Mathematical software

TABI
Referenced in 32 articles [sw18194]
solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a well-conditioned ... integral equations are discretized by centroid collocation. The linear system is solved by GMRES iteration ... compare results for the Poisson-Boltzmann and Poisson equations. We show that the treecode approximation...

AFMPB
Referenced in 12 articles [sw08875]
described an adaptive fast multipole Poisson-Boltzmann solver for computing the electrostatics in biomolecules. This ... boundary integral equation of the linearized Poisson-Boltzmann equation. Numerical experiments show the efficiency...

MIBPB
Referenced in 58 articles [sw08106]
package for electrostatic analysis. The Poisson–Boltzmann equation (PBE) is an established model ... further accelerates the rate of convergence of linear equation systems resulting from the MIBPB...

TMSmesh
Referenced in 21 articles [sw14719]
surface points by solving a nonlinear equation directly, polygonizes by connecting surface points through ... outputs a triangulated mesh. TMSmesh has a linear complexity with respect to the number ... boundary element solutions of the Poisson−Boltzmann equation, which directly gives rise to a route...

PB-AM
Referenced in 1 article [sw16459]
fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes...

DAFMPB
Referenced in 1 article [sw40371]
biomolecular systems modeled by the linearized Poisson-Boltzmann (LPB) equation. DAFMPB first reformulates ... patch scheme [33]. It solves the resulting linear system using GMRES, where it adopts...

PyCosmo
Referenced in 1 article [sw21683]
solution of the Einstein-Boltzmann equations governing the evolution of linear perturbations in the Universe ... based framework to solve this set of equations using a special purpose solver based ... uses a consistency relation of the field equations to adapt the time step and does ... symbolic representation of the Einstein-Boltzmann equation system in PyCosmo provides a convenient interface...

ORB5
Referenced in 12 articles [sw10369]
presented. It solves the gyrokinetic electrostatic equations including zonal flows in axisymmetric magnetic geometry ... present version of the code assumes a Boltzmann electron response on magnetic surfaces. It uses ... against other codes for a selection of linear and nonlinear tests...

DENOVO
Referenced in 13 articles [sw18081]
obtain accurate solutions to the Boltzmann transport equation. Denovo uses the Koch-Baker-Alcouffe parallel ... Krylov methods to solve the within-group equations. Krylov methods are far more efficient than ... provides diamond-difference, theta-weighted diamond-difference, linear-discontinuous finite element, trilinear-discontinuous finite element...

FeatLBE
Referenced in 1 article [sw31316]
numerical simulation of the Lattice Boltzmann equation (LBE). In Hübner and Turek (Computing ... intensity had been proposed for radiative transfer equations which we adapt here ... analogous (semi-discretized) integro-differential equation with constant characteristics. Thus, we combine an efficient finite ... short-characteristic upwinding, we obtain an efficient linear solver for transport dominated configurations (macroscopic Stokes...

TABI