Journal of Computational Physics: X最新文献

{"title":"Computational fluid dynamics on 3D point set surfaces","authors":"Hassan Bouchiba ,&nbsp;Simon Santoso ,&nbsp;Jean-Emmanuel Deschaud ,&nbsp;Luisa Rocha-Da-Silva ,&nbsp;François Goulette ,&nbsp;Thierry Coupez","doi":"10.1016/j.jcpx.2020.100069","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100069","url":null,"abstract":"<div><p>Computational fluid dynamics (CFD) in many cases requires designing 3D models manually, which is a tedious task that requires specific skills. In this paper, we present a novel method for performing CFD directly on scanned 3D point clouds. The proposed method builds an anisotropic volumetric tetrahedral mesh adapted around a point-sampled surface, without an explicit surface reconstruction step. The surface is represented by a new extended implicit moving least squares (EIMLS) scalar representation that extends the definition of the function to the entire computational domain, which makes it possible for use in immersed boundary flow simulations. The workflow we present allows us to compute flows around point-sampled geometries automatically. It also gives a better control of the precision around the surface with a limited number of computational nodes, which is a critical issue in CFD.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"7 ","pages":"Article 100069"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72230723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive dynamic multilevel simulation of fractured geothermal reservoirs","authors":"Mousa HosseiniMehr ,&nbsp;Cornelis Vuik ,&nbsp;Hadi Hajibeygi","doi":"10.1016/j.jcpx.2020.100061","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100061","url":null,"abstract":"<div><p>An algebraic dynamic multilevel (ADM) method for fully-coupled simulation of flow and heat transport in heterogeneous fractured geothermal reservoirs is presented. Fractures are modeled explicitly using the projection-based embedded discrete method (pEDFM), which accurately represents fractures with generic conductivity values, from barriers to highly-conductive manifolds. A fully implicit scheme is used to obtain the coupled discrete system including mass and energy balance equations with two main unknowns (i.e., pressure and temperature) at fine-scale level. The ADM method is then developed to map the fine-scale discrete system to a dynamic multilevel coarse grid, independently for matrix and fractures. To obtain the ADM map, multilevel multiscale coarse grids are constructed for matrix as well as for each fracture at all coarsening levels. On this hierarchical nested grids, multilevel multiscale basis functions (for flow and heat) are solved locally at the beginning of the simulation. They are used during the ADM simulation to allow for accurate multilevel systems in presence of parameter heterogeneity. The resolution of ADM simulations is defined dynamically based on the solution gradient (i.e. front tracking technique) using a user-defined threshold. The ADM mapping occurs algebraically using the so-called ADM prolongation and restriction operators, for all unknowns. A variety of 2D and 3D fractured test cases with homogeneous and heterogeneous permeability maps are studied. It is shown that ADM is able to model the coupled mass-heat transport accurately by employing only a fraction of fine-scale grid cells. Therefore, it promises an efficient approach for simulation of large and real-field scale fractured geothermal reservoirs. All software developments of this paper is publicly available at <span>https://gitlab.com/DARSim2simulator</span><svg><path></path></svg>.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"7 ","pages":"Article 100061"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72266784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Height-function curvature estimation with arbitrary order on non-uniform Cartesian grids","authors":"Fabien Evrard,&nbsp;Fabian Denner,&nbsp;Berend van Wachem","doi":"10.1016/j.jcpx.2020.100060","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100060","url":null,"abstract":"<div><p>This paper proposes a height-function algorithm to estimate the curvature of two-dimensional curves and three-dimensional surfaces that are defined implicitly on two- and three-dimensional non-uniform Cartesian grids. It relies on the reconstruction of local heights, onto which polynomial height-functions are fitted. The algorithm produces curvature estimates of order <span><math><mi>N</mi><mo>−</mo><mn>1</mn></math></span> anywhere in a stencil of <span><math><msup><mrow><mo>(</mo><mi>N</mi><mo>+</mo><mn>1</mn><mo>)</mo></mrow><mrow><mi>d</mi><mo>−</mo><mn>1</mn></mrow></msup></math></span> heights computed from the volume-fraction data available on a <em>d</em>-dimensional non-uniform Cartesian grid. These estimates are of order <em>N</em> at the centre of the stencil when it is symmetric about its main axis. This is confirmed by a comprehensive convergence analysis conducted on the errors associated with the application of the algorithm to a fabricated test-curve and test-surface.