Binarized-octree generation for Cartesian adaptive mesh refinement around immersed geometries

We revisit the generation of balanced octrees for adaptive mesh refinement (AMR) of Cartesian domains with immersed complex geometries. In a recent short note (Hasbestan and Senocak, 2017) [42], we showed that the data locality of the Z-order curve in a hashed linear-octree generation method may not be perfect because of potential collisions in the hash table. Building on that observation, we propose a binarized-octree generation method that complies with the Z-order curve exactly. Similar to a hashed linear-octree generation method, we use Morton encoding to index the nodes of an octree, but use a red-black tree in place of the hash table. Red-black tree is a special kind of a binary tree, which we use for insertion and deletion of elements during mesh adaptation. By strictly working with the bitwise representation of an octree, we remove computer hardware limitations on the depth of adaptation on a single processor. Additionally, we introduce a geometry encoding technique for rapidly tagging a solid geometry for mesh refinement. Our results for several geometries with different levels of adaptations show that the binarized-octree generation method outperforms the linear-octree generation method in terms of runtime performance at the expense of only a slight increase in memory usage. The current AMR capability, rebl-AMR, is available as open-source software

A simple multigrid scheme for solving the Poisson equation with arbitrary domain boundaries

We present a new multigrid scheme for solving the Poisson equation with Dirichlet boundary conditions on a Cartesian grid with irregular domain boundaries. This scheme was developed in the context of the Adaptive Mesh Refinement (AMR) schemes based on a graded-octree data structure. The Poisson equation is solved on a level-by-level basis, using a "one-way interface" scheme in which boundary conditions are interpolated from the previous coarser level solution. Such a scheme is particularly well suited for self-gravitating astrophysical flows requiring an adaptive time stepping strategy. By constructing a multigrid hierarchy covering the active cells of each AMR level, we have designed a memory-efficient algorithm that can benefit fully from the multigrid acceleration. We present a simple method for capturing the boundary conditions across the multigrid hierarchy, based on a second-order accurate reconstruction of the boundaries of the multigrid levels. In case of very complex boundaries, small scale features become smaller than the discretization cell size of coarse multigrid levels and convergence problems arise. We propose a simple solution to address these issues. Using our scheme, the convergence rate usually depends on the grid size for complex grids, but good linear convergence is maintained. The proposed method was successfully implemented on distributed memory architectures in the RAMSES code, for which we present and discuss convergence and accuracy properties as well as timing performances.Comment: 33 pages, 15 figures, accepted for publication in Journal of Computational Physic

Afivo: a framework for quadtree/octree AMR with shared-memory parallelization and geometric multigrid methods

Afivo is a framework for simulations with adaptive mesh refinement (AMR) on quadtree (2D) and octree (3D) grids. The framework comes with a geometric multigrid solver, shared-memory (OpenMP) parallelism and it supports output in Silo and VTK file formats. Afivo can be used to efficiently simulate AMR problems with up to about $10^{8}$ unknowns on desktops, workstations or single compute nodes. For larger problems, existing distributed-memory frameworks are better suited. The framework has no built-in functionality for specific physics applications, so users have to implement their own numerical methods. The included multigrid solver can be used to efficiently solve elliptic partial differential equations such as Poisson's equation. Afivo's design was kept simple, which in combination with the shared-memory parallelism facilitates modification and experimentation with AMR algorithms. The framework was already used to perform 3D simulations of streamer discharges, which required tens of millions of cells

RADAMESH: Cosmological Radiative Transfer for Adaptive Mesh Refinement Simulations

We present a new three-dimensional radiative transfer (RT) code, RADAMESH, based on a ray-tracing, photon-conserving and adaptive (in space and time) scheme. RADAMESH uses a novel Monte Carlo approach to sample the radiation field within the computational domain on a "cell-by-cell" basis. Thanks to this algorithm, the computational efforts are now focused where actually needed, i.e. within the Ionization-fronts (I-fronts). This results in an increased accuracy level and, at the same time, a huge gain in computational speed with respect to a "classical" Monte Carlo RT, especially when combined with an Adaptive Mesh Refinement (AMR) scheme. Among several new features, RADAMESH is able to adaptively refine the computational mesh in correspondence of the I-fronts, allowing to fully resolve them within large, cosmological boxes. We follow the propagation of ionizing radiation from an arbitrary number of sources and from the recombination radiation produced by H and He. The chemical state of six species (HI, HII, HeI, HeII, HeIII, e) and gas temperatures are computed with a time-dependent, non-equilibrium chemistry solver. We present several validating tests of the code, including the standard tests from the RT Code Comparison Project and a new set of tests aimed at substantiating the new characteristics of RADAMESH. Using our AMR scheme, we show that properly resolving the I-front of a bright quasar during Reionization produces a large increase of the predicted gas temperature within the whole HII region. Also, we discuss how H and He recombination radiation is able to substantially change the ionization state of both species (for the classical Stroemgren sphere test) with respect to the widely used "on-the-spot" approximation.Comment: 19 pages, 24 figures; accepted for publication in MNRAS, version with high-resolution figures is avalaible at http://www.ast.cam.ac.uk/~cantal/Papers/CP10.pd

Multigrid elliptic equation solver with adaptive mesh refinement

In this paper we describe in detail the computational algorithm used by our parallel multigrid elliptic equation solver with adaptive mesh refinement. Our code uses truncation error estimates to adaptively refine the grid as part of the solution process. The presentation includes a discussion of the orders of accuracy that we use for prolongation and restriction operators to ensure second order accurate results and to minimize computational work. Code tests are presented that confirm the overall second order accuracy and demonstrate the savings in computational resources provided by adaptive mesh refinement.Comment: 12 pages, 9 figures, Modified in response to reviewer suggestions, added figure, added references. Accepted for publication in J. Comp. Phy

An adaptive Cartesian embedded boundary approach for fluid simulations of two- and three-dimensional low temperature plasma filaments in complex geometries

We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal fluid-plasma model on adaptive Cartesian grids, extended to also account for charging of insulating surfaces. We discuss the spatial and temporal discretization methods, and show that the resulting overall method is second order convergent, monotone, and conservative (for smooth solutions). Weak scalability with parallel efficiencies over 70\% are demonstrated up to 8192 cores and more than one billion cells. We then demonstrate the use of adaptive mesh refinement in multiple two- and three-dimensional simulation examples at modest cores counts. The examples include two-dimensional simulations of surface streamers along insulators with surface roughness; fully three-dimensional simulations of filaments in experimentally realizable pin-plane geometries, and three-dimensional simulations of positive plasma discharges in multi-material complex geometries. The largest computational example uses up to $800$ million mesh cells with billions of unknowns on $4096$ computing cores. Our use of computer-aided design (CAD) and constructive solid geometry (CSG) combined with capabilities for parallel computing offers possibilities for performing three-dimensional transient plasma-fluid simulations, also in multi-material complex geometries at moderate pressures and comparatively large scale.Comment: 40 pages, 21 figure