Provides the keyword DISTANCE_MATRIX More...

Inheritance diagram for PLMD::adjmat::DistanceMatrix:

[legend]

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

Public Member Functions
	DistanceMatrix (const ActionOptions &)
	Constructor. More...

virtual bool	actionHasForces ()

bool	actionInChain () const
	Are we running this command in a chain. More...

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	addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f)
	Add force to an atom. More...

void	addForcesOnArguments (const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)
	Add forces to arguments (used in apply) 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...

virtual void	apply ()
	Apply the forces on this data. More...

virtual void	areAllTasksRequired (std::vector< ActionWithVector * > &task_reducing_actions)
	Do we always need to do all the tasks for this action. More...

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

double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...

virtual void	calculate () override
	Run the calculation. More...

void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...

virtual bool	calculateConstantValues (const bool &have_atoms)
	Used to calculate constant values in startup. More...

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

void	calculateNumericalDerivatives (ActionWithValue *av) override
	N.B. More...

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

double	calculateWeight (const Vector &pos1, const Vector &pos2, const unsigned &natoms, MultiValue &myvals) const
	This does nothing. More...

virtual bool	canBeAfterInChain (ActionWithVector *av)
	Check if we can be after another ActionWithVector. More...

ActionAtomistic *	castToActionAtomistic () noexcept final

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

ActionWithArguments *	castToActionWithArguments () noexcept final

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

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

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

void	changeBox (const Tensor &newbox)
	Change the box shape. More...

virtual void	checkFieldsAllowed ()

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

bool	checkForTaskForce (const unsigned &itask, const Value *myval) const override
	Check if there are forces we need to account for on this task. More...

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

virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...

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

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

virtual int	checkTaskStatus (const unsigned &taskno, int &flag) const
	Check the status of the ith task. 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
	We override clearDerivatives here to prevent data in streams from being deleted. More...

void	clearInputForces (const bool &force=false) override
	We override clearInputForces here to ensure that forces are deleted from all 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...

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

double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...

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

void	doNotForce ()
	Skip atom forces - use with care. More...

void	doNotRetrieve ()
	Skip atom retrieval - use with care. 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...

void	finishChainBuild (ActionWithVector *act)
	This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions. More...

void	finishComputations (const std::vector< double > &buf)
	This is to transfer data from the buffer to the final value. More...

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

void	gatherForcesOnStoredValue (const Value *myval, const unsigned &itask, const MultiValue &myvals, std::vector< double > &forces) const override
	This gathers the force on a particular value. More...

void	gatherProcesses (std::vector< double > &buffer) override
	Gather all the data from the MPI processes. More...

void	gatherStoredValue (const unsigned &valindex, const unsigned &code, const MultiValue &myvals, const unsigned &bufstart, std::vector< double > &buffer) const override
	Gather a row of the matrix. More...

void	gatherThreads (const unsigned &nt, const unsigned &bufsize, const std::vector< double > &omp_buffer, std::vector< double > &buffer, MultiValue &myvals) override
	Gather all the data from the threads. More...

AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...

virtual const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...

void	getAdditionalTasksRequired (ActionWithVector *action, std::vector< unsigned > &atasks) override
	Get the additional tasks that are required here. More...

void	getAllActionLabelsInChain (std::vector< std::string > &mylabels) const
	Get every the label of every value that is calculated in this chain. More...

void	getAllActionLabelsInMatrixChain (std::vector< std::string > &mylabels) const override
	This is overridden in ActionWithMatrix. More...

double	getArgument (const unsigned n) const
	Returns the value of an argument. More...

virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...

const Tensor &	getBox () const
	Get box shape. More...

double	getCharge (int i) const
	Get charge of i-th atom. 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...

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

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

const double &	getEnergy () const
	Get energy. More...

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

ActionWithVector *	getFirstActionInChain ()

const ActionWithVector *	getFirstActionInChain () const
	Return a pointer to the first action in the chain. More...

const ActionWithMatrix *	getFirstMatrixInChain () const
	Get the first matrix in this chain. More...

Vector	getForce (const std::pair< std::size_t, std::size_t > &a) const
	Get the force acting on a particular atom. More...

Vector	getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const
	Get position of i-th atom (access by absolute AtomNumber). More...

void	getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const
	Transfer the gradients. More...

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...

double	getMass (int i) const
	Get mass of i-th atom. 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...

virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...

unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...

unsigned	getNumberOfColumns () const override
	This should return the number of columns to help with sparse storage of matrices. More...