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"7 ","pages":"Article 100060"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72230725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parallel-in-time integration of kinematic dynamos","authors":"Andrew T. Clarke ,&nbsp;Christopher J. Davies ,&nbsp;Daniel Ruprecht ,&nbsp;Steven M. Tobias","doi":"10.1016/j.jcpx.2020.100057","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100057","url":null,"abstract":"<div><p>The precise mechanisms responsible for the natural dynamos in the Earth and Sun are still not fully understood. Numerical simulations of natural dynamos are extremely computationally intensive, and are carried out in parameter regimes many orders of magnitude away from real conditions. Parallelization in space is a common strategy to speed up simulations on high performance computers, but eventually hits a scaling limit. Additional directions of parallelization are desirable to utilise the high number of processor cores now available. Parallel-in-time methods can deliver speed up in addition to that offered by spatial partitioning but have not yet been applied to dynamo simulations. This paper investigates the feasibility of using the parallel-in-time algorithm Parareal to speed up initial value problem simulations of the kinematic dynamo, using the open source Dedalus spectral solver. Both the time independent Roberts and time dependent Galloway-Proctor 2.5D dynamos are investigated over a range of magnetic Reynolds numbers. Speedups beyond those possible from spatial parallelisation are found in both cases. Results for the Galloway-Proctor flow are promising, with Parareal efficiency found to be close to 0.3. Roberts flow results are less efficient, but Parareal still shows some speed up over spatial parallelisation alone. Parallel in space and time speed ups of ∼300 were found for 1600 cores for the Galloway-Proctor flow, with total parallel efficiency of ∼0.16.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"7 ","pages":"Article 100057"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72230722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An implicit local time-stepping method based on cell reordering for multiphase flow in porous media","authors":"Gaute Linga ,&nbsp;Olav Møyner ,&nbsp;Halvor Møll Nilsen ,&nbsp;Arthur Moncorgé ,&nbsp;Knut-Andreas Lie","doi":"10.1016/j.jcpx.2020.100051","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100051","url":null,"abstract":"<div><p>We discuss how to introduce local time-step refinements in a sequential implicit method for multiphase flow in porous media. Our approach relies heavily on causality-based optimal ordering, which implies that cells can be ordered according to total fluxes after the pressure field has been computed, leaving the transport problem as a sequence of ordinary differential equations, which can be solved cell-by-cell or block-by-block. The method is suitable for arbitrary local time steps and grids, is mass-conservative, and reduces to the standard implicit upwind finite-volume method in the case of equal time steps in adjacent cells. The method is validated by a series of numerical simulations. We discuss various strategies for selecting local time steps and demonstrate the efficiency of the method and several of these strategies by through a series of numerical examples.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"6 ","pages":"Article 100051"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72232701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Massively parallel implicit equal-weights particle filter for ocean drift trajectory forecasting","authors":"Håvard Heitlo Holm ,&nbsp;Martin Lilleeng Sætra ,&nbsp;Peter Jan van Leeuwen","doi":"10.1016/j.jcpx.2020.100053","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100053","url":null,"abstract":"<div><p>Forecasting of ocean drift trajectories are important for many applications, including search and rescue operations, oil spill cleanup and iceberg risk mitigation. In an operational setting, forecasts of drift trajectories are produced based on computationally demanding forecasts of three-dimensional ocean currents. Herein, we investigate a complementary approach for shorter time scales by using the recently proposed two-stage implicit equal-weights particle filter applied to a simplified ocean model. To achieve this, we present a new algorithmic design for a data-assimilation system in which all components – including the model, model errors, and particle filter – take advantage of massively parallel compute