#include <DomainDecomposition.h>

Inheritance diagram for PLMD::DomainDecomposition:

[legend]

Classes
class	DomainComms

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	DomainDecomposition (const ActionOptions &ao)

virtual void	activate ()
	Set action to active. More...

void	addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name. More...

virtual void	addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name that has derivatives. More...

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label. More...

virtual void	addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label that has derivatives. More...

void	apply () override
	Apply an Action. More...

virtual void	beforeUpdate ()
	Before Update. More...

void	broadcastToDomains (Value *val)

void	calculate () override
	Actually set the values for the output. More...

void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...

virtual bool	calculateOnUpdate ()
	This is used to check if we run calculate during the update step. More...

virtual ActionAtomistic *	castToActionAtomistic () noexcept

ActionForInterface *	castToActionForInterface () noexcept final

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

ActionWithValue *	castToActionWithValue () noexcept final
	Specialized casts, to make PlumedMain run faster. More...

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

DomainDecomposition *	castToDomainDecomposition () noexcept final

virtual PbcAction *	castToPbcAction () noexcept

virtual void	checkFieldsAllowed ()

bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. More...

virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...

bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used. More...

void	checkRead ()
	Check if Action was properly read. More...

bool	checkUpdate () const
	Check if action should be updated. More...

std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...

void	clearDependencies ()
	Clear the dependence list for this Action. More...

void	clearDerivatives (const bool &force=false) override
	Override clear the input data. More...

void	clearFullList ()

virtual void	clearInputForces (const bool &force=false)
	Clear the forces on the values. More...

virtual void	clearOptions ()

void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...

void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

void	createFullList (const TypesafePtr &x)

virtual void	deactivate ()
	Set action to inactive. More...

virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...

void	error (const std::string &msg) const
	Crash calculation and print documentation. More...

bool	exists (const std::string &name) const
	Check if a value with a particular name is present. More...

void	exit (int c=0)
	Exit with error code c. More...

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

void	fflush ()
	Tell to the Action to flush open files. More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

std::string	getComponentsList () const
	get a string that contains all the available components More...

std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components More...

bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...

const long int &	getDdStep () const

std::string	getDefaultString () const
	Get the defaults. More...

const Dependencies &	getDependencies () const
	Return dependencies. More...

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

void	getFullList (const TypesafePtr &x)

const std::vector< int > &	getGatindex () const

double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. More...

std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...

const std::string &	getLabel () const
	Returns the label. More...

virtual void	getMatrixColumnTitles (std::vector< std::string > &argnames) const
	Get the titles to use for the columns of the matrix. More...

const std::string &	getName () const
	Returns the name. More...

unsigned	getNumberOfAtoms () const

int	getNumberOfComponents () const
	Returns the number of values defined. More...

unsigned	getNumberOfDerivatives () override
	The number of derivatives. More...

unsigned	getNumberOfForcesToRescale () const override
	This get the number of forces that need to be rescaled in rescale forces. More...

double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...

double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...

bool	getRestart () const
	Return true if we are doing a restart. More...

std::string	getRole () const

long long int	getStep () const
	Return the present timestep. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

bool	hasBeenSet () const
	Check if the value has been set. More...

bool	isActive () const
	Check if action is active. More...

bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...

virtual void	lockRequests ()

bool	onStep () const override

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...

void	readBinary (std::istream &i) override

void	reset () override

void	resetForStepStart () override

virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...

void	Set_comm (Communicator &comm) override

void	setAtomsContiguous (int start)

void	setAtomsGatindex (const TypesafePtr &g, bool fortran)

void	setAtomsNlocal (int n)

bool	setForcePointer (const std::string &name, const TypesafePtr &) override
	Set the force to the value that contains this data. More...

void	setGradientsIfNeeded () override
	Override the need to deal with gradients. More...

void	setNotPeriodic ()
	Set your default value to have no periodicity. More...

virtual void	setOption (const std::string &s)

void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

void	setStart (const std::string &name, const unsigned &sss) override
	Set the start point for the memory if needed. More...

void	setStride (const std::string &name, const unsigned &sss) override
	Set the stride for the memory if needed. More...

void	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...

void	setValue (Value *, double)
	Set the value. More...

