GlobalSearch::Structure Class Reference

Generic molecule object. More...

#include <globalsearch/structure.h>

Public Types
enum	State { Optimized = 0, StepOptimized, WaitingForOptimization, InProcess, Empty, Updating, Error, Submitted, Killed, Removed, Duplicate, Restart, Preoptimizing }
Public Slots
virtual void	setupConnections ()
virtual void	enableAutoHistogramGeneration (bool)
virtual void	requestHistogramGeneration ()
virtual void	generateDefaultHistogram ()
virtual void	structureChanged ()
static bool	compareIADDistributions (const std::vector< double > &d, const std::vector< double > &f1, const std::vector< double > &f2, double decay, double smear, double *error)
static bool	compareIADDistributions (const QList< double > &d, const QList< double > &f1, const QList< double > &f2, double decay, double smear, double *error)
static bool	compareIADDistributions (const QList< QVariant > &d, const QList< QVariant > &f1, const QList< QVariant > &f2, double decay, double smear, double *error)
virtual void	writeSettings (const QString &filename)
virtual void	readSettings (const QString &filename)
virtual void	updateAndSkipHistory (const QList< unsigned int > &atomicNums, const QList< Eigen::Vector3d > &coords, const double energy=0, const double enthalpy=0, const Eigen::Matrix3d &cell=Eigen::Matrix3d::Zero())
virtual void	updateAndAddToHistory (const QList< unsigned int > &atomicNums, const QList< Eigen::Vector3d > &coords, const double energy=0, const double enthalpy=0, const Eigen::Matrix3d &cell=Eigen::Matrix3d::Zero())
virtual void	deleteFromHistory (unsigned int index)
virtual void	retrieveHistoryEntry (unsigned int index, QList< unsigned int > atomicNums, QList< Eigen::Vector3d > coords, double energy, double enthalpy, Eigen::Matrix3d *cell)
virtual unsigned int	sizeOfHistory ()
void	setHasBestOffspring (bool b=true)
void	setEnthalpy (double enthalpy)
void	setPV (double pv)
void	resetEnthalpy ()
void	resetEnergy ()
void	setOBEnergy (const QString &ff=QString("UFF"))
void	setRank (uint rank)
void	setJobID (uint id)
void	setGeneration (uint gen)
void	setIDNumber (uint id)
void	setIndex (int index)
void	setParents (const QString &p)
void	setRempath (const QString &p)
void	setStatus (State status)
void	setCurrentOptStep (uint i)
void	setFailCount (uint count)
void	resetFailCount ()
void	addFailure ()
void	setDuplicateString (const QString &s)
void	setChangedSinceDupChecked (bool b)
void	startOptTimer ()
void	stopOptTimer ()
void	setOptTimerStart (const QDateTime &d)
void	setOptTimerEnd (const QDateTime &d)
virtual void	setNeedsPreoptimization (bool b)
virtual void	abortPreoptimization () const
void	emitPreoptimizationStarted ()
void	emitPreoptimizationFinished ()
virtual void	load (QTextStream &in)
Signals
void	preoptimizationStarted ()
void	preoptimizationFinished ()
Public Member Functions
	Structure (QObject *parent=0)
	Structure (const Structure &other)
	Structure (const Avogadro::Molecule &other)
virtual	~Structure ()
Structure &	operator= (const Structure &other)
Structure &	operator= (const Avogadro::Molecule &other)
virtual Structure &	copyStructure (const Structure &other)
bool	hasBestOffspring () const
bool	hasEnthalpy () const
double	getEnergy () const
double	getEnthalpy () const
double	getPV () const
uint	getRank () const
uint	getJobID () const
uint	getGeneration () const
uint	getIDNumber () const
int	getIndex () const
QString	getDuplicateString () const
QString	getParents () const
QString	getRempath () const
State	getStatus () const
uint	getCurrentOptStep ()
virtual bool	isPreoptimizing () const
virtual int	getPreOptProgress () const
virtual bool	needsPreoptimization () const
uint	getFailCount ()
QDateTime	getOptTimerStart () const
QDateTime	getOptTimerEnd () const
QString	getIDString () const
virtual QString	getResultsHeader () const
virtual QString	getResultsEntry () const
QHash< int, int > *	getOptimizerLookupTable ()
void	resetOptimizerLookupTable ()
virtual bool	getNearestNeighborDistances (QList< double > *list) const
virtual bool	getShortestInteratomicDistance (double &shortest) const
virtual bool	getNearestNeighborDistance (const double x, const double y, const double z, double &shortest) const
virtual bool	getNearestNeighborDistance (const Avogadro::Atom *atom, double &shortest) const
QList< Avogadro::Atom * >	getNeighbors (const double x, const double y, const double z, const double cutoff, QList< double > *distances=0) const
QList< Avogadro::Atom * >	getNeighbors (const Avogadro::Atom atom, const double cutoff, QList< double > distances=0) const
virtual void	getDefaultHistogram (QList< double > dist, QList< double > freq) const
virtual void	getDefaultHistogram (QList< QVariant > dist, QList< QVariant > freq) const
virtual bool	isHistogramGenerationPending () const
virtual bool	generateIADHistogram (QList< double > distance, QList< double > frequency, double min=0.0, double max=10.0, double step=0.01, Avogadro::Atom *atom=0) const
virtual bool	generateIADHistogram (QList< QVariant > distance, QList< QVariant > frequency, double min=0.0, double max=10.0, double step=0.01, Avogadro::Atom *atom=0) const
virtual bool	addAtomRandomly (uint atomicNumber, double minIAD=0.0, double maxIAD=0.0, int maxAttempts=1000, Avogadro::Atom **atom=0)
QList< QString >	getSymbols () const
QList< uint >	getNumberOfAtomsAlpha () const
QString	getOptElapsed () const
virtual QHash< QString, QVariant >	getFingerprint () const
bool	hasChangedSinceDupChecked ()
Static Public Member Functions
static void	sortByEnthalpy (QList< Structure * > *structures)
static void	rankByEnthalpy (const QList< Structure * > &structures)
static void	sortAndRankByEnthalpy (QList< Structure * > *structures)
Protected Slots
void	writeStructureSettings (const QString &filename)
void	readStructureSettings (const QString &filename)

Detailed Description

Generic molecule object.

