Performance evaluation of a parallel algorithm for simultaneous untangling and smoothing of tetrahedral meshes

[EN]A new parallel algorithm for simultaneous untangling and smoothing of tetrahedral meshes is proposed in this paper. We provide a detailed analysis of its performance on shared-memory many-core computer architectures. This performance analysis includes the evaluation of execution time, parallel scalability, load balancing, and parallelism bottlenecks. Additionally, we compare the impact of three previously published graph coloring procedures on the performance of our parallel algorithm. We use six benchmark meshes with a wide range of sizes. Using these experimental data sets, we describe the behavior of the parallel algorithm for different data sizes. We demonstrate that this algorithm is highly scalable when it runs on two different high-performance many-core computers with up to 128 processors...

T-spline parameterization of 2D geometries based on the meccano method with a new T-mesh optimization algorithm

[EN]We present a new method, based on the idea of the meccano method and a novel T-mesh optimization procedure, to construct a T-spline parameterization of 2D geometries for the application of isogeometric analysis. The proposed method only demands a boundary representation of the geometry as input data. The algorithm obtains, as a result, high quality parametric transformation between 2D objects and the parametric domain, the unit square. First, we define a parametric mapping between the input boundary of the object and the boundary of the parametric domain. Then, we build a T-mesh adapted to the geometric singularities of the domain in order to preserve the features of the object boundary with a desired tolerance…

A multilevel converter structure for grid-connected PV plants

A new conversion structure for three-phase grid-connected photovoltaic (PV) generation plants is presented and discussed in this Thesis. The conversion scheme is based on two insulated PV arrays, each one feeding the dc bus of a standard 2-level three-phase voltage source inverter (VSI). Inverters are connected to the grid by a traditional three-phase transformer having open-end windings at inverters side and either star or delta connection at the grid side. The resulting conversion structure is able to perform as a multilevel VSI, equivalent to a 3-level inverter, doubling the power capability of a single VSI with given voltage and current ratings. Different modulation schemes able to generate proper multilevel voltage waveforms have been discussed and compared. They include known algorithms, some their developments, and new original approaches. The goal was to share the grid power with a given ratio between the two VSI within each cycle period of the PWM, being the PWM pattern suitable for the implementation in industrial DSPs. It has been shown that an extension of the modulation methods for standard two-level inverter can provide a elegant solution for dual two-level inverter. An original control method has been introduced to regulate the dc-link voltages of each VSI, according to the voltage reference given by a single MPPT controller. A particular MPPT algorithm has been successfully tested, based on the comparison of the operating points of the two PV arrays. The small deliberately introduced difference between two operating dc voltages leads towards the MPP in a fast and accurate manner. Either simulation or experimental tests, or even both, always accompanied theoretical developments. For the simulation, the Simulink tool of Matlab has been adopted, whereas the experiments have been carried out by a full-scale low-voltage prototype of the whole PV generation system. All the research work was done at the Lab of the Department of Electrical Engineering, University of Bologna.

Preliminary studies for the establishment of a tsunami early detection algorithm to be used in the frame of a Tsunami Warning System

This thesis presents and discusses TEDA, an algorithm for the automatic detection in real-time of tsunamis and large amplitude waves on sea level records. TEDA has been developed in the frame of the Tsunami Research Team of the University of Bologna for coastal tide gauges and it has been calibrated and tested for the tide gauge station of Adak Island, in Alaska. A preliminary study to apply TEDA to offshore buoys in the Pacific Ocean is also presented.

