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Use this search facility to find out more about the profile of our HPC-Europa2 visitors, the type of work they have been doing, and their project achievements.
The importance of the spin state of iron on the behaviour of a class of α-diimine iron catalysts  was to be studied computationally. The main method of research was the application of quantum chemical density functional theory (DFT) on this class of compounds.
Traditional DFT methods, which are available in standard program packages, suffer from three short-comings that are especially troublesome when considering metal complexes in different spin states, their reactions, and interaction with the environment:
The host group has recently developed a DFT method which addresses all of the above problematic cases. The Swart-Solà-Bickelhaupt (SSB-D) functional is very new , but has already shown great potential for tackling the problems at hand. Thus, by visiting the host group, the objective was to provide the applicant with first-hand introduction to the details of method and its applicability, by studying a relevant and much discussed real-world catalytic process.
Further, as the computations involved are very demanding, access to the computer facilities at the Barcelona Supercomputing Centre was critical for carrying out the proposed study.
 L.E.N. Allan, M.P. Shaver, A.J.P. White, V.C. Gibson, "Correlation of Metal Spin-State in α-diimine Iron Catalysts with Polymerization Mechanism", Inorg. Chem. 46 (2007) 8963–8970.
 M. Swart, M. Solà, F.M. Bickelhaupt, “A new all-round density functional based on spin states and SN2 barriers”, J. Chem. Phys. 131 (2009) 094103.
The two distinct reaction pathways discussed in reference , the catalytic chain transfer (CCT) mechanism, which was proposed to take place via intermediate-spin state complexes, and the atom transfer radical polymerization (ATRP), proposed to be favoured when the metal complex is in a high-spin state, were studied. To be able to confidently assess the results, four different complexes were studied, two that have been shown to follow the CCT pathway, and two that follow the ATRP pathway.
The computational results strongly suggest that all of the parent complexes have a high-spin ground state, in contrast to the suggestions in the literature. However, the CCT mechanism does follow an intermediate-spin transitional complex pathway. The hypothetical high-spin intermediate, which is not seen experimentally but can of course be studied theoretically, is much higher in energy, that is, unstable, compared to the intermediate-spin complex.
On the other hand, the study could not directly distinguish between the high- and intermediate-spin transitional complexes of the ATRP pathway, which are energetically quite close. Further study of this pathway is necessary to elucidate and fully explain the differences between the two catalytic routes. Discussions lead to several hypotheses about the origin of the effect, all of which will be explored in the near future.
In addition to the progress for the specific case-study discussed above, the other major achievement of the visit was the establishment of a new and exciting collaboration between host and guest. Technical issues with the newly developed method were also identified and remedied. The good performance of the SSB-D functional  was further established. This indirectly also led to a new collaboration partnership with Prof. G. Gutsev (Florida, USA) and a side project on the spin states of small pure-iron clusters.
The plasma state —ionised gas— is ubiquitous in the Universe. In particular the ionosphere is the plasma embedded in the high altitude atmosphere of a planet. Ionospheres (and magnetospheres) play a key role in mediating the interaction between space and planetary environments through complex dynamic processes that involve interactions between electromagnetic waves and charged particles.One way to investigate the physics of such plasma is computer modelling simulation, where PDE’s of different approximations, full kinetic to fluid descriptions are solved numerically. Alternatively Lagrangian particle methods aim at time-integrating the dynamics of ‘macro-particles’. One particle method widely used in plasma simulation is the Particle-In-Cell (PIC) method.PicSim is a collection of 2D and 3D parallel plasma PIC C++ codes where the internal electrostatic field is updated on a fixed Eulerian mesh, and external uniform electromagnetic, electric and gravitation fields can be enabled. PicSim has been used for various studies of plasma complex dynamic processes involving wave-particle interactions and resulted in over nine publications.Nevertheless the PicSim code suite has never been through a `rigorous review' and examination by experts in high performance computing. The main objective of this project is to port PicSim onto the CINECA high performance computing facility, in order to make profiling, looking for improved efficiency (optimisation) and finally to benchmark and measure the parallel scalability of the code. This process should lead to a better life cycle and science return of the code and foster stronger collaboration between UCL and CINECA.
