One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the current simulation. More...

#include "brains/SimInfo.hpp"

Public Types
using	MoleculeIterator = std::map<int, Molecule*>::iterator

Public Member Functions
	SimInfo (ForceField ff, Globals simParams)
	Constructor of SimInfo.
bool	addMolecule (Molecule *mol)
	Adds a molecule.
bool	removeMolecule (Molecule *mol)
	Removes a molecule from SimInfo.
int	getNGlobalMolecules ()
	Returns the total number of molecules in the system.
int	getNGlobalAtoms ()
	Returns the total number of atoms in the system.
int	getNGlobalCutoffGroups ()
	Returns the total number of cutoff groups in the system.
int	getNGlobalIntegrableObjects ()
	Returns the total number of integrable objects (total number of rigid bodies plus the total number of atoms which do not belong to the rigid bodies) in the system.
int	getNGlobalRigidBodies ()
	Returns the total number of integrable objects (total number of rigid bodies plus the total number of atoms which do not belong to the rigid bodies) in the system.
unsigned int	getNGlobalBonds ()
	Returns the number of global bonds.
unsigned int	getNGlobalBends ()
	Returns the number of global bends.
unsigned int	getNGlobalTorsions ()
	Returns the number of global torsions.
unsigned int	getNGlobalInversions ()
	Returns the number of global inversions.
unsigned int	getNGlobalConstraints ()
size_t	getNMolecules ()
	Returns the number of local molecules.
unsigned int	getNAtoms ()
	Returns the number of local atoms.
unsigned int	getNLocalCutoffGroups ()
	Returns the number of effective cutoff groups on local processor.
unsigned int	getNBonds ()
	Returns the number of local bonds.
unsigned int	getNBends ()
	Returns the number of local bends.
unsigned int	getNTorsions ()
	Returns the number of local torsions.
unsigned int	getNInversions ()
	Returns the number of local inversions.
unsigned int	getNRigidBodies ()
	Returns the number of local rigid bodies.
unsigned int	getNIntegrableObjects ()
	Returns the number of local integrable objects.
unsigned int	getNCutoffGroups ()
	Returns the number of local cutoff groups.
unsigned int	getNConstraints ()
	Returns the total number of constraints in this SimInfo.
Molecule *	beginMolecule (MoleculeIterator &i)
	Returns the first molecule in this SimInfo and intialize the iterator.
Molecule *	nextMolecule (MoleculeIterator &i)
	Returns the next avaliable Molecule based on the iterator.
int	getNFluctuatingCharges ()
	Returns the total number of fluctuating charges that are present.
int	getNdf ()
	Returns the number of degrees of freedom.
int	getNdfLocal ()
	Returns the number of degrees of freedom (LOCAL).
int	getNdfRaw ()
	Returns the number of raw degrees of freedom.
int	getNdfTrans ()
	Returns the number of translational degrees of freedom.
void	setFdf (int fdf)
	sets the current number of frozen degrees of freedom
int	getFdf ()
int	getNZconstraint ()
	Returns the total number of z-constraint molecules in the system.
void	setNZconstraint (int nZconstraint)
	Sets the number of z-constraint molecules in the system.
SnapshotManager *	getSnapshotManager ()
	Returns the snapshot manager.
int	getAtomStorageLayout ()
	Returns the storage layouts (computed by SimCreator).
int	getRigidBodyStorageLayout ()
int	getCutoffGroupStorageLayout ()
void	setAtomStorageLayout (int asl)
	Sets the storage layouts (computed by SimCreator).
void	setRigidBodyStorageLayout (int rbsl)
void	setCutoffGroupStorageLayout (int cgsl)
void	setSnapshotManager (SnapshotManager *sman)
	Sets the snapshot manager.
ForceField *	getForceField ()
	Returns the force field.
Globals *	getSimParams ()
Utils::RandNumGenPtr	getRandomNumberGenerator () const
void	update ()
	update
void	prepareTopology ()
	Do final bookkeeping before Force managers need their data.
LocalIndexManager *	getLocalIndexManager ()
	Returns the local index manager.
int	getMoleculeStampId (int globalIndex)
MoleculeStamp *	getMoleculeStamp (int id)
	Returns the molecule stamp.
size_t	getNMoleculeStamp ()
	Return the total number of the molecule stamps.
Molecule *	getMoleculeByGlobalIndex (int index)
	Finds a molecule with a specified global index.
int	getGlobalMolMembership (int id)
std::vector< int >	getGlobalAtomIndices ()
	returns a vector which maps the local atom index on this processor to the global atom index.
std::vector< int >	getGlobalGroupIndices ()
	returns a vector which maps the local cutoff group index on this processor to the global cutoff group index.
std::string	getFinalConfigFileName ()
void	setFinalConfigFileName (const std::string &fileName)
std::string	getRawMetaData ()
void	setRawMetaData (const std::string &rawMetaData)
std::string	getDumpFileName ()
void	setDumpFileName (const std::string &fileName)
std::string	getStatFileName ()
void	setStatFileName (const std::string &fileName)
std::string	getReportFileName ()
void	setReportFileName (const std::string &fileName)
std::string	getRestFileName ()
void	setRestFileName (const std::string &fileName)
void	setGlobalGroupMembership (const std::vector< int > &ggm)
	Sets GlobalGroupMembership.
void	setGlobalMolMembership (const std::vector< int > &gmm)
	Sets GlobalMolMembership.
bool	isTopologyDone ()
bool	getCalcBoxDipole ()
bool	getCalcBoxQuadrupole ()
bool	getUseAtomicVirial ()
void	addProperty (std::shared_ptr< GenericData > genData)
	Adds property into property map.
void	removeProperty (const std::string &propName)
	Removes property from PropertyMap by name.
std::vector< std::string >	getPropertyNames ()
	Returns all names of properties.
std::vector< std::shared_ptr< GenericData > >	getProperties ()
	Returns all of the properties in PropertyMap.
std::shared_ptr< GenericData >	getPropertyByName (const std::string &propName)
	Returns property.
void	addInteractionPairs (Molecule *mol)
	add all special interaction pairs (including excluded interactions) in a molecule into the appropriate lists.
void	removeInteractionPairs (Molecule *mol)
	remove all special interaction pairs which belong to a molecule from the appropriate lists.
AtomTypeSet	getSimulatedAtomTypes ()
	Returns the set of atom types present in this simulation.
int	getGlobalCountOfType (AtomType *atype)
	Returns the global count of atoms of a particular type.
void	getCutoff (RealType &rcut, RealType &rsw)
bool	usesElectrostaticAtoms ()
bool	usesDirectionalAtoms ()
bool	usesFluctuatingCharges ()
bool	usesAtomicVirial ()
bool	requiresPrepair ()
bool	requiresSkipCorrection ()
bool	requiresSelfCorrection ()
std::vector< int >	getGlobalGroupMembership ()
std::vector< int >	getIdentArray ()
std::vector< int >	getRegions ()
std::vector< RealType >	getMassFactors ()
PairList *	getExcludedInteractions ()
PairList *	getOneTwoInteractions ()
PairList *	getOneThreeInteractions ()
PairList *	getOneFourInteractions ()
StuntDouble *	getIOIndexToIntegrableObject (int index)
	return an integral objects by its global index.
void	setIOIndexToIntegrableObject (const std::vector< StuntDouble * > &v)
int	getMolToProc (int globalIndex)
	Finds the processor where a molecule resides.
void	setMolToProcMap (const std::vector< int > &molToProcMap)
	Set MolToProcMap array.