bool	setValuePointer (const std::string &name, const TypesafePtr &) override
	Set the pointer to the value that contains this data. More...

void	share () override
	Overriding this method from ActionWithValue ensures that taskLists that are set during share are not updated during calculate loop. More...

void	shareAll () override

void	sumOverDomains (Value *val)

virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives. More...

virtual void	unlockRequests ()

virtual void	update ()
	Update. More...

void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...

void	wait () override
	Get the data to share. More...

void	warning (const std::string &msg)
	Issue a warning. More...

void	writeBinary (std::ostream &o) override
	For replica exchange. More...

virtual std::string	writeInGraph () const
	Get the info on what to calculate. More...

Static Public Member Functions
static void	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...

static void	registerKeywords (Keywords &keys)

static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

Log &	log
	Reference to the log stream. More...

Communicator &	multi_sim_comm

PlumedMain &	plumed
	Reference to main plumed object. More...

Protected Member Functions
bool	checkForForces ()
	Accumulate the forces from the Values. More...

const Value *	getConstPntrToComponent (int i) const
	Get a const pointer to the ith component. More...

const std::vector< double > &	getForcesToApply () const
	Get the forces to apply. More...

double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...

Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...

Value *	getPntrToValue ()
	Get a pointer to the default value. More...

const Units &	getUnits () const
	Get the units that we are operating in. More...

void	setValue (const double &d)
	Set the default value (the one without name) More...

bool	usingNaturalUnits () const
	Are we using natural units. More...

Protected Attributes
bool	firststep

std::string	role
	The role this plays. More...

bool	wasscaled
	Have the forces in this action been scaled by another action. More...

bool	wasset
	Action has been set. More...

Private Member Functions
void	getAllActiveAtoms (std::vector< AtomNumber > &u)
	Get all the atoms in the input that are active at this time. More...

int	getComponent (const std::string &name) const
	Return the index for the component named name. More...

void	share (const std::vector< AtomNumber > &unique)
	This actually does the sharing of the data across the domains. More...

Private Attributes
std::vector< ActionAtomistic * >	actions
	This holds all the actions that read atoms. More...

bool	active
	Switch to activate Action on this step. More...

Dependencies	after
	Actions on which this Action depends. More...

bool	asyncSent

DomainComms	dd

long int	ddStep

std::string	defaults
	The set of default arguments that we are using. More...

bool	doCheckPoint

std::vector< AtomNumber >	forced_unique
	This holds the list of atoms that have a force on. More...

std::vector< double >	forcesForApply
	A vector that is used to hold the forces that we will apply on the input quantities. More...

std::vector< int >	fullList
	The list that holds all the atom indexes we need. More...

std::vector< int >	g2l
	Map global indexes to local indexes E.g. More...

std::vector< int >	gatindex

std::vector< ActionToPutData * >	inputs
	This holds the list of actions that are set from this action. More...

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

std::vector< std::string >	line
	Directive line. More...

const std::string	name
	Name of the directive in the plumed.dat file. More...

bool	never_activate

bool	noderiv
	Are we skipping the calculation of the derivatives. More...

bool	numericalDerivatives
	Are we using numerical derivatives to differentiate. More...

std::set< std::string >	options
	Option that you might have enabled. More...

int	replica_index

bool	restart

unsigned	shuffledAtoms

double	timestep
	Save the timestep here. More...

std::vector< unsigned >	uniq_index

std::vector< AtomNumber >	unique
	This holds the list of unique atoms. More...

bool	unique_serial

double	update_from
	Update only after this time. More...

double	update_until
	Update only until this time. More...

std::vector< unsigned >	valsToForce

std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action. More...

Member Typedef Documentation

◆ Dependencies

typedef std::vector<Action*> PLMD::Action::Dependencies

inherited

Constructor & Destructor Documentation

◆ DomainDecomposition()

PLMD::DomainDecomposition::DomainDecomposition ( const ActionOptions & ao )

explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

virtualinherited

Add a value with a name like label.name that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ addDependency()

void PLMD::Action::addDependency ( Action * action )

inherited

Specify that this Action depends on another one.