Novel simulation methods for Coulomb and hydrodynamic interactions

This thesis presents new methods to simulate systems with hydrodynamic and electrostatic interactions. Part 1 is devoted to computer simulations of Brownian particles with hydrodynamic interactions. The main influence of the solvent on the dynamics of Brownian particles is that it mediates hydrodynamic interactions. In the method, this is simulated by numerical solution of the Navier--Stokes equation on a lattice. To this end, the Lattice--Boltzmann method is used, namely its D3Q19 version. This model is capable to simulate compressible flow. It gives us the advantage to treat dense systems, in particular away from thermal equilibrium. The Lattice--Boltzmann equation is coupled to the particles via a friction force. In addition to this force, acting on {it point} particles, we construct another coupling force, which comes from the pressure tensor. The coupling is purely local, i.~e. the algorithm scales linearly with the total number of particles. In order to be able to map the physical properties of the Lattice--Boltzmann fluid onto a Molecular Dynamics (MD) fluid, the case of an almost incompressible flow is considered. The Fluctuation--Dissipation theorem for the hybrid coupling is analyzed, and a geometric interpretation of the friction coefficient in terms of a Stokes radius is given. Part 2 is devoted to the simulation of charged particles. We present a novel method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. This algorithm scales linearly, too. We focus on the Molecular Dynamics version of the method and show that it is intimately related to the Car--Parrinello approach, while being equivalent to solving Maxwell's equations with freely adjustable speed of light. The Lagrangian formulation of the coupled particles--fields system is derived. The quasi--Hamiltonian dynamics of the system is studied in great detail. For implementation on the computer, the equations of motion are discretized with respect to both space and time. The discretization of the electromagnetic fields on a lattice, as well as the interpolation of the particle charges on the lattice is given. The algorithm is as local as possible: Only nearest neighbors sites of the lattice are interacting with a charged particle. Unphysical self--energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green's function. The method allows easy parallelization using standard domain decomposition. Some benchmarking results of the algorithm are presented and discussed.

Detecting interfaces in a parabolic-elliptic problem from surface measurements

Assuming that the heat capacity of a body is negligible outside certain inclusions the heat equation degenerates to a parabolic-elliptic interface problem. In this work we aim to detect these interfaces from thermal measurements on the surface of the body. We deduce an equivalent variational formulation for the parabolic-elliptic problem and give a new proof of the unique solvability based on Lions’s projection lemma. For the case that the heat conductivity is higher inside the inclusions, we develop an adaptation of the factorization method to this time-dependent problem. In particular this shows that the locations of the interfaces are uniquely determined by boundary measurements. The method also yields to a numerical algorithm to recover the inclusions and thus the interfaces. We demonstrate how measurement data can be simulated numerically by a coupling of a finite element method with a boundary element method, and finally we present some numerical results for the inverse problem.

A parallel community detection algorithm

Complex networks analysis is a very popular topic in computer science. Unfortunately this networks, extracted from different contexts, are usually very large and the analysis may be very complicated: computation of metrics on these structures could be very complex. Among all metrics we analyse the extraction of subnetworks called communities: they are groups of nodes that probably play the same role within the whole structure. Communities extraction is an interesting operation in many different fields (biology, economics,...). In this work we present a parallel community detection algorithm that can operate on networks with huge number of nodes and edges. After an introduction to graph theory and high performance computing, we will explain our design strategies and our implementation. Then, we will show some performance evaluation made on a distributed memory architectures i.e. the supercomputer IBM-BlueGene/Q "Fermi" at the CINECA supercomputing center, Italy, and we will comment our results.

Coordination and Control of Autonomous Mobile Robots Swarms by using Particle Swarm Optimization Algorithm and Consensus Theory

This thesis presents some different techniques designed to drive a swarm of robots in an a-priori unknown environment in order to move the group from a starting area to a final one avoiding obstacles. The presented techniques are based on two different theories used alone or in combination: Swarm Intelligence (SI) and Graph Theory. Both theories are based on the study of interactions between different entities (also called agents or units) in Multi- Agent Systems (MAS). The first one belongs to the Artificial Intelligence context and the second one to the Distributed Systems context. These theories, each one from its own point of view, exploit the emergent behaviour that comes from the interactive work of the entities, in order to achieve a common goal. The features of flexibility and adaptability of the swarm have been exploited with the aim to overcome and to minimize difficulties and problems that can affect one or more units of the group, having minimal impact to the whole group and to the common main target. Another aim of this work is to show the importance of the information shared between the units of the group, such as the communication topology, because it helps to maintain the environmental information, detected by each single agent, updated among the swarm. Swarm Intelligence has been applied to the presented technique, through the Particle Swarm Optimization algorithm (PSO), taking advantage of its features as a navigation system. The Graph Theory has been applied by exploiting Consensus and the application of the agreement protocol with the aim to maintain the units in a desired and controlled formation. This approach has been followed in order to conserve the power of PSO and to control part of its random behaviour with a distributed control algorithm like Consensus.

