Universidad de Zaragoza - Caesaraugusta Node

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CAESARAUGUSTA II supercomputer (a.k.a. "Memento")

The Institute for Biocomputation and Physics of Complex Systems of the University of Zaragoza (BIFI-UNIZAR) is a research organisation that promotes interdisciplinarity to develop competitive research in computation applied to physics of complex systems and biological systems. Despite its youth, the Institute has already developed intensive research activity in several fields of computation: HPC, grid computing, cloud computing, GPUs, dedicated computers (FPGAs) and volunteer computing.

CAESARAUGUSTA II (locally also known as "Memento") at the University of Zaragoza, is a founding node of the Spanish Supercomputing Network (RES). The supercomputer, located at BIFI's premises in the Río Ebro Campus of the University, is managed by the High Performance Computing group of the Institute. It is equipped with 3072 computing cores, 12TB of RAM memory, 72TB of raw storage and Infiniband QDR interconnection network (40Gb/s), offering an overall raw performance (Rpeak) of 25,8 TFLOPS (Rmax is 20 TFLOPS). The portion of CAESARAUGUSTA II shared through the RES during 2014 was equal to 768 cores; 512 for RES users and 256 for local users.
This second version of Caesaraugusta superseded the former Caesaraugusta (2007-2013), PowerPC-based, hosted in the Faculty of Science of the University of Zaragoza.

Organisational Structure

CAESARAUGUSTA Operations Team (from left to right): Arturo Giner (BIFI's HPC sysadmin), Alfonso Tarancón (BIFI's Director), Guillermo Losilla (BIFI's HPC group manager), Patricia Santos (BIFI's HPC sysadmin)

CAESARAUGUSTA is maintained by technical staff of the Computing Area at BIFI, namely the HPC group. This includes hardware and software administration as well as first level user support, all of which are coordinated with the BSC-CNS Operations Department.

There is also a local Access Committee which periodically (each four months, coinciding with RES schedule) allocates the CPU time reserved for local projects (the portion equivalent to 256 cores mentioned above) among applicant activities. This time is assigned by the Committee after evaluating the applications received. During 2014, the members of the local Access Committee were: Prof. Pablo Ibáñez Marín, Prof. Luis Rández García, and Prof. Alfonso Tarancón Lafita.

Technical and Scientific Highlights 2014

In 2014 CAESARAUGUSTA's local Access Committee granted a total of 20 local projects, consuming 1.878.000 hours of CPU time. These activities have produced numerous scientific results and publications.

Key Publications 2014

  • Structure and magnetism of Tm atoms and monolayers on W(110); Corneliu Nistor, Aitor Mugarza, Sebastian Stepanow, and Pietro Gambardella1, Kurt Kummer, José Luis Diez-Ferrer, David Coffey, César de la Fuente, Miguel Ciria, and Jose I. Arnaudas; PHYSICAL REVIEW B 90, 064423 (2014), DOI: 10.1103/PhysRevB.90.064423
  • Roca-Lopez, D.; Tejero, T.; Merino, P. DFT Investigation of the Mechanism of E/Z Isomerization of Nitrones. J. Org. Chem. 2014, 79, 8358-8365.
  • Roca-López, D.; Tejero, T.; Caramella, P.; Merino, P., [2n2π + 2n2π] Cycloadditions: An alternative to forbidden [4π + 4π] processes. The Case of Nitrones Dimerizations. Org. Biomol. Chem. 2014, 12, 517-525.
  • Roca-López, D.; Marqués-López, E.; Alcaine, A.; Merino, P.; Herrera, R. P., Friedel-Crafts alkylation mechanism using aminoindanol derived thiourea catalyst. Org. Biomol. Chem. 2014, 12, 4503-4510.
  • Merino, P.; Tejero, T.; Diez Martinez, A., Theoretical Elucidation of the Mechanism of the Cycloaddition between Nitrone Ylides and Electron-deficient Alkenes. J. Org. Chem. 2014, 79, 2189-2202.
  • Majer, R.; Konechnaya, O.; Delso, I.; Tejero, T.; Attanasi, O. A.; Santeusanio, S.; Merino, P., Highly Diastereoselective 1,3-Dipolar Cycloadditions of Chiral Non-Racemic Nitrones to 1,2-Diaza-1,3-dienes: An Experimental and Computational Investigation. Org. Biomol. Chem. 2014, 12, 8888-8901.
  • Nguyen, D. H.; Greger, I.; Perez-Torrente, J. J.; Jiménez, M. V.; Modrego, F. J.; Lahoz, F. J.; Oro, L. A. Organometallics 2013, 32, 6903–6917. ONO Dianionic Pincer-Type Ligand Precursors for the Synthesis of σ,π-Cyclooctenyl Iridium(III) Complexes: Formation Mechanism and Coordination Chemistry DOI:10.1021/om400767d
  • Jiménez, M. V.; Bartolomé, M. I.; Perez-Torrente, J. J.; Gómez, D.; Modrego, F. J.; Oro, L. A. ChemCatChem 2013, 5, 263–276. Mechanistic Studies on the Catalytic Oxidative Amination of Alkenes by Rhodium(I) Complexes with Hemilabile Phosphines DOI:10.1002/cctc.201200510
  • Baya, M.; Belío, U.; Martín, A. Synthesis, Characterization, And Computational Study of Complexes Containing Pt···H Hydrogen Bonding Interactions Inorg. Chem. 2014, 53, 189-200.
  • García-Monforte, M. A.; Baya, M.; Betoré, M. P.; Martín, A.; Menjón, B. Mononuclear anionic AO2X3 compounds with non-VSEPR structure Dalton Trans. 2014, 43, 7615-7621.
  • Sabater, S.; Baya, M.; Mata, J. A. Highly Active Cp*Ir Catalyst at Low Temperatures Bearing an N-Heterocyclic Carbene Ligand and a Chelated Primary Benzylamine in Transfer Hydrogenation Organometallics 2014, 33, 6830-6839.

