A unification of least-squares and Green-Gauss gradients under a common projection-based gradient reconstruction frameworkWe propose a family of gradient reconstruction schemes based on the solution of over-determined systems by orthogonal or oblique projections. In the case of orthogonal projections, we retrieve…Alexandros Syrakos, Oliver Oxtoby, Eugene de Villiers et al.·Nov 3, 2021SaveLearn
gVOF: An open-source package for unsplit geometric volume of fluid methods on arbitrary gridsThe gVOF package includes a complete and self-contained set of routines for volume of fluid initialization, interface reconstruction and fluid advection, which are used to implement several accurate…Joaquín López, Julio Hernández·Nov 2, 2021SaveLearn
H2ZIXY: Pauli spin matrix decomposition of real symmetric matricesWe present a code in Python3 which takes a square real symmetric matrix, of arbitrary size, and decomposes it as a tensor product of Pauli spin matrices. The application to the decomposition of a…Rocco Monteiro Nunes Pesce, Paul D. Stevenson·Oct 31, 2021SaveLearn
TTDFT: A GPU accelerated Tucker tensor DFT code for large-scale Kohn-Sham DFT calculationsWe present the Tucker tensor DFT (TTDFT) code which uses a tensor-structured algorithm with graphic processing unit (GPU) acceleration for conducting ground-state DFT calculations on large-scale…Chih-Chuen Lin, Vikram Gavini·Oct 29, 2021SaveLearn
IRA: A shape matching approach for recognition and comparison of generic atomic patternsWe propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm…Miha Gunde, Nicolas Salles, Anne Hémeryck et al.·Oct 29, 2021SaveLearn
The Hubbard model with fermionic tensor networksMany electromagnetic properties of graphene can be described by the Hubbard model on a honeycomb lattice. However, this system suffers strongly from the sign problem if a chemical potential is…Manuel Schneider, Johann Ostmeyer, Karl Jansen et al.·Oct 28, 2021SaveLearn
Semi-Lagrangian 4d, 5d, and 6d kinetic plasma simulation on large scale GPU equipped supercomputerRunning kinetic plasma physics simulations using grid-based solvers is very demanding both in terms of memory as well as computational cost. This is primarily due to the up to six-dimensional phase…Lukas Einkemmer, Alexander Moriggl·Oct 27, 2021SaveLearn
A2I Transformer: Permutation-equivariant attention network for pairwise and many-body interactions with minimal featurizationThe combination of neural network potential (NNP) with molecular simulations plays an important role in an efficient and thorough understanding of a molecular system's potential energy surface (PES).…Ji Woong Yu, Min Young Ha, Bumjoon Seo et al.·Oct 27, 2021SaveLearn
A random batch Ewald method for charged particles in the isothermal-isobaric ensembleWe develop an accurate, highly efficient and scalable random batch Ewald (RBE) method to conduct simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic…Jiuyang Liang, Pan Tan, Liang Hong et al.·Oct 27, 2021SaveLearn
Impact of Orientation Misalignments on Black Phosphorus Ultrascaled Field-effect TransistorsTwo-dimensional materials with strong bandstructure anisotropy such as black phosphorus BP have been identified as attractive candidates for logic application due to their potential high carrier…Cedric Klinkert, Sara Fiore, Jonathan Backmann et al.·Oct 27, 2021SaveLearn
On Computing the Hyperparameter of Extreme Learning Machines: Algorithm and Application to Computational PDEs, and Comparison with Classical and High-Order Finite ElementsWe consider the use of extreme learning machines (ELM) for computational partial differential equations (PDE). In ELM the hidden-layer coefficients in the neural network are assigned to random values…Suchuan Dong, Jielin Yang·Oct 27, 2021SaveLearn
Nonintrusive Manufactured Solutions for Non-Decomposing Ablation in Two DimensionsCode verification is a necessary step towards establishing credibility in computational physics simulations. It is used to assess the correctness of the implementation of the numerical methods within…Brian A. Freno, Brian R. Carnes, Victor E. Brunini et al.·Oct 26, 2021SaveLearn