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

unsigned	getNumberOfDerivatives () override

void	getNumberOfStreamedDerivatives (unsigned &nderivatives, Value *stopat)
	Get the number of derivatives in the stream. More...

virtual void	getNumberOfTasks (unsigned &ntasks)
	Find out how many tasks we need to perform in this loop. More...

virtual std::string	getOutputComponentDescription (const std::string &cname, const Keywords &keys) const
	Get the description of this component. 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...

const Pbc &	getPbc () const
	Get reference to Pbc. More...

Value *	getPntrToArgument (const unsigned n) const
	Return a pointer to specific argument. More...

const Vector &	getPosition (int) const
	Get position of i-th atom (access by relative index) More...

const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...

double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...

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

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...

unsigned	getTotAtoms () const
	Get total number of atoms, including virtual ones. More...

const std::vector< AtomNumber > &	getUnique () const

const std::vector< AtomNumber > &	getUniqueLocal () const

Tensor	getVirial () const
	Get the virial that is acting. More...

bool	hasStoredArguments () const
	Check if there are any stored values in arguments. More...

void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this. More...

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

bool	isAdjacencyMatrix () const override

virtual bool	isInSubChain (unsigned &nder)
	Check if we are in a subchain. More...

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

void	lockRequests () override

void	makeWhole ()
	Make atoms whole, assuming they are in the proper order. More...

double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...

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

bool	parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
	Parse a numbered list of arguments. More...

void	parseArgumentList (const std::string &key, std::vector< Value * > &args)
	Parse a list of arguments. More...

void	parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
	Parse an list of atom with a numbred keyword. More...

void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. 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...

void	pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
	Applies PBCs to a seriens of positions or distances. More...

Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...

void	performTask (const std::string &controller, const unsigned &index1, const unsigned &index2, MultiValue &myvals) const override
	This is the virtual that will do the calculation of the task for a particular matrix element. More...

void	performTask (const unsigned &task_index, MultiValue &myvals) const override
	Run over one row of the matrix. More...

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

void	readAtomsFromPDB (const PDB &pdb) override
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...

void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies. More...

void	requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
	Request an array of atoms. More...

void	requestExtraDependencies (const std::vector< Value * > &extra)

void	resetStoredTimestep ()
	Set the timestep that is stored in the action to the correct value. More...

void	retrieveAtoms (const bool &force=false) override

unsigned	retrieveNeighbours (const unsigned &current, std::vector< unsigned > &indices) const

void	runEndOfRowJobs (const unsigned &ival, const std::vector< unsigned > &indices, MultiValue &myvals) const override
	This is the jobs that need to be done when we have run all the jobs in a row of the matrix. More...

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

void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the forces to the atoms. More...

void	setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind)
	Add the virial forces (span-like syntax) More...

void	setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the virial forces. More...

void	setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos)
	Modify position of i-th atom (access by absolute AtomNumber). More...

void	setGradients (Value *myval, unsigned &start) const
	Get the gradient for this action. More...

virtual void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) 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	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	setupForTask (const unsigned &current, std::vector< unsigned > &indices, MultiValue &myvals) const override

void	setupStreamedComponents (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping) override
	This requires some thought. More...

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

virtual void	switchTaskReduction (const bool &task_reduction, ActionWithVector *aselect)
	Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere. More...

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

void	unlockRequests () override

virtual void	update ()
	Update. More...

virtual void	updateAdditionalIndices (const unsigned &ostrn, MultiValue &myvals) const
	This is used to ensure that all indices are updated when you do local average. More...

virtual void	updateForceTasksFromValue (const Value *myval, std::vector< unsigned > &force_tasks) const
	Get the force tasks that are active for this action. More...

void	updateNeighbourList () override
	This is overwritten in Adjacency matrix where we have a neighbour list. More...

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

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

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

Static Public Member Functions
static void	getAtomValuesFromPlumedObject (const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev)
	This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges. More...

static void	interpretArgumentList (const std::vector< std::string > &c, const ActionSet &as, Action action, std::vector< Value > &arg)
	Convert a list of argument names into a list of pointers to the values. More...

static void	interpretAtomList (std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) 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)
	Create manual. More...

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
void	addAtomDerivatives (const unsigned &indno, const Vector &der, MultiValue &myvals) const

void	addBoxDerivatives (const Tensor &vir, MultiValue &myvