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The objective of this project's study is description of turbulent flow characteristics over realistic complex terrain by means of high resolution numerical simulation. It is a logical continuation of the study done during the previous HPC-Europa visit. During this visit besides Bolund, a hill in Denmark, the subject of a recent full-scale measurement campaign, we did simulations of flow over a matrix of cubic obstacles representing urban environment. It was a subject of water tunnel experiment done by Coanda R&D Corp. who provided detailed measurement data for model validation. The flow in both cases has been computed using structured finite-volume Navier-Stokes code. Turbulence was accounted using Reynolds averaged Navier-Stokes (RANS) models, as well as with hybrid T-RANS/LES models (Transient RANS/Large Eddy Simulation). The applications of results of flow over realistic complex topogaphy are pertinent to energy production (siting of wind farms, prediction of wind loads on stuctures etc). Urban flow studies are related to prediction of pollutant dispersion.
For the case of complex realistic hill, the effects of non-smoothness of topography and the way it is affecting the air flow is studied. In the case of complex non-smooth terrain the effect of stagnation points is taken into account trough realizability constraints on turbulence production, i.e. using Durbin time scale limiters. These limit the excessive production of turbulence kinetic energy in the stagnation regions, present in many turbulence models. This approach relies on the use of high resolution numerical meshes, capable of capturing steep slopes in topography. Bolund hill, otherwise low and smooth in the back side preventing forming of separation region has almost vertical upstream escarpment forming stagnation region. Simulations gave deep insights how incorporating different effects of turbulence physics helps in prediction of turbulent environmental flows of practical interest.Dispersion by turbulent environmental flow over urban environment represented by a group of cubic obstacles was studied next. Long term statistics was colected from a number of continued simulations until reaching the convergence of statistics of monitored values. These were turbulence characteristics like turbulence kinetic energy and concentration of passive scalar at several monitoring locations. These simulations gave better matching than other similar simulations present in the literature.
Formation of various surface (H)COx type species on cerium dioxide was clearly established in the last decades of the 20th century mainly by infrared spectroscopy (IR) and different oxidation states of carbon in these species was confirmed by electronic core level spectroscopy. Due to the importance of those species in various catalytic applications of ceria, they have been extensively studied since then. The assignment of the observed IR bands to certain type of surface species is based on comparison with the spectra of related molecules or materials, on the symmetry of the vibrations, and on the general observations about the relative positions of the IR bands of carbonates. The goal of the present work is to assign properly the vibrational modes to each type of surface species using state-of-the-art computational modeling. Our calculations contribute in clarifying the structures of the surface species by modeling of different type of oxocarbonates presumed on the base of the observed experimental frequencies: carbonates CO32-, formates HCO2-, and hydrogen carbonates CO2(OH)-, bound in various coordination modes to the surface.
The proposed re-assignment of the vibrational frequencies allows correct determination of the surface species using IR or other vibrational spectroscopies, which is of crucial importance for the meaningful analysis of the reactivity of these species on ceria surface and the clarification of the mechanisms of the various surface processes. The results are expected to have large impact on the research activities/area, having in mind the growing interest on various oxocarbonate species on ceria and their reactivity. If such definite assignment could be done solely with the available experimental methods, this would be already accomplished having in mind the extraordinary scientific, technological and industrial interest in this field. Similar approach for clarification of the structure of surface carbonates using computational modeling was applied for other metal oxide surfaces as MgO, CaO, RuO2, etc.
Measured vibrational frequencies and their assignment to various surface species from minor part of the published papers with such results are summarized below:
- two bands at ca. 2950 and 2850 cm-1, consensually assigned to the valence C-H mode of the formates;
- weak bands at ca. 1730 cm-1, which together with the bands at ca. 1135 (and in some papers also with bands at ca. 1395 and ca. 1220 cm-1) are assigned to “bridged” carbonates;
- two bands at 1590-1599 and ca. 1612 cm-1 assigned to hydrogen carbonates together with bands at 3617, 1390-1413, 1025-1045 and ca. 830 cm-1;
- strong bands ca. 1580 cm-1, which is considered to have two components: due to formates (together with the bands at ca. 1370 and/or ca. 1320 cm-1, and in some cases with a band at 790 or 771 cm-1) and due to “bidentate” carbonates (together with the bands at ca. 1290, 1020, and 856 cm-1);
- bands in the region 1460-1510, which together with the bands at ca. 1350, 1060, and 856 cm-1 are assigned by different groups to “monodentate”, “polydentate” or polymeric carbonate, or together with a band at 1310-1316 cm-1, to carboxylate species coordinated via the carbon atom to cerium ion from the surface.
- Three groups of carbonite (CO22-) species are also suggested: at 1465 cm-1; at 1317 and 1150 cm-1; and at 1266, 1071 and 773 cm-1.
In order to check these assignments we modeled all types of suggested species and check their different location and orientation with respect to the ceria nanoparticle. As a model of support we used ceria nanoparticle with composition Ce21O42, which is one of the smallest example with the crystallinity inherent to the fluorite structure of CeO2 as described earlier. On the surface of this nanoparticle, in addition to the oxygen centers coordinated to three cerium cations, we have two-coordinated oxygens at the edges.
In order to facilitate the description of the various optimized structures of the surface carbonates and the discussion of the results we introduce a more general notation, which shows to how many cerium ions each of the three carbonate oxygen atoms is bound: lmn, where l,m,n = 0 – 3. The integer, showing the oxygen atom of the carbonate with highest coordination (typically originating from the ceria surface) is written in the middle. The formation of bidentate moieties to one cerium ion from the surface is denoted by a point between the corresponding carbonate oxygen atoms, e.g. 1.3.1 or 1.30.
