OpenMD::SimInfo Class Reference

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 93 of file SimInfo.hpp.

Member Typedef Documentation

MoleculeIterator

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

Definition at line 95 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 79 of file SimInfo.cpp.

~SimInfo()

OpenMD::SimInfo::~SimInfo ( )

virtual

Definition at line 179 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 376 of file SimInfo.cpp.

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

Referenced by 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 187 of file SimInfo.cpp.

References addInteractionPairs(), 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().

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 950 of file SimInfo.cpp.

References OpenMD::PropertyMap::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 240 of file SimInfo.cpp.

Referenced by OpenMD::SimCreator::createSim(), OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getBoundingBox(), OpenMD::Thermo::getCom(), OpenMD::Thermo::getComAll(), OpenMD::Thermo::getComVel(), getGlobalAtomIndices(), getGlobalGroupIndices(), OpenMD::Thermo::getInertiaTensor(), getNLocalCutoffGroups(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getPressureTensor(), getSimulatedAtomTypes(), OpenMD::Thermo::getSystemDipole(), OpenMD::Thermo::getSystemQuadrupole(), prepareTopology(), OpenMD::Velocitizer::randomize(), OpenMD::Velocitizer::randomizeChargeVelocity(), OpenMD::Velocitizer::removeAngularDrift(), OpenMD::Velocitizer::removeComDrift(), OpenMD::Velocitizer::scale(), and setSnapshotManager().

getAtomStorageLayout()

int OpenMD::SimInfo::getAtomStorageLayout ( )

inline

Returns the storage layouts (computed by SimCreator)

Definition at line 251 of file SimInfo.hpp.

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

getCalcBoxDipole()

bool OpenMD::SimInfo::getCalcBoxDipole ( )

inline

Definition at line 378 of file SimInfo.hpp.

getCalcBoxQuadrupole()

bool OpenMD::SimInfo::getCalcBoxQuadrupole ( )

inline

Definition at line 379 of file SimInfo.hpp.

getCutoffGroupStorageLayout()

int OpenMD::SimInfo::getCutoffGroupStorageLayout ( )

inline

Definition at line 253 of file SimInfo.hpp.

getDumpFileName()

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

inline

Definition at line 335 of file SimInfo.hpp.

getExcludedInteractions()

PairList * OpenMD::SimInfo::getExcludedInteractions ( )

inline

Definition at line 594 of file SimInfo.hpp.

getFdf()

int OpenMD::SimInfo::getFdf

(

)

Definition at line 302 of file SimInfo.cpp.

getFinalConfigFileName()

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

inline

Definition at line 323 of file SimInfo.hpp.

getForceField()

ForceField * OpenMD::SimInfo::getForceField ( )

inline

Returns the force field.

Definition at line 266 of file SimInfo.hpp.

Referenced by OpenMD::ForceMatrixDecomposition::distributeInitialData().

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 862 of file SimInfo.cpp.

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

Referenced by OpenMD::ForceMatrixDecomposition::distributeInitialData().

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 878 of file SimInfo.cpp.

References beginMolecule(), and nextMolecule().

Referenced by OpenMD::ForceMatrixDecomposition::distributeInitialData().

getGlobalGroupMembership()

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

inline

Definition at line 549 of file SimInfo.hpp.

getGlobalMolMembership()

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

inline

Definition at line 307 of file SimInfo.hpp.

getIdentArray()

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

inline

Definition at line 569 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 1027 of file SimInfo.cpp.

getLocalIndexManager()

LocalIndexManager * OpenMD::SimInfo::getLocalIndexManager ( )

inline

Returns the local index manager.

Definition at line 282 of file SimInfo.hpp.

getMassFactors()

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

inline

Definition at line 592 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 300 of file SimInfo.hpp.

Referenced by OpenMD::ZConsVisitor::ZConsVisitor().

getMoleculeStamp()

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

inline

Returns the molecule stamp.

Definition at line 290 of file SimInfo.hpp.

getMoleculeStampId()

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

inline

Definition at line 284 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 667 of file SimInfo.hpp.

getNAtoms()

unsigned int OpenMD::SimInfo::getNAtoms ( )

inline

Returns the number of local atoms.