Non-Linear Analysis and Design of Synchronous Bearingless Multiphase Permanent Magnet Machines and Drives

A two-dimensional model to analyze the distribution of magnetic fields in the airgap of a PM electrical machines is studied. A numerical algorithm for non-linear magnetic analysis of multiphase surface-mounted PM machines with semi-closed slots is developed, based on the equivalent magnetic circuit method. By using a modular structure geometry, whose the basic element can be duplicated, it allows to design whatever typology of windings distribution. In comparison to a FEA, permits a reduction in computing time and to directly changing the values of the parameters in a user interface, without re-designing the model. Output torque and radial forces acting on the moving part of the machine can be calculated. In addition, an analytical model for radial forces calculation in multiphase bearingless Surface-Mounted Permanent Magnet Synchronous Motors (SPMSM) is presented. It allows to predict amplitude and direction of the force, depending on the values of torque current, of levitation current and of rotor position. It is based on the space vectors method, letting the analysis of the machine also during transients. The calculations are conducted by developing the analytical functions in Fourier series, taking all the possible interactions between stator and rotor mmf harmonic components into account and allowing to analyze the effects of electrical and geometrical quantities of the machine, being parametrized. The model is implemented in the design of a control system for bearingless machines, as an accurate electromagnetic model integrated in a three-dimensional mechanical model, where one end of the motor shaft is constrained to simulate the presence of a mechanical bearing, while the other is free, only supported by the radial forces developed in the interactions between magnetic fields, to realize a bearingless system with three degrees of freedom. The complete model represents the design of the experimental system to be realized in the laboratory.

Parallelization of the algorithm WHAM with NVIDIA CUDA.

The aim of my thesis is to parallelize the Weighting Histogram Analysis Method (WHAM), which is a popular algorithm used to calculate the Free Energy of a molucular system in Molecular Dynamics simulations. WHAM works in post processing in cooperation with another algorithm called Umbrella Sampling. Umbrella Sampling has the purpose to add a biasing in the potential energy of the system in order to force the system to sample a specific region in the configurational space. Several N independent simulations are performed in order to sample all the region of interest. Subsequently, the WHAM algorithm is used to estimate the original system energy starting from the N atomic trajectories. The parallelization of WHAM has been performed through CUDA, a language that allows to work in GPUs of NVIDIA graphic cards, which have a parallel achitecture. The parallel implementation may sensibly speed up the WHAM execution compared to previous serial CPU imlementations. However, the WHAM CPU code presents some temporal criticalities to very high numbers of interactions. The algorithm has been written in C++ and executed in UNIX systems provided with NVIDIA graphic cards. The results were satisfying obtaining an increase of performances when the model was executed on graphics cards with compute capability greater. Nonetheless, the GPUs used to test the algorithm is quite old and not designated for scientific calculations. It is likely that a further performance increase will be obtained if the algorithm would be executed in clusters of GPU at high level of computational efficiency. The thesis is organized in the following way: I will first describe the mathematical formulation of Umbrella Sampling and WHAM algorithm with their apllications in the study of ionic channels and in Molecular Docking (Chapter 1); then, I will present the CUDA architectures used to implement the model (Chapter 2); and finally, the results obtained on model systems will be presented (Chapter 3).