Author:: David C. Lonie

The Structure class provides a generic data object for storing information about a molecule. It derives from Avogadro::Molecule, adding new functionality to help with common tasks during a global structure search.

Definition at line 49 of file structure.h.

Member Enumeration Documentation

enum GlobalSearch::Structure::State

Enum containing possible optimization statuses.

See also:: setStatus; getStatus

Enumerator:

Optimized	Structure has completed all optimization steps
StepOptimized	Structure has completed an optimization step but may still have some to complete. getCurrentOptStep() shows the step that has just completed.
WaitingForOptimization	Structure is waiting to start an optimization step. getCurrentOptStep() shows the step it will start next.
InProcess	Structure is currently queued or running an optimization step on the PBS server (if applicable).
Empty	Structure has just been generated, and has not yet been initialized
Updating	The Structure has completed it's current optimization step, and the results of the calculation are being transferred and applied.
Error	The optimization is failing.
Submitted	The Structure has been submitted to the PBS server, but has not appeared in the queue yet.
Killed	The Structure has been killed before finishing all optimization steps.
Removed	The Structure has been killed after finishing all optimization steps.
Duplicate	The Structure has been found to be a duplicate of another. The other structure's information can be found in getDuplicateString().
Restart	The Structure is about to restart it's current optimization step.
Preoptimizing	The Structure is undergoing a preoptimization step.

Definition at line 103 of file structure.h.

Constructor & Destructor Documentation

GlobalSearch::Structure::Structure ( QObject * parent = 0 )

Constructor.

Parameters:

parent

The object parent.

Definition at line 42 of file structure.cpp.

References Empty, resetFailCount(), and setStatus().

GlobalSearch::Structure::Structure ( const Structure & other )

Copy constructor.

Definition at line 62 of file structure.cpp.

GlobalSearch::Structure::Structure ( const Avogadro::Molecule & other )

Explicit copy constructor for Molecules.

Definition at line 79 of file structure.cpp.

GlobalSearch::Structure::~Structure ( ) [virtual]

Destructor.

Definition at line 192 of file structure.cpp.

Member Function Documentation

virtual void GlobalSearch::Structure::abortPreoptimization ( ) const [inline, virtual, slot]

Abort the preoptimization running on this structure.

Definition at line 1098 of file structure.h.

Referenced by GlobalSearch::QueueManager::stopJob(), and GlobalSearch::QueueManager::~QueueManager().

virtual bool GlobalSearch::Structure::addAtomRandomly	(	uint	atomicNumber,
		double	minIAD = `0.0`,
		double	maxIAD = `0.0`,
		int	maxAttempts = `1000`,
		Avogadro::Atom **	atom = `0`
	)			`[virtual]`

Add an atom to a random position in the Structure. If no other atoms exist in the Structure, the new atom is placed at (0,0,0).

Returns:: true if the atom was sucessfully added within the specified interatomic distances.

Parameters:

	atomicNumber	Atomic number of atom to add.
	minIAD	Smallest interatomic distance allowed (NULL or omit for no limit)
	maxIAD	Largest interatomic distance allowed (NULL or omit for no limit)
	maxAttempts	Maximum number of tries before giving up.
	atom	Returns a pointer to the new atom.

void GlobalSearch::Structure::addFailure ( ) [inline, slot]

Increase the number of times this Structure has failed the current optimization step by one.

See also:: resetFailCount; setFailCount; getFailCount

Definition at line 1019 of file structure.h.

References getFailCount(), and setFailCount().

bool GlobalSearch::Structure::compareIADDistributions	(	const QList< QVariant > &	d,
		const QList< QVariant > &	f1,
		const QList< QVariant > &	f2,
		double	decay,
		double	smear,
		double *	error
	)			`[static, slot]`

Compare two IAD histograms.

Given two histograms over the same range with the same step, this function calculates an error value to measure the differences between the two. A boxcar smoothing is performed using a width of "smear", and an optional weight can be applied. The weight is a standard exponential decay with a halflife of "decay".

Parameters:

	d	List of distances
	f1	First list of frequencies
	f2	Second list of frequencies
	decay	Exponential decay parameter for lowering weight of large IADs
	smear	Boxcar smoothing width in Angstroms
	error	Return error value

Returns:: Whether or not the operation could be performed.

Definition at line 1109 of file structure.cpp.

References compareIADDistributions().

bool GlobalSearch::Structure::compareIADDistributions	(	const QList< double > &	d,
		const QList< double > &	f1,
		const QList< double > &	f2,
		double	decay,
		double	smear,
		double *	error
	)			`[static, slot]`

Compare two IAD histograms.

Given two histograms over the same range with the same step, this function calculates an error value to measure the differences between the two. A boxcar smoothing is performed using a width of "smear", and an optional weight can be applied. The weight is a standard exponential decay with a halflife of "decay".

Parameters:

	d	List of distances
	f1	First list of frequencies
	f2	Second list of frequencies
	decay	Exponential decay parameter for lowering weight of large IADs
	smear	Boxcar smoothing width in Angstroms
	error	Return error value

Returns:: Whether or not the operation could be performed.