Friends
ostream &	operator<< (ostream &o, SimInfo &info)

Detailed Description

One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the current simulation.

This includes the primary list of Molecules. The Molecule class maintains all of the concrete objects (Atoms, Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups, Constraints). In both the single and parallel versions, Atoms and RigidBodies have both global and local indices.

Definition at line 96 of file SimInfo.hpp.

Member Typedef Documentation

◆ MoleculeIterator

using OpenMD::SimInfo::MoleculeIterator = std::map<int, Molecule*>::iterator

Definition at line 98 of file SimInfo.hpp.

Constructor & Destructor Documentation

◆ SimInfo()

OpenMD::SimInfo::SimInfo	(	ForceField *	ff,
		Globals *	simParams )

Constructor of SimInfo.

Parameters

ff	pointer to a concrete ForceField instance
simParams	pointer to the simulation parameters in a Globals object

Definition at line 82 of file SimInfo.cpp.

Referenced by getGlobalCountOfType().

◆ ~SimInfo()

OpenMD::SimInfo::~SimInfo ( )

virtual

Definition at line 182 of file SimInfo.cpp.

Member Function Documentation

◆ addInteractionPairs()

void OpenMD::SimInfo::addInteractionPairs ( Molecule * mol )

add all special interaction pairs (including excluded interactions) in a molecule into the appropriate lists.

Definition at line 379 of file SimInfo.cpp.

References addInteractionPairs(), OpenMD::RigidBody::getAtoms(), OpenMD::StuntDouble::getGlobalIndex(), and OpenMD::StuntDouble::isRigidBody().