A multi-objective genetic algorithm optimisation using variable speed pumps in water distribution systems

Due to its practical importance and inherent complexity, the optimisation of distribution networks for supplying drinking water has been the subject of extensive study for the past 30 years. The optimization is governed by sizing the pipes in the water distribution network (WDN) and / or optimises specific parts of the network such as pumps, tanks etc. or try to analyse and optimise the reliability of a WDN. In this thesis, the author has analysed two different WDNs (Anytown City and Cabrera city networks), trying to solve and optimise a multi-objective optimisation problem (MOOP). The main two objectives in both cases were the minimisation of Energy Cost (€) or Energy consumption (kWh), along with the total Number of pump switches (TNps) during a day. For this purpose, a decision support system generator for Multi-objective optimisation used. Its name is GANetXL and has been developed by the Center of Water System in the University of Exeter. GANetXL, works by calling the EPANET hydraulic solver, each time a hydraulic analysis has been fulfilled. The main algorithm used, was a second-generation algorithm for multi-objective optimisation called NSGA_II that gave us the Pareto fronts of each configuration. The first experiment that has been carried out was the network of Anytown city. It is a big network with a pump station of four fixed speed parallel pumps that are boosting the water dynamics. The main intervention was to change these pumps to new Variable speed driven pumps (VSDPs), by installing inverters capable to diverse their velocity during the day. Hence, it’s been achieved great Energy and cost savings along with minimisation in the number of pump switches. The results of the research are thoroughly illustrated in chapter 7, with comments and a variety of graphs and different configurations. The second experiment was about the network of Cabrera city. The smaller WDN had a unique FS pump in the system. The problem was the same as far as the optimisation process was concerned, thus, the minimisation of the energy consumption and in parallel the minimisation of TNps. The same optimisation tool has been used (GANetXL).The main scope was to carry out several and different experiments regarding a vast variety of configurations, using different pump (but this time keeping the FS mode), different tank levels, different pipe diameters and different emitters coefficient. All these different modes came up with a large number of results that were compared in the chapter 8. Concluding, it should be said that the optimisation of WDNs is a very interested field that has a vast space of options to deal with. This includes a large number of algorithms to choose from, different techniques and configurations to be made and different support system generators. The researcher has to be ready to “roam” between these choices, till a satisfactory result will convince him/her that has reached a good optimisation point.

An optical sensor for online hematocrit measurement: characterization and fitting algorithm development

Lo scopo del presente lavoro di tesi riguarda la caratterizzazione di un sensore ottico per la lettura di ematocrito e lo sviluppo dell’algoritmo di calibrazione del dispositivo. In altre parole, utilizzando dati ottenuti da una sessione di calibrazione opportunamente pianificata, l’algoritmo sviluppato ha lo scopo di restituire la curva di interpolazione dei dati che caratterizza il trasduttore. I passi principali del lavoro di tesi svolto sono sintetizzati nei punti seguenti: 1) Pianificazione della sessione di calibrazione necessaria per la raccolta dati e conseguente costruzione di un modello black box.  Output: dato proveniente dal sensore ottico (lettura espressa in mV)  Input: valore di ematocrito espresso in punti percentuali ( questa grandezza rappresenta il valore vero di volume ematico ed è stata ottenuta con un dispositivo di centrifugazione sanguigna) 2) Sviluppo dell’algoritmo L’algoritmo sviluppato e utilizzato offline ha lo scopo di restituire la curva di regressione dei dati. Macroscopicamente, il codice possiamo distinguerlo in due parti principali: 1- Acquisizione dei dati provenienti da sensore e stato di funzionamento della pompa bifasica 2- Normalizzazione dei dati ottenuti rispetto al valore di riferimento del sensore e implementazione dell’algoritmo di regressione. Lo step di normalizzazione dei dati è uno strumento statistico fondamentale per poter mettere a confronto grandezze non uniformi tra loro. Studi presenti, dimostrano inoltre un mutazione morfologica del globulo rosso in risposta a sollecitazioni meccaniche. Un ulteriore aspetto trattato nel presente lavoro, riguarda la velocità del flusso sanguigno determinato dalla pompa e come tale grandezza sia in grado di influenzare la lettura di ematocrito.