Definition at line 1088 of file structure.cpp.

References compareIADDistributions().

bool GlobalSearch::Structure::compareIADDistributions	(	const std::vector< double > &	d,
		const std::vector< double > &	f1,
		const std::vector< double > &	f2,
		double	decay,
		double	smear,
		double *	error
	)			`[static, slot]`

Compare two IAD histograms.

Given two histograms over the same range with the same step, this function calculates an error value to measure the differences between the two. A boxcar smoothing is performed using a width of "smear", and an optional weight can be applied. The weight is a standard exponential decay with a halflife of "decay".

Parameters:

	d	List of distances
	f1	First list of frequencies
	f2	Second list of frequencies
	decay	Exponential decay parameter for lowering weight of large IADs
	smear	Boxcar smoothing width in Angstroms
	error	Return error value

Returns:: Whether or not the operation could be performed.

Definition at line 1017 of file structure.cpp.

Referenced by compareIADDistributions().

Structure & GlobalSearch::Structure::copyStructure ( const Structure & other ) [virtual]

Only update this structure's atoms, bonds, and residue information from other.

See also:: operator=

Definition at line 228 of file structure.cpp.

References operator=().

Referenced by operator=().

void GlobalSearch::Structure::deleteFromHistory ( unsigned int index ) [virtual, slot]

Parameters:

index

Index of entry to remove from structure's history.

Definition at line 597 of file structure.cpp.

References sizeOfHistory().

void GlobalSearch::Structure::emitPreoptimizationFinished ( ) [inline, slot]

Emits the preoptimizationFinished signal

Definition at line 1107 of file structure.h.

void GlobalSearch::Structure::emitPreoptimizationStarted ( ) [inline, slot]

Emits the preoptimizationStarted signal

Definition at line 1101 of file structure.h.

void GlobalSearch::Structure::enableAutoHistogramGeneration ( bool b ) [virtual, slot]

Set whether the default histogram generation should be performed (default is off)

Definition at line 135 of file structure.cpp.

References requestHistogramGeneration().

void GlobalSearch::Structure::generateDefaultHistogram ( ) [virtual, slot]

Generate default histogram data (0:10 A, 0.01 A step)

See also:: isHistogramGenerationPending(); getDefaultHistogram()

Definition at line 852 of file structure.cpp.

References generateIADHistogram().

Referenced by requestHistogramGeneration().

bool GlobalSearch::Structure::generateIADHistogram	(	QList< QVariant > *	distance,
		QList< QVariant > *	frequency,
		double	min = `0.0`,
		double	max = `10.0`,
		double	step = `0.01`,
		Avogadro::Atom *	atom = `0`
	)			const `[virtual]`

Generate data for a histogram of the distances between all atoms, or between one atom and all others.

If the parameter atom is specified, the resulting data will represent the distance distribution between that atom and all others. If omitted (or NULL), a histogram of all interatomic distances is calculated.

Useful for estimating the coordination number of an atom from a plot.

Warning:: This algorithm is not thoroughly tested and should not be relied upon. It is merely an estimation.

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than one atom present)

Parameters:

	distance	List of distance values for the histogram bins.
	frequency	Number of Atoms within the corresponding distance bin.
	min	Value of starting histogram distance.
	max	Value of ending histogram distance.
	step	Increment between bins.
	atom	Optional: Atom to calculate distances from.

See also:: getShortestInteratomicDistance; requestHistogramGeneration; getNearestNeighborDistance

Definition at line 948 of file structure.cpp.

bool GlobalSearch::Structure::generateIADHistogram	(	QList< double > *	distance,
		QList< double > *	frequency,
		double	min = `0.0`,
		double	max = `10.0`,
		double	step = `0.01`,
		Avogadro::Atom *	atom = `0`
	)			const `[virtual]`

Generate data for a histogram of the distances between all atoms, or between one atom and all others.

If the parameter atom is specified, the resulting data will represent the distance distribution between that atom and all others. If omitted (or NULL), a histogram of all interatomic distances is calculated.

Useful for estimating the coordination number of an atom from a plot.

Warning:: This algorithm is not thoroughly tested and should not be relied upon. It is merely an estimation.

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than one atom present)

Parameters:

	distance	List of distance values for the histogram bins.
	frequency	Number of Atoms within the corresponding distance bin.
	min	Value of starting histogram distance.
	max	Value of ending histogram distance.
	step	Increment between bins.
	atom	Optional: Atom to calculate distances from.

See also:: getShortestInteratomicDistance; requestHistogramGeneration; getNearestNeighborDistance

Definition at line 874 of file structure.cpp.

Referenced by generateDefaultHistogram().

uint GlobalSearch::Structure::getCurrentOptStep ( ) [inline]

Returns:: The current optimization step of the Structure.

See also:: setCurrentOptStep

Definition at line 287 of file structure.h.

Referenced by GlobalSearch::Optimizer::getInterpretedTemplates(), GlobalSearch::OptBase::interpretKeyword_base(), GlobalSearch::QueueManager::startJob(), and writeStructureSettings().

void GlobalSearch::Structure::getDefaultHistogram	(	QList< QVariant > *	dist,
		QList< QVariant > *	freq
	)			const `[virtual]`

Get the default histogram data.

Definition at line 868 of file structure.cpp.

void GlobalSearch::Structure::getDefaultHistogram	(	QList< double > *	dist,
		QList< double > *	freq
	)			const `[virtual]`

Get the default histogram data.

Definition at line 858 of file structure.cpp.