I was given a thorough introduction to the IBM SP6 system at CINECA. The first step was to compile both sequential and parallel versions of PicSim without optimisation and test the validity of the results.I was also given an introduction on how to make a parallelism profiling with Scalasca to allow identification of potential performance bottlenecks —in particular those concerning communication and synchronisation— and offers guidance in exploring their causes.We profiled both non-optimised and optimised versions of PicSim and identified the two most time consuming parts of the code (63% of the computing time used to interpolate the electric field from the grid to particle positions and then move particles, while 31% is used to compute the source).We spotted a minor imbalance in the tested configuration (that can eventually become more important in different configuration) and decided to modify the code to reduce the imbalance and prepare the code for further parallelisation of some components in the future.We performed a series of benchmarks for different problem size and a wide range of number of CPUs on the SP6 system as we originally planned. But we ended up having time to also benchmark PicSim on the PLX systems also available. The results of our benchmarks have been analysed and successfully fitted to theoretical speed-up law. Results are very encouraging and show linear speedup to several thousands of CPUs.Thanks to a fruitful collaboration and visits at CINECA, PicSim has been benchmarked for parallelism for the first time.
The main objectives from this study are :
The properties of interest are :
Thermodynamic and structural properties. Investigating these properties we may gain insight for the interactions at microscopic level and how the ions interact each other. Using these properties, we may obtain information on the efficiency of the available interaction potential models in description of these systems.
Single particle dynamic properties. These include velocity power spectra, diffusion coefficients and molecular reorientational correlation times. These properties will be investigated mainly using the appropriate single particle time correlation functions.
Collective dynamic properties. These include dielectric relaxation, conductivity, viscosity, etc. and they will be investigated using the appropriate collective time correlation functions.
Dependence of all these properties on the size and complexity of cations and anions.
Similar properties for solutions of ionic liquids as well as additional properties resulting from the two component systems.
Molecular Dynamics simulations of 1-alkyl-3-methyl imidazolium based ionic liquids were performed using existing in the literature forcefields. It was found that the existing forcefields are not accurate enough in the prediction of some basic properties of these liquids like density or self diffusion coefficient. Forcefield development found to be necessary to obtain a forcefield that, at least, is accurate in the prediction of these basic – simple properties. At the same time, a number of publications noting this problem of the existing forcefields appeared in the literature as well as few attempts to propose a forcefield. Most of these proposed forcefields were focused in the improvement of localized partial charges of ions, using van der Waals parameters from existing forcefields like AMBER/OPLS. In one publication, the enhancement of the van der Waals parameters only of few atoms was attempted, using the charges from literature. Additional publications using ab-initio molecular dynamics using small number of molecules pointed out the problem of the existing classical forcefields in the prediction of ionic liquids properties. Several levels of forcefield enhancement were attempted in the framework of this project. First, a massive optimization of all the atomic van der Waals parameters using the existing in the literature charges and bonded interactions was attempted. Next, using quantum mechanics calculations, the isolated ions geometry was optimized. Using this optimized geometry the partial atomic charges were fitted to reproduce the quantum mechanical potential energy surface. A massive optimization of all the atomic van der Waals parameters applied again using the partial charges obtained from the quantum mechanics calculations. Both resulting forcefields were verified for their ability to predict few basic properties of the systems. It was found that these forcefields perform much better in the prediction of the temperature/pressure dependence of the density. These new forcefields were used in the long time molecular dynamics simulation of the systems under investigation. From these runs, a number of trajectories was produced for each system at selected thermodynamic states were experimental data are available in the literature, that will be used for the calculation of thermodynamic, structural, single and collective dynamic properties of the systems. These properties will be compared with existing in the literature experimental results. Some of these properties are already calculated on Marenostrum, other properties will be calculated off site using the trajectories obtained using the BSC hardware.
Few molecular dynamics codes were examined for their parallel efficiency and speed on HPC hardware. It was found, as it was expected, that gromacs 4.0.4 is the faster for this type of systems on HPC hardware. Parallel scaling found to be linear up to 28 processors for the systems under investigation.