architectures, such as graphical processing units. Faster computations can enable in-situ and ad-hoc model runs for emergency management, and larger ensembles for better uncertainty quantification. Using a challenging test case with near-realistic chaotic instabilities, we run data-assimilation experiments based on synthetic observations from drifting and moored buoys, and analyze the trajectory forecasts for the drifters. Our results show that even sparse drifter observations are sufficient to significantly improve short-term drift forecasts up to twelve hours. With equidistant moored buoys observing only 0.1% of the state space, the ensemble gives an accurate description of the true state after data assimilation followed by a high-quality probabilistic forecast.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"6 ","pages":"Article 100053"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72232700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive multilevel space-time-stepping scheme for transport in heterogeneous porous media (ADM-LTS)","authors":"Ludovica Delpopolo Carciopolo ,&nbsp;Matteo Cusini ,&nbsp;Luca Formaggia ,&nbsp;Hadi Hajibeygi","doi":"10.1016/j.jcpx.2020.100052","DOIUrl":"https://doi.org/10.1016/j.jcpx.2020.100052","url":null,"abstract":"<div><p>We present ADM-LTS, an adaptive multilevel space-time-stepping scheme for transport in heterogeneous porous media. At each time step, firstly, the flow (pressure) solution is obtained. Then, the transport equation is solved using the ADM-LTS method, which consists of two stages. In the first stage, an initial solution is obtained by imposing the coarsest space-time grid. This initial solution is then improved, in the second stage, by imposing a space-time adaptive grid on the cells where the solution does not satisfy the desired quality. The quality control is based on error estimators with user-defined threshold values. The time-integration procedure, in which the coarsest-scale solution provides local flux boundary conditions for sub-domains with local time refinement, is strictly mass conservative. In addition, the method employs space-time fine grid cells only at the moving saturation fronts. In order to ensure local mass conservation at all levels, finite-volume restriction operators and unity prolongation operators are developed. Several numerical experiments have been performed to analyze the efficiency and accuracy of the proposed ADM-LTS method for both homogeneous and heterogeneous permeability fields on two and three dimensional domains. The results show that the method provides accurate solutions, at the same time it maintains the computational efficiency. The ADM-LTS implementation is publicly available at <span>https://gitlab.com/darsim2simulator</span><svg><path></path></svg>.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"6 ","pages":"Article 100052"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2020.100052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72232690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implicit hybridized discontinuous Galerkin methods for compressible magnetohydrodynamics","authors":"C. Ciucă ,&nbsp;P. Fernandez ,&nbsp;A. Christophe ,&nbsp;N.C. Nguyen ,&nbsp;J. Peraire","doi":"10.1016/j.jcpx.2019.100042","DOIUrl":"https://doi.org/10.1016/j.jcpx.2019.100042","url":null,"abstract":"<div><p>We present hybridized discontinuous Galerkin (HDG) methods for ideal and resistive compressible magnetohydrodynamics (MHD). The HDG methods are fully implicit, high-order accurate and endowed with a unique feature which distinguishes themselves from other discontinuous Galerkin (DG) methods. In particular, they reduce the globally coupled unknowns to the approximate trace of the solution on element boundaries, thereby resulting in considerably smaller global degrees of freedom than other DG methods. Furthermore, we develop a shock capturing method to deal with shocks by appropriately adding artificial bulk viscosity, molecular viscosity, thermal conductivity, and electric resistivity to the physical viscosities in the MHD equations. We show the optimal convergence of the HDG methods for ideal MHD problems and validate our resistive implementation for a magnetic reconnection problem. For smooth problems, we observe that employing a generalized Lagrange multiplier (GLM) formulation can reduce the errors in the divergence of the magnetic field by two orders of magnitude. We demonstrate the robustness of our shock capturing method on a number of test cases and compare our results, both qualitatively and quantitatively, with other MHD solvers. For shock problems, we observe that an effective treatment of both the shock wave and the divergence-free constraint is crucial to ensuring numerical stability.