QString GlobalSearch::Structure::getDuplicateString ( ) const [inline]

Returns:: A string naming the Structure that this Structure is a duplicate of.

See also:: setDuplicateString

Definition at line 265 of file structure.h.

double GlobalSearch::Structure::getEnergy ( ) const [inline]

Return the energy value of the first conformer in eV. This is a convenience function.

Note:: The energies of the other conformers are still available using energy(int). Be aware that energy(int) returns kcal/mol. The multiplicative factor EV_TO_KCAL_PER_MOL has been defined to aid conversion.

Returns:: The energy of the first conformer in eV.

See also:: setEnthalpy; hasEnthalpy; setPV; getPV; setEnergy; getEnergy

Definition at line 178 of file structure.h.

Referenced by getEnthalpy().

double GlobalSearch::Structure::getEnthalpy ( ) const [inline]

Return the enthalpy value of the first conformer in eV.

Note:: If the enthalpy is not set but the energy is set, this function assumes that the system is at zero-pressure and returns the energy.

Returns:: The enthalpy of the first conformer in eV.

See also:: setEnthalpy; hasEnthalpy; setPV; getPV; setEnergy; getEnergy

Definition at line 194 of file structure.h.

References getEnergy().

Referenced by getFingerprint(), GlobalSearch::OptBase::getProbabilityList(), getResultsEntry(), rankByEnthalpy(), and sortByEnthalpy().

uint GlobalSearch::Structure::getFailCount ( ) [inline]

Returns:: The number of times this Structure has failed the current optimization step.

See also:: setFailCount; addFailure; resetFailCount

Definition at line 306 of file structure.h.

Referenced by addFailure(), GlobalSearch::QueueManager::checkPopulation(), and writeStructureSettings().

QHash< QString, QVariant > GlobalSearch::Structure::getFingerprint ( ) const [virtual]

A "fingerprint" hash of the structure. Returns "enthalpy" key with the enthalpy value as a double wrapped in a QVariant. May be extended in derived classes.

Used for checking if two Structures are similar enough to be marked as duplicates.

Returns:: A hash of key/value pairs containing data that is representative of the Structure.

Definition at line 1232 of file structure.cpp.

References getEnthalpy().

uint GlobalSearch::Structure::getGeneration ( ) const [inline]

Returns the generation number of the structure. Only useful for genetic/evolutionary algorithms.

Returns:: Generation number

See also:: setGeneration; getIDNumber; getIndex; setIDNumber; setIndex; getIDString

Definition at line 232 of file structure.h.

Referenced by getIDString(), getResultsEntry(), GlobalSearch::OptBase::interpretKeyword_base(), and writeStructureSettings().

uint GlobalSearch::Structure::getIDNumber ( ) const [inline]

Returns an ID number associated with the Structure.

Note:: If a generation number is used as well, this may not be unique.

Returns:: Identification number

See also:: setGeneration; getGeneration; getIndex; setIDNumber; setIndex; getIDString

Definition at line 246 of file structure.h.

Referenced by getIDString(), getResultsEntry(), GlobalSearch::OptBase::interpretKeyword_base(), and writeStructureSettings().

QString GlobalSearch::Structure::getIDString ( ) const [inline]

Returns a unique identification string. Defaults to [generation]x[IDNumber]. Handy for debugging/error output.

Returns:: Unique identification string.

See also:: setGeneration; getGeneration; setIndex; getIndex; setIDNumber; getIDNumber

Definition at line 338 of file structure.h.

References getGeneration(), and getIDNumber().

Referenced by GlobalSearch::Optimizer::getInterpretedTemplates(), GlobalSearch::Optimizer::read(), readStructureSettings(), GlobalSearch::QueueManager::startJob(), GlobalSearch::QueueManager::unlockForNaming(), and GlobalSearch::Optimizer::update().

int GlobalSearch::Structure::getIndex ( ) const [inline]

Returns a unique ID number associated with the Structure. This is typically assigned in order of introduction to a tracker.

Returns:: Unique identification number

See also:: setGeneration; getGeneration; getIndex; setIDNumber; getIDNumber; getIDString

Definition at line 259 of file structure.h.

Referenced by writeStructureSettings().

uint GlobalSearch::Structure::getJobID ( ) const [inline]

Returns the Job ID of the Structure's current running optimization. Returns zero is not running.

Returns:: Job ID of the structure's optimization process.

See also:: setJobID

Definition at line 220 of file structure.h.

Referenced by writeStructureSettings().

bool GlobalSearch::Structure::getNearestNeighborDistance	(	const Avogadro::Atom *	atom,
		double &	shortest
	)			const `[virtual]`

Find the nearest neighbor distance of a specified atom.

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than one atom present)

Parameters:

	atom	Atom of interest
	shortest	An empty double to be overwritten with the nearest neighbor distance.

See also:: getShortestInteratomicDistance; getNearestNeighborHistogram; getNeighbors

Definition at line 799 of file structure.cpp.

References getNearestNeighborDistance().

bool GlobalSearch::Structure::getNearestNeighborDistance	(	const double	x,
		const double	y,
		const double	z,
		double &	shortest
	)			const `[virtual]`

Find the distance to the nearest atom from a specified point.

Useful for checking if an atom will be too close to another atom before adding it.

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than one atom present)

Parameters:

	x	Cartesian coordinate
	y	Cartesian coordinate
	z	Cartesian coordinate
	shortest	An empty double to be overwritten with the nearest neighbor distance.

See also:: getShortestInteratomicDistance; getNearestNeighborHistogram; getNeighbors

Definition at line 773 of file structure.cpp.

