GlobalSearch::OptBase Class Reference

The OptBase class stores variables and helper functions for global searches. More...

#include <globalsearch/optbase.h>

Public Types
enum	FailActions { FA_DoNothing = 0, FA_KillIt, FA_Randomize, FA_NewOffspring }
Public Slots
virtual void	reset ()
virtual void	startSearch ()=0
virtual void	generateNewStructure ()
virtual void	preoptimizeStructure (Structure *s)
void	debug (const QString &s)
void	warning (const QString &s)
void	error (const QString &s)
void	emitSessionStarted ()
void	emitReadOnlySessionStarted ()
void	emitStartingSession ()
void	setIsStartingTrue ()
void	setIsStartingFalse ()
void	setReadOnlyTrue ()
void	setReadOnlyFalse ()
void	printBackTrace ()
void	setQueueInterface (QueueInterface *q)
void	setOptimizer (Optimizer *o)
void	promptForBoolean (const QString &message, bool *ok=0)
void	promptForPassword (const QString &message, QString newPassword, bool ok=0)
void	setClipboard (const QString &text) const
Signals
void	startingSession ()
void	sessionStarted ()
void	readOnlySessionStarted ()
void	queueInterfaceChanged (QueueInterface *)
void	optimizerChanged (Optimizer *)
void	debugStatement (const QString &s)
void	warningStatement (const QString &s)
void	errorStatement (const QString &s)
void	needBoolean (const QString &message, bool *ok)
void	needPassword (const QString &message, QString newPassword, bool ok)
void	refreshAllStructureInfo ()
Public Member Functions
	OptBase (AbstractDialog *parent)
virtual	~OptBase ()
QString	getIDString ()
virtual Structure *	replaceWithRandom (Structure *s, const QString &reason="")
virtual Structure *	replaceWithOffspring (Structure *s, const QString &reason="")
virtual bool	checkLimits ()=0
virtual bool	checkStepOptimizedStructure (Structure s, QString err=NULL)
virtual bool	save (const QString &filename="", bool notify=false)
virtual bool	postSave (const QString &filename)
virtual bool	load (const QString &filename, const bool forceReadOnly=false)
virtual QString	interpretTemplate (const QString &templateString, Structure *structure)
virtual QString	getTemplateKeywordHelp ()
AbstractDialog *	dialog ()
Tracker *	tracker ()
QueueManager *	queue ()
QueueInterface *	queueInterface ()
Optimizer *	optimizer ()
SSHManager *	ssh ()
Static Public Member Functions
static QList< double >	getProbabilityList (const QList< Structure * > &structures)
Public Attributes
bool	limitRunningJobs
	Whether to impose the running job limit.
uint	runningJobLimit
	Number of concurrent jobs allowed.
uint	contStructs
	Number of continuous structures generated.
int	cutoff
	How many structures to produce before halting search. -1 for no limit.
bool	testingMode
	Whether to run benchmarking tests.
uint	test_nRunsStart
	Starting run number for benchmark.
uint	test_nRunsEnd
	Ending run number for benchmark.
uint	test_nStructs
	Number of Structures per run when benchmarking.
uint	failLimit
FailActions	failAction
QString	filePath
	Local directory to work in.
QString	description
	Terse description of current search.
QString	host
	Host name or IP address of remote PBS server.
int	port
	Port on remote PBS server used for SSH communication.
QString	username
	Username for ssh login on remote PBS server.
QString	rempath
QMutex *	sOBMutex
QMutex *	stateFileMutex
QMutex *	backTraceMutex
	This is locked when generating a backtrace.
bool	usePreopt
	True if a preoptimization should be used.
bool	savePending
	True if there is a save requested or in progress.
bool	isStarting
	True if a session is starting or being loaded.
bool	readOnly
	Whether readOnly mode is enabled (e.g. no connection to server).
Protected Member Functions
void	interpretKeyword_base (QString &keyword, Structure *structure)
	Hidden call to interpretKeyword.
QString	getTemplateKeywordHelp_base ()
	Hidden call to getTemplateKeywordHelp.
Protected Attributes
QString	m_idString
SSHManager *	m_ssh
AbstractDialog *	m_dialog
Tracker *	m_tracker
QThread *	m_queueThread
	Thread to run the QueueManager.
QueueManager *	m_queue
QueueInterface *	m_queueInterface
Optimizer *	m_optimizer
unsigned int	m_schemaVersion
	Current version of save/resume schema.
bool	m_isDestroying

Detailed Description

The OptBase class stores variables and helper functions for global searches.