A two-body study of dynamical expansion in the XXZ spin chain and equivalent interacting fermion models

Lo scopo di questa tesi è studiare l'espansione dinamica di due fermioni interagenti in una catena unidimensionale cercando di definire il ruolo degli stati legati durante l'evoluzione temporale del sistema. Lo studio di questo modello viene effettuato a livello analitico tramite la tecnica del Bethe ansatz, che ci fornisce autovalori ed autovettori dell'hamiltoniana, e se ne valutano le proprietà statiche. Particolare attenzione è stata dedicata alle caratteristiche dello spettro al variare dell'interazione tra le due particelle e alle caratteristiche degli autostati. Dalla risoluzione dell'equazione di Bethe vengono ricercate le soluzioni che danno luogo a stati legati delle due particelle e se ne valuta lo spettro energetico in funzione del momento del centro di massa. Si è studiato inoltre l'andamento del numero delle soluzioni, in particolare delle soluzioni che danno luogo ad uno stato legato, al variare della lunghezza della catena e del parametro di interazione. La valutazione delle proprietà dinamiche del modello è stata effettuata tramite l'utilizzo dell'algoritmo t-DMRG (time dependent - Density Matrix Renormalization Group). Questo metodo numerico, che si basa sulla decimazione dello spazio di Hilbert, ci permette di avere accesso a quantità che caratterizzano la dinamica quali la densità e la velocità di espansione. Da queste sono stati estratti i proli dinamici della densità e della velocità di espansione al variare del valore del parametro di interazione.

Image quality and dose evaluation of filtered back projection versus iterative reconstruction algorithm in multislice computed tomography.

Il presente lavoro di tesi è stato svolto presso il servizio di Fisica Sanitaria del Policlinico Sant'Orsola-Malpighi di Bologna. Lo studio si è concentrato sul confronto tra le tecniche di ricostruzione standard (Filtered Back Projection, FBP) e quelle iterative in Tomografia Computerizzata. Il lavoro è stato diviso in due parti: nella prima è stata analizzata la qualità delle immagini acquisite con una CT multislice (iCT 128, sistema Philips) utilizzando sia l'algoritmo FBP sia quello iterativo (nel nostro caso iDose4). Per valutare la qualità delle immagini sono stati analizzati i seguenti parametri: il Noise Power Spectrum (NPS), la Modulation Transfer Function (MTF) e il rapporto contrasto-rumore (CNR). Le prime due grandezze sono state studiate effettuando misure su un fantoccio fornito dalla ditta costruttrice, che simulava la parte body e la parte head, con due cilindri di 32 e 20 cm rispettivamente. Le misure confermano la riduzione del rumore ma in maniera differente per i diversi filtri di convoluzione utilizzati. Lo studio dell'MTF invece ha rivelato che l'utilizzo delle tecniche standard e iterative non cambia la risoluzione spaziale; infatti gli andamenti ottenuti sono perfettamente identici (a parte le differenze intrinseche nei filtri di convoluzione), a differenza di quanto dichiarato dalla ditta. Per l'analisi del CNR sono stati utilizzati due fantocci; il primo, chiamato Catphan 600 è il fantoccio utilizzato per caratterizzare i sistemi CT. Il secondo, chiamato Cirs 061 ha al suo interno degli inserti che simulano la presenza di lesioni con densità tipiche del distretto addominale. Lo studio effettuato ha evidenziato che, per entrambi i fantocci, il rapporto contrasto-rumore aumenta se si utilizza la tecnica di ricostruzione iterativa. La seconda parte del lavoro di tesi è stata quella di effettuare una valutazione della riduzione della dose prendendo in considerazione diversi protocolli utilizzati nella pratica clinica, si sono analizzati un alto numero di esami e si sono calcolati i valori medi di CTDI e DLP su un campione di esame con FBP e con iDose4. I risultati mostrano che i valori ricavati con l'utilizzo dell'algoritmo iterativo sono al di sotto dei valori DLR nazionali di riferimento e di quelli che non usano i sistemi iterativi.