Referenced by getNearestNeighborDistance(), and getNearestNeighborDistances().

bool GlobalSearch::Structure::getNearestNeighborDistances ( QList< double > * list ) const [virtual]

Find the smallest separation between all atoms in the Structure.

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than two atoms present)

Parameters:

list

list of distances in Angstrom

See also:: getNearestNeighborDistance; getNearestNeighborHistogram; getNeighbors

Definition at line 728 of file structure.cpp.

References getNearestNeighborDistance().

QList< Atom * > GlobalSearch::Structure::getNeighbors	(	const Avogadro::Atom *	atom,
		const double	cutoff,
		QList< double > *	distances = `0`
	)			const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Returns:: a list of all atoms within cutoff of atom and, optionally, their distances.

Definition at line 833 of file structure.cpp.

References getNeighbors().

QList< Atom * > GlobalSearch::Structure::getNeighbors	(	const double	x,
		const double	y,
		const double	z,
		const double	cutoff,
		QList< double > *	distances = `0`
	)			const

Returns:: a list of all atoms within cutoff of (x,y,z) and, optionally, their distances.

Definition at line 808 of file structure.cpp.

Referenced by getNeighbors().

QList< uint > GlobalSearch::Structure::getNumberOfAtomsAlpha ( ) const

Returns:: A list of the number of species present that corresponds to the symbols listed in getSymbols().

See also:: getSymbols

Definition at line 1146 of file structure.cpp.

References getSymbols().

QString GlobalSearch::Structure::getOptElapsed ( ) const

Returns:: A string formated "HH:MM:SS" indicating the amount of time spent in the current optimization step

See also:: setOptTimerStart; getOptTimerStart; setOptTimerEnd; getOptTimerEnd; startOptTimer; stopOptTimer

Definition at line 1166 of file structure.cpp.

QHash<int, int>* GlobalSearch::Structure::getOptimizerLookupTable ( ) [inline]

Returns:: a lookup table for mapping atoms indices between structure index (value) and the optimizer index (key).

Definition at line 362 of file structure.h.

Referenced by GlobalSearch::OptBase::interpretKeyword_base().

QDateTime GlobalSearch::Structure::getOptTimerEnd ( ) const [inline]

Returns:: The time that the current optimization step ended.

See also:: getOptTimerStart; startOptTimer; stopOptTimer; setOptTimerStart; setOptTimerEnd; getOptElapsed

Definition at line 326 of file structure.h.

Referenced by writeStructureSettings().

QDateTime GlobalSearch::Structure::getOptTimerStart ( ) const [inline]

Returns:: The time that the current optimization step started.

See also:: getOptTimerEnd; startOptTimer; stopOptTimer; setOptTimerStart; setOptTimerEnd; getOptElapsed

Definition at line 316 of file structure.h.

Referenced by writeStructureSettings().

QString GlobalSearch::Structure::getParents ( ) const [inline]

Returns:: a string describing the ancestory of the Structure.

See also:: setParents

Definition at line 270 of file structure.h.

Referenced by writeStructureSettings().

virtual int GlobalSearch::Structure::getPreOptProgress ( ) const [inline, virtual]

Returns:: The percentage completion of the preoptimization step. -1 if this is not Preoptimizing.

Definition at line 295 of file structure.h.

double GlobalSearch::Structure::getPV ( ) const [inline]

Returns the value PV term from an enthalpy calculation (H = U + PV) in eV.

Returns:: The PV term in eV.

See also:: getEnthalpy; setEnthalpy; hasEnthalpy; setPV; setEnergy; getEnergy

Definition at line 207 of file structure.h.

uint GlobalSearch::Structure::getRank ( ) const [inline]

Returns an energetic ranking set by setRank(uint).

Returns:: the energetic ranking.

See also:: setRank

Definition at line 213 of file structure.h.

Referenced by getResultsEntry(), and writeStructureSettings().

QString GlobalSearch::Structure::getRempath ( ) const [inline]

Returns:: The path on the remote server to write this Structure for optimization.

See also:: setRempath

Definition at line 276 of file structure.h.

Referenced by GlobalSearch::OptBase::interpretKeyword_base(), and writeStructureSettings().

QString GlobalSearch::Structure::getResultsEntry ( ) const [virtual]

Returns:: A structure-specific entry for a results printout

See also:: getResultsHeader; OptBase::save

Definition at line 687 of file structure.cpp.

References Duplicate, Empty, Error, getEnthalpy(), getGeneration(), getIDNumber(), getRank(), getStatus(), InProcess, Killed, Optimized, Preoptimizing, Removed, Restart, StepOptimized, Submitted, Updating, and WaitingForOptimization.

Referenced by GlobalSearch::OptBase::save().

virtual QString GlobalSearch::Structure::getResultsHeader ( ) const [inline, virtual]

Returns:: A header line for a results printout

See also:: getResultsEntry; OptBase::save

Definition at line 345 of file structure.h.

bool GlobalSearch::Structure::getShortestInteratomicDistance ( double & shortest ) const [virtual]

Return a list of nearest neighbor distances for each atom in the Structure

Returns:: true if the operation makes sense for this Structure, false otherwise (i.e. fewer than two atoms present)

Parameters:

shortest

An empty double to be overwritten with the shortest interatomic distance.

See also:: getNearestNeighborDistance; getNearestNeighborHistogram; getNeighbors

Definition at line 747 of file structure.cpp.

State GlobalSearch::Structure::getStatus ( ) const [inline]

Returns:: The current status of the Structure.

See also:: setStatus; State

Definition at line 282 of file structure.h.

