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Dataset posted on 2025-03-04, 15:29 authored by Henry La Pierre, Andrew Boggiano, Chad Studvick, Sabyasachi Roy Chowdhury, Julie Niklas, Haruko Tateyama, Hongwei Wu, Johannes Leisen, Florian Kleemiss, Bess Vlaisavljevich, Ivan Popov
Geographic data, such as seismic event locations, station locations, etc., are generally given in geographic latitude Φ ’, longitude θ , and depth below sea level, ζ , using the WGS84 ellipsoid as a reference. In software systems that use this type of geographic data, it is necessary to manipulate the data mathematically in order to perform such tasks as finding the angular distance or azimuth from one point to another, to find an array of points along a great circle, to rotate a point about a pole of rotation, to move a point some angular distance in a specified direction, to find the intersections of two great circles or to find the intersections of a great circle and a small circle. In this paper, equations are presented that convert geographic locations first to geocentric coordinates and then to Earth-centered Cartesian coordinates where many mathematical manipulations can be performed conveniently and efficiently.
The streaming operator, which generates a displacement of a particle on a straight line at a constant speed in transport theory, is derived algebraically from a spherical coordinate formulation of Newton’s second law. This derivation leads to an operator that has more partial derivatives than a Cartesian coordinate formulation of the operator. The additional partial derivatives, which are with respect to the normalized velocity variables of a particle, take into account the intrinsic curvature of a ball. Moreover, these partial derivatives mitigate ray effects, which arise when a finite number of normalized velocities (also called directions or discrete ordinates) are used to simulate a continuous S 2 sphere of directions, by rotating the polar axis of the S 2 sphere into the radial direction of the coordinate system. As a consequence of this rotation, the number of actual discrete ordinates is greatly amplified to an enormous number of effective discrete ordinates by a multiplier that is equal to the number of patches that partitions a spherical surface. In addition to the derivation of the streaming operator, we provide in closed form a solution to the system of characteristic equations that is equivalent to the streaming operator. Furthermore, the solution to the system of characteristic equations enables the construction of an integral operator that is the inverse to the streaming operator. Examples in which ray effects are immensely mitigated by spherical coordinates are presented.
The streaming operator of the transport equation is derived for spherical coordinates by starting from Newton’s second law for a free particle expressed in spherical coordinates. We shall show that the partial derivatives with respect to the velocity variables of the particle, which are absent in the Cartesian coordinate formulation of the transport equation, arise in the spherical coordinate formulation of the transport equation in response to the centrifugal force which prevents a free particle from ‘falling into the origin’ of the coordinate system.
The concept of capacitive-sharing readout, described in detail in a previous study, offers the possibility for the development of high-performance three-coordinates (X--Y--U)-strip readout for Micro Pattern Gaseous Detectors (MPGDs) using simple standard PCB fabrication techniques. Capacitive-sharing (X--Y--U)-strip readout allows simultaneous measurement of the Cartesian coordinates x and y of the position of the particles together with a third coordinate u along the diagonal axis in a single readout PCB. This provides a powerful tool to address multiple-hit ambiguity and enable pattern recognition capabilities in moderate particle flux environment of collider or fixed target experiments in high energy physics HEP) and nuclear physics (NP). We present in this paper the performance of a 10 cm × 10 cm triple-GEM detector with capacitive-sharing (X--Y--U)-strip anode readout. Spatial resolutions of the order of $\sigma_{x}^{res}$ = 71.6 $\pm$ 0.8 $\mu$m for X-strips, $\sigma_{y}^{res}$ = 56.2 $\pm$ 0.9 $\mu$m for Y-strips and $\sigma_{u}^{res}$ = 75.2 $\pm$ 0.9 $\mu$m for U-strips have been obtained at a beam test at Thomas Jefferson National Accelerator Facility (Jefferson Lab). Modifications of the readout design of future prototypes to improve the spatial resolution and challenges in scaling to large-area MPGDs are discussed.
