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 lowlevel 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, multidimensional
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 quasiinternal frame.

ffx.numerics.optimization 
The Optimization package implements the limitedmemory BroydenFletcherGoldfarbShanno (LBFGS)
algorithm for largescale 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 Bsplines 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 Xray package implements support for Xray and Neutron refinement.

ffx.xray.cli 
The Xray CLI package defines options for PicoCLI command line scripts.

ffx.xray.parsers 
The Parsers package reads CNS files and reads/writes MTZ files.