Referenced by GlobalSearch::QueueManager::checkPopulation(), GlobalSearch::QueueManager::checkRunning(), GlobalSearch::QueueManager::getAllDuplicateStructures(), GlobalSearch::QueueManager::getAllOptimizedStructures(), getResultsEntry(), GlobalSearch::QueueManager::killStructure(), and writeStructureSettings().

QList< QString > GlobalSearch::Structure::getSymbols ( ) const

Returns:: An alphabetized list of the atomic symbols for the atomic species present in the Structure.

See also:: getNumberOfAtomsAlpha

Definition at line 1130 of file structure.cpp.

Referenced by getNumberOfAtomsAlpha(), and GlobalSearch::OptBase::interpretKeyword_base().

bool GlobalSearch::Structure::hasBestOffspring ( ) const [inline]

Returns:: Whether or not the "best" offspring (an optimized mutation) has been generated for this structure.

Definition at line 149 of file structure.h.

Referenced by writeStructureSettings().

bool GlobalSearch::Structure::hasChangedSinceDupChecked ( ) [inline]

Structure can track if it has changed since it was last checked in a duplicate finding routine. This is useful for cutting down on the number of comparisons needed.

Must call setupConnections() before using this function.

See also:: setChangedSinceDupChecked()

Definition at line 623 of file structure.h.

bool GlobalSearch::Structure::hasEnthalpy ( ) const [inline]

Whether the Structure has an enthalpy value set.

Returns:: true if enthalpy has been set, false otherwise

See also:: setEnthalpy; getEnthalpy; setPV; getPV; setEnergy; getEnergy

Definition at line 160 of file structure.h.

virtual bool GlobalSearch::Structure::isHistogramGenerationPending ( ) const [inline, virtual]

Returns:: True is histogram generation is pending.

Definition at line 473 of file structure.h.

virtual bool GlobalSearch::Structure::isPreoptimizing ( ) const [inline, virtual]

Returns:: true if running, false otherwise.

Definition at line 290 of file structure.h.

Referenced by GlobalSearch::QueueManager::stopJob().

void GlobalSearch::Structure::load ( QTextStream & in ) [virtual, slot]

Load data into Structure.

Attention:: Do not use this function in new code, as it has been replaced by readSettings. Old code should be rewritten to use readSettings as well.

Deprecated:: Use readSettings instead, and call this only as a backup for outdates .state files

Parameters:

in

QTextStream containing load data.

See also:: readSettings

Definition at line 1181 of file structure.cpp.

References InProcess, setCurrentOptStep(), setFailCount(), setGeneration(), setIDNumber(), setIndex(), setJobID(), setOptTimerEnd(), setOptTimerStart(), setParents(), setRank(), setRempath(), and setStatus().

Referenced by readStructureSettings().

virtual bool GlobalSearch::Structure::needsPreoptimization ( ) const [inline, virtual]

Returns:: Whether or not this needs to be preoptimized.

Definition at line 298 of file structure.h.

Referenced by GlobalSearch::QueueManager::checkPopulation(), GlobalSearch::QueueManager::startJob(), GlobalSearch::QueueManager::startPreoptimization(), and writeStructureSettings().

Structure & GlobalSearch::Structure::operator= ( const Avogadro::Molecule & other )

Assignment operator. Makes a new structure with all Molecule specific information copied from other.

See also:: copyStructure

Definition at line 222 of file structure.cpp.

References copyStructure().

Structure & GlobalSearch::Structure::operator= ( const Structure & other )

Assignment operator. Makes a new structure with all Structure specific information copied from other.

See also:: copyStructure

Definition at line 196 of file structure.cpp.

References copyStructure().

Referenced by copyStructure().

void GlobalSearch::Structure::rankByEnthalpy ( const QList< Structure * > & structures ) [static]

Rank the listed structures by their enthalpies

Parameters:

structures

List of structures to assign ranks

See also:: sortEnthalpies; sortAndRankByEnthalpy; setRank; getRank

Definition at line 1277 of file structure.cpp.

References getEnthalpy().

virtual void GlobalSearch::Structure::readSettings ( const QString & filename ) [inline, virtual, slot]

Read supplementary data about this Structure from a file. All data that is not stored in the OpenBabel-readable optimizer output file should be read here.

If reimplementing this in a derived class, call readStructureSettings(filename) to read inherited data.

Parameters:

filename

Filename to read data from.

See also:: readStructureSettings; writeSettings

Definition at line 797 of file structure.h.

References readStructureSettings().

void GlobalSearch::Structure::readStructureSettings ( const QString & filename ) [protected, slot]

Read data concerning the Structure class from a file.

Parameters:

filename

Filename to read data from.

See also:: writeSettings; readSettings

Definition at line 342 of file structure.cpp.

References getIDString(), load(), setCurrentOptStep(), setFailCount(), setGeneration(), setHasBestOffspring(), setIDNumber(), setIndex(), setJobID(), setNeedsPreoptimization(), setOptTimerEnd(), setOptTimerStart(), setParents(), setRank(), setRempath(), and setStatus().

Referenced by readSettings().

void GlobalSearch::Structure::requestHistogramGeneration ( ) [virtual, slot]

Request that histogram data be regenerated. This is connected to Molecule::update() and calls generateDefaultHistogram(). This function is throttled to only run every 250 ms.

Definition at line 843 of file structure.cpp.

References generateDefaultHistogram().

Referenced by enableAutoHistogramGeneration().

void GlobalSearch::Structure::resetEnergy ( ) [inline, slot]

Reset the Structure's energy to zero

See also:: setEnergy; getEnergy

Definition at line 912 of file structure.h.

void GlobalSearch::Structure::resetEnthalpy ( ) [inline, slot]

Reset the Structure's enthalpy and PV term to zero and clear hasEnthalpy()

See also:: setEnthalpy; getEnthalpy; hasEnthalpy; setPV; getPV

Definition at line 906 of file structure.h.

void GlobalSearch::Structure::resetFailCount ( ) [inline, slot]

Reset the number of times this Structure has failed the current optimization step.