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"5 ","pages":"Article 100042"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2019.100042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72270300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modelling binary alloy solidification with adaptive mesh refinement","authors":"James R.G. Parkinson ,&nbsp;Daniel F. Martin ,&nbsp;Andrew J. Wells ,&nbsp;Richard F. Katz","doi":"10.1016/j.jcpx.2019.100043","DOIUrl":"https://doi.org/10.1016/j.jcpx.2019.100043","url":null,"abstract":"<div><p>The solidification of a binary alloy results in the formation of a porous mushy layer, within which spontaneous localisation of fluid flow can lead to the emergence of features over a range of spatial scales. We describe a finite volume method for simulating binary alloy solidification in two dimensions with local mesh refinement in space and time. The coupled heat, solute, and mass transport is described using an enthalpy method with flow described by a Darcy-Brinkman equation for flow across porous and liquid regions. The resulting equations are solved on a hierarchy of block-structured adaptive grids. A projection method is used to compute the fluid velocity, whilst the viscous and nonlinear diffusive terms are calculated using a semi-implicit scheme. A series of synchronization steps ensure that the scheme is flux-conservative and correct for errors that arise at the boundaries between different levels of refinement. We also develop a corresponding method using Darcy's law for flow in a porous medium/narrow Hele-Shaw cell. We demonstrate the accuracy and efficiency of our method using established benchmarks for solidification without flow and convection in a fixed porous medium, along with convergence tests for the fully coupled code. Finally, we demonstrate the ability of our method to simulate transient mushy layer growth with narrow liquid channels which evolve over time.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"5 ","pages":"Article 100043"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2019.100043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72233850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A fast solver for the narrow capture and narrow escape problems in the sphere","authors":"Jason Kaye ,&nbsp;Leslie Greengard","doi":"10.1016/j.jcpx.2019.100047","DOIUrl":"https://doi.org/10.1016/j.jcpx.2019.100047","url":null,"abstract":"<div><p>We present an efficient method to solve the narrow capture and narrow escape problems for the sphere. The <em>narrow capture</em> problem models the equilibrium behavior of a Brownian particle in the exterior of a sphere whose surface is reflective, except for a collection of small absorbing patches. The <em>narrow escape</em> problem is the dual problem: it models the behavior of a Brownian particle confined to the interior of a sphere whose surface is reflective, except for a collection of small patches through which it can escape.</p><p>Mathematically, these give rise to mixed Dirichlet/Neumann boundary value problems of the Poisson equation. They are numerically challenging for two main reasons: (1) the solutions are non-smooth at Dirichlet-Neumann interfaces, and (2) they involve adaptive mesh refinement and the solution of large, ill-conditioned linear systems when the number of small patches is large.</p><p>By using the Neumann Green's functions for the sphere, we recast each boundary value problem as a system of first-kind integral equations on the collection of patches. A block-diagonal preconditioner together with a multiple scattering formalism leads to a well-conditioned system of second-kind integral equations and a very efficient approach to discretization. This system is solved iteratively using GMRES. We develop a hierarchical, fast multipole method-like algorithm to accelerate each matrix-vector product. Our method is insensitive to the patch size, and the total cost scales with the number <em>N</em> of patches as <span><math><mi>O</mi><mo>(</mo><mi>N</mi><mi>log</mi><mo>⁡</mo><mi>N</mi><mo>)</mo></math></span>, after a precomputation whose cost depends only on the patch size and not on the number or arrangement of patches. We demonstrate the method with several numerical examples, and are able to achieve highly accurate solutions with 100<!--> <!-->000 patches in one hour on a 60-core workstation. For that case, adaptive discretization of each patch would lead to a dense linear system with about 360 million degrees of freedom. Our preconditioned system uses only 13.6 million “compressed” degrees of freedom and a few dozen GMRES iterations.</p></div>","PeriodicalId":37045,"journal":{"name":"Journal of Computational Physics: X","volume":"5 ","pages":"Article 100047"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.jcpx.2019.100047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72233851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}