Mesh generation for confined fusion plasma simulation

XGC1 and M3D-C ¹ are two fusion plasma simulation codes being developed at Princeton Plasma Physics Laboratory. XGC1 uses the particle-in-cell method to simulate gyrokinetic neoclassical physics and turbulence (Chang et al. Phys Plasmas 16(5):056108, 2009; Ku et al. Nucl Fusion 49:115021, 2009; Admas et al. J Phys 180(1):012036, 2009). M3D-\(C^1\) solves the two-fluid resistive magnetohydrodynamic equations with the \(C^1\) finite elements (Jardin J comput phys 200(1):133–152, 2004; Jardin et al. J comput Phys 226(2):2146–2174, 2007; Ferraro and Jardin J comput Phys 228(20):7742–7770, 2009; Jardin J comput Phys 231(3):832–838, 2012; Jardin et al. Comput Sci Discov 5(1):014002, 2012; Ferraro et al. Sci Discov Adv Comput, 2012; Ferraro et al. International sherwood fusion theory conference, 2014). This paper presents the software tools and libraries that were combined to form the geometry and automatic meshing procedures for these codes. Specific consideration has been given to satisfy the mesh configuration and element shape quality constraints of XGC1 and M3D-\(C^1\).     

The computational capability of chemical reaction automata

We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant of reaction automata (RAs) studied in recent literature (Okubo in RAIRO Theor Inform Appl 48:23–38 2014; Okubo et al. in Theor Comput Sci 429:247–257 2012a, Theor Comput Sci 454:206–221 2012b). We show that CRAs in maximally parallel manner are computationally equivalent to Turing machines, while the computational power of CRAs in sequential manner coincides with that of the class of Petri nets, which is in marked contrast to the result that RAs (in both maximally parallel and sequential manners) have the computing power of Turing universality (Okubo 2014; Okubo et al. 2012a). Intuitively, CRAs are defined as RAs without inhibitor functioning in each reaction, providing an offline model of computing by chemical reaction networks (CRNs). Thus, the main results in this paper not only strengthen the previous result on Turing computability of RAs but also clarify the computing powers of inhibitors in RA computation.     

Error Inhibiting Block One-step Schemes for Ordinary Differential Equations

The commonly used one step methods and linear multi-step methods all have a global error that is of the same order as the local truncation error (as defined in [1, 6, 8, 13, 15]). In fact, this is true of the entire class of general linear methods. In practice, this means that the order of the method is typically defined solely by order conditions which are derived by studying the local truncation error. In this work we investigate the interplay between the local truncation error and the global error, and develop a methodology which defines the construction of explicit error inhibiting block one-step methods (alternatively written as explicit general linear methods [2]). These error inhibiting schemes are constructed so that the accumulation of the local truncation error over time is controlled, which results in a global error that is one order higher than the local truncation error. In this work, we delineate how to carefully choose the coefficient matrices so that the growth of the local truncation error is inhibited. We then use this theoretical understanding to construct several methods that have higher order global error than local truncation error, and demonstrate their enhanced order of accuracy on test cases. These methods demonstrate that the error inhibiting concept is realizable. Future work will further develop new error inhibiting methods and will analyze the computational efficiency and linear stability properties of these methods.     

<Emphasis Type="Italic">δ</Emphasis>-equality of intuitionistic fuzzy sets: a new proximity measure and applications in medical diagnosis

Intuitionistic fuzzy set is capable of handling uncertainty with counterpart falsities which exist in nature. Proximity measure is a convenient way to demonstrate impractical significance of values of memberships in the intuitionistic fuzzy set. However, the related works of Pappis (Fuzzy Sets Syst 39(1):111–115, 1991), Hong and Hwang (Fuzzy Sets Syst 66(3):383–386, 1994), Virant (2000) and Cai (IEEE Trans Fuzzy Syst 9(5):738–750, 2001) did not model the measure in the context of the intuitionistic fuzzy set but in the Zadeh’s fuzzy set instead. In this paper, we examine this problem and propose new notions of δ-equalities for the intuitionistic fuzzy set and δ-equalities for intuitionistic fuzzy relations. Two fuzzy sets are said to be δ-equal if they are equal to an extent of δ. The applications of δ-equalities are important to fuzzy statistics and fuzzy reasoning. Several characteristics of δ-equalities that were not discussed in the previous works are also investigated. We apply the δ-equalities to the application of medical diagnosis to investigate a patient’s diseases from symptoms. The idea is using δ-equalities for intuitionistic fuzzy relations to find groups of intuitionistic fuzzified set with certain equality or similar degrees then combining them. Numerical examples are given to illustrate validity of the proposed algorithm. Further, we conduct experiments on real medical datasets to check the efficiency and applicability on real-world problems. The results obtained are also better in comparison with 10 existing diagnosis methods namely De et al. (Fuzzy Sets Syst 117:209–213, 2001), Samuel and Balamurugan (Appl Math Sci 6(35):1741–1746, 2012), Szmidt and Kacprzyk (2004), Zhang et al. (Procedia Eng 29:4336–4342, 2012), Hung and Yang (Pattern Recogn Lett 25:1603–1611, 2004), Wang and Xin (Pattern Recogn Lett 26:2063–2069, 2005), Vlachos and Sergiadis (Pattern Recogn Lett 28(2):197–206, 2007), Zhang and Jiang (Inf Sci 178(6):4184–4191, 2008), Maheshwari and Srivastava (J Appl Anal Comput 6(3):772–789, 2016) and Support Vector Machine (SVM).     