◆ addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ apply()

void PLMD::DomainDecomposition::apply ( )

overridevirtual

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

◆ broadcastToDomains()

void PLMD::DomainDecomposition::broadcastToDomains ( Value * val )

◆ calculate()

void PLMD::ActionForInterface::calculate ( )

inlineoverridevirtualinherited

Actually set the values for the output.

Implements PLMD::Action.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB & pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives()

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::analysis::Accumulate, and PLMD::analysis::Collect.

◆ castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionForInterface()

ActionForInterface* PLMD::ActionForInterface::castToActionForInterface ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments()

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithValue()

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )

inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

DomainDecomposition* PLMD::DomainDecomposition::castToDomainDecomposition ( )

inlinefinalvirtualnoexcept

Reimplemented from PLMD::Action.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action * action )

inherited

Check that this action does not depend on the action in the argument.

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )

protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

virtual bool PLMD::Action::checkNeedsGradients ( ) const

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives()

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionForInterface::clearDerivatives ( const bool & force = false )

inlineoverridevirtualinherited

Override clear the input data.

Reimplemented from PLMD::ActionWithValue.

◆ clearFullList()

void PLMD::DomainDecomposition::clearFullList ( )

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( const bool & force = false )

virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string & name )

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic	(	const std::string &	name,
		const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords & keys )

staticinherited

Puts a message into the manual that the components always output.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string & name ) const

inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned & n ) const

inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ createFullList()

void PLMD::DomainDecomposition::createFullList ( const TypesafePtr & x )

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

◆ error()

void PLMD::Action::error ( const std::string & msg ) const

inherited

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string & name ) const

inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

void PLMD::Action::exit ( int c = 0 )

inherited

Exit with error code c.

◆ fclose()

int PLMD::Action::fclose ( FILE * fp )

inherited

Closes a file opened with Action::fclose().

◆ fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

◆ fopen()

FILE * PLMD::Action::fopen	(	const char *	path,
		const char *	mode
	)

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

When opened for writing, processors other than the one with rank 0 just open /dev/null
PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

◆ getAllActiveAtoms()

void PLMD::DomainDecomposition::getAllActiveAtoms ( std::vector< AtomNumber > & u )

private

Get all the atoms in the input that are active at this time.

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string & name ) const

privateinherited

Return the index for the component named name.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const

inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const

inherited

get a vector that contains the label for all the components

◆ getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int i ) const

protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDdStep()

const long int & PLMD::DomainDecomposition::getDdStep ( ) const

◆ getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const

inlineinherited

Get the defaults.

◆ getDependencies()

const Dependencies& PLMD::Action::getDependencies ( ) const

inlineinherited

Return dependencies.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const

inlineprotectedinherited

Get the forces to apply.

◆ getFullList()

void PLMD::DomainDecomposition::getFullList ( const TypesafePtr & x )

◆ getGatindex()

const std::vector< int > & PLMD::DomainDecomposition::getGatindex ( ) const

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )

inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

◆ getKeyword()

std::string PLMD::Action::getKeyword ( const std::string & key )

inherited

Just read one of the keywords and return the whole thing as a string.

◆ getLabel()

const std::string & PLMD::Action::getLabel ( ) const

inlineinherited

Returns the label.

◆ getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > & argnames ) const

virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::adjmat::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

const std::string & PLMD::Action::getName ( ) const

inlineinherited

Returns the name.

◆ getNumberOfAtoms()

unsigned PLMD::DomainDecomposition::getNumberOfAtoms ( ) const

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::ActionForInterface::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

The number of derivatives.

Implements PLMD::ActionWithValue.

◆ getNumberOfForcesToRescale()

unsigned PLMD::DomainDecomposition::getNumberOfForcesToRescale ( ) const

overridevirtual

This get the number of forces that need to be rescaled in rescale forces.

Reimplemented from PLMD::ActionForInterface.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string & name ) const

inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned j ) const

inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string & name )

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int i )

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

inlineprotectedinherited

Get a pointer to the default value.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getRole()

std::string PLMD::ActionForInterface::getRole ( ) const

inherited

◆ getStep()

long long int PLMD::Action::getStep ( ) const

inherited

Return the present timestep.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const

protectedinherited

Get the units that we are operating in.