See also:: addFailure; setFailCount; getFailCount

Definition at line 1010 of file structure.h.

References setFailCount().

Referenced by Structure().

void GlobalSearch::Structure::resetOptimizerLookupTable ( ) [inline]

Reset the optimizer lookup table to set the optimizer indicies to the structure indices.

Definition at line 370 of file structure.h.

void GlobalSearch::Structure::retrieveHistoryEntry	(	unsigned int	index,
		QList< unsigned int > *	atomicNums,
		QList< Eigen::Vector3d > *	coords,
		double *	energy,
		double *	enthalpy,
		Eigen::Matrix3d *	cell
	)			`[virtual, slot]`

This function is used to retrieve data from the structure's history. All non-zero pointers will be modified to contain the information at the specified index of the history.

Parameters:

	index	Entry in history to return
	atomicNums	Pointer to a list that will be filled with atomic numbers. Can be zero if this is not needed.
	coords	Pointer to a list that will be filled with cartesian atomic coordinates. Can be zero if this is not needed.
	energy	Pointer to a double that will contain the entry's energy in eV. Can be zero if this is not needed.
	enthalpy	Pointer to a double that will contain the entry's enthalpy in eV. Can be zero if this is not needed.
	cell	Pointer to an Eigen::Matrix3f filled with the unit cell vectors (row vectors). Can be zero if this is not needed.

Note:: If the system is not periodic, the cell matrix will be a zero matrix. Use Eigen::Matrix3d::isZero() to test for a valid cell.

Definition at line 608 of file structure.cpp.

References sizeOfHistory().

void GlobalSearch::Structure::setChangedSinceDupChecked ( bool b ) [inline, slot]

Structure can track if it has changed since it was last checked in a duplicate finding routine. This is useful for cutting down on the number of comparisons needed.

Must call setupConnections() before using this function.

See also:: hasChangedSinceDupChecked()

Definition at line 1035 of file structure.h.

void GlobalSearch::Structure::setCurrentOptStep ( uint i ) [inline, slot]

Parameters:

i

The current optimization step of the Structure.

See also:: getCurrentOptStep

Definition at line 993 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setDuplicateString ( const QString & s ) [inline, slot]

Parameters:

s

A string naming the Structure that this Structure is a duplicate of.

See also:: getDuplicateString

Definition at line 1025 of file structure.h.

void GlobalSearch::Structure::setEnthalpy ( double enthalpy ) [inline, slot]

Set the enthalpy of the Structure.

Parameters:

enthalpy

The Structure's enthalpy

See also:: getEnthalpy

Definition at line 890 of file structure.h.

void GlobalSearch::Structure::setFailCount ( uint count ) [inline, slot]

Parameters:

count

The number of times this Structure has failed the current optimization step.

See also:: addFailure; getFailCount; resetFailCount

Definition at line 1001 of file structure.h.

Referenced by addFailure(), load(), readStructureSettings(), and resetFailCount().

void GlobalSearch::Structure::setGeneration ( uint gen ) [inline, slot]

Set the generation number of the Structure.

Parameters:

gen

The generation number.

See also:: setGeneration; getGeneration; setIndex; getIndex; setIDNumber; getIDNumber; getIDString

Definition at line 942 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setHasBestOffspring ( bool b = true ) [inline, slot]

Parameters:

b

Whether or not the "best" offspring (an optimized mutation) has been generated for this structure.

Definition at line 881 of file structure.h.

Referenced by readStructureSettings().

void GlobalSearch::Structure::setIDNumber ( uint id ) [inline, slot]

Set the ID number associated with the Structure.

Note:: If a generation number is used as well, this may not be unique.

Returns:: Identification number

See also:: setGeneration; getGeneration; setIndex; getIndex; getIDNumber; getIDString

Definition at line 956 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setIndex ( int index ) [inline, slot]

Set a unique ID number associated with the Structure. This is typically assigned in order of introduction to a tracker.

Note:: If a generation number is used as well, this may not be unique.

Parameters:

index

Identification number

See also:: setGeneration; getGeneration; getIndex; setIDNumber; getIDNumber; getIDString

Definition at line 971 of file structure.h.

Referenced by load(), readStructureSettings(), and GlobalSearch::OptBase::save().

void GlobalSearch::Structure::setJobID ( uint id ) [inline, slot]

Set the Job ID of the current optimization process.

Parameters:

id

The current optimization process's Job ID.

See also:: getJobID

Definition at line 930 of file structure.h.

Referenced by load(), readStructureSettings(), and GlobalSearch::Optimizer::update().

virtual void GlobalSearch::Structure::setNeedsPreoptimization ( bool b ) [inline, virtual, slot]

Parameters:

b

Whether or not this needs to be preoptimized.

Definition at line 1089 of file structure.h.

Referenced by readStructureSettings().

void GlobalSearch::Structure::setOBEnergy ( const QString & ff = QString("UFF") ) [slot]

Determine and set the energy using a forcefield method from OpenBabel.

Parameters:

ff

A string identifying the forcefield to use (default: UFF).

Definition at line 674 of file structure.cpp.

void GlobalSearch::Structure::setOptTimerEnd ( const QDateTime & d ) [inline, slot]

Parameters:

d

The time that the current optimization process stopped.

See also:: setOptTimerStart; getOptTimerStart; getOptTimerEnd; startOptTimer; stopOptTimer; getOptElapsed

Definition at line 1085 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setOptTimerStart ( const QDateTime & d ) [inline, slot]

Parameters:

d

The time that the current optimization process started.