Author:: David C. Lonie

OptBase is the main class in libglobalsearch. It contains the variables that define a search, as well as handling structure generation. This class ties all others together.

Definition at line 53 of file optbase.h.

Member Enumeration Documentation

enum GlobalSearch::OptBase::FailActions

Actions to take when a structure has failed optimization too many times.

See also:: OptBase::failAction; OptBase::failLimit

Enumerator:

FA_DoNothing	Do nothing; keep submitting for optimization.
FA_KillIt	Kill the structure.
FA_Randomize	Replace the failing structure with a new random one.
FA_NewOffspring	Replace with a new offspring structure.

Definition at line 77 of file optbase.h.

Constructor & Destructor Documentation

GlobalSearch::OptBase::OptBase ( AbstractDialog * parent ) [explicit]

Constructor

Parameters:

parent

Dialog window of GUI.

Definition at line 48 of file optbase.cpp.

References m_queueThread, needBoolean(), needPassword(), promptForBoolean(), promptForPassword(), readOnlySessionStarted(), sessionStarted(), setIsStartingFalse(), setIsStartingTrue(), and startingSession().

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

Destructor

Definition at line 100 of file optbase.cpp.

References m_optimizer, m_queue, m_queueInterface, m_queueThread, and m_tracker.

Member Function Documentation

virtual bool GlobalSearch::OptBase::checkLimits ( ) [pure virtual]

Before starting an optimization, this function will check the parameters of the search to ensure that they are within a reasonable range.

Returns:: True if the search parameters are valid, false otherwise.

virtual bool GlobalSearch::OptBase::checkStepOptimizedStructure	(	Structure *	s,
		QString *	err = `NULL`
	)			`[inline, virtual]`

Perform any post-optimization checks that need to be performed when a structure enters the Structure::StepOptimized state.

Parameters:

	s	Structure to check
	err	If non-NULL, will be overwritten with an explaination of why the check failed.

Returns:: True if structure passes, false otherwise.

Definition at line 140 of file optbase.h.

void GlobalSearch::OptBase::debug ( const QString & s ) [slot]

Prints a debug message to the terminal and emits debugStatement

Parameters:

s

The debug statement.

See also:: debug; debugStatement; warning; warningStatement; error; errorStatement

Definition at line 631 of file optbase.cpp.

References debugStatement().

void GlobalSearch::OptBase::debugStatement ( const QString & s ) [signal]

Emitted when debug(const QString&) is called.

Parameters:

s

The debugging statement.

See also:: debug; debugStatement; warning; warningStatement; error; errorStatement

Referenced by debug().

AbstractDialog* GlobalSearch::OptBase::dialog ( ) [inline]

Returns:: A pointer to the main dialog..

Definition at line 242 of file optbase.h.

References m_dialog.

Referenced by GlobalSearch::Optimizer::dialog(), promptForBoolean(), and promptForPassword().

void GlobalSearch::OptBase::emitReadOnlySessionStarted ( ) [inline, slot]

Emits the readOnlySessionStarted signal.

See also:: sessionStarted; emitSessionStarted; readOnlySessionStarted; startingSession; emitStartingSession

Definition at line 557 of file optbase.h.

References readOnlySessionStarted().

Referenced by GlobalSearch::AbstractDialog::resumeSession_().

void GlobalSearch::OptBase::emitSessionStarted ( ) [inline, slot]

Emits the sessionStarted signal.

See also:: sessionStarted; readOnlySessionStarted; emitReadOnlySessionStarted; startingSession; emitStartingSession

Definition at line 547 of file optbase.h.

References sessionStarted().

Referenced by GlobalSearch::AbstractDialog::resumeSession_().

void GlobalSearch::OptBase::emitStartingSession ( ) [inline, slot]

Emits the startingSession signal.

See also:: sessionStarted; emitSessionStarted; startingSession; emitStartingSession

Definition at line 566 of file optbase.h.

References startingSession().

Referenced by GlobalSearch::AbstractDialog::resumeSession_().

void GlobalSearch::OptBase::error ( const QString & s ) [slot]

Prints a error message to the terminal and emits errorStatement

Parameters:

s

The error statement.

See also:: debug; debugStatement; warning; warningStatement; error; errorStatement

Definition at line 636 of file optbase.cpp.