Referenced by addInteractionPairs(), addMolecule(), and OpenMD::SimCreator::createSim().

◆ addMolecule()

bool OpenMD::SimInfo::addMolecule ( Molecule * mol )

Adds a molecule.

Returns: return true if adding successfully, return false if the molecule is already in SimInfo

Parameters

mol	Molecule to be added

Definition at line 190 of file SimInfo.cpp.

References addInteractionPairs(), addMolecule(), OpenMD::Molecule::getGlobalIndex(), OpenMD::Molecule::getNAtoms(), OpenMD::Molecule::getNBends(), OpenMD::Molecule::getNBonds(), OpenMD::Molecule::getNConstraintPairs(), OpenMD::Molecule::getNCutoffGroups(), OpenMD::Molecule::getNIntegrableObjects(), OpenMD::Molecule::getNInversions(), OpenMD::Molecule::getNRigidBodies(), and OpenMD::Molecule::getNTorsions().

Referenced by addMolecule().

◆ addProperty()

void OpenMD::SimInfo::addProperty ( std::shared_ptr< GenericData > genData )

Adds property into property map.

Parameters

genData GenericData to be added into PropertyMap

Definition at line 954 of file SimInfo.cpp.

References addProperty().

Referenced by addProperty().

◆ beginMolecule()

Molecule * OpenMD::SimInfo::beginMolecule ( MoleculeIterator & i )

Returns the first molecule in this SimInfo and intialize the iterator.

Returns: the first molecule, return NULL if there is not molecule in this SimInfo

Parameters

i	the iterator of molecule array (user shouldn't change it)

Definition at line 243 of file SimInfo.cpp.

References beginMolecule().

Referenced by beginMolecule(), OpenMD::SimCreator::createSim(), getGlobalAtomIndices(), getGlobalGroupIndices(), getNLocalCutoffGroups(), getSimulatedAtomTypes(), prepareTopology(), and setSnapshotManager().

◆ getAtomStorageLayout()

int OpenMD::SimInfo::getAtomStorageLayout ( )

inline

Returns the storage layouts (computed by SimCreator).

Definition at line 254 of file SimInfo.hpp.

Referenced by OpenMD::SimCreator::createSim().

◆ getCalcBoxDipole()

bool OpenMD::SimInfo::getCalcBoxDipole ( )

inline

Definition at line 381 of file SimInfo.hpp.

◆ getCalcBoxQuadrupole()

bool OpenMD::SimInfo::getCalcBoxQuadrupole ( )

inline

Definition at line 382 of file SimInfo.hpp.

◆ getCutoffGroupStorageLayout()

int OpenMD::SimInfo::getCutoffGroupStorageLayout ( )

inline

Definition at line 256 of file SimInfo.hpp.

◆ getDumpFileName()

std::string OpenMD::SimInfo::getDumpFileName ( )

inline

Definition at line 338 of file SimInfo.hpp.

◆ getExcludedInteractions()

PairList * OpenMD::SimInfo::getExcludedInteractions ( )

inline

Definition at line 597 of file SimInfo.hpp.

◆ getFdf()

int OpenMD::SimInfo::getFdf ( )

Definition at line 305 of file SimInfo.cpp.

◆ getFinalConfigFileName()

std::string OpenMD::SimInfo::getFinalConfigFileName ( )

inline

Definition at line 326 of file SimInfo.hpp.

◆ getForceField()

ForceField * OpenMD::SimInfo::getForceField ( )

inline

Returns the force field.

Definition at line 269 of file SimInfo.hpp.

◆ getGlobalAtomIndices()

vector< int > OpenMD::SimInfo::getGlobalAtomIndices ( )

returns a vector which maps the local atom index on this processor to the global atom index.

With only one processor, these should be identical.

Definition at line 866 of file SimInfo.cpp.

References beginMolecule(), getGlobalAtomIndices(), OpenMD::StuntDouble::getGlobalIndex(), OpenMD::StuntDouble::getLocalIndex(), getNAtoms(), and nextMolecule().

Referenced by getGlobalAtomIndices().

◆ getGlobalGroupIndices()

vector< int > OpenMD::SimInfo::getGlobalGroupIndices ( )

returns a vector which maps the local cutoff group index on this processor to the global cutoff group index.

With only one processor, these should be identical.

Definition at line 882 of file SimInfo.cpp.

References beginMolecule(), getGlobalGroupIndices(), and nextMolecule().

Referenced by getGlobalGroupIndices().

◆ getGlobalGroupMembership()

std::vector< int > OpenMD::SimInfo::getGlobalGroupMembership ( )

inline

Definition at line 552 of file SimInfo.hpp.

◆ getGlobalMolMembership()

int OpenMD::SimInfo::getGlobalMolMembership ( int id )

inline

Definition at line 310 of file SimInfo.hpp.

◆ getIdentArray()

std::vector< int > OpenMD::SimInfo::getIdentArray ( )

inline

Definition at line 572 of file SimInfo.hpp.

◆ getIOIndexToIntegrableObject()

StuntDouble * OpenMD::SimInfo::getIOIndexToIntegrableObject ( int index )

return an integral objects by its global index.

In MPI version, if the StuntDouble with specified global index does not belong to local processor, a NULL will be return.

Definition at line 1031 of file SimInfo.cpp.

References getIOIndexToIntegrableObject().

Referenced by getIOIndexToIntegrableObject().

◆ getLocalIndexManager()

LocalIndexManager * OpenMD::SimInfo::getLocalIndexManager ( )

inline

Returns the local index manager.

Definition at line 285 of file SimInfo.hpp.

◆ getMassFactors()

std::vector< RealType > OpenMD::SimInfo::getMassFactors ( )

inline

Definition at line 595 of file SimInfo.hpp.

◆ getMoleculeByGlobalIndex()

Molecule * OpenMD::SimInfo::getMoleculeByGlobalIndex ( int index )

inline

Finds a molecule with a specified global index.

Returns: a pointer point to found molecule

Parameters

index

Definition at line 303 of file SimInfo.hpp.

◆ getMoleculeStamp()

MoleculeStamp * OpenMD::SimInfo::getMoleculeStamp ( int id )

inline

Returns the molecule stamp.

Definition at line 293 of file SimInfo.hpp.

◆ getMoleculeStampId()

int OpenMD::SimInfo::getMoleculeStampId ( int globalIndex )

inline

Definition at line 287 of file SimInfo.hpp.

◆ getMolToProc()

int OpenMD::SimInfo::getMolToProc ( int globalIndex )

inline

Finds the processor where a molecule resides.

Returns: the id of the processor which contains the molecule

Parameters

globalIndex global Index of the molecule

Definition at line 670 of file SimInfo.hpp.

◆ getNAtoms()

unsigned int OpenMD::SimInfo::getNAtoms ( )

inline

Returns the number of local atoms.

Definition at line 175 of file SimInfo.hpp.

Referenced by getGlobalAtomIndices(), and prepareTopology().

◆ getNBends()

unsigned int OpenMD::SimInfo::getNBends ( )

inline

Returns the number of local bends.

Definition at line 184 of file SimInfo.hpp.

◆ getNBonds()

unsigned int OpenMD::SimInfo::getNBonds ( )

inline

Returns the number of local bonds.

Definition at line 181 of file SimInfo.hpp.

◆ getNConstraints()

unsigned int OpenMD::SimInfo::getNConstraints ( )

inline

Returns the total number of constraints in this SimInfo.

Definition at line 201 of file SimInfo.hpp.

◆ getNCutoffGroups()

unsigned int OpenMD::SimInfo::getNCutoffGroups ( )

inline

Returns the number of local cutoff groups.

Definition at line 198 of file SimInfo.hpp.

◆ getNdf()

int OpenMD::SimInfo::getNdf ( )

inline

Returns the number of degrees of freedom.

Definition at line 223 of file SimInfo.hpp.

◆ getNdfLocal()

int OpenMD::SimInfo::getNdfLocal ( )

inline

Returns the number of degrees of freedom (LOCAL).

Definition at line 226 of file SimInfo.hpp.

◆ getNdfRaw()

int OpenMD::SimInfo::getNdfRaw ( )

inline

Returns the number of raw degrees of freedom.

Definition at line 229 of file SimInfo.hpp.

◆ getNdfTrans()

int OpenMD::SimInfo::getNdfTrans ( )

inline

Returns the number of translational degrees of freedom.

Definition at line 232 of file SimInfo.hpp.

◆ getNFluctuatingCharges()

int OpenMD::SimInfo::getNFluctuatingCharges ( )

inline

Returns the total number of fluctuating charges that are present.

Definition at line 220 of file SimInfo.hpp.

◆ getNGlobalAtoms()

int OpenMD::SimInfo::getNGlobalAtoms ( )

inline

Returns the total number of atoms in the system.

Definition at line 132 of file SimInfo.hpp.

◆ getNGlobalBends()

unsigned int OpenMD::SimInfo::getNGlobalBends ( )

inline

Returns the number of global bends.

Definition at line 155 of file SimInfo.hpp.

◆ getNGlobalBonds()

unsigned int OpenMD::SimInfo::getNGlobalBonds ( )

inline

Returns the number of global bonds.

Definition at line 152 of file SimInfo.hpp.

◆ getNGlobalConstraints()

unsigned int OpenMD::SimInfo::getNGlobalConstraints ( )

inline

Definition at line 163 of file SimInfo.hpp.

◆ getNGlobalCutoffGroups()

int OpenMD::SimInfo::getNGlobalCutoffGroups ( )

inline

Returns the total number of cutoff groups in the system.

Definition at line 135 of file SimInfo.hpp.

◆ getNGlobalIntegrableObjects()

int OpenMD::SimInfo::getNGlobalIntegrableObjects ( )

inline

Returns the total number of integrable objects (total number of rigid bodies plus the total number of atoms which do not belong to the rigid bodies) in the system.

Definition at line 142 of file SimInfo.hpp.

◆ getNGlobalInversions()

unsigned int OpenMD::SimInfo::getNGlobalInversions ( )

inline

Returns the number of global inversions.

Definition at line 161 of file SimInfo.hpp.

◆ getNGlobalMolecules()

int OpenMD::SimInfo::getNGlobalMolecules ( )

inline

Returns the total number of molecules in the system.

Definition at line 129 of file SimInfo.hpp.

◆ getNGlobalRigidBodies()

int OpenMD::SimInfo::getNGlobalRigidBodies ( )

inline

Returns the total number of integrable objects (total number of rigid bodies plus the total number of atoms which do not belong to the rigid bodies) in the system.

Definition at line 149 of file SimInfo.hpp.

◆ getNGlobalTorsions()

unsigned int OpenMD::SimInfo::getNGlobalTorsions ( )

inline

Returns the number of global torsions.

Definition at line 158 of file SimInfo.hpp.

◆ getNIntegrableObjects()

unsigned int OpenMD::SimInfo::getNIntegrableObjects ( )

inline

Returns the number of local integrable objects.

Definition at line 195 of file SimInfo.hpp.

◆ getNInversions()

unsigned int OpenMD::SimInfo::getNInversions ( )

inline

Returns the number of local inversions.

Definition at line 190 of file SimInfo.hpp.

◆ getNLocalCutoffGroups()

unsigned int OpenMD::SimInfo::getNLocalCutoffGroups ( )

Returns the number of effective cutoff groups on local processor.

Definition at line 314 of file SimInfo.cpp.

References beginMolecule(), getNLocalCutoffGroups(), and nextMolecule().

Referenced by getNLocalCutoffGroups().

◆ getNMolecules()

size_t OpenMD::SimInfo::getNMolecules ( )

inline

Returns the number of local molecules.

Returns: the number of local molecules

Definition at line 172 of file SimInfo.hpp.

◆ getNMoleculeStamp()

size_t OpenMD::SimInfo::getNMoleculeStamp ( )

inline

Return the total number of the molecule stamps.

Definition at line 296 of file SimInfo.hpp.

◆ getNRigidBodies()

unsigned int OpenMD::SimInfo::getNRigidBodies ( )

inline

Returns the number of local rigid bodies.

Definition at line 192 of file SimInfo.hpp.

◆ getNTorsions()

unsigned int OpenMD::SimInfo::getNTorsions ( )

inline

Returns the number of local torsions.

Definition at line 187 of file SimInfo.hpp.

◆ getNZconstraint()

int OpenMD::SimInfo::getNZconstraint ( )

inline

Returns the total number of z-constraint molecules in the system.

Definition at line 243 of file SimInfo.hpp.

◆ getOneFourInteractions()

PairList * OpenMD::SimInfo::getOneFourInteractions ( )

inline

Definition at line 600 of file SimInfo.hpp.

◆ getOneThreeInteractions()

PairList * OpenMD::SimInfo::getOneThreeInteractions ( )

inline

Definition at line 599 of file SimInfo.hpp.

◆ getOneTwoInteractions()

PairList * OpenMD::SimInfo::getOneTwoInteractions ( )

inline

Definition at line 598 of file SimInfo.hpp.

◆ getProperties()

std::vector< std::shared_ptr< GenericData > > OpenMD::SimInfo::getProperties ( )

Returns all of the properties in PropertyMap.

Returns: all of the properties in PropertyMap

Definition at line 966 of file SimInfo.cpp.

References getProperties().

Referenced by getProperties().

◆ getPropertyByName()

std::shared_ptr< GenericData > OpenMD::SimInfo::getPropertyByName ( const std::string & propName )

Returns property.

Parameters

propName name of property

Returns: a pointer point to property with propName. If no property named propName exists, return NULL

Definition at line 970 of file SimInfo.cpp.

References getPropertyByName().

Referenced by getPropertyByName().

◆ getPropertyNames()

std::vector< string > OpenMD::SimInfo::getPropertyNames ( )

Returns all names of properties.

Returns: all names of properties

Definition at line 962 of file SimInfo.cpp.

References getPropertyNames().

Referenced by getPropertyNames().

◆ getRandomNumberGenerator()

Utils::RandNumGenPtr OpenMD::SimInfo::getRandomNumberGenerator ( ) const

inline

Definition at line 273 of file SimInfo.hpp.

◆ getRawMetaData()

std::string OpenMD::SimInfo::getRawMetaData ( )

inline

Definition at line 332 of file SimInfo.hpp.

◆ getRegions()

std::vector< int > OpenMD::SimInfo::getRegions ( )

inline

Definition at line 582 of file SimInfo.hpp.

◆ getReportFileName()

std::string OpenMD::SimInfo::getReportFileName ( )

inline

Definition at line 350 of file SimInfo.hpp.

◆ getRestFileName()

std::string OpenMD::SimInfo::getRestFileName ( )

inline

Definition at line 356 of file SimInfo.hpp.

◆ getRigidBodyStorageLayout()

int OpenMD::SimInfo::getRigidBodyStorageLayout ( )

inline

Definition at line 255 of file SimInfo.hpp.

◆ getSimParams()

Globals * OpenMD::SimInfo::getSimParams ( )

inline

Definition at line 271 of file SimInfo.hpp.

◆ getSimulatedAtomTypes()

AtomTypeSet OpenMD::SimInfo::getSimulatedAtomTypes ( )

Returns the set of atom types present in this simulation.

getSimulatedAtomTypes

Returns an STL set of AtomType* that are actually present in this simulation. Must query all processors to assemble this information.

Definition at line 716 of file SimInfo.cpp.

References beginMolecule(), OpenMD::Atom::getAtomType(), getSimulatedAtomTypes(), and nextMolecule().

Referenced by getSimulatedAtomTypes().

◆ getSnapshotManager()

SnapshotManager * OpenMD::SimInfo::getSnapshotManager ( )

inline

Returns the snapshot manager.

Definition at line 251 of file SimInfo.hpp.

◆ getStatFileName()

std::string OpenMD::SimInfo::getStatFileName ( )

inline

Definition at line 344 of file SimInfo.hpp.

◆ getUseAtomicVirial()

bool OpenMD::SimInfo::getUseAtomicVirial ( )

inline

Definition at line 384 of file SimInfo.hpp.

◆ isTopologyDone()

bool OpenMD::SimInfo::isTopologyDone ( )

inline

Definition at line 379 of file SimInfo.hpp.

◆ nextMolecule()

Molecule * OpenMD::SimInfo::nextMolecule ( MoleculeIterator & i )

Returns the next avaliable Molecule based on the iterator.

Returns: the next avaliable molecule, return NULL if reaching the end of the array

Parameters

i	the iterator of molecule array

Definition at line 248 of file SimInfo.cpp.

References nextMolecule().

Referenced by OpenMD::SimCreator::createSim(), getGlobalAtomIndices(), getGlobalGroupIndices(), getNLocalCutoffGroups(), getSimulatedAtomTypes(), nextMolecule(), prepareTopology(), and setSnapshotManager().

◆ prepareTopology()

void OpenMD::SimInfo::prepareTopology ( )

Do final bookkeeping before Force managers need their data.

The mass factor is the relative mass of an atom to the total mass of the cutoff group it belongs to. By default, all atoms are their own cutoff groups, and therefore have mass factors of

We need some special handling for massless atoms, which will be treated as carrying the entire mass of the cutoff group.

Definition at line 901 of file SimInfo.cpp.

References beginMolecule(), OpenMD::StuntDouble::getLocalIndex(), OpenMD::StuntDouble::getMass(), getNAtoms(), nextMolecule(), and prepareTopology().

Referenced by prepareTopology().

◆ removeInteractionPairs()

void OpenMD::SimInfo::removeInteractionPairs ( Molecule * mol )

remove all special interaction pairs which belong to a molecule from the appropriate lists.

Definition at line 535 of file SimInfo.cpp.

References OpenMD::RigidBody::getAtoms(), OpenMD::StuntDouble::getGlobalIndex(), OpenMD::StuntDouble::isRigidBody(), and removeInteractionPairs().

Referenced by removeInteractionPairs(), and removeMolecule().

◆ removeMolecule()

bool OpenMD::SimInfo::removeMolecule ( Molecule * mol )

Removes a molecule from SimInfo.

Returns: true if removing successfully, return false if molecule is not in this SimInfo

Definition at line 215 of file SimInfo.cpp.

References OpenMD::Molecule::getGlobalIndex(), OpenMD::Molecule::getNAtoms(), OpenMD::Molecule::getNBends(), OpenMD::Molecule::getNBonds(), OpenMD::Molecule::getNConstraintPairs(), OpenMD::Molecule::getNCutoffGroups(), OpenMD::Molecule::getNIntegrableObjects(), OpenMD::Molecule::getNInversions(), OpenMD::Molecule::getNRigidBodies(), OpenMD::Molecule::getNTorsions(), removeInteractionPairs(), and removeMolecule().

Referenced by removeMolecule().

◆ removeProperty()

void OpenMD::SimInfo::removeProperty ( const std::string & propName )

Removes property from PropertyMap by name.

Parameters

propName the name of property to be removed

Definition at line 958 of file SimInfo.cpp.

References removeProperty().

Referenced by removeProperty().

◆ requiresPrepair()

bool OpenMD::SimInfo::requiresPrepair ( )

inline

Definition at line 526 of file SimInfo.hpp.

◆ requiresSelfCorrection()

bool OpenMD::SimInfo::requiresSelfCorrection ( )

inline

Definition at line 528 of file SimInfo.hpp.

◆ requiresSkipCorrection()

bool OpenMD::SimInfo::requiresSkipCorrection ( )

inline

Definition at line 527 of file SimInfo.hpp.

◆ setAtomStorageLayout()

void OpenMD::SimInfo::setAtomStorageLayout ( int asl )

inline

Sets the storage layouts (computed by SimCreator).

Definition at line 259 of file SimInfo.hpp.

◆ setCutoffGroupStorageLayout()

void OpenMD::SimInfo::setCutoffGroupStorageLayout ( int cgsl )

inline

Definition at line 261 of file SimInfo.hpp.

◆ setDumpFileName()

void OpenMD::SimInfo::setDumpFileName ( const std::string & fileName )

inline

Definition at line 340 of file SimInfo.hpp.

◆ setFdf()

void OpenMD::SimInfo::setFdf ( int fdf )

inline

sets the current number of frozen degrees of freedom

Definition at line 235 of file SimInfo.hpp.

◆ setFinalConfigFileName()

void OpenMD::SimInfo::setFinalConfigFileName ( const std::string & fileName )

inline

Definition at line 328 of file SimInfo.hpp.

◆ setGlobalGroupMembership()

void OpenMD::SimInfo::setGlobalGroupMembership ( const std::vector< int > & ggm )

inline

Sets GlobalGroupMembership.

Definition at line 365 of file SimInfo.hpp.

◆ setGlobalMolMembership()

void OpenMD::SimInfo::setGlobalMolMembership ( const std::vector< int > & gmm )

inline

Sets GlobalMolMembership.

Definition at line 373 of file SimInfo.hpp.

◆ setIOIndexToIntegrableObject()

void OpenMD::SimInfo::setIOIndexToIntegrableObject ( const std::vector< StuntDouble * > & v )

Definition at line 1044 of file SimInfo.cpp.

◆ setMolToProcMap()

void OpenMD::SimInfo::setMolToProcMap ( const std::vector< int > & molToProcMap )

inline

Set MolToProcMap array.

Definition at line 678 of file SimInfo.hpp.

◆ setNZconstraint()

void OpenMD::SimInfo::setNZconstraint ( int nZconstraint )

inline

Sets the number of z-constraint molecules in the system.

Definition at line 248 of file SimInfo.hpp.

◆ setRawMetaData()

void OpenMD::SimInfo::setRawMetaData ( const std::string & rawMetaData )

inline

Definition at line 334 of file SimInfo.hpp.

◆ setReportFileName()

void OpenMD::SimInfo::setReportFileName ( const std::string & fileName )

inline

Definition at line 352 of file SimInfo.hpp.

◆ setRestFileName()

void OpenMD::SimInfo::setRestFileName ( const std::string & fileName )

inline

Definition at line 358 of file SimInfo.hpp.

◆ setRigidBodyStorageLayout()

void OpenMD::SimInfo::setRigidBodyStorageLayout ( int rbsl )

inline

Definition at line 260 of file SimInfo.hpp.

◆ setSnapshotManager()

void OpenMD::SimInfo::setSnapshotManager ( SnapshotManager * sman )

Sets the snapshot manager.

Definition at line 975 of file SimInfo.cpp.

References beginMolecule(), nextMolecule(), OpenMD::CutoffGroup::setSnapshotManager(), OpenMD::ShortRangeInteraction::setSnapshotManager(), setSnapshotManager(), and OpenMD::StuntDouble::setSnapshotManager().

Referenced by OpenMD::SimCreator::createSim(), and setSnapshotManager().

◆ setStatFileName()

void OpenMD::SimInfo::setStatFileName ( const std::string & fileName )

inline

Definition at line 346 of file SimInfo.hpp.

◆ update()

void OpenMD::SimInfo::update ( )

update

Performs the global checks and variable settings after the objects have been created.

Definition at line 701 of file SimInfo.cpp.

References update().

Referenced by OpenMD::SimCreator::createSim(), and update().

◆ usesAtomicVirial()

bool OpenMD::SimInfo::usesAtomicVirial ( )

inline

Definition at line 525 of file SimInfo.hpp.

◆ usesDirectionalAtoms()

bool OpenMD::SimInfo::usesDirectionalAtoms ( )

inline

Definition at line 523 of file SimInfo.hpp.

◆ usesElectrostaticAtoms()

bool OpenMD::SimInfo::usesElectrostaticAtoms ( )

inline

Definition at line 522 of file SimInfo.hpp.

◆ usesFluctuatingCharges()

bool OpenMD::SimInfo::usesFluctuatingCharges ( )

inline

Definition at line 524 of file SimInfo.hpp.

◆ operator<<

ostream & operator<<	(	ostream &	o,
		SimInfo &	info )

friend

Definition at line 1029 of file SimInfo.cpp.

The documentation for this class was generated from the following files:

brains/SimInfo.hpp
brains/SimInfo.cpp

Public Types

Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ MoleculeIterator

Constructor & Destructor Documentation

◆ SimInfo()

◆ ~SimInfo()

Member Function Documentation

◆ addInteractionPairs()

◆ addMolecule()

◆ addProperty()

◆ beginMolecule()

◆ getAtomStorageLayout()

◆ getCalcBoxDipole()

◆ getCalcBoxQuadrupole()

◆ getCutoffGroupStorageLayout()

◆ getDumpFileName()

◆ getExcludedInteractions()

◆ getFdf()

◆ getFinalConfigFileName()

◆ getForceField()

◆ getGlobalAtomIndices()

◆ getGlobalGroupIndices()

◆ getGlobalGroupMembership()

◆ getGlobalMolMembership()

◆ getIdentArray()

◆ getIOIndexToIntegrableObject()

◆ getLocalIndexManager()

◆ getMassFactors()

◆ getMoleculeByGlobalIndex()

◆ getMoleculeStamp()

◆ getMoleculeStampId()

◆ getMolToProc()

◆ getNAtoms()

◆ getNBends()

◆ getNBonds()

◆ getNConstraints()

◆ getNCutoffGroups()

◆ getNdf()

◆ getNdfLocal()

◆ getNdfRaw()

◆ getNdfTrans()

◆ getNFluctuatingCharges()

◆ getNGlobalAtoms()

◆ getNGlobalBends()

◆ getNGlobalBonds()

◆ getNGlobalConstraints()

◆ getNGlobalCutoffGroups()

◆ getNGlobalIntegrableObjects()

◆ getNGlobalInversions()

◆ getNGlobalMolecules()

◆ getNGlobalRigidBodies()

◆ getNGlobalTorsions()

◆ getNIntegrableObjects()

◆ getNInversions()

◆ getNLocalCutoffGroups()

◆ getNMolecules()

◆ getNMoleculeStamp()

◆ getNRigidBodies()

◆ getNTorsions()

◆ getNZconstraint()

◆ getOneFourInteractions()

◆ getOneThreeInteractions()

◆ getOneTwoInteractions()

◆ getProperties()

◆ getPropertyByName()

◆ getPropertyNames()

◆ getRandomNumberGenerator()

◆ getRawMetaData()

◆ getRegions()

◆ getReportFileName()

◆ getRestFileName()

◆ getRigidBodyStorageLayout()

◆ getSimParams()

◆ getSimulatedAtomTypes()

◆ getSnapshotManager()

◆ getStatFileName()

◆ getUseAtomicVirial()