Publikační činnost Úseku superpočítačových služeb / Publications of Supercomputining Services (96300)

Permanent URI for this collectionhttp://hdl.handle.net/10084/96085

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Now showing 1 - 8 out of 8 results

The Dalton quantum chemistry program system
(Wiley, 2014) Aidas, Kestutis; Angeli, Celestino; Bak, Keld L.; Bakken, Vebjørn; Bast, Radovan; Boman, Linus; Christiansen, Ove; Cimiraglia, Renzo; Coriani, Sonia; Dahle, Pal; Dalskov, Erik K.; Ekström, Ulf; Enevoldsen, Thomas; Eriksen, Janus J.; Ettenhuber, Patrick; Fernández, Berta; Ferrighi, Lara; Fliegl, Heike; Frediani, Luca; Hald, Kasper; Halkier, Asger; Hättig, Christof; Heiberg, Hanne; Helgaker, Trygve; Hennum, Alf Christian; Hettema, Hinne; Hjertenæs, Eirik; Høst, Stinne; Høyvik, Ida-Marie; Iozzi, Maria Francesca; Jansík, Branislav; Jensen, Hans Jørgen Aa.; Jonsson, Dan; Jørgensen, Poul; Kauczor, Joanna; Kirpekar, Sheela; Kjærgaard, Thomas; Klopper, Wim; Knecht, Stefan; Kobayashi, Rika; Koch, Henrik; Kongsted, Jacob; Krapp, Andreas; Kristensen, Kasper; Ligabue, Andrea; Lutnæs, Ola B.; Melo, Juan I.; Mikkelsen, Kurt V.; Myhre, Rolf H.; Neiss, Christian; Nielsen, Christian B.; Norman, Patrick; Olsen, Jeppe; Olsen, Jógvan Magnus H.; Osted, Anders; Packer, Martin J.; Pawlowski, Filip; Pedersen, Thomas B.; Provasi, Patricio F.; Reine, Simen; Rinkevicius, Zilvinas; Ruden, Torgeir A.; Ruud, Kenneth; Rybkin, Vladimir V.; Sałek, Pawel; Samson, Claire C. M.; Sanchez de Merás, Alfredo; Saue, Trond; Sauer, Stephan P. A.; Schimmelpfennig, Bernd; Sneskov, Kristian; Steindal, Arnfinn H.; Sylvester-Hvid, Kristian O.; Taylor, Peter R.; Teale, Andrew M.; Tellgren, Erik I.; Tew, David P.; Thorvaldsen, Andreas J.; Thøgersen, Lea; Vahtras, Olav; Watson, Mark A.; Wilson, David J. D.; Ziolkowski, Marcin; Ågren, Hans
Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
Light commodity devices for building vehicular ad hoc networks: An experimental study
(Elsevier, 2016) Toutouh, Jamal; Alba, Enrique
Vehicular communication networks represent both an opportunity and a challenge for providing smart mobility services by using a hybrid solution that relies on cellular connectivity and short range communications. The evaluation of this kind of network is overwhelmingly carried out in the present literature with simulations. However, the degree of realism of the results obtained is limited because simulations simplify real world interactions too much in many cases. In this article, we define an outdoor testbed to evaluate the performance of short range vehicular communications by using real world personal portable devices (smartphones, tablets, and laptops), two different PHY standards (IEEE 802.11g and IEEE 802.11a), and vehicles. Our test results on the 2.4 GHz band show that smartphones can be used to communicate vehicles within a range up to 75 m, while tablets can attain up to 125 m in mobility conditions. Moreover, we observe that vehicles equipped with laptops exchange multimedia information with nodes located further than 150 m. The communications on the 5 GHz band achieved an effective transmission range of up to 100 m. This, together with the optimization of the protocols used, could take our commodity lightweight devices to a new realm of use in the next generation of ad hoc mobility communications for moving through the city.
Random neural network model for supervised learning problems
(Czech Technical University in Prague, VSB - Technical University of Ostrava, 2015) Basterrech, Sebastián; Rubino, Gerardo
Random Neural Networks (RNNs) area classof Neural Networks (NNs) that can also be seen as a specific type of queuing network. They have been successfully used in several domains during the last 25 years, as queuing networks to analyze the performance of resource sharing in many engineering areas, as learning tools and in combinatorial optimization, where they are seen as neural systems, and also as models of neurological aspects of living beings. In this article we focus on their learning capabilities, and more specifically, we present a practical guide for using the RNN to solve supervised learning problems. We give a general description of these models using almost indistinctly the terminology of Queuing Theory and the neural one. We present the standard learning procedures usedby RNNs, adapted from similar well-established improvements in the standard NN field. We describe in particular a set of learning algorithms covering techniques based on the use of first order and, then, of second order derivatives. We also discuss some issues related to these objects and present new perspectives about their use in supervised learning problems. The tutorial describes their most relevant applications, and also provides a large bibliography.
Photodissociation of medium-sized argon cluster cations in the visible region
(Royal Society of Chemistry, 2015) Stachoň, Martin; Vítek, Aleš; Kalus, René