A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solverThe Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in…Jiahui Chen, Johannes Tausch, Weihua Geng·Oct 26, 2021SaveLearn
Quantifying biomolecular diffusion with a "spherical cow" modelThe dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their…Frederico Campos Freitas, Sandra Byju, Asem Hassan et al.·Oct 26, 2021SaveLearn
A Metalearning Approach for Physics-Informed Neural Networks (PINNs): Application to Parameterized PDEsPhysics-informed neural networks (PINNs) as a means of discretizing partial differential equations (PDEs) are garnering much attention in the Computational Science and Engineering (CS&E) world. At…Michael Penwarden, Shandian Zhe, Akil Narayan et al.·Oct 26, 2021SaveLearn
libcommute/pycommute: A quantum operator algebra domain-specific language and exact diagonalization toolkitI present libcommute, a C++11/14/17 template library that implements a domain-specific language for easy manipulating of polynomial operators used in the quantum many-body theory, as well as a…Igor Krivenko·Oct 25, 2021SaveLearn
Resolution Exchange with Tunneling for Enhanced Sampling of Protein LandscapesSimulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of…Fatih Yasar, Alan J. Ray, Ulrich H. E. Hansmann·Oct 24, 2021SaveLearn
Resonant mode coupling approximation for calculation of optical spectra of photonic crystal slabsWe develop the resonant mode coupling approximation to calculate the optical spectra of a stack of two photonic crystal slabs. The method is based on a derivation of the input and output resonant…Dmitrii A. Gromyko, Sergey A. Dyakov, Sergei G. Tikhodeev et al.·Oct 23, 2021SaveLearn
Large-scale earthquake sequence simulations on 3D nonplanar faults using the boundary element method accelerated by lattice H-matricesLarge-scale earthquake sequence simulations using the boundary element method (BEM) incur extreme computational costs through multiplying a dense matrix with a slip rate vector. Hierarchical matrices…So Ozawa, Akihiro Ida, Tetsuya Hoshino et al.·Oct 23, 2021SaveLearn
Velocity Discretization for Lattice Boltzmann Method for Noncontinuum Bounded Gas Flows at the Micro and NanoscaleThe lattice Boltzmann (LB) method intrinsically links to the Boltzmann equation with the Bhatnagar-Gross-Krook collision operator; however, it has been questioned to be able to simulate noncontinuum…Yong Shi·Oct 23, 2021SaveLearn
High-Order Curvilinear Finite Element Magneto-Hydrodynamics I: A Conservative Lagrangian SchemeMagneto-hydrodynamics is one of the foremost models in plasma physics with applications in inertial confinement fusion, astrophysics and elsewhere. Advanced numerical methods are needed to get an…Jan Nikl, Milan Kuchařík, Stefan Weber·Oct 22, 2021SaveLearn
Computing the Invariant Distribution of Randomly Perturbed Dynamical Systems Using Deep LearningThe invariant distribution, which is characterized by the stationary Fokker-Planck equation, is an important object in the study of randomly perturbed dynamical systems. Traditional numerical methods…Bo Lin, Qianxiao Li, Weiqing Ren·Oct 22, 2021SaveLearn
A conservative level set method for liquid-gas flows with application in liquid jet atomisationIn this paper, a methodology for modelling two-phase flows based on a conservative level set method in the framework of finite volume method is presented. The novelty of the interface capturing…Panagiotis Lyras, Antoine Hubert, Konstantinos G. Lyras·Oct 20, 2021SaveLearn
Strong phase correlation between diffusons governs heat conduction in amorphous siliconUnderstanding the thermal vibrations and thermal transport in amorphous materials is an important but long-standing issue in several theoretical and practical fields. Using direct molecular dynamic…Zhongwei Zhang, Yangyu Guo, Marc Bescond et al.·Oct 20, 2021SaveLearn
Divergence error based p-adaptive discontinuous Galerkin solution of time-domain Maxwell's equationsA p-adaptive discontinuous Galerkin time-domain method is developed to obtain high-order solutions to electromagnetic scattering problems. A novel feature of the proposed method is the use of…Apurva Tiwari, Avijit Chatterjee·Oct 19, 2021SaveLearn