See also:: getOptTimerStart; setOptTimerEnd; getOptTimerEnd; startOptTimer; stopOptTimer; getOptElapsed

Definition at line 1073 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setParents ( const QString & p ) [inline, slot]

Parameters:

p

A string describing the ancestory of the Structure.

See also:: getParents

Definition at line 976 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setPV ( double pv ) [inline, slot]

Set the PV term of the Structure's enthalpy (see getPV()).

Parameters:

pv

The PV term

See also:: getPV

Definition at line 896 of file structure.h.

void GlobalSearch::Structure::setRank ( uint rank ) [inline, slot]

Set the Structure's energetic ranking.

Parameters:

rank

The Structure's energetic ranking.

See also:: getRank

Definition at line 924 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setRempath ( const QString & p ) [inline, slot]

Parameters:

p

The path on the remote server to write this Structure for optimization.

See also:: getRempath

Definition at line 982 of file structure.h.

Referenced by load(), and readStructureSettings().

void GlobalSearch::Structure::setStatus ( State status ) [inline, slot]

Parameters:

status

The current status of the Structure.

See also:: getStatus; State

Definition at line 988 of file structure.h.

Referenced by GlobalSearch::QueueManager::killStructure(), load(), readStructureSettings(), GlobalSearch::QueueManager::startJob(), GlobalSearch::QueueManager::startPreoptimization(), and Structure().

void GlobalSearch::Structure::setupConnections ( ) [virtual, slot]

Connect slots/signals within the molecule. This must be called AFTER moving the Structure to it's final thread.

Definition at line 96 of file structure.cpp.

References structureChanged().

virtual unsigned int GlobalSearch::Structure::sizeOfHistory ( ) [inline, virtual, slot]

Returns:: Number of history entries available

Definition at line 876 of file structure.h.

Referenced by deleteFromHistory(), and retrieveHistoryEntry().

void GlobalSearch::Structure::sortAndRankByEnthalpy ( QList< Structure * > * structures ) [static]

Sort and rank the listed structures by their enthalpies

Parameters:

structures

List of structures to sort and assign rank

See also:: sortByEnthalpy; rankEnthalpies; setRank; getRank

Definition at line 1311 of file structure.cpp.

References sortByEnthalpy().

Referenced by GlobalSearch::OptBase::save().

void GlobalSearch::Structure::sortByEnthalpy ( QList< Structure * > * structures ) [static]

Sort the listed structures by their enthalpies

Parameters:

structures

List of structures to sort

See also:: rankEnthalpies; sortAndRankByEnthalpy

Definition at line 1239 of file structure.cpp.

References getEnthalpy().

Referenced by sortAndRankByEnthalpy().

void GlobalSearch::Structure::startOptTimer ( ) [inline, slot]

Record the current time as when the current optimization process started.

See also:: setOptTimerStart; getOptTimerStart; setOptTimerEnd; getOptTimerEnd; stopOptTimer; getOptElapsed

Definition at line 1047 of file structure.h.

void GlobalSearch::Structure::stopOptTimer ( ) [inline, slot]

Record the current time as when the current optimization process stopped.

See also:: setOptTimerStart; getOptTimerStart; setOptTimerEnd; getOptTimerEnd; startOptTimer; getOptElapsed

Definition at line 1060 of file structure.h.

Referenced by GlobalSearch::QueueManager::killStructure(), and GlobalSearch::Optimizer::update().

void GlobalSearch::Structure::structureChanged ( ) [virtual, slot]

After calling setupConnections(), this will be called when the structure is update, atoms moved, added, etc...

Definition at line 481 of file structure.cpp.

Referenced by setupConnections().

void GlobalSearch::Structure::updateAndAddToHistory	(	const QList< unsigned int > &	atomicNums,
		const QList< Eigen::Vector3d > &	coords,
		const double	energy = `0`,
		const double	enthalpy = `0`,
		const Eigen::Matrix3d &	cell = `Eigen::Matrix3d::Zero()`
	)			`[virtual, slot]`

Update the coordinates, enthalpy and/or energy, and optionally unit cell of the structure, appending the data to the structure's history.

Parameters:

	atomicNums	List of atomic numbers
	coords	List of cartesian coordinates
	energy	in eV
	enthalpy	in eV
	cell	Matrix of cell vectors (row vectors)

Definition at line 538 of file structure.cpp.

Referenced by GlobalSearch::Optimizer::read().

void GlobalSearch::Structure::updateAndSkipHistory	(	const QList< unsigned int > &	atomicNums,
		const QList< Eigen::Vector3d > &	coords,
		const double	energy = `0`,
		const double	enthalpy = `0`,
		const Eigen::Matrix3d &	cell = `Eigen::Matrix3d::Zero()`
	)			`[virtual, slot]`

Update the coordinates, enthalpy and/or energy, and optionally unit cell of the structure, without adding the data to the structure's history.

Parameters:

	atomicNums	List of atomic numbers
	coords	List of cartesian coordinates
	energy	in eV
	enthalpy	in eV
	cell	Matrix of cell vectors (row vectors)

Definition at line 486 of file structure.cpp.

Referenced by GlobalSearch::Optimizer::read().

virtual void GlobalSearch::Structure::writeSettings ( const QString & filename ) [inline, virtual, slot]

Write supplementary data about this Structure to a file. All data that is not stored in the OpenBabel-readable optimizer output file should be written here.

If reimplementing this in a derived class, call writeStructureSettings(filename) to write inherited data.

Parameters:

filename

Filename to write data to.