Krack, Matthias, Carolini, Paolo, and Parrinello, Michele

Subjects
Zinc compounds -- Structure, Alcohol dehydrogenase -- Structure, Alcohol dehydrogenase -- Spectra, Chemicals, plastics and rubber industries
Abstract

First principles quantum chemical calculations based on both localized (G) and delocalized (PW) basis sets are carried out for models of increasing complexity representing the LADH ternary complex, which features the Zn-His-Asp-water motif. The calculations suggest that second (Asp49) and third- shell (WAT) ligands affect the structure, electronic properties and energetics of the LADH active site.

Published
2003

45. An adaptive numerical integrator for molecular integrals.

Author

Krack, Matthias and Koster, Andreas M.

Subjects
*INTEGRALS, *NUMERICAL integration, *NUMERICAL grid generation (Numerical analysis)
Abstract

Presents the numerical integrator for molecular integrals generating an adaptive molecular grid. Identification of input parameters of integrator; Implementation of adaptive numerical integrator in density-functional theory method; Reliability of numerical integration; Reduction of expensive reference grid calculations.

Published
1998
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