DdMd::AtomContext Struct Reference

Detailed Description

Descriptor for context of an Atom within a molecule and species.

The information in the AtomContext struct is not used by any of the essential algorithms of ddSim, but may be used by some analyzers or modifiers.

Definition at line 21 of file AtomContext.h.

#include <AtomContext.h>

Public Member Functions
	AtomContext ()
	Default constructor. More...
void	clear ()
	Set all data members to null default values. More...

Public Attributes
int	speciesId
	Index of the species of molecule. More...
int	moleculeId
	Index of molecule within its molecular species. More...
int	atomId
	Index of atom within its parent molecule. More...

Constructor & Destructor Documentation

DdMd::AtomContext::AtomContext ( )

inline

Default constructor.

Definition at line 61 of file AtomContext.h.

Member Function Documentation

void DdMd::AtomContext::clear ( )

inline

Set all data members to null default values.

Definition at line 70 of file AtomContext.h.

References atomId, moleculeId, and speciesId.

Referenced by DdMd::AtomArray::allocate().

Member Data Documentation

int DdMd::AtomContext::speciesId

Index of the species of molecule.

Definition at line 27 of file AtomContext.h.

Referenced by clear(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), and DdMd::DdMdConfigIo::writeConfig().

int DdMd::AtomContext::moleculeId

Index of molecule within its molecular species.

Definition at line 32 of file AtomContext.h.

Referenced by clear(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), and DdMd::DdMdConfigIo::writeConfig().

int DdMd::AtomContext::atomId

Index of atom within its parent molecule.

Note: This takes on values from zero to one less than the number of of atoms within the molecule. Corresponding atoms in identical molecules have the same atomId. This index is thus distinct from the global atom id returned by Atom::id(), which is unique within the system.

Definition at line 43 of file AtomContext.h.

Referenced by clear(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), and DdMd::DdMdConfigIo::writeConfig().

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

• AtomContext.h