Tools Namespace Reference

Single-processor classes for pre- and post-processing MD trajectories. More...

Classes
class	Analyzer
	Abstract base for periodic output and/or analysis actions. More...
class	AnalyzerManager
	Manager for a list of Analyzer objects. More...
struct	Atom
	A point particle in an MD simulation. More...
class	AtomMSD
	Mean-squared displacement of specific atoms in specific species. More...
class	AtomStorage
	Container for a set of atoms. More...
class	Cell
	A single cell in a CellList. More...
class	CellAtom
	Data for an atom in a CellList. More...
class	CellList
	A cell list used only to identify nearby atom pairs. More...
class	ChainMaker
	Generates a simulation box full of randomly generated linear polymers. More...
class	ConfigReader
	Abstract reader/writer for configuration files. More...
class	ConfigReaderFactory
	Default Factory for subclasses of ConfigReader. More...
class	Configuration
	An instantaneous molecular dynamics configuration. More...
class	ConfigWriter
	Abstract reader/writer for configuration files. More...
class	ConfigWriterFactory
	Default Factory for subclasses of ConfigWriter. More...
class	DdMdConfigReader
	Native / default DdMd format for configuration files. More...
class	DdMdConfigWriter
	Native / default DdMd format for configuration files. More...
class	DdMdTrajectoryReader
	Reader for lammps dump trajectory file format. More...
class	Group
	A group of covalently interacting atoms. More...
class	GroupStorage
	A container for Group<N> objects. More...
class	HoomdConfigReader
	Reader for Hoomd-blue XML configuration files. More...
class	HoomdConfigWriter
	Hoomd-blue XML format for configuration files. More...
class	LammpsDumpReader
	Reader for lammps dump trajectory file format. More...
class	LammpsDumpWriter
	Write a trajectory in the Lammps dump format. More...
class	LogStep
	Write step number to log. More...
class	Molecule
	An Molecule has a sequence of atoms, and belongs to an Species. More...
class	PairEnergy
	Analyzer to compute total nonbonded pair energy. More...
class	Processor
	A post-processor for analyzing outputs of MD simulations. More...
class	ProcessorAnalyzerFactory
	Factory for Tools::Analyzer objects. More...
class	ProcessorAnalyzerManager
	Manager for a list of Analyzer objects. More...
class	Species
	A set of identical molecules. More...
class	TrajectoryReader
	Abstract trajectory file reader. More...
class	TrajectoryReaderFactory
	Default Factory for subclasses of TrajectoryReader. More...
class	TrajectoryWriter
	Based class for classes that write trajectories to a single file. More...
class	TypeMap
	Map between type names and type ids. More...

Functions
template<int N>
std::istream &	operator>> (std::istream &in, Group< N > &group)
	istream extractor (>>) for a Group. More...
template<int N>
std::ostream &	operator<< (std::ostream &out, const Group< N > &group)
	ostream inserter (<<) for a Group. More...
std::istream &	operator>> (std::istream &in, Species &species)
	istream extractor (>>) for a Species. More...
std::ostream &	operator<< (std::ostream &out, const Species &species)
	ostream inserter (<<) for a Species. More...

Detailed Description

Single-processor classes for pre- and post-processing MD trajectories.

Function Documentation

template<int N>

std::istream& Tools::operator>>	(	std::istream &	in,
		Group< N > &	group
	)

istream extractor (>>) for a Group.

Parameters

in	input stream
group	Group to be read from stream

Returns

modified input stream

Definition at line 52 of file tools/chemistry/Group.h.

References Tools::Group< N >::atomIds, Tools::Group< N >::id, and Tools::Group< N >::typeId.

template<int N>

std::ostream& Tools::operator<<	(	std::ostream &	out,
		const Group< N > &	group
	)

ostream inserter (<<) for a Group.

Format on one line with no line break:

Parameters

out	output stream
group	Group to be written to stream

Returns

modified output stream

Definition at line 72 of file tools/chemistry/Group.h.

std::istream & Tools::operator>>	(	std::istream &	in,
		Species &	species
	)

istream extractor (>>) for a Species.

Parameters

in	input stream
species	Species to be read from stream

Returns

modified input stream

Definition at line 206 of file tools/chemistry/Species.cpp.

References Simp::Species::nAtom_.

std::ostream & Tools::operator<<	(	std::ostream &	out,
		const Species &	species
	)

ostream inserter (<<) for a Species.

Format on one line with no line break:

Parameters

out	output stream
species	Species to be written to stream

Returns

modified output stream

Definition at line 217 of file tools/chemistry/Species.cpp.

References Simp::Species::nAtom_.