Modeling and Simulation of Laser Processing of Particulate-Functionalized Materials

The objective of this paper is to focus on one of the “building blocks” of additive manufacturing technologies, namely selective laser-processing of particle-functionalized materials. Following a series of work in Zohdi (Int J Numer Methods Eng 53:1511–1532, 2002; Philos Trans R Soc Math Phys Eng Sci 361(1806):1021–1043, 2003; Comput Methods Appl Mech Eng 193(6–8):679–699, 2004; Comput Methods Appl Mech Eng 196:3927–3950, 2007; Int J Numer Methods Eng 76:1250–1279, 2008; Comput Methods Appl Mech Eng 199:79–101, 2010; Arch Comput Methods Eng 1–17. doi: 10.1007/s11831-013-9092-6, 2013; Comput Mech Eng Sci 98(3):261–277, 2014; Comput Mech 54:171–191, 2014; J Manuf Sci Eng ASME doi: 10.1115/1.4029327, 2015; CIRP J Manuf Sci Technol 10:77–83, 2015; Comput Mech 56:613–630, 2015; Introduction to computational micromechanics. Springer, Berlin, 2008; Introduction to the modeling and simulation of particulate flows. SIAM (Society for Industrial and Applied Mathematics), Philadelphia, 2007; Electromagnetic properties of multiphase dielectrics: a primer on modeling, theory and computation. Springer, Berlin, 2012), a laser-penetration model, in conjunction with a Finite Difference Time Domain Method using an immersed microstructure method, is developed. Because optical, thermal and mechanical multifield coupling is present, a recursive, staggered, temporally-adaptive scheme is developed to resolve the internal microstructural fields. The time step adaptation allows the numerical scheme to iteratively resolve the changing physical fields by refining the time-steps during phases of the process when the system is undergoing large changes on a relatively small time-scale and can also enlarge the time-steps when the processes are relatively slow. The spatial discretization grids are uniform and dense enough to capture fine-scale changes in the fields. The microstructure is embedded into the spatial discretization and the regular grid allows one to generate a matrix-free iterative formulation which is amenable to rapid computation, with minimal memory requirements, making it ideal for laptop computation. Numerical examples are provided to illustrate the modeling and simulation approach, which by design, is straightforward to computationally implement, in order to be easily utilized by researchers in the field. More advanced conduction models, based on thermal-relaxation, which are a key feature of fast-pulsing laser technologies, are also discussed.     

Method of Lines Transpose: An Efficient Unconditionally Stable Solver for Wave Propagation

Building upon recent results obtained in Causley and Christlieb (SIAM J Numer Anal 52(1):220–235, 2014), Causley et al. (Math Comput 83(290):2763–2786, 2014, Method of lines transpose: high order L-stable O(N) schemes for parabolic equations using successive convolution, 2015), we describe an efficient second-order, unconditionally stable scheme for solving the wave equation, based on the method of lines transpose (MOL\(^T\)), and the resulting semi-discrete (i.e. continuous in space) boundary value problem. In Causley and Christlieb (SIAM J Numer Anal 52(1):220–235, 2014), unconditionally stable schemes of high order were derived, and in Causley et al. (Method of lines transpose: high order L-stable O(N) schemes for parabolic equations using successive convolution, 2015) a high order, fast \(\mathcal {O}(N)\) spatial solver was derived, which is matrix-free and is based on dimensional-splitting. In this work, are interested in building a wave solver, and our main concern is the development of boundary conditions. We demonstrate all desired boundary conditions for a wave solver, including outflow boundary conditions, in 1D and 2D. The scheme works in a logically Cartesian fashion, and the boundary points are embedded into the regular mesh, without incurring stability restrictions, so that boundary conditions are imposed without any reduction in the order of accuracy. We demonstrate how the embedded boundary approach works in the cases of Dirichlet and Neumann boundary conditions. Further, we develop outflow and periodic boundary conditions for the MOL\(^T\) formulation. Our solver is designed to couple with particle codes, and so special attention is also paid to the implementation of point sources, and soft sources which can be used to launch waves into waveguides.     