Semiclassical methods for non-adiabatic dynamics simulations, based on a semiempirical diatomics-in-molecules model of intracluster interactions and the mean-field dynamical approach with the inclusion of quantum decoherence, have been used to study the photodissociation of argon cluster cations, ArN+(N = 6–19), at Ephot = 2.35 eV. Time periods upto t = 200 ps have been considered and abundance of ionic and neutral fragments, their time evolution and stability have been investigated and compared with available experimental data as well as earlier theoretical studies. A good agreement has been achieved between our predictions and the experimental data and deviations from earlier dynamical calculations are discussed.
The divide–expand–consolidate MP2 scheme goes massively parallel
(Taylor & Francis, 2013) Kristensen, Kasper; Kjærgaard, Thomas; Høyvik, Ida-Marie; Ettenhuber, Patrick; Jørgensen, Poul; Jansík, Branislav; Reine, Simen; Jakowski, Jacek
For large molecular systems conventional implementations of second order Møller–Plesset (MP2) theory encounter a scaling wall, both memory- and time-wise. We describe how this scaling wall can be removed. We present a massively parallel algorithm for calculating MP2 energies and densities using the divide–expand–consolidate scheme where a calculation on a large system is divided into many small fragment calculations employing local orbital spaces. The resulting algorithm is linear-scaling with system size, exhibits near perfect parallel scalability, removes memory bottlenecks and does not involve any I/O. The algorithm employs three levels of parallelisation combined via a dynamic job distribution scheme. Results on two molecular systems containing 528 and 1056 atoms (4278 and 8556 basis functions) using 47,120 and 94,240 cores are presented. The results demonstrate the scalability of the algorithm both with respect to the number of cores and with respect to system size. The presented algorithm is thus highly suited for large super computer architectures and allows MP2 calculations on large molecular systems to be carried out within a few hours – for example, the correlated calculation on the molecular system containing 1056 atoms took 2.37 hours using 94240 cores.
Pipek–Mezey localization of occupied and virtual orbitals
(Wiley, 2013) Høyvik, Ida-Marie; Jansík, Branislav; Jørgensen, Poul
Recent advances in orbital localization algorithms are used to minimize the Pipek–Mezey localization function for both occupied and virtual Hartree–Fock orbitals. Virtual Pipek–Mezey orbitals for large molecular systems have previously not been considered in the literature. For this work, the Pipek–Mezey (PM) localization function is implemented for both the Mulliken and a Löwdin population analysis. The results show that the standard PM localization function (using either Mulliken or Löwdin population analyses) may yield local occupied orbitals, although for some systems the occupied orbitals are only semilocal as compared to state-of-the-art localized occupied orbitals. For the virtual orbitals, a Löwdin population analysis shows improvement in locality compared to a Mulliken population analysis, but for both Mulliken and Löwdin population analyses, the virtual orbitals are seen to be considerably less local compared to state-of-the-art localized orbitals.
Local hartree-fock orbitals using a three-level optimization strategy for the energy
(Wiley, 2013) Høyvik, Ida-Marie; Jansík, Branislav; Kristensen, Kasper; Jørgensen, Poul
Using the three-level energy optimization procedure combined with a refined version of the least-change strategy for the orbitals—where an explicit localization is performed at the valence basis level—it is shown how to more efficiently determine a set of local Hartree–Fock orbitals. Further, a core–valence separation of the least-change occupied orbital space is introduced. Numerical results comparing valence basis localized orbitals and canonical molecular orbitals as starting guesses for the full basis localization are presented. The results show that the localization of the occupied orbitals may be performed at a small computational cost if valence basis localized orbitals are used as a starting guess. For the unoccupied space, about half the number of iterations are required if valence localized orbitals are used as a starting guess compared to a canonical set of unoccupied Hartree–Fock orbitals. Different local minima may be obtained when different starting guesses are used. However, the different minima all correspond to orbitals with approximately the same locality.
Orbital localization using fourth central moment minimization
(American Institute of Physics, 2012) Høyvik, Ida-Marie; Jansík, Branislav; Jørgensen, Poul
We present a new orbital localization function based on the sum of the fourth central moments of the orbitals. To improve the locality, we impose a power on the fourth central moment to act as a penalty on the least local orbitals. With power two, the occupied and virtual Hartree-Fock orbitals exhibit a more rapid tail decay than orbitals from other localization schemes, making them suitable for use in local correlation methods. We propose that the standard orbital spread (the square root of the second central moment) and fourth moment orbital spread (the fourth root of the fourth central moment) are used as complementary measures to characterize the locality of an orbital, irrespective of localization scheme.

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