
SpaceEx
 Referenced in 67 articles
[sw10939]
 hybrid systems with piecewise affine, nondeterministic dynamics. It combines polyhedra and support function representations ... over previous work by using variable time steps to guarantee a given local error bound...

TINKER
 Referenced in 10 articles
[sw04095]
 general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER ... space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise...

CellPLoc
 Referenced in 90 articles
[sw09126]
 subcellular locations. Proteins with multiple locations or dynamic features of this kind are particularly interesting ... drug discovery. This protocol is a stepbystep guide ... CellPLoc package. The computational time for each prediction is less than...

XTOR
 Referenced in 19 articles
[sw03221]
 time steps are only weakly limited by the departure of the nonlinear MHD dynamics from...

Nek5000
 Referenced in 66 articles
[sw08064]
 spectralelement code Nek5000 to investigate the dynamics of nonlinear flows in moderately complex geometries ... using matrixfree methods adopting the timestepping Arnoldi approach. We present here our implementation...

WIGGLE
 Referenced in 10 articles
[sw02594]
 coordinate. The theory of conventional constrained molecular dynamics (MD) simulations is reexamined based ... simulations with internal constraints. At each time step, the algorithm utilizes the constrained accelerations derived...

GSHMC
 Referenced in 16 articles
[sw02631]
 momentum refreshment step. This property seems desirable for keeping some of the dynamic information throughout ... process similar to stochastic Langevin and Brownian dynamics simulations. It is, however, ultimate ... that the rejection rate in the molecular dynamics part is kept at a minimum. Otherwise ... dynamics trajectories. The modified energy is based on backward error results for symplectic timestepping...

Featherweight Java
 Referenced in 90 articles
[sw16204]
 type safety. We carry this process a step further, omitting almost all features ... feel,” providing classes, methods, fields, inheritance, and dynamic typecasts with a semantics closely following Java ... extended system formalizes for the first time some of the key features...

M.DynaMix
 Referenced in 3 articles
[sw09596]
 mixtures. A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures ... treat the Coulombic interactions. Double timestep or constrained dynamics schemes are included. An external...

MDVRY
 Referenced in 2 articles
[sw00566]
 dipoles are calculated at each time step of the dynamics through the dynamics of additional ... with the dipoles. This method saves computer time and allows to study polarized solvated proteins...

OpenAD/F
 Referenced in 21 articles
[sw09380]
 sequences of vertex, edge, and face elimination steps. Specifically, for the generation of adjoint codes ... example from geophysical fluid dynamics, a nonlinear timedependent scalable, yet simple, barotropic ocean model...

nsCouette
 Referenced in 1 article
[sw32576]
 pseudospectral spatial discretization and dynamic timestepping. It is implemented in modern Fortran with...

Hondo
 Referenced in 22 articles
[sw08706]
 large deformation elastic and inelastic transient dynamic response of two dimensional solids. To accommodate ... time, the program performs the integration using a central difference method time integrator ... Since the time integration scheme is only conditionally stable with respect to step size...

ALPS
 Referenced in 22 articles
[sw08907]
 dynamic timeevolving block decimation (TEBD) code, and quantum Monte Carlo solvers for dynamical mean ... applications, which, for instance, greatly simplify the steps of porting a serial code onto...

AHFinderDirect
 Referenced in 25 articles
[sw04972]
 relativity. In 3 + 1 numerical simulations of dynamic blackhole spacetimes, it is useful ... each slice of a time evolution. A number of AH finders are available, but they ... practically usable at each time step. Here I present a new AH finder, AHFINDERDIRECT, which...

OPTCON
 Referenced in 14 articles
[sw02660]
 algorithm for the optimal control of nonlinear dynamic control that allows for additive uncertainty ... system equations. The first step consists in approximating the timeinvariant nonlinear system...

TREE
 Referenced in 2 articles
[sw03080]
 times requiring millions of time steps. Appropriate domain decomposition and dynamic data management were employed ... million particles and a half million time steps. For the long temporal trajectories of relaxation...

real2dXZcuda
 Referenced in 2 articles
[sw18231]
 time over small time steps. The method yields the solution of dynamical problems...

SALE3D
 Referenced in 11 articles
[sw23716]
 simplified numerical fluiddynamics computing technique for calculating timedependent flows in three dimensions ... subsonic without stringent constraints on the time step. In addition, the grid vertices...

YADE
 Referenced in 13 articles
[sw06761]
 integration scheme (Lagrangian method). The threedimensional dynamics equations based on the classical Newtonian approach ... each particle is kept at every time step. Contact forces depend on the particle geometry...