One the base of the calculated vibrational frequencies we may suggest the following assignment of the experimentally observed infrared frequencies of different oxocarbonate species on ceria (see Fig. 2):
- 3610 – 3700, 1630 – 1590, 1408 – 1330, 1190 – 1170, 1020 – 1000, and 790 – 770 cm-1 to hydrogen carbonates;
- 2950 – 2850, 1570 – 1530, 1360 – 1340, 1340 – 1290, 1020 – 1000, and 750 – 700 cm-1 to formates;
- 1850 – 1830, 1160 – 1120, and 740 cm-1 to terminal carbonate moiety of polycarbonates and the band at 1370 – 1330 cm-1 to C-O-C bridge of the polycarbonates;
- 1740 – 1730, 1200 – 1130, 870 – 810, and 780 – 770 cm-1 to carbonates bound by two oxygen centers to ceria (types 1.30, 1.20);
- 1590 – 1490, 1297 – 1227, 1000 – 930, and 820 – 790 cm-1, to carbonates bound by three oxygen centers to ceria (types 1.3.1, 1.21, 1.2.1).
Due to the limited accuracy of the calculations, some of these regions may be shifted in the actual experimental spectra by at most 2%. Since monodentate carbonate, carboxylate or carbonite species were found unstable on ceria surface, they are unlikely to be formed and identified experimentally. According to the computational results discussed above, the bands in different regions of the IR spectra assigned earlier to some of these species actually corresponds to some of the stable species on ceria surface – carbonates, hydrogen carbonates, or formates.
For each type of modeled stable species we can suggest specific characteristic frequencies, which are not part of the spectra of the competitive species, bands at 2950 – 2850 cm-1 for formates, 1300 – 1200 and 1000 – 930 cm-1 for carbonates bound by three oxygens, 1740 – 1700 cm-1 for carbonates bound by two oxygens, about 3700 and 1630 – 1600 cm-1 for hydrogen carbonates, and 1850 – 1830 cm-1 for terminal carbonate moiety of polycarbonates.
The calculations are performed with periodic plane-wave DFT method with PW91 exchange-correlation functional as implemented in VASP program. The kinetic energy cut-off was selected at 415 eV and a cube with dimensions of 2.00 nm each side was selected as the unit cell for the calculations. This size provides ca. 1.00 nm distance between nanoparticles in two neighboring unit cells. Due to the internal deficiency of pure DFT functionals to describe localized electrons, we applied the DFT+U approach in order to provide proper localization of the extra electron on the individual Ce(III) cations.
The investigation is supported by HPC-Europa2 program at Barcelona Supercomputer Center.
In the past decade an increased interest has been exhibited in spatiotemporal epidemic spread from the scope of stochastic approaches. To this end, the most commonly employed algorithms are variations of the Monte Carlo (MC) random sampling method. For systems out-of-equilibrium in particular, the Kinetic MC (KMC) algorithm gives a much more accurate picture than the traditional MC one.
In our case, we shall study a Susceptible-Infected-Recovered-Susceptible (SIRS) kinetic transitional model using traditional MC algorithms as well as the KMC variation. The kinetic scheme is as follows:
S+I-->I+I through a transitional rate k1 (we assume that an I site is in the first neighbour proximity of an Site)
I-->R through a transitional rate k2
R-->S through a transitional rate k3
We shall assume both parallel (traditional MC code) and sequential updates (KMC code) of the system for each MC step. In addition, we include mobility dynamics (diffusion) for each site of the distributed population.
A serial code has been developed with sequential updating of the system on a 1D chain and 2D square lattice (grid), much in the fashion of the respective Ising models.
With the expertise of our host in Florence (Politi-Torcini), our collaborators from the physics department in Bologna (Turchetti et al.) and the HPC group of CINECA we aim to optimise the existing serial code for the KMC case and to develop a highly efficient one for an implementation with parallel updating of the system (traditional MC sampling method).
Finally, a crucial goal will be to speed up our large scale runs of the KMC case via parallelisation of the code for both cases of the system update. Currently, a single (serial) run on a square grid of 103x103 lattice points (individuals) and for 100 MC steps exceeds 23 hours, a score which we expect to reduce vastly with the use of the CINECA resources. The final results should be temporal evolutions of the different species of the system for different realisations (parameter values).
To begin with, the collaboration with our host and department of physics in Bologna was successful in the development of the serial code for the case of the parallel update of the system, and therefore a comparison with the respective sequential update case was realised. As suspected, the two methods led to different results (specifically different steady states for the same parameter values), but surprisingly the sequential update case reached a noisy steady state instead of a constantly evolving (at least oscillatory if not chaotic) as was expected. This is something to be further investigated in future work. For debugging purposes, the gdb package was employed from the GNU suite of the PLX cluster in CINECA.
Furthermore, extensive discussions and prospects on statistical data analysis as well as theoretical derivations from these results were exchanged with our host in Florence and our collaborators at the department of physics in Bologna which will certainly be studied in work to follow.
As far as parallelisation is concerned, a lengthy search in the literature and discussions with Andrew Emerson of the HPC group of CINECA took place in order to decide which would be the best implementation of parallelisation on the SIRS simulations under study. The conclusion was that a modified Game of Life (Conway 1970) code would be the best for the SIRS simulations, both for the sequential and parallel updating of the system. A lot of time has been spent on debugging and profiling (for scalability) the code using the DDT debugging package and the gprof profiler available from the PLX cluster in CINECA.
Due to no prior experience in parallel programming at the beginning of the visit in CINECA and due to extensive search and theoretical work before venturing into the parallel implementation, the codes are in a final form but in the process of debugging and trial runs. Within the end of the following month we expect to have a working code scaled to finalise within the span of an hour, thus fulfilling our initial expectations. This short term work shall continue via remote access of the PLX cluster of CINECA from our home institute in Athens.