Definition at line 172 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 181 of file SimInfo.hpp.

getNBonds()

unsigned int OpenMD::SimInfo::getNBonds ( )

inline

Returns the number of local bonds.

Definition at line 178 of file SimInfo.hpp.

getNConstraints()

unsigned int OpenMD::SimInfo::getNConstraints ( )

inline

Returns the total number of constraints in this SimInfo.

Definition at line 198 of file SimInfo.hpp.

getNCutoffGroups()

unsigned int OpenMD::SimInfo::getNCutoffGroups ( )

inline

Returns the number of local cutoff groups.

Definition at line 195 of file SimInfo.hpp.

getNdf()

int OpenMD::SimInfo::getNdf ( )

inline

Returns the number of degrees of freedom.

Definition at line 220 of file SimInfo.hpp.

Referenced by OpenMD::Velocitizer::randomize().

getNdfLocal()

int OpenMD::SimInfo::getNdfLocal ( )

inline

Returns the number of degrees of freedom (LOCAL)

Definition at line 223 of file SimInfo.hpp.

getNdfRaw()

int OpenMD::SimInfo::getNdfRaw ( )

inline

Returns the number of raw degrees of freedom.

Definition at line 226 of file SimInfo.hpp.

Referenced by OpenMD::Velocitizer::randomize().

getNdfTrans()

int OpenMD::SimInfo::getNdfTrans ( )

inline

Returns the number of translational degrees of freedom.

Definition at line 229 of file SimInfo.hpp.

getNFluctuatingCharges()

int OpenMD::SimInfo::getNFluctuatingCharges ( )

inline

Returns the total number of fluctuating charges that are present.

Definition at line 217 of file SimInfo.hpp.

getNGlobalAtoms()

int OpenMD::SimInfo::getNGlobalAtoms ( )

inline

Returns the total number of atoms in the system.

Definition at line 129 of file SimInfo.hpp.

getNGlobalBends()

unsigned int OpenMD::SimInfo::getNGlobalBends ( )

inline

Returns the number of global bends.

Definition at line 152 of file SimInfo.hpp.

getNGlobalBonds()

unsigned int OpenMD::SimInfo::getNGlobalBonds ( )

inline

Returns the number of global bonds.

Definition at line 149 of file SimInfo.hpp.

getNGlobalConstraints()

unsigned int OpenMD::SimInfo::getNGlobalConstraints ( )

inline

Definition at line 160 of file SimInfo.hpp.

getNGlobalCutoffGroups()

int OpenMD::SimInfo::getNGlobalCutoffGroups ( )

inline

Returns the total number of cutoff groups in the system.

Definition at line 132 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 139 of file SimInfo.hpp.

Referenced by OpenMD::Thermo::getGyrationalVolume(), and OpenMD::Thermo::getGyrationalVolume().

getNGlobalInversions()

unsigned int OpenMD::SimInfo::getNGlobalInversions ( )

inline

Returns the number of global inversions.

Definition at line 158 of file SimInfo.hpp.

getNGlobalMolecules()

int OpenMD::SimInfo::getNGlobalMolecules ( )

inline

Returns the total number of molecules in the system.

Definition at line 126 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 146 of file SimInfo.hpp.

getNGlobalTorsions()

unsigned int OpenMD::SimInfo::getNGlobalTorsions ( )

inline

Returns the number of global torsions.

Definition at line 155 of file SimInfo.hpp.

getNIntegrableObjects()

unsigned int OpenMD::SimInfo::getNIntegrableObjects ( )

inline

Returns the number of local integrable objects.

Definition at line 192 of file SimInfo.hpp.

getNInversions()

unsigned int OpenMD::SimInfo::getNInversions ( )

inline

Returns the number of local inversions.

Definition at line 187 of file SimInfo.hpp.

getNLocalCutoffGroups()

unsigned int OpenMD::SimInfo::getNLocalCutoffGroups

(

)

Returns the number of effective cutoff groups on local processor.

Definition at line 311 of file SimInfo.cpp.

References beginMolecule(), and nextMolecule().

Referenced by OpenMD::ForceMatrixDecomposition::distributeInitialData().

getNMolecules()

size_t OpenMD::SimInfo::getNMolecules ( )

inline

Returns the number of local molecules.

