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.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.
|
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