J. J. Mortensen

Technical University of Denmark, Copenhagen, Capital Region, Denmark

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Publications (28)44.15 Total impact

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    ABSTRACT: Density function theory (DFT) is the most widely employed electronic structure method because of its favorable scaling with system size and accuracy for a broad range of molecular and condensed-phase systems. The advent of massively parallel supercomputers has enhanced the scientific community's ability to study larger system sizes. Ground-state DFT calculations on ∼ 103 valence electrons using traditional algorithms can be routinely performed on present-day supercomputers. The performance characteristics of these massively parallel DFT codes on > 104 computer cores are not well understood. The GPAW code was ported an optimized for the Blue Gene/P architecture. We present our algorithmic parallelization strategy and interpret the results for a number of benchmark test cases.Copyright © 2013 John Wiley & Sons, Ltd.
    Concurrency and Computation Practice and Experience 12/2013; · 0.85 Impact Factor
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    ABSTRACT: We present an implementation of localized atomic-orbital basis sets in the projector augmented wave (PAW) formalism within the density-functional theory. The implementation in the real-space GPAW code provides a complementary basis set to the accurate but computationally more demanding grid representation. The possibility to switch seamlessly between the two representations implies that simulations employing the local basis can be fine tuned at the end of the calculation by switching to the grid, thereby combining the strength of the two representations for optimal performance. The implementation is tested by calculating atomization energies and equilibrium bulk properties of a variety of molecules and solids, comparing to the grid results. Finally, it is demonstrated how a grid-quality structure optimization can be performed with significantly reduced computational effort by switching between the grid and basis representations.
    Physical review. B, Condensed matter 03/2013; 80(19).
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    ABSTRACT: Density functional theory has became the workhorse for simulations of catalytic reactions and computational design of novel catalysis. The generally applied semi-local exchange-correlation functionals have successfully predicted catalytic reaction trends over a variety of surfaces. However, in order to achieve quantitative predictions of reaction rates for molecule-surface systems, in particular where there is weak Van der Waals interactions or strong correlation, it is of vital importance to include non-local correlation effects. The use of random phase approximation (RPA) to construct the correlation energy, combined with the exact, self-interaction free exchange energy, offers a non-empirical way for accurately describe the adsorption energies [1] and dispersion forces [2]. We have recently implemented RPA in the GPAW code [3-4], an electronic structure package using projector augmented wave method and real space grids. In this talk I will present our initial results comparing RPA and generalized gradient functionals for the activation energies and reaction energies for transition metal or metal oxide surfaces. [4pt] [1] L. Schimka, et.al, Nature Mat. 9, 741 (2010) [2] T. Olsen, et.al, Phys. Rev. Lett. 107, 156401 (2011) [3] J. Yan, et.al, Phys. Rev. B 83, 245122 (2011). [4] J. Yan, et.al, Phys. Rev. Lett. 106, 146803 (2011)
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    ABSTRACT: Density function theory (DFT) is the most widely employed electronic structure method due to its favorable scaling with system size and accuracy for a broad range of molecular and condensed-phase systems. The advent of massively parallel supercomputers have enhanced the scientific community's ability to study larger system sizes. Ground state DFT calculations of systems with O(10^3) valence electrons can be routinely performed on present-day supercomputers. The performance of these massively parallel DFT codes at the scale of 1 - 10K execution threads are not well understood; even experienced DFT users are unaware of Amdahl's Law and the non-trivial scaling bottlenecks that are present in standard O(N^3) DFT algorithms. The GPAW code was ported an optimized for the Blue Gene/P. We present our algorithmic parallelization strategy and interpret the results for a number of benchmark tests cases. Lastly, I will describe opportunities for computer allocations at the Argonne Leadership Computing Facility.
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    ABSTRACT: We describe the implementation of K-shell core level spectroscopies (X-ray absorption (XAS), X-ray emission (XES), and X-ray photoemission (XPS)) in the real-space-grid-based Projector Augmented Wave (PAW) GPAW code. The implementation for XAS is based on the Haydock recursion method avoiding computation of unoccupied states. The absolute energy scale is computed with the Delta Kohn–Sham method which is possible using specific PAW setups for the core-hole states. We show computed spectra for selected test cases (gas phase H2O and bulk diamond) and discuss the dependence on grid spacing and box size. In the case of diamond we include vibrational effects by sampling spectra from the ground state vibrational distribution and discuss the importance of those effects for the experimentally observed features. We apply the method to XPS, XES and XAS of CO adsorbed on Ni(100) and compare to experimental data where possible.
