Modules

Here is a list of all modules:

[detail level 123]

Programs	Executable simulation and analysis programs
▼Util namespace	Group of modules containing classes in the Util namespace
Accumulators	Statistical operations (e.g., averages or autocorrelations) on a data sequence
Serialization	Serialization of C++ objects to/from file or memory
▼Container Templates	Container and iterator class templates
Object Arrays	Array containers that store objects by value, and related iterators
Pointer Arrays	Array containers that store pointers to objects, and related iterators
Matrix Containers	Two-dimensional array containers that store by objects value
Linked List	A simple linked list implementation and associated iterator
Iterators	Iterators for use with particular containers
Crystal	Crystal periodicity and symmetry groups
Output Format	Utilities to simplify formatted C++ stream output
Mathematics	Mathematical constants and utilities
Miscellaneous Utilities	Miscellaneous utility classes and functions
Managers and Factories	A Manager is a container for items with a common base class
Parameter File IO	Classes used to read parameters from a parameter file
Random	Random numbers and processes
Signals (Observer Pattern)	Classes used to implement the observer design pattern
Space (Vector, Tensor)	Classes that represent spatial Vectors, Tensors, etc
Xml Tag Parsers	Classes to verify and parse XML markup tags
▼Simp namespace	Simp namespace
Boundary	Unit cells for periodic boundary conditions
Statistical Ensembles	Statistical mechanical ensembles for specific macro-variables
▼Interactions	Potential energy functions
Angle Interactions	Potential functions for covalent angle interactions
Bond Interactions	Covalent bond interaction potential energy functions
Dihedral Interactions	Potential functions for covalent dihedral interactions
External Interactions	Potential functions for external one-body interactions
Pair Interactions	Potential functions for non-bonded pair interactions
Species	Classes that represent molecular species
▼McMd namespace	McMd namespace (single-processor MC and MD)
▼Analyzers	Classes that implement data analysis or output operations
MD Analyzers	Analyzers for molecular dynamics (MD) simulations with mdSim
MC Analyzers	Analyzers for Monte Carlo (MC) simulations with mcSim
MC/MD Analyzers	Analyzers for either MC or MD simulations
Chemical Structure	Classes that describe atoms, molecules, and groups of atoms
▼Commands	Operations that can be invoked from the command script
MD Commands	Commands for molecular dynamics (MD) simulations with mdSim
MC Commands	Commands for Monte Carlo (MC) simulations with mcSim
MC/MD Commands	Commands for either MC or MD simulations
Configuration File IO	A ConfigIo object can read and write the configuration file for a System
Generators	Classes that generate random initial configurations
Monte Carlo Moves	This module contains all McMove (Monte Carlo Move) classes
Molecular Dynamics Integrators	Molecular dynamics integration algorithms
Nonbonded Neighbors	Classes used to keep track of nonbonded neighbors
Free Energy Perturbation	Classes that implement free energy perturbation theory and replica exchange
▼Potential Energies	Classes used by a System calculate potential energies
Pair Potentials	Nonbonded pair potentials
Bond Potentials	Covalent 2-body bond potentials
Angle Potentials	Covalent 3-body angle potentials
Dihedral Potentials	Covalent 4-body dihedral potentials
Coulomb Potentials	Coulomb potentials, implemented using Ewald separation
External Potentials	External one-body potentials
Special Potentials	Special (i.e., specialized) potentials
Managers	A Manager is a container for objects with a common base class
Simulations	A Simulation object represents a complete simulation
Systems	A System is a set of interacting Molecules enclosed by a Boundary
Trajectory Readers	Classes that can read trajectory files for analysis
▼DdMd namespace	DdMd namespace (parallel domain-decomposition MD)
▼Analyzers	Classes that implement data analysis or output operations
Analyzer Base	Base classes for analyzers
Energy Analyzers	Analyzer classes that analyze energies
Miscellaneous Analyzers	Analyzer classes (miscellaneous)
Scattering Analyzers	Analyzer classes that analyze spatial correlations
Stress Analyzers	Analyzer classes that analyze stress or boundary dimensions
Trajectory Analyzers	Analyzer classes that write trajectories to file
Chemical Structure	Classes that describe atoms, molecules, and groups of atoms
MPI Communication	Classes that control interprocessor communication
ConfigIos	Config file reader / writers
MD Integrators	Molecular dynamics integration algorithms
Modifiers	Actions that can modify the state of the system
Nonbonded Neighbors	Classes used to keep track of nonbonded neighbors
▼Potential Energies	Classes used to calculate potential energies
Pair Potentials	Classes that represent non-bonded pair potentials
Bond Potentials	Classes that represent covalent bond potentials
Angle Potentials	Classes that represent covalent angle potentials
Dihedral Potentials	Classes that represent covalent dihedral potentials
External Potentials	Classes that represent external one-body potentials
Simulations	Complete simulations
▼Storage	Containers and iterators for atoms and groups
Atom Storage	Containers and iterators for atoms
Group Storage	Containers and iterators for covalent groups (bonds etc.)
▼Tools namespace	Tools namespace (post-processing for MD trajectories)
Analyzers	Single-processor Classes for data analysis or data output operations
Chemical Structure	Classes that model atoms, groups, molecules, and species
▼Config File IO	Configuration file readers and writers
Config File Readers	Configuration file readers
Config File Writers	Configuration file writers
Nonbonded Neighbors	Classes to efficiently identify non-bonded neighbors
Storage	Classes that store atoms and groups
Trajectory File Readers
Unit Test Framework	A framework for constructing unit tests for other classes