References errorStatement().

Referenced by GlobalSearch::Optimizer::read(), and save().

void GlobalSearch::OptBase::errorStatement ( const QString & s ) [signal]

Emitted when error(const QString&) is called.

Parameters:

s

The error statement.

See also:: debug; debugStatement; warning; warningStatement; error; errorStatement

Referenced by error().

virtual void GlobalSearch::OptBase::generateNewStructure ( ) [inline, virtual, slot]

Called when the QueueManager requests more Structures.

See also:: QueueManager

Definition at line 491 of file optbase.h.

QString GlobalSearch::OptBase::getIDString ( ) [inline]

Returns:: An ID string that uniquely identifies this OptBase.

Definition at line 91 of file optbase.h.

References m_idString.

Referenced by GlobalSearch::AbstractEditTab::loadScheme(), GlobalSearch::Optimizer::readDataFromSettings(), GlobalSearch::Optimizer::readTemplatesFromSettings(), GlobalSearch::Optimizer::readUserValuesFromSettings(), GlobalSearch::AbstractDialog::resumeSession(), GlobalSearch::AbstractEditTab::saveScheme(), GlobalSearch::AbstractDialog::updateGUI(), GlobalSearch::Optimizer::writeDataToSettings(), GlobalSearch::Optimizer::writeTemplatesToSettings(), and GlobalSearch::Optimizer::writeUserValuesToSettings().

QList< double > GlobalSearch::OptBase::getProbabilityList ( const QList< Structure * > & structures ) [static]

Generate a probability list using the enthalpies of a collection of structures.

The probability is calculated by:

p_i = N * (1 - (H_i - H_min) / (H_max - H_min) )

where p_i is the probability of selecting structure i, H_i is the enthalpy of structure i, H_min and H_max are the lowest and highest enthalpies in the collection, and N is a normalization factor.

To use the probability list generated by this function, run

double r = RANDDOUBLE();
int ind;
for (ind = 0; ind < probs.size(); ind++)
  if (r < probs.at(ind)) break;

ind will hold the chosen index.

Parameters:

structures

Collection of Structure objects to use. Must be sorted by enthalpy

See also:: Structure::sortByEnthalpy()

Note:: IMPORTANT: structures must contain one more structure than needed -- the last structure in the list will be removed from the probability list! (e.g. return list has size (structure.size()-1)).

Returns:

Definition at line 150 of file optbase.cpp.

References GlobalSearch::Structure::getEnthalpy().

virtual QString GlobalSearch::OptBase::getTemplateKeywordHelp ( ) [inline, virtual]

Returns:: A QString defining all known keywords.

Definition at line 236 of file optbase.h.

References getTemplateKeywordHelp_base().

Referenced by GlobalSearch::AbstractEditTab::showHelp().

QString GlobalSearch::OptBase::interpretTemplate	(	const QString &	templateString,
		Structure *	structure
	)			`[virtual]`

Takes a template and inserts structure specific information by replacing keywords.

Parameters:

	templateString	Template
	structure	Structure of interest

Returns:: Interpreted template with structure information included

See also:: getTemplateKeywordHelp; getTemplateKeywordHelp_base; interpretTemplate_base

Definition at line 343 of file optbase.cpp.

References interpretKeyword_base().

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

virtual bool GlobalSearch::OptBase::load	(	const QString &	filename,
		const bool	forceReadOnly = `false`
	)			`[inline, virtual]`

Load a search session from the specified filename.

Parameters:

	filename	State file to resume.
	forceReadOnly	Set to true to skip any prompts and load the session readonly

Returns:: True is successful, false otherwise.

Definition at line 213 of file optbase.h.

Referenced by GlobalSearch::AbstractDialog::resumeSession_().

void GlobalSearch::OptBase::needBoolean	(	const QString &	message,
		bool *	ok
	)			`[signal]`

Prompts user with an "Yes/No" dialog

Parameters:

	message	Message to the user.
	ok	True if user accepts dialog, false if they cancel.

See also:: promptForBoolean

Referenced by OptBase().

void GlobalSearch::OptBase::needPassword	(	const QString &	message,
		QString *	newPassword,
		bool *	ok
	)			`[signal]`

Request a password from the user, used for libssh authentication.

Parameters:

	message	Message to the user.
	newPassword	pointer to the QString that will hold the new password.
	ok	True if user accepts dialog, false if they cancel.