    Fuel and Energy Abstracts 01/2011; 184(8):427-439.
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    ABSTRACT: AbstractWe address the fundamental question of which size a metallic nano-particle needs to have before its surface chemical properties can be considered to be those of a solid, rather than those of a large molecule. Calculations of adsorption energies for carbon monoxide and oxygen on a series of gold nanoparticles ranging from 13 to 1,415 atoms, or 0.8–3.7nm, have been made possible by exploiting massively parallel computing on up to 32,768 cores on the Blue Gene/P computer at Argonne National Laboratory. We show that bulk surface properties are obtained for clusters larger than ca. 560 atoms (2.7nm). Below that critical size, finite-size effects can be observed, and we show those to be related to variations in the local atomic structure augmented by quantum size effects for the smallest clusters. Graphical Abstract KeywordsNano-particle–Size effects–DFT
    Catalysis Letters 01/2011; 141(8):1067-1071. · 2.24 Impact Factor
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    ABSTRACT: Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.
    Journal of Physics Condensed Matter 06/2010; 22(25):253202. · 2.36 Impact Factor
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    ABSTRACT: We use density functional theory (DFT) with a recently developed van der Waals density functional (vdW-DF) to study the adsorption of graphene on Al, Cu, Ag, Au, Pt, Pd, Co and Ni(111) surfaces. In constrast to the local density approximation (LDA) which predicts relatively strong binding for Ni,Co and Pd, the vdW-DF predicts weak binding for all metals and metal-graphene distances in the range 3.40-3.72 \AA. At these distances the graphene bandstructure as calculated with DFT and the many-body G$_0$W$_0$ method is basically unaffected by the substrate, in particular there is no opening of a band gap at the $K$-point. Comment: 4 pages, 3 figures
    Physical review. B, Condensed matter 12/2009;
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    ABSTRACT: We present a computational screening study of ternary metal borohydrides for reversible hydrogen storage based on density functional theory. We investigate the stability and decomposition of alloys containing 1 alkali metal atom, Li, Na, or K (M(1)); and 1 alkali, alkaline earth or 3d/4d transition metal atom (M(2)) plus two to five (BH(4))(-) groups, i.e., M(1)M(2)(BH(4))(2-5), using a number of model structures with trigonal, tetrahedral, octahedral, and free coordination of the metal borohydride complexes. Of the over 700 investigated structures, about 20 were predicted to form potentially stable alloys with promising decomposition energies. The M(1)(Al/Mn/Fe)(BH(4))(4), (Li/Na)Zn(BH(4))(3), and (Na/K)(Ni/Co)(BH(4))(3) alloys are found to be the most promising, followed by selected M(1)(Nb/Rh)(BH(4))(4) alloys.
    The Journal of Chemical Physics 08/2009; 131(1):014101. · 3.16 Impact Factor
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    Physical Review B (Condensed Matter and Materials Physics). 01/2009; 80(19):195112.
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    ABSTRACT: We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.
    Physical Review Letters 12/2005; 95(21):216401. · 7.94 Impact Factor
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    J. J. Mortensen, L. B. Hansen, K. W. Jacobsen
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    ABSTRACT: A grid-based real-space implementation of the Projector Augmented Wave (PAW) method of P. E. Blochl [Phys. Rev. B 50, 17953 (1994)] for Density Functional Theory (DFT) calculations is presented. The use of uniform 3D real-space grids for representing wave functions, densities and potentials allows for flexible boundary conditions, efficient multigrid algorithms for solving Poisson and Kohn-Sham equations, and efficient parallelization using simple real-space domain-decomposition. We use the PAW method to perform all-electron calculations in the frozen core approximation, with smooth valence wave functions that can be represented on relatively coarse grids. We demonstrate the accuracy of the method by calculating the atomization energies of twenty small molecules, and the bulk modulus and lattice constants of bulk aluminum. We show that the approach in terms of computational efficiency is comparable to standard plane-wave methods, but the memory requirements are higher. Comment: 13 pages, 3 figures, accepted for publication in Physical Review B
    Physical review. B, Condensed matter 11/2004;
  • Physical Review B (Condensed Matter and Materials Physics). 01/2004; 69(21):214104.
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    ABSTRACT: The quasicontinuum method is a way of reducing the number of degrees of freedom in an atomistic simulation by removing the majority of the atoms in regions of slowly varying strain fields. Due to the different ways the energy of the atoms is calculated in the coarse-grained regions and the regions where all the atoms are present, unphysical forces called “ghost forces” arise at the interfaces. Corrections may be used to almost remove the ghost forces, but the correction forces are nonconservative, ruining energy conservation in dynamic simulations. We show that it is possible to formulate the quasicontinuum method without these problems by introducing a buffer layer between the two regions of space. The method is applicable to short-ranged potentials in the face-centered cubic, body-centered cubic, and hexagonal close-packed crystal structures.