Key Projects 2014

The Figure shows both ELF and NCI analyses of the cycloaddition reaction between a nitrone ylide and methyl acrylate.

Theoretical study of chemical and enzymatic reactions

Led by Pedro Merino (UNIZAR). Investigations on several reaction mechanism regarding organic reactions including nucleophilic additions, cycloadditions and rearrangements were carried out. Particular attention was focused on the mechanism of enzymatic reactions, e.g. transglycosylation reactions and protein-glycosylation reactions and small systems including organocatalytic reactions resembling enzymatic processes. Enzymes that can transfer single or multiple activated carbohydrate units to a range of substrates are involved in important biological processes and therefore are potential pharmaceutical targets. Transglycosylases are crucial membrane-bound enzymes for the remodelling of bacterial and fungal cell wall, which is an essential structure in scaffolding the cytoplasmatic membrane and maintaining structural integrity of those microorganisms. Glycosyltransferases (GTs) are involved in the biosynthesis of poly- and oligosaccharides, as well as glycoconjugates. In particular, protein glycosylation is the most abundant post-translational modification in nature. GTs use activated sugar donors to drive the reaction in the direction of glycosidic bond synthesis. The study in detail of the model reactions is crucial for understanding the mechanism of action of the enzymes and it can serve as the basis for the design of specific therapeutic agents acting as inhibitors and/or modulators of the target proteins.

Detailed long-term weather predictions for the construction of a Typical Meteorological Year for Spain

The figure shows the average wind speed at 80 meters in Spain (calculated with a spatial resolution of 2.5 km and a time resolution of 1 h.)

Led by Norberto Fueyo Díaz (UNIZAR). The project involves performing highly detailed Numerical Weather Predictions (NWP) simulations for Spain for the construction of a high-resolution Typical Meteorological Year, TMY. The overarching aim is the re-evaluation of the potential and cost of renewable energies in Spain, using the calculated TMY. It is part of the wider project ENE2011-27264: Rigorous quantification of energy scenarios for Spain, funded by the Spanish Ministry for Science and Innovation for the development of a rigourous energy model for Spainto explore the implications of several energy scenarios in the time horizons of 2020, 2030 and 2050. The proposed model combines a detailed evaluation of the potential and cost of renewable energies (obtained through the use of high resolution geographical and climate data) with an economic model of the Spanish energy system.

The computational resources of BIFI have been used to obtain the TMY employing the WRF software (Weather Research and Forecasting Model). We calculated:

Meteorological data for 15 years in Spain, with a spatial resolution of 10 km and a time resolution of 1 h.

Meteorological data for 10 years in Spain, with a spatial resolution of 5 km and a time resolution of 1 h.

Meteorological data for 7 years in Spain, with a spatial resolution of 2.5 km and a time resolution of 1 h.

We observed an improvement in the quality of the simulated wind data compared to measurements as the spatial resolution increased. Eventually, we elaborated a TMY of Spain with a spatial resolution of 2.5 km and a time resolution of 1 h. This TMY will be available free in the web page of the Fluid Numerical Group (gfn.unizar.es) of the University of Zaragoza. The availability of these data can help develop research activities by other groups. A paper on the intermittency of wind generation in Spain is foreseen to be published in forthcoming months as a direct result of the application of the data from the calculated TMY.

Modellization of Chemical Processes of Theoretical and Practical Importance

Molecular Orbitals describing the pi-bonding of the molybdenyl unit in complex [MoO2(C6F5)3]

Led by Miguel Baya García (ISQCH). Our scientific interests are centred in the study of chemical reactions involving organometallics. These include processes of theoretical interest and of practical applicability. During the course of our investigations modelling of these reactions by means of DFT calculations is crucial in order to gain insight onto the chemical processes. For example, we described and characterized hydrogen-bonding interactions in platinum (II) square-planar systems. The referred interactions were observed both in the solid state and in the solution. We also prepared and studied a rare mononuclear molybdenum (IV) dioxo complex, which shows an unusual structure that can be described as an edge-capped tetrahedron. Furthermore we designed novel Iridium (III) catalysts active in transfer hydrogenation reactions, which showed to induce moderate enantiomeric excesses in the reduction of prochiral ketones. DFT studies support a mechanism through a hydrogen-bonded organized transition state which has no precedent in the scientific literature.