See also:: promptForPassword

Referenced by OptBase().

Optimizer* GlobalSearch::OptBase::optimizer ( ) [inline]

Returns:: A pointer to the current Optimizer.

See also:: setOptimizer; optimizerChanged

Definition at line 266 of file optbase.h.

References m_optimizer.

void GlobalSearch::OptBase::optimizerChanged ( Optimizer * ) [signal]

Emitted when the current Optimizer changed

See also:: setOptimizer; optimizer

Referenced by setOptimizer().

virtual bool GlobalSearch::OptBase::postSave ( const QString & filename ) [inline, virtual]

Override with any saving operations that derived classes need.

Definition at line 198 of file optbase.h.

Referenced by save().

virtual void GlobalSearch::OptBase::preoptimizeStructure ( Structure * s ) [inline, virtual, slot]

Perform a background preoptimization on Structure s. This may not be implemented for all search types, and does nothing by default.

Parameters:

s

the Structure to preoptimize.

Definition at line 498 of file optbase.h.

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

void GlobalSearch::OptBase::printBackTrace ( ) [slot]

Prints a backtrace to the terminal

Definition at line 142 of file optbase.cpp.

References backTraceMutex.

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

void GlobalSearch::OptBase::promptForBoolean	(	const QString &	message,
		bool *	ok = `0`
	)			`[slot]`

Prompt user with a "Yes/No" dialog.

Parameters:

	message	Message to the user.
	ok	True if user accepts dialog, false if they cancel.

See also:: needBoolean

Definition at line 515 of file optbase.cpp.

References dialog(), and m_idString.

Referenced by OptBase().

void GlobalSearch::OptBase::promptForPassword	(	const QString &	message,
		QString *	newPassword,
		bool *	ok = `0`
	)			`[slot]`

Request a password from the user, used for libssh authentication.

Parameters:

	message	Message to the user.
	newPassword	pointer to the QString that will hold the new password.
	ok	True if user accepts dialog, false if they cancel.

See also:: needPassword

Definition at line 507 of file optbase.cpp.

References dialog().

Referenced by OptBase().

QueueManager* GlobalSearch::OptBase::queue ( ) [inline]

Returns:: A pointer to the associated QueueManager.

Definition at line 252 of file optbase.h.

References m_queue.

Referenced by GlobalSearch::AbstractDialog::initialize().

QueueInterface* GlobalSearch::OptBase::queueInterface ( ) [inline]

Returns:: A pointer to the associated QueueManager.

See also:: setQueueInterface; queueInterfaceChanged

Definition at line 259 of file optbase.h.

References m_queueInterface.

void GlobalSearch::OptBase::queueInterfaceChanged ( QueueInterface * ) [signal]

Emitted when the current QueueInterface changes

See also:: setQueueInterface; queueInterface

Referenced by setQueueInterface().

void GlobalSearch::OptBase::readOnlySessionStarted ( ) [signal]

Emitted when a read-only session finishes loading.

See also:: sessionStarted; emitSessionStarted; readOnlySessionStarted; emitReadOnlySessionStarted; startingSession; emitStartingSession

Referenced by emitReadOnlySessionStarted(), and OptBase().

void GlobalSearch::OptBase::refreshAllStructureInfo ( ) [signal]

Emitted when a major change has occurred affecting many structures, e.g. when duplicates are set/reset. It is recommended that any user-visible structure data is rebuilt from scratch when this is called.

virtual Structure* GlobalSearch::OptBase::replaceWithOffspring	(	Structure *	s,
		const QString &	reason = `""`
	)			`[inline, virtual]`

Replace the Structure with a new offspring. This only makes sense if the search method uses offspring (e.g. a GA). The default implementation of this method calls replaceWithRandom().

Parameters:

	s	The Structure to be replaced. This pointer remains valid -- the structure it points to will be modified.
	reason	Reason for replacing. This will appear in the Structure::getParents() string. (Optional)

Returns:: The pointer to the structure (same as s).

Definition at line 119 of file optbase.h.

References replaceWithRandom().

virtual Structure* GlobalSearch::OptBase::replaceWithRandom	(	Structure *	s,
		const QString &	reason = `""`
	)			`[inline, virtual]`

Replace the Structure with an appropriate random Structure.

Parameters:

	s	The Structure to be replaced. This pointer remains valid -- the structure it points to will be modified.
	reason	Reason for replacing. This will appear in the Structure::getParents() string. (Optional)