Packages 
Package Description
edu.rit.http
The HTTP package provides a lightweight HTTP/1.0 server.
edu.rit.io
The IO package provides the DataOutputStream and DataInputStream classes to read/write primitive data types and strings in binary form.
edu.rit.mp
The MP package provides low-level support for Message Passing.
edu.rit.mp.buf
The BUF package provides data buffers for Message Passing.
edu.rit.pj
The PJ package (Parallel Java) support shared memory, message passing and hybrid shared memory/message passing parallelization in pure Java.
edu.rit.pj.cluster
The Cluster package contains the Parallel Java cluster middleware and the main program for the PJ Job Scheduler Daemon process for a parallel computer.
edu.rit.pj.io
The IO package represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
edu.rit.pj.job
The Job package encapsulates a job and its attributes.
edu.rit.pj.reduction
The Reduction package provides a variety of reduction variables.
edu.rit.pj.replica
The Replica package provides replicated, shared reduction variables.
edu.rit.util
The Util package contains utilities that support the PJ API.
ffx
Force Field X implements fixed charge and polarizable atomic multipole molecular mechanics potentials, local and global optimization, molecular dynamics, free energy differences, etc, with special support for crystal space groups.
ffx.algorithms
The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli
The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics
The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators
The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats
The Thermostats package implements thermostats for molecular dynamics simulations.
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.optimize.anneal  
ffx.algorithms.optimize.manybody  
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).
ffx.crystal
The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.numerics
The Numerics package has support for atomic double arrays, FFTs (1D and 3D), numerical integration (1D), complex numbers, vector operations, multipole tensors, multi-dimensional optimization, special functions, splines and switching functions.
ffx.numerics.atomic
The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.numerics.estimator  
ffx.numerics.fft
The FFT package implements 1D and 3D FFTs of real or complex valued data, including SMP parallelization of 3D transforms and convolution using the Parallel Java library.
ffx.numerics.func1d  
ffx.numerics.integrate
The Integrate package implements 1D numerical integration.
ffx.numerics.math
The Math package implements complex numbers, a software square root, and vector operations.
ffx.numerics.multipole
The Multipole package computes derivatives of 1/|r| via recursion to arbitrary order using Cartesian multipoles in either a global frame or a quasi-internal frame.
ffx.numerics.optimization
The Optimization package implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
ffx.numerics.special
The Special package implements special functions including the complex error function (Erf) and the modified Bessel functions.
ffx.numerics.spline
The Spline package implements implements B-splines and Tricubic splines.
ffx.numerics.switching
The Switching package implements univariate switching functions.
ffx.numerics.tornado  
ffx.potential
The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli
The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands  
ffx.potential.constraint  
ffx.potential.extended
The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e.
ffx.potential.nonbonded
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit  
ffx.potential.nonbonded.octree  
ffx.potential.nonbonded.pme  
ffx.potential.parameters
The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers
The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils
The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace
The Real Space package implements real space structure refinement.
ffx.realspace.cli
The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.parsers
The Parsers package reads and writes CCP4 map files.
ffx.ui
The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.behaviors
The Behaviors package contains Java3D Behaviors that turn user actions into scenegraph changes.
ffx.ui.commands
The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.ui.properties
The Properties package will eventually encapsulate internationalization features.
ffx.utilities
The Utilities package implements a variety of useful Directory, File, Port, String, etc functionality.
ffx.xray
The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli
The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.parsers
The Parsers package reads CNS files and reads/writes MTZ files.