Direct Discontinuous Galerkin Method and Its Variations for Second Order Elliptic Equations

In this paper, we study direct discontinuous Galerkin method (Liu and Yan in SIAM J Numer Anal 47(1):475–698, 2009) and its variations (Liu and Yan in Commun Comput Phys 8(3):541–564, 2010; Vidden and Yan in J Comput Math 31(6):638–662, 2013; Yan in J Sci Comput 54(2–3):663–683, 2013) for 2nd order elliptic problems. A priori error estimate under energy norm is established for all four methods. Optimal error estimate under \(L^2\) norm is obtained for DDG method with interface correction (Liu and Yan in Commun Comput Phys 8(3):541–564, 2010) and symmetric DDG method (Vidden and Yan in J Comput Math 31(6):638–662, 2013). A series of numerical examples are carried out to illustrate the accuracy and capability of the schemes. Numerically we obtain optimal \((k+1)\)th order convergence for DDG method with interface correction and symmetric DDG method on nonuniform and unstructured triangular meshes. An interface problem with discontinuous diffusion coefficients is investigated and optimal \((k+1)\)th order accuracy is obtained. Peak solutions with sharp transitions are captured well. Highly oscillatory wave solutions of Helmholz equation are well resolved.     

Superconvergent Two-Grid Methods for Elliptic Eigenvalue Problems

Some numerical algorithms for elliptic eigenvalue problems are proposed, analyzed, and numerically tested. The methods combine advantages of the two-grid algorithm (Xu and Zhou in Math Comput 70(233):17–25, 2001), the two-space method (Racheva and Andreev in Comput Methods Appl Math 2:171–185, 2002), the shifted inverse power method (Hu and Cheng in Math Comput 80:1287–1301, 2011; Yang and Bi in SIAM J Numer Anal 49:1602–1624, 2011), and the polynomial preserving recovery enhancing technique (Naga et al. in SIAM J Sci Comput 28:1289–1300, 2006). Our new algorithms compare favorably with some existing methods and enjoy superconvergence property.     

Content-Based Image Retrieval Using Iterative Search

The aim of Content-based Image Retrieval (CBIR) is to find a set of images that best match the query based on visual features. Most existing CBIR systems find similar images in low level features, while Text-based Image Retrieval (TBIR) systems find images with relevant tags regardless of contents in the images. Generally, people are more interested in images with similarity both in contours and high-level concepts. Therefore, we propose a new strategy called Iterative Search to meet this requirement. It mines knowledge from the similar images of original queries, in order to compensate for the missing information in feature extraction process. To evaluate the performance of Iterative Search approach, we apply this method to four different CBIR systems (HOF Zhou et al. in ACM international conference on multimedia, 2012; Zhou and Zhang in Neural information processing—international conference, ICONIP 2011, Shanghai, 2011, HOG Dalal and Triggs in IEEE computer society conference on computer vision pattern recognition, 2005, GIST Oliva and Torralba in Int J Comput Vision 42:145–175, 2001 and CNN Krizhevsky et al. in Adv Neural Inf Process Syst 25:2012, 2012) in our experiments. The results show that Iterative Search improves the performance of original CBIR features by about \(20\%\) on both the Oxford Buildings dataset and the Object Sketches dataset. Meanwhile, it is not restricted to any particular visual features.     

Stability and Scepticism in the Modelling of Doxastic States: Probabilities and Plain Beliefs

There are two prominent ways of formally modelling human belief. One is in terms of plain beliefs (yes-or-no beliefs, beliefs simpliciter), i.e., sets of propositions. The second one is in terms of degrees of beliefs, which are commonly taken to be representable by subjective probability functions. In relating these two ways of modelling human belief, the most natural idea is a thesis frequently attributed to John Locke: a proposition is or ought to be believed (accepted) just in case its subjective probability exceeds a contextually fixed probability threshold \(t<1\). This idea is known to have two serious drawbacks: first, it denies that beliefs are closed under conjunction, and second, it may easily lead to sets of beliefs that are logically inconsistent. In this paper I present two recent accounts of aligning plain belief with subjective probability: the Stability Theory of Leitgeb (Ann Pure Appl Log 164(12):1338–1389, 2013; Philos Rev 123(2):131–171, 2014; Proc Aristot Soc Suppl Vol 89(1):143–185, 2015a; The stability of belief: an essay on rationality and coherence. Oxford University Press, Oxford, 2015b) and the Probalogical Theory (or Tracking Theory) of Lin and Kelly (Synthese 186(2):531–575, 2012a; J Philos Log 41(6):957–981, 2012b). I argue that Leitgeb’s theory may be too sceptical for the purposes of real life.     