Computational Modelling of Homogeneous Catalytic Reactions

Led by Francisco Javier Modrego Pérez (ISQCH). The project was developed along the research line "Catalysis and catalytic processes" within the ISQCH. The computational chemistry methodology allowed for a detailed analysis of the reaction mechanisms and the homogeneous catalysis processes as a whole, obtaining results which are not amenable to experimental studies alone. The use of the supercomputing facilities at CAESARAGUSTA enabled us to use realistic models of the molecules and processes avoiding simplifications which are not always advisable. Several papers were published. One of them reports the necessity of explicit inclusion of solvent in an, apparently simple, process of oxidative addition of a carboxilate group to an iridium centre. The proton transfer to the metal atom in the complex is mediated by a methanol molecule while the direct oxidative is not possible. Also a mechanistic analysis of the catalytic oxidative amination of alkenes by rhodium(I) complexes with hemilabile phosphine ligands were carried out buy extensive computational studies. In these processes the N-H group is activated by the metal and transfers a proton to an olefin directly, avoiding the more energetically costly oxidative addition of the N-H bond to the metal. These computational studies complement the experimental results in a synergistic way in order to get a deeper understanding of the catalytic processes.

First-principles calculations of the spin coupling between lanthanide adatoms and iron islands

Experimental average spin polarized conductance for Tm/Fe-ML/ (110)W, with the tip between 2.5 Å - 3.0 Å over the sample.

Led by Cesar de la Fuente. By using non-collinear spin polarized (SP) DFT-based first-principles calculations, we performed a study of the electronic properties of Tm and Lu adatoms over an Fe monolayer (ML) on (110) W. The LSDA+U is introduced for including the corresponding corrections when GGA fails, by using U = 0.8 eV for the Fe d-states and U = 5.0 eV for the adatoms f-states. The spin-orbit coupling was also included to analyse the dependence of Khon-Sham ground state energy on the direction of the magnetic moments. After a 3D structural optimization, the equilibrium position found for the adatoms is the hollow site at Fe pseudomorphic monolayer, which only gets a small structural in-plane relaxation for those Fe atoms close to the Rare Earth adatom. The spacing between Fe and W layers is very close to the reference system, Fe (ML)/(110)W. The 4f magnetic moment of Tm adatom is almost fully aligned along [1-10], the easy axis direction of Fe monolayer. It is tilted about 10 degrees out to (110) plane and towards [110] direction. The electronic structure of Tm adatom, is Tm3+, but the total angular momentum and spin are reduced by almost a 50% with respect to Tm in bulk. The Campbell mechanism proposed for Rare Earth-Transition Metal intermetallics, consisting in the antiferromagnetic coupling between the 5d Rare Earth spins and the 3d Fe spins, is found to hold in our system, at the single atom limit. The conductance at different bias is calculated (see Figure), too; the analysis of d-PDOS indicates that the major contribution is coming from dxz+dyz -states. The agreement with the spin-polarized scanning tunneling microscopy (SP-STM) experimental results is fine, showing important contribution at positive bias that well accounted when the SP-STM tip is simulated at approximately 3.0 Å over the adatom. All first principle calculations were done at the cluster “Memento” of Zaragoza’s University.

Structure and magnetism of Tm atoms and monolayers on W(110)

Led by Cesar de la Fuente. We investigated the growth and magnetic properties of Tm atoms and monolayers deposited on a W(110) surface using scanning tunnelling microscopy and x-ray magnetic circular and linear dichroism. The equilibrium structure of Tm monolayer films is found and calculated by first principle calculations. It is strongly distorted hexagonal lattice with a Moiré pattern due to the overlap with the rectangular W(110) substrate. Monolayer as well as isolated Tm adatoms on W present a trivalent ground-state electronic configuration, contrary to divalent gas phase Tm and weakly coordinated atoms in quench-condensed Tm films. Ligand field multiplet simulations of the x-ray absorption spectra further show that Tm has a |J = 6,Jz = ±5> electronic ground state separated by a few meV from the next lowest substates |J = 6,Jz = ±4> and |J = 6,Jz = ±6>. Accordingly, both the Tm atoms and monolayer films exhibit large spin and orbital moments with out-of-plane uniaxial magnetic anisotropy. X-ray magnetic dichroism measurements as a function of temperature show that the Tm monolayers develop antiferromagnetic correlations at about 50 K. The triangular structure of the Tm lattice suggests the presence of significant magnetic frustration in this system, which may lead to either a non-collinear staggered spin structure or intrinsic disorder. All first principle calculations were done at the cluster “Memento” of Zaragoza’s University.

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