◆ hasBeenSet()

bool PLMD::ActionForInterface::hasBeenSet ( ) const

inlineinherited

Check if the value has been set.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string & s ) const

inlineinherited

Check if an option is on.

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords & keys )

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ onStep()

bool PLMD::DomainDecomposition::onStep ( ) const

inlineoverridevirtual

Implements PLMD::ActionForInterface.

◆ parse()

template<class T >

void PLMD::Action::parse	(	const std::string &	key,
		T &	t
	)

inherited

Parse one keyword as generic type.

◆ parseFlag()

void PLMD::Action::parseFlag	(	const std::string &	key,
		bool &	t
	)

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

bool PLMD::Action::parseNumbered	(	const std::string &	key,
		const int	no,
		T &	t
	)

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector	(	const std::string &	key,
		const int	no,
		std::vector< T > &	t
	)

inherited

Parse a vector with a number.

◆ parseVector()

template<class T >

void PLMD::Action::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

inherited

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::adjmat::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::adjmat::DiagonalizeMatrix, PLMD::analysis::CreateMask, PLMD::adjmat::OuterProduct, PLMD::adjmat::VStack, PLMD::adjmat::MatrixTimesVector, PLMD::analysis::FarthestPointSampling, PLMD::adjmat::TransposeMatrix, PLMD::colvar::CoordinationBase, PLMD::adjmat::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ readBinary()

void PLMD::DomainDecomposition::readBinary ( std::istream & i )

overridevirtual

Implements PLMD::ActionForInterface.

◆ registerKeywords()

void PLMD::DomainDecomposition::registerKeywords ( Keywords & keys )

static

◆ reset()

void PLMD::DomainDecomposition::reset ( )

overridevirtual

Reimplemented from PLMD::ActionForInterface.

◆ resetForStepStart()

void PLMD::DomainDecomposition::resetForStepStart ( )

overridevirtual

Implements PLMD::ActionForInterface.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

◆ Set_comm()

void PLMD::DomainDecomposition::Set_comm ( Communicator & comm )

overridevirtual

Implements PLMD::ActionForInterface.

◆ setAtomsContiguous()

void PLMD::DomainDecomposition::setAtomsContiguous ( int start )

◆ setAtomsGatindex()

void PLMD::DomainDecomposition::setAtomsGatindex	(	const TypesafePtr &	g,
		bool	fortran
	)

◆ setAtomsNlocal()

void PLMD::DomainDecomposition::setAtomsNlocal ( int n )

◆ setForcePointer()

bool PLMD::DomainDecomposition::setForcePointer	(	const std::string &	name,
		const TypesafePtr &
	)

overridevirtual

Set the force to the value that contains this data.

Implements PLMD::ActionForInterface.

◆ setGradientsIfNeeded()

void PLMD::ActionForInterface::setGradientsIfNeeded ( )

inlineoverridevirtualinherited

Override the need to deal with gradients.

Reimplemented from PLMD::ActionWithValue.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

void PLMD::Action::setOption ( const std::string & s )

virtualinherited

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic	(	const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ setStart()

void PLMD::DomainDecomposition::setStart	(	const std::string &	name,
		const unsigned &	sss
	)

overridevirtual

Set the start point for the memory if needed.

Implements PLMD::ActionForInterface.

◆ setStride()

void PLMD::DomainDecomposition::setStride	(	const std::string &	name,
		const unsigned &	sss
	)

overridevirtual

Set the stride for the memory if needed.

Implements PLMD::ActionForInterface.

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool & have_atoms )

inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double & d )

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue	(	Value *	,
		double
	)

inherited

Set the value.

◆ setValuePointer()

bool PLMD::DomainDecomposition::setValuePointer	(	const std::string &	name,
		const TypesafePtr &
	)

overridevirtual

Set the pointer to the value that contains this data.

Implements PLMD::ActionForInterface.

◆ share() [1/2]

void PLMD::DomainDecomposition::share ( )

overridevirtual

Overriding this method from ActionWithValue ensures that taskLists that are set during share are not updated during calculate loop.

Get the data

Implements PLMD::ActionForInterface.

◆ share() [2/2]

void PLMD::DomainDecomposition::share ( const std::vector< AtomNumber > & unique )

private

This actually does the sharing of the data across the domains.

◆ shareAll()

void PLMD::DomainDecomposition::shareAll ( )

overridevirtual

Implements PLMD::ActionForInterface.

◆ sumOverDomains()

void PLMD::DomainDecomposition::sumOverDomains ( Value * val )

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::Read, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfScalar< T >, PLMD::adjmat::Neighbors, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ update()

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

This method is called one time per step. The set of all Actions is updated in forward order.

Reimplemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::generic::DumpPDB, PLMD::analysis::Accumulate, PLMD::analysis::Collect, PLMD::generic::PrintNDX, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords & keys )

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

◆ wait()

void PLMD::DomainDecomposition::wait ( )

overridevirtual

Get the data to share.

Implements PLMD::ActionForInterface.

◆ warning()

void PLMD::Action::warning ( const std::string & msg )

inherited

Issue a warning.

◆ writeBinary()

void PLMD::DomainDecomposition::writeBinary ( std::ostream & o )

overridevirtual

For replica exchange.

Implements PLMD::ActionForInterface.

◆ writeInGraph()

std::string PLMD::Action::writeInGraph ( ) const

virtualinherited

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Member Data Documentation

◆ actions

std::vector<ActionAtomistic*> PLMD::DomainDecomposition::actions

private

This holds all the actions that read atoms.

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ asyncSent

bool PLMD::DomainDecomposition::asyncSent

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ dd

DomainComms PLMD::DomainDecomposition::dd

private

◆ ddStep

long int PLMD::DomainDecomposition::ddStep

private

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ files

std::set<FILE*> PLMD::Action::files

inherited

◆ firststep

bool PLMD::ActionForInterface::firststep

protectedinherited

◆ forced_unique

std::vector<AtomNumber> PLMD::DomainDecomposition::forced_unique

private

This holds the list of atoms that have a force on.

◆ forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply

privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

◆ fullList

std::vector<int> PLMD::DomainDecomposition::fullList

private

The list that holds all the atom indexes we need.

◆ g2l

std::vector<int> PLMD::DomainDecomposition::g2l

private

Map global indexes to local indexes E.g.

g2l[i] is the position of atom i in the array passed from the MD engine. Called "global to local" since originally it was used to map global indexes to local ones used in domain decomposition. However, it is now also used for the NAMD-like interface, where only a small number of atoms is passed to plumed.

◆ gatindex

std::vector<int> PLMD::DomainDecomposition::gatindex

private

◆ inputs

std::vector<ActionToPutData*> PLMD::DomainDecomposition::inputs

private

This holds the list of actions that are set from this action.

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ name

const std::string PLMD::Action::name

privateinherited

Name of the directive in the plumed.dat file.

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

◆ options

std::set<std::string> PLMD::Action::options

privateinherited

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ role

std::string PLMD::ActionForInterface::role

protectedinherited

The role this plays.

◆ shuffledAtoms

unsigned PLMD::DomainDecomposition::shuffledAtoms

private

◆ timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

◆ uniq_index

std::vector<unsigned> PLMD::DomainDecomposition::uniq_index

private

◆ unique

std::vector<AtomNumber> PLMD::DomainDecomposition::unique

private

This holds the list of unique atoms.

◆ unique_serial

bool PLMD::DomainDecomposition::unique_serial

private

◆ update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

◆ valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce

privateinherited

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values

privateinherited

An array containing the values for this action.

◆ wasscaled

bool PLMD::ActionForInterface::wasscaled

protectedinherited

Have the forces in this action been scaled by another action.

◆ wasset

bool PLMD::ActionForInterface::wasset

protectedinherited

Action has been set.

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

core/DomainDecomposition.h
core/DomainDecomposition.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ DomainDecomposition()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ broadcastToDomains()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateOnUpdate()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments()

◆ castToActionWithValue()

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ checkFieldsAllowed()

◆ checkForDependency()

◆ checkForForces()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearFullList()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ createFullList()

◆ deactivate()

◆ doNotCalculateDerivatives()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getAllActiveAtoms()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getConstPntrToComponent()

◆ getCPT()

◆ getDdStep()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getForcesToApply()

◆ getFullList()

◆ getGatindex()

◆ getKBoltzmann()

◆ getkBT()

◆ getKeyword()