Information Lower Bounds via Self-Reducibility

We use self-reduction methods to prove strong information lower bounds on two of the most studied functions in the communication complexity literature: Gap Hamming Distance (GHD) and Inner Product (IP). In our first result we affirm the conjecture that the information cost of GHD is linear even under the uniform distribution, which strengthens the Ω(n) bound recently shown by Kerenidis et al. (2012), and answers an open problem from Chakrabarti et al. (2012). In our second result we prove that the information cost of IP_n is arbitrarily close to the trivial upper bound n as the permitted error tends to zero, again strengthening the Ω(n) lower bound recently proved by Braverman and Weinstein (Electronic Colloquium on Computational Complexity (ECCC) 18, 164 2011). Our proofs demonstrate that self-reducibility makes the connection between information complexity and communication complexity lower bounds a two-way connection. Whereas numerous results in the past (Chakrabarti et al. 2001; Bar-Yossef et al. J. Comput. Syst. Sci. 68(4), 702–732 2004; Barak et al. 2010) used information complexity techniques to derive new communication complexity lower bounds, we explore a generic way in which communication complexity lower bounds imply information complexity lower bounds in a black-box manner.     

On Optimally Partitioning a Text to Improve Its Compression

In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once. This problem was introduced in Buchsbaum et al. (Proc. of 11th ACM-SIAM Symposium on Discrete Algorithms, pp. 175–184, 2000; J. ACM 50(6):825–851, 2003) in the context of table compression, and then further elaborated and extended to strings and trees by Ferragina et al. (J. ACM 52:688–713, 2005; Proc. of 46th IEEE Symposium on Foundations of Computer Science, pp. 184–193, 2005) and Mäkinen and Navarro (Proc. of 14th Symposium on String Processing and Information Retrieval, pp. 229–241, 2007). Unfortunately, the literature offers poor solutions: namely, we know either a cubic-time algorithm for computing the optimal partition based on dynamic programming (Buchsbaum et al. in J. ACM 50(6):825–851, 2003; Giancarlo and Sciortino in Proc. of 14th Symposium on Combinatorial Pattern Matching, pp. 129–143, 2003), or few heuristics that do not guarantee any bounds on the efficacy of their computed partition (Buchsbaum et al. in Proc. of 11th ACM-SIAM Symposium on Discrete Algorithms, pp. 175–184, 2000; J. ACM 50(6):825–851, 2003), or algorithms that are efficient but work in some specific scenarios (such as the Burrows-Wheeler Transform, see e.g. Ferragina et al. in J. ACM 52:688–713, 2005; Mäkinen and Navarro in Proc. of 14th Symposium on String Processing and Information Retrieval, pp. 229–241, 2007) and achieve compression performance that might be worse than the optimal-partitioning by a Ω(log?n/log?log?n) factor. Therefore, computing efficiently the optimal solution is still open (Buchsbaum and Giancarlo in Encyclopedia of Algorithms, pp. 939–942, 2008). In this paper we provide the first algorithm which computes in O(nlog?_1+ε n) time and O(n) space, a partition of T whose compressed output is guaranteed to be no more than (1+ε)-worse the optimal one, where ε may be any positive constant fixed in advance. This result holds for any base-compressor C whose compression performance can be bounded in terms of the zero-th or the k-th order empirical entropy of the text T. We will also discuss extensions of our results to BWT-based compressors and to the compression booster of Ferragina et al. (J. ACM 52:688–713, 2005).     

Comments on the Authors’ Reply by T. Sokół and T. Lewiñski (2011) to a Discussion by Vazquez and Cervera (2011) on their Research Paper (Sokół and Lewiñski 2010)

Sokó? and Lewiñski (Struct Multidisc Optim 42:835–853, Sokó? and Lewiñski 2010) published a paper on Michell trusses for three forces in the plane, with an application to a class of symmetric trusses. Vazquez Espi and Cervera Bravo (2011) have written a Discussion on the above paper, which was replied by Sokó? and Lewiñski (2011). In the current Discussion, some comments on the above exchange are offered, because it involves some fundamental issues of topology optimization.     

