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Register a new userImplicit temporal discretization and exact energy conservation for particle methods applied to the Poisson-Boltzmann equation
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Wereportonanewmultiscalemethodapproachforthestudyofsystemswith wide separation of short-range forces acting on short time scales and long-range forces acting on much slower scales. We consider the case of the Poisson-Boltzmann equation that describes the long-range forces using the Boltzmann formula (i.e. we assume the medium to be in quasi local thermal equilibrium). We developed a new approach where fields and particle information (mediated by the equations for their moments) are solved self-consistently. The new approach is implicit and numerically stable, providing exact energy conservation. We tested different implementations all leading to exact energy conservation. The new method requires the solution of a large set of non-linear equations. We considered three solution strategies: Jacobian Free Newton Krylov, an alternative, called field hiding, based on hiding part of the residual calculation and replacing them with direct solutions and a Direct Newton Schwarz solver that considers simplified single particle-based Jacobian. The field hiding strategy proves to be the most efficient approach.
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Recently, a family of models that couple multifluid systems to the full Maxwell equations draw a lot of attention in laboratory, space, and astrophysical plasma modeling. These models are more complete descriptions of the plasma than reduced models like magnetohydrodynamic (MHD) since they naturally retain non-ideal effects like electron inertia, Hall term, pressure anisotropy/nongyrotropy, etc. One obstacle to broader application of these model is that an explicit treatment of their source terms leads to the need to resolve rapid kinetic processes like plasma oscillation and electron cyclotron motion, even when they are not important. In this paper, we suggest two ways to address this issue. First, we derive the analytic forms solutions to the source update equations, which can be implemented as a practical, but less generic solver. We then develop a time-centered, locally implicit algorithm to update the source terms, allowing stepping over the fast kinetic time-scales. For a plasma with $S$ species, the locally implict algorithm involves inverting a local $3S+3$ matrix only, thus is very efficient. The performance can be further elevated by using the direct update formulas to skip null calculations. Benchmarks illustrated the exact energy-conservation of the locally implicit solver, as well as its efficiency and robustness for both small-scale, idealized problems and large-scale, complex systems. The locally implicit algorithm can be also easily extended to include other local sources, like collisions and ionization, which are difficult to solve analytically.
Based on the previously developed Energy Conserving Semi Implicit Method (ECsim) code, we present its cylindrical implementation, called ECsim-CYL, to be used for axially symmetric problems. The main motivation for the development of the cylindrical version is to greatly improve the computational speed by utilizing cylindrical symmetry. The ECsim-CYL discretizes the field equations in two-dimensional cylindrical coordinates using the finite volume method . For the particle mover, it uses a modification of ECsims mover for cylindrical coordinates by keeping track of all three components of velocity vectors, while only keeping radial and axial coordinates of particle positions. In this paper, we describe the details of the algorithm used in the ECsim-CYL and present a series of tests to validate the accuracy of the code including a wave spectrum in a homogeneous plasmas inside a cylindrical waveguide and free expansion of a spherical plasma ball in vacuum. The ECsim-CYL retains the stability properties of ECsim and conserves the energy within machine precision, while accurately describing the plasma behavior in the test cases.
This work presents new parallelizable numerical schemes for the integration of Dissipative Particle Dynamics with Energy conservation (DPDE). So far, no numerical scheme introduced in the literature is able to correctly preserve the energy over long times and give rise to small errors on average properties for moderately small timesteps, while being straightforwardly parallelizable. We present in this article two new methods, both straightforwardly parallelizable, allowing to correctly preserve the total energy of the system. We illustrate the accuracy and performance of these new schemes both on equilibrium and nonequilibrium parallel simulations.
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties, such as exponential nonlinear term, strong singularity by the source terms, and complex dielectric interface. Recently, a pseudo-time ghost-fluid method (GFM) has been developed in [S. Ahmed Ullah and S. Zhao, Applied Mathematics and Computation, 380, 125267, (2020)], by analytically handling both nonlinearity and singular sources. The GFM interface treatment not only captures the discontinuity in the regularized potential and its flux across the molecular surface, but also guarantees the stability and efficiency of the time integration. However, the molecular surface definition based on the MSMS package is known to induce instability in some cases, and a nontrivial Lagrangian-to-Eulerian conversion is indispensable for the GFM finite difference discretization. In this paper, an Eulerian Solvent Excluded Surface (ESES) is implemented to replace the MSMS for defining the dielectric interface. The electrostatic analysis shows that the ESES free energy is more accurate than that of the MSMS, while being free of instability issues. Moreover, this work explores, for the first time in the PBE literature, adaptive time integration techniques for the pseudo-transient simulations. A major finding is that the time increment $Delta t$ should become smaller as the time increases, in order to maintain the temporal accuracy. This is opposite to the common practice for the steady state convergence, and is believed to be due to the PBE nonlinearity and its time splitting treatment. Effective adaptive schemes have been constructed so that the pseudo-time GFM methods become more efficient than the constant $Delta t$ ones.
We describe how regularization of lattice Boltzmann methods can be achieved by modifying dissipation. Classes of techniques used to try to improve regularization of LBMs include flux limiters, enforcing the exact correct production of entropy and manipulating non-hydrodynamic modes of the system in relaxation. Each of these techniques corresponds to an additional modification of dissipation compared with the standard LBGK model. Using some standard 1D and 2D benchmarks including the shock tube and lid driven cavity, we explore the effectiveness of these classes of methods.
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