    Physical Review B 01/2004; 69(21). · 3.77 Impact Factor
  • Jens Jo̸rgen Mortensen, Jakob Schiøtz, Karsten W Jacobsen
    Proceedings; 01/2002
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    ABSTRACT: The diffusion of individual N adatoms on Fe(100) has been studied using scanning tunneling microscopy and ab initio density functional theory (DFT) calculations. The measured diffusion barrier for isolated N adatoms is E(d) = (0.92+/-0.04) eV, with a prefactor of nu(0) = 4.3x10(12) s(-1), which is in quantitative agreement with the DFT calculations. The diffusion is strongly coupled to lattice distortions, and, as a consequence, the presence of other N adatoms introduces an anisotropy in the diffusion. Based on experimentally determined values of the diffusion barriers and adsorbate-adsorbate interactions, the potential energy surface experienced by a N adatom is determined.
    Physical Review Letters 06/2000; 84(21):4898-901. · 7.94 Impact Factor
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    ABSTRACT: Adsorption energies and structures for N atoms on three low-index surfaces of Fe have been calculated using density functional theory (DFT) and the generalized gradient approximation (GGA). At low N coverage the adsorption energy on Fe(100) is found to be ∼0.7eV higher than on the (111) and (110) surfaces – particularly the c(2×2)-N/Fe(100) structure with the N atoms in four-fold sites is very stable. We attribute the differences in adsorption energy to the lack of four-fold sites on the (111) and (110) surfaces. We suggest that at higher N coverages, islands with a structure similar to the c(2×2)-N/Fe(100) structure will form on the (111) and (110) surfaces.
    Surface Science - SURFACE SCI. 01/1999; 422(1):8-16.
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    ABSTRACT: We report extensive density functional calculations of the energetics of N2adsorption and dissociation on a Fe(111) surface. From the calculations we can present a detailed picture of the rate limiting step in the ammonia synthesis which is consistent with available experimental observations. Four different molecularly adsorbed states are identified, including a new state not seen by experiment. The new state is the true precursor to dissociation. We find that there are two dissociation channels, one going through all the molecular states sequentially with a low energy barrier, but a high entropy barrier, and the other a direct channel into the new precursor, which is highly activated. In this way we can explain both the measured sticking probability for a thermal gas of N2above a Fe(111) surface and the molecular beam scattering experiments. During ammonia synthesis conditions the low barrier channel is expected to dominate, but at the highest synthesis temperatures, the high barrier channels may become the most effective. The origin of the alkali promotion of the N2dissociation process is also discussed.
    Journal of Catalysis - J CATAL. 01/1999; 182(2):479-488.
  • J. J Mortensen, B Hammer, J. K Nørskovi
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    ABSTRACT: Using density functional theory we study the effect of pre-adsorbed atoms on the dissociation of N2 and the adsorption of N, N2, and CO on Ru(0001). We have done calculations for pre-adsorbed Na, Cs, and S, and find that alkali atoms adsorbed close to a dissociating N2 molecule will lower the barrier for dissociation, whereas S will increase it. The interaction with alkali atoms is mainly of an electrostatic nature. The poisoning by S is due to two kinds of repulsive interactions: a Pauli repulsion and a reduced covalent bond strength between the adsorbate and the surface d-electrons. In order to investigate these different interactions in more detail, we look at three different species (N atoms, and terminally bonded N2 and CO) and use them as probes to study their interaction with two modifier atoms (Na and S). The two modifier atoms have very different properties, which allows us to decouple the different types of interactions. Adsorbed Na induces large electrostatic fields, which S does not, and S interacts strongly with Ru(4d) states and broadens and shifts the d band, which Na does not do.
    Surface Science - SURFACE SCI. 01/1998; 414(3):315-329.
  • J. J. Mortensen, B. Hammer, J. K. Nørskov
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    ABSTRACT: Using self-consistent density functional calculations, we show that adsorbed Na and Cs lower the barrier for dissociation of N2 on Ru(0001). Since N2 dissociation is a crucial step in the ammonia synthesis reaction, we explain in this way the experimental observation that alkali metals promote the ammonia synthesis reaction over Ru catalysts. We also show that the origin of this effect is predominantly a direct electrostatic attraction between the adsorbed alkali atoms and the dissociating molecule.
    Physical Review Letters 01/1998; 80(19):4333-4336. · 7.94 Impact Factor

Publication Stats

309 Citations
44.15 Total Impact Points


  • 1997–2013
    • Technical University of Denmark
      • • Center for Atomic-scale Materials Design
      • • Department of Physics
      Copenhagen, Capital Region, Denmark
  • 2011
    • Stanford University
      Palo Alto, California, United States
  • 2010
    • CSC-IT Center for Science Ltd
      Esbo, Southern Finland Province, Finland
  • 2000
    • Aarhus University
      • Department of Physics and Astronomy
      Århus, Central Jutland, Denmark