Worlds,Events, and Inertia

The semantics of progressive sentences presents a challenge to linguists and philosophers alike. According to a widely accepted view, the truth-conditions of progressive sentences rely essentially on a notion of inertia. Dowty (Word meaning and Montague grammar: the semantics of verbs and times in generative grammar and in Montague’s PTQ, D. Reidel Publishing Company, Dordrecht, 1979) suggested inertia worlds to implement this “inertia idea” in a formal semantic theory of the progressive. The main thesis of the paper is that the notion of inertia went through a subtle, but crucial change when worlds were replaced by events in Landman (Nat Lang Semant 1:1–32, 1992) and Portner (Language 74(4):760–787, 1998), and that this new, event-related concept of inertia results in a possibility-based theory of the progressive. An important case in point in the paper is a proof that, despite its surface structure, the theory presented in Portner (1998) does not implement the notion of inertia in Dowty (1979); rather, it belongs together with Dowty’s earlier, 1977 theory according to which the progressive is a possibility operator.     

Pupil detection for head-mounted eye tracking in the wild: an evaluation of the state of the art

Robust and accurate detection of the pupil position is a key building block for head-mounted eye tracking and prerequisite for applications on top, such as gaze-based human–computer interaction or attention analysis. Despite a large body of work, detecting the pupil in images recorded under real-world conditions is challenging given significant variability in the eye appearance (e.g., illumination, reflections, occlusions, etc.), individual differences in eye physiology, as well as other sources of noise, such as contact lenses or make-up. In this paper we review six state-of-the-art pupil detection methods, namely ElSe (Fuhl et al. in Proceedings of the ninth biennial ACM symposium on eye tracking research & applications, ACM. New York, NY, USA, pp 123–130, 2016), ExCuSe (Fuhl et al. in Computer analysis of images and patterns. Springer, New York, pp 39–51, 2015), Pupil Labs (Kassner et al. in Adjunct proceedings of the 2014 ACM international joint conference on pervasive and ubiquitous computing (UbiComp), pp 1151–1160, 2014. doi: 10.1145/2638728.2641695), SET (Javadi et al. in Front Neuroeng 8, 2015), Starburst (Li et al. in Computer vision and pattern recognition-workshops, 2005. IEEE Computer society conference on CVPR workshops. IEEE, pp 79–79, 2005), and ?wirski (?wirski et al. in Proceedings of the symposium on eye tracking research and applications (ETRA). ACM, pp 173–176, 2012. doi: 10.1145/2168556.2168585). We compare their performance on a large-scale data set consisting of 225,569 annotated eye images taken from four publicly available data sets. Our experimental results show that the algorithm ElSe (Fuhl et al. 2016) outperforms other pupil detection methods by a large margin, offering thus robust and accurate pupil positions on challenging everyday eye images.     

Complexity of Fixed-Size Bit-Vector Logics

Bit-precise reasoning is important for many practical applications of Satisfiability Modulo Theories (SMT). In recent years, efficient approaches for solving fixed-size bit-vector formulas have been developed. From the theoretical point of view, only few results on the complexity of fixed-size bit-vector logics have been published. Some of these results only hold if unary encoding on the bit-width of bit-vectors is used. In our previous work (Kovásznai et al. 2012), we have already shown that binary encoding adds more expressiveness to various fixed-size bit-vector logics with and without quantification. In a follow-up work (Fröhlich et al. 2013), we then gave additional complexity results for several fragments of the quantifier-free case. In this paper, we revisit our complexity results from (Fröhlich et al. 2013; Kovásznai et al. 2012) and go into more detail when specifying the underlying logics and presenting the proofs. We give a better insight in where the additional expressiveness of binary encoding comes from. In order to do this, we bring together our previous work and propose several new complexity results for new fragments and extensions of earlier bit-vector logics. We also discuss the expressiveness of various bit-vector operations in more detail. Altogether, we provide the currently most complete overview on the complexity of common bit-vector logics.     

Connectivity Preserving Multivalued Functions in Digital Topology

We study connectivity preserving multivalued functions (Kovalevsky in A new concept for digital geometry, shape in picture, 1994) between digital images. This notion generalizes that of continuous multivalued functions (Escribano et al. in Discrete geometry for computer imagery, lecture notes in computer science, 2008; Escribano et al. in J Math Imaging Vis 42:76–91, 2012) studied mostly in the setting of the digital plane \({\mathbb {Z}}^2\). We show that connectivity preserving multivalued functions, like continuous multivalued functions, are appropriate models for digital morphological operations. Connectivity preservation, unlike continuity, is preserved by compositions, and generalizes easily to higher dimensions and arbitrary adjacency relations.