Returns

the number of local molecules

Definition at line 169 of file SimInfo.hpp.

getNMoleculeStamp()

size_t OpenMD::SimInfo::getNMoleculeStamp ( )

inline

Return the total number of the molecule stamps.

Definition at line 293 of file SimInfo.hpp.

getNRigidBodies()

unsigned int OpenMD::SimInfo::getNRigidBodies ( )

inline

Returns the number of local rigid bodies.

Definition at line 189 of file SimInfo.hpp.

getNTorsions()

unsigned int OpenMD::SimInfo::getNTorsions ( )

inline

Returns the number of local torsions.

Definition at line 184 of file SimInfo.hpp.

getNZconstraint()

int OpenMD::SimInfo::getNZconstraint ( )

inline

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

Definition at line 240 of file SimInfo.hpp.

getOneFourInteractions()

PairList * OpenMD::SimInfo::getOneFourInteractions ( )

inline

Definition at line 597 of file SimInfo.hpp.

getOneThreeInteractions()

PairList * OpenMD::SimInfo::getOneThreeInteractions ( )

inline

Definition at line 596 of file SimInfo.hpp.

getOneTwoInteractions()

PairList * OpenMD::SimInfo::getOneTwoInteractions ( )

inline

Definition at line 595 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 962 of file SimInfo.cpp.

References OpenMD::PropertyMap::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 966 of file SimInfo.cpp.

References OpenMD::PropertyMap::getPropertyByName().

getPropertyNames()

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

(

)

Returns all names of properties.

Returns

all names of properties

Definition at line 958 of file SimInfo.cpp.

References OpenMD::PropertyMap::getPropertyNames().

getRandomNumberGenerator()

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

inline

Definition at line 270 of file SimInfo.hpp.

getRawMetaData()

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

inline

Definition at line 329 of file SimInfo.hpp.

getRegions()

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

inline

Definition at line 579 of file SimInfo.hpp.

getReportFileName()

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

inline

Definition at line 347 of file SimInfo.hpp.

getRestFileName()

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

inline

Definition at line 353 of file SimInfo.hpp.

getRigidBodyStorageLayout()

int OpenMD::SimInfo::getRigidBodyStorageLayout ( )

inline

Definition at line 252 of file SimInfo.hpp.

getSimParams()

Globals * OpenMD::SimInfo::getSimParams ( )

inline

Definition at line 268 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 712 of file SimInfo.cpp.

References beginMolecule(), OpenMD::ForceField::getAtomType(), and nextMolecule().

Referenced by OpenMD::ForceManager::setupCutoffs().

getSnapshotManager()

SnapshotManager * OpenMD::SimInfo::getSnapshotManager ( )

inline

Returns the snapshot manager.

Definition at line 248 of file SimInfo.hpp.

Referenced by OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getBoundingBox(), OpenMD::Thermo::getCom(), OpenMD::Thermo::getComAll(), OpenMD::Thermo::getComVel(), OpenMD::Thermo::getGyrationalVolume(), OpenMD::Thermo::getGyrationalVolume(), OpenMD::Thermo::getInertiaTensor(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getSystemDipole(), OpenMD::Thermo::getSystemQuadrupole(), OpenMD::BoxObjectiveFunction::gradient(), OpenMD::PotDiff::PotDiff(), OpenMD::PotDiff::process(), OpenMD::BoxObjectiveFunction::value(), OpenMD::BoxObjectiveFunction::valueAndGradient(), and OpenMD::ZConsVisitor::ZConsVisitor().

getStatFileName()

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

inline

Definition at line 341 of file SimInfo.hpp.

getUseAtomicVirial()

bool OpenMD::SimInfo::getUseAtomicVirial ( )

inline

Definition at line 381 of file SimInfo.hpp.

isTopologyDone()

bool OpenMD::SimInfo::isTopologyDone ( )

inline

Definition at line 376 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 245 of file SimInfo.cpp.

Referenced by OpenMD::SimCreator::createSim(), OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getBoundingBox(), OpenMD::Thermo::getCom(), OpenMD::Thermo::getComAll(), OpenMD::Thermo::getComVel(), getGlobalAtomIndices(), getGlobalGroupIndices(), OpenMD::Thermo::getInertiaTensor(), getNLocalCutoffGroups(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getPressureTensor(), getSimulatedAtomTypes(), OpenMD::Thermo::getSystemDipole(), OpenMD::Thermo::getSystemQuadrupole(), prepareTopology(), OpenMD::Velocitizer::randomize(), OpenMD::Velocitizer::randomizeChargeVelocity(), OpenMD::Velocitizer::removeAngularDrift(), OpenMD::Velocitizer::removeComDrift(), OpenMD::Velocitizer::scale(), 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

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

Definition at line 897 of file SimInfo.cpp.

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

Referenced by OpenMD::ForceManager::initialize().

removeInteractionPairs()

void OpenMD::SimInfo::removeInteractionPairs

(

Molecule *

mol

)

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

Definition at line 532 of file SimInfo.cpp.

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

Referenced by 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 212 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(), and removeInteractionPairs().

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 954 of file SimInfo.cpp.

References OpenMD::PropertyMap::removeProperty().

requiresPrepair()

bool OpenMD::SimInfo::requiresPrepair ( )

inline

Definition at line 523 of file SimInfo.hpp.

requiresSelfCorrection()

bool OpenMD::SimInfo::requiresSelfCorrection ( )

inline

Definition at line 525 of file SimInfo.hpp.

requiresSkipCorrection()

bool OpenMD::SimInfo::requiresSkipCorrection ( )

inline

Definition at line 524 of file SimInfo.hpp.

setAtomStorageLayout()

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

inline

Sets the storage layouts (computed by SimCreator)

Definition at line 256 of file SimInfo.hpp.

Referenced by OpenMD::PotDiff::PotDiff().

setCutoffGroupStorageLayout()

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

inline

Definition at line 258 of file SimInfo.hpp.

setDumpFileName()

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

inline

Definition at line 337 of file SimInfo.hpp.

setFdf()

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

inline

sets the current number of frozen degrees of freedom

Definition at line 232 of file SimInfo.hpp.

setFinalConfigFileName()

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

inline

Definition at line 325 of file SimInfo.hpp.

setGlobalGroupMembership()

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

inline

Sets GlobalGroupMembership.

Definition at line 362 of file SimInfo.hpp.

setGlobalMolMembership()

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

inline

Sets GlobalMolMembership.

Definition at line 370 of file SimInfo.hpp.

setIOIndexToIntegrableObject()

void OpenMD::SimInfo::setIOIndexToIntegrableObject

(

const std::vector< StuntDouble * > &

v

)

Definition at line 1040 of file SimInfo.cpp.

setMolToProcMap()

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

inline

Set MolToProcMap array.

Definition at line 675 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 245 of file SimInfo.hpp.

Referenced by OpenMD::ForceManager::initialize().

setRawMetaData()

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

inline

Definition at line 331 of file SimInfo.hpp.

setReportFileName()

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

inline

Definition at line 349 of file SimInfo.hpp.

setRestFileName()

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

inline

Definition at line 355 of file SimInfo.hpp.

setRigidBodyStorageLayout()

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

inline

Definition at line 257 of file SimInfo.hpp.

setSnapshotManager()

void OpenMD::SimInfo::setSnapshotManager

(

SnapshotManager *

sman

)

Sets the snapshot manager.

Definition at line 971 of file SimInfo.cpp.

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

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

setStatFileName()

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

inline

Definition at line 343 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 697 of file SimInfo.cpp.

Referenced by OpenMD::ForceManager::initialize().

usesAtomicVirial()

bool OpenMD::SimInfo::usesAtomicVirial ( )

inline

Definition at line 522 of file SimInfo.hpp.

usesDirectionalAtoms()

bool OpenMD::SimInfo::usesDirectionalAtoms ( )

inline

Definition at line 520 of file SimInfo.hpp.

usesElectrostaticAtoms()

bool OpenMD::SimInfo::usesElectrostaticAtoms ( )

inline

Definition at line 519 of file SimInfo.hpp.

usesFluctuatingCharges()

bool OpenMD::SimInfo::usesFluctuatingCharges ( )

inline

Definition at line 521 of file SimInfo.hpp.

Friends And Related Symbol Documentation

operator<<

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

friend

Definition at line 1025 of file SimInfo.cpp.

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

• brains/SimInfo.hpp
• brains/SimInfo.cpp