The LANL fork of the AthenaPK project, which contains curvlinear coordinates The Code is a set of modifications to AthenaPK, an existing open source 3D hydrodynamics and magnetohydrodynamics simulation software for astrophysics, which enable simulation with uniform curvilinear geometries. Specifically it extends the existing Cartesian coordinates to uniform spherical coordinate and uniform cylindrical coordinate systems
The gyrokinetic (GK) field equation is a three-dimensional (3D) elliptic equation, but it is often simplified to a set of two-dimensional (2D) equations by assuming that the field does not vary along a specific direction. However, this simplification can introduce inevitable 0th-order numerical errors, as nonlinear mode coupling in toroidal geometry can produce undesirable harmonic modes that violate the assumption. In this work, we propose a novel directional finite difference method (FDM) with a local coordinate transformation to better resolve the target field of interest. The directional FDM can accurately solve 3D GK field equations without simplifications, which can overcome the limitations of conventional methods. The accuracy and efficiency of different FDMs are analyzed in great detail for a variety of geometries, from simple 2D Cartesian coordinates to realistic 3D curvilinear coordinates. The 0th-order numerical errors of simplified 2D GK equations were found to be more problematic for low-harmonic modes and low aspect ratio geometries such as spherical tokamaks. On the other hand, the directional 3D FDM can accurately resolve a much wider range of harmonic modes aligned to the direction of interest, including the low-harmonic modes. In conclusion, we demonstrate that the directional 3D FDM is a highly effective algorithm for solving the 3D GK field equations, achieving accuracy improvements of 10 to 100 times or more, particularly for low-harmonic modes in spherical tokamaks.
Here, in this article, we investigate the transverse dynamics of a single particle in a model integrable accelerator lattice, based on a McMillan axially-symmetric electron lens. Although the McMillan e-lens has been considered as a device potentially capable of mitigating collective space charge forces, some of its fundamental properties have not been described yet. The main goal of our work is to close this gap and understand the limitations and potentials of this device. It is worth mentioning that the McMillan axially symmetric map provides the first-order approximations of dynamics for a general linear lattice plus an arbitrary thin lens with motion separable in polar coordinates. Therefore, advancements in its understanding should give us a better picture of more generic and not necessarily integrable round beams. In the first part of the article, we classify all possible regimes with stable trajectories and find the canonical action-angle variables. This provides an evaluation of the dynamical aperture, Poincaré rotation numbers as functions of amplitudes, and thus determines the spread in nonlinear tunes. Also, we provide a parameterization of invariant curves, allowing for the immediate determination of the map image forward and backward in time. The second part investigates the particle dynamics as a function of system parameters. We show that there are three fundamentally different configurations of the accelerator optics causing different regimes of nonlinear oscillations. Each regime is considered in great detail, including the limiting cases of large and small amplitudes. In addition, we analyze the dynamics in Cartesian coordinates and provide a description of observable variables and corresponding spectra.
Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.
Machine learning potential (MLP) has been a popular topic in recent years for its capability to replace expensive first-principles calculations in some large systems. Meanwhile, message passing networks have gained significant attention due to their remarkable accuracy, and a wave of message passing networks based on Cartesian coordinates has emerged. However, the information of the node in these models is usually limited to scalars, and vectors. In this work, we propose High-order Tensor message Passing interatomic Potential (HotPP), an E(n) equivariant message passing neural network that extends the node embedding and message to an arbitrary order tensor. By performing some basic equivariant operations, high order tensors can be coupled very simply and thus the model can make direct predictions of high-order tensors such as dipole moments and polarizabilities without any modifications. The tests in several datasets show that HotPP not only achieves high accuracy in predicting target properties, but also successfully performs tasks such as calculating phonon spectra, infrared spectra, and Raman spectra, demonstrating its potential as a tool for future research.
