Package ffx.algorithms.cli

@ParametersAreNonnullByDefault package ffx.algorithms.cli

The Algorithms CLI package defines options for PicoCLI command line scripts.

Since:

1.0

Related Packages

Package	Description
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).

Class	Description
AlgorithmsScript	Base class for scripts in the Algorithms package, providing some key functions.
AnnealOptions	Represents command line options for scripts that utilize simulated annealing.
BarostatOptions	Represents command line options for scripts that use a barostat/NPT.
DynamicsOptions	Represents command line options for scripts that run molecular dynamics.
LambdaParticleOptions	Represents command line options for scripts that utilize a mobile lambda particle, such as Thermodynamics.
ManyBodyOptions	Represents command line options for scripts that use a many-body expansion for global optimization.
MinimizeOptions	Represents command line options for scripts that involve local energy minimization.
MultiDynamicsOptions	Represents command line options for scripts that can create multiple walkers, such as multi-walker OST.
OSTOptions	Represents command line options for scripts that utilize variants of the Orthogonal Space Tempering (OST) algorithm.
RandomUnitCellOptions	Represents command line options for scripts that create randomized unit cells.
RepExOptions
RepexOSTOptions
ThermodynamicsOptions	Represents command line options for scripts that calculate thermodynamics.
ThermodynamicsOptions.ThermodynamicsAlgorithm	Represents categories of thermodynamics algorithms that must be handled differentially.