• 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...
  • BEMLIB

  • Referenced in 115 articles [sw00005]
  • BEMLIB is a boundary-element software library of...
  • FIDAP

  • Referenced in 37 articles [sw00006]
  • FIDAP (A Fluid Dynamics Analysis Program). This paper...
  • ADOL-C

  • Referenced in 257 articles [sw00019]
  • ADOL-C: Automatic Differentiation of C/C++. We present...
  • ANSYS

  • Referenced in 713 articles [sw00044]
  • ANSYS offers a comprehensive software suite that spans...
  • ATLAS

  • Referenced in 199 articles [sw00056]
  • This paper describes the Automatically Tuned Linear Algebra...
  • BoomerAMG

  • Referenced in 200 articles [sw00086]
  • BoomerAMG: A parallel algebraic multigrid solver and preconditioner...
  • CASA

  • Referenced in 111 articles [sw00108]
  • CASA is a special-purpose system for computational...
  • CGAL

  • Referenced in 402 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • Chaste

  • Referenced in 54 articles [sw00122]
  • Chaste: incorporating a novel multi-scale spatial and...