The authors present SHarmonic, a new implementation of the spherical harmonics targeted for electronic-structure calculations. Their approach is to use explicit formulas for the harmonics written in terms of normalized Cartesian coordinates. This approach results in a code that is as precise as other implementations while being at least one order of magnitude more computationally efficient. The library can run on graphics processing units as well, achieving an additional order of magnitude in execution speed. This new implementation is simple to use and is provided under an open-source license; it can be readily used by other codes to avoid the error-prone and cumbersome implementation of the spherical harmonics.
Theoretically and computationally describing the operation of nanodiodes requires characterizing the transitions between multiple electron emission mechanisms for nanodiodes with complicated geometries. This motivates our development of techniques to determine when simplified theories for individual mechanisms suffice compared to more complete, but more computationally expensive, models. Leveraging recent theories that define a canonical gap distance to translate planar theory to nonplanar diodes, we derive the conditions for the transitions among thermal emission, field emission, and space-charge-limited current density (SCLCD) in vacuum and with collisions for non-Cartesian coordinate systems, including spherical, cylindrical, and prolate spheroidal coordinate systems. Particle-in-cell (PIC) simulations of the current density as a function of applied voltage for a tip-to-plate geometry in vacuum agreed qualitatively with the asymptotes for thermal emission at low voltage and SCLCD at higher voltage using the canonical gap distance. As a result, this demonstrates the utility of this approach for guiding system design and suggests future extensions to save simulation time for more realistic geometries that are more computationally expensive.
Fringe fields in quadrupole magnets are usually neglected in studies of beam dynamics at accelerators. However, the extreme optical parameters present in the final focus of a collider such as the Electron–Ion Collider (EIC) may give rise to effects that should not be overlooked. The calculation of quadrupole fringe fields presented in this study follows the procedure outlined in Ref. [1], specialized to the case of a straight reference orbit (i.e., with no dipole field component). A right-handed Cartesian coordinate system is employed, with the $z$-axis aligned with the quadrupole axis and $x$ and $y$ denoting the horizontal and vertical transverse coordinates, respectively. The magnetic quadrupole field gradient, $G = \partial B_y / \partial x$, transitions from its peak value inside the quadrupole—where it is nearly independent of the longitudinal coordinate $z$—to zero at some distance beyond the magnet edge. Consequently, $G$ is treated as a function of $z$. The region over which this variation occurs is defined as the quadrupole fringe field region. The study begins with the development of a description of the magnetic field in the fringe region using a power-series expansion in the transverse coordinates $x$and $y$, consistent with the longitudinally varying gradient. A model for the $z$-dependence of the gradient is then proposed and adjusted to reproduce magnetic field data obtained from three-dimensional field calculations. To evaluate the impact of the fringe fields on beam dynamics, the corresponding vector potential is derived and incorporated into a Hamiltonian formulation of particle motion. The significance of the fringe fields is quantified by calculating the amplitude-dependent tune shift from the Hamiltonian. Using linear beam optics parameters of the Hadron Storage Ring (HSR) of the EIC, the tune shift due to the fringe fields of all quadrupole magnets in the IR-6 interaction region is evaluated. Finally, the resulting tune shifts are compared with those arising from other nonlinear field components present in the HSR.
The tritium migration analysis program (TMAP) has been used for tritium inventory tracking and analysis for several years, and the Multiphysics Object Oriented Simulation Environment (MOOSE)-based TMAP8 has several improvements over TMAP4 and TMAP7, such as support for multiple dimensions and non-cartesian coordinate systems, as well as interoperability with sub-apps at higher and lower length scales. We demonstrate that TMAP8 has the additional capacity to solve systems-level problems using zero-dimensional ordinary differential equations by reproducing a literature model which describes a systems-level fuel-cycle of tritium inventory in a hypothetical fusion power plant. The capacity to run several coupled multi-scale physics calculations as part of a single package will be necessary for accurate blanket and fuel-cycle design.
A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.
