Tools::Atom Struct Reference

Detailed Description

A point particle in an MD simulation.

Definition at line 23 of file tools/chemistry/Atom.h.

#include <Atom.h>

Public Attributes
Vector	position
	Atom position. More...
Vector	velocity
	Atom velocity. More...
int	typeId
	Atom type index. More...
int	id
	Unique global index (tag) More...
int	speciesId
	Index for species of parent molecule. More...
int	moleculeId
	Index of molecule with its species. More...
int	atomId
	Index of atom within its molecule. More...

Member Data Documentation

Vector Tools::Atom::position

Atom position.

Definition at line 29 of file tools/chemistry/Atom.h.

Referenced by Tools::CellList::placeAtom(), Tools::DdMdConfigReader::readConfig(), Tools::HoomdConfigReader::readConfig(), Tools::LammpsDumpReader::readFrame(), Tools::DdMdTrajectoryReader::readFrame(), and Tools::PairEnergy::sample().

Vector Tools::Atom::velocity

Atom velocity.

Definition at line 32 of file tools/chemistry/Atom.h.

Referenced by Tools::DdMdConfigReader::readConfig(), and Tools::HoomdConfigReader::readConfig().

int Tools::Atom::typeId

Atom type index.

Definition at line 35 of file tools/chemistry/Atom.h.

Referenced by Tools::DdMdConfigReader::readConfig(), Tools::HoomdConfigReader::readConfig(), and Tools::PairEnergy::sample().

int Tools::Atom::id

Unique global index (tag)

Definition at line 38 of file tools/chemistry/Atom.h.

Referenced by Tools::AtomStorage::add(), Tools::DdMdConfigReader::readConfig(), and Tools::HoomdConfigReader::readConfig().

int Tools::Atom::speciesId

Index for species of parent molecule.

Definition at line 41 of file tools/chemistry/Atom.h.

Referenced by Tools::Species::addAtom(), Tools::Species::begin(), Tools::DdMdConfigReader::readConfig(), and Tools::ConfigReader::setAtomContexts().

int Tools::Atom::moleculeId

Index of molecule with its species.

Definition at line 44 of file tools/chemistry/Atom.h.

Referenced by Tools::Species::addAtom(), Tools::Species::begin(), Tools::DdMdConfigReader::readConfig(), and Tools::ConfigReader::setAtomContexts().

int Tools::Atom::atomId

Index of atom within its molecule.

Definition at line 47 of file tools/chemistry/Atom.h.

Referenced by Tools::Species::addAtom(), Tools::Species::begin(), Tools::DdMdConfigReader::readConfig(), and Tools::ConfigReader::setAtomContexts().

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The documentation for this struct was generated from the following file:

• tools/chemistry/Atom.h