Entity is a new-generation, fully open-source particle-in-cell (PIC) code developed to overcome key limitations in astrophysical plasma modeling, particularly the extreme separation of scales and the performance challenges associated with evolving, GPU-centric computing infrastructures. It achieves hardware-agnostic performance portability across various GPU and CPU architectures using the Kokkos library. Crucially, Entity maintains a high standard for usability, clarity, and customizability, offering a robust and easy-to-use framework for developing new algorithms and grid geometries, which allows extensive control without requiring edits to the core source code. This paper details the core general-coordinate special relativistic module. Entity is the first PIC code designed to solve the Vlasov–Maxwell system in general coordinates, enabling a coordinate-agnostic framework that provides the foundational structure for straightforward extension to arbitrary coordinate geometries. The core methodology achieves numerical stability by solving particle equations of motion in the global orthonormal Cartesian basis, despite using generalized coordinates like Cartesian, axisymmetric spherical, and quasi-spherical grids. Charge conservation is ensured via a specialized current deposition technique using conformal currents. The code exhibits robust scalability and performance portability on major GPU platforms (AMD MI250X, NVIDIA A100, and Intel Max Series), with the 3D particle pusher and the current deposition operating efficiently at about 2 ns per particle per time step. Functionality is validated through a comprehensive suite of standard Cartesian plasma tests and the accurate modeling of relativistic magnetospheres in curvilinear axisymmetric geometries.
We introduce Mahakala, a Python-based, modular, radiative ray-tracing code for curved spacetimes. We employ Google's JAX framework for accelerated automatic differentiation, which can efficiently compute Christoffel symbols directly from the metric, allowing the user to easily and quickly simulate photon trajectories through non-Kerr spacetimes. JAX also enables Mahakala to run in parallel on both CPUs and GPUs. Mahakala natively uses the Cartesian Kerr–Schild coordinate system, which avoids numerical issues caused by the pole in spherical coordinate systems. We demonstrate Mahakala's capabilities by simulating 1.3 mm wavelength images (the wavelength of Event Horizon Telescope observations) of general relativistic magnetohydrodynamic simulations of low-accretion rate supermassive black holes. The modular nature of Mahakala allows us to quantitatively explore how different regions of the flow influence different image features. We show that most of the emission seen in 1.3 mm images originates close to the black hole and peaks near the photon orbit. We also quantify the relative contribution of the disk, forward jet, and counterjet to 1.3 mm images.
A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code, utilizes a set of field scalings and a coordinate mapping, reducing the Maxwell field problem in a cylindrical system to a Cartesian finite element Maxwell solver in the meridian plane. The latter obviates the cylindrical coordinate singularity in the symmetry axis. The choice of an unstructured finite element discretization enhances the geometrical flexibility of the BORPIC++ solver compared to the more traditional finite difference solvers. Symmetries in Maxwell’s equations are explored to decompose the problem into two dual polarization states with isomorphic representations that enable code reuse. The particle-in-cell scatter and gather steps preserve charge conservation at the discrete level. Our previous algorithm (BORPIC+) discretized the E and B field components of TE Φ and TM Φ polarizations on the finite element (primal) mesh. Here, we employ a new field-update scheme. Using the same finite element (primal) mesh, this scheme advances two sets of field components independently: (1) E and B of TE Φ polarized fields, (E z , E ρ , B Φ ) and (2) D and H of TM Φ polarized fields, (D Φ , H z , H ρ ). Since these field updates are not explicitly coupled, the new field solver obviates the coordinate singularity, which otherwise arises at the cylindrical symmetric axis, ρ = 0 when defining the discrete Hodge matrices (generalized finite element mass matrices). Here, a cylindrical perfectly matched layer is implemented as a boundary condition in the radial direction to simulate open space problems, with periodic boundary conditions in the axial direction. We investigate effects of charged particles moving next to the cylindrical perfectly matched layer. We model azimuthal currents arising from rotational motion of charged rings, which produce TMΦ polarized fields. Several numerical examples are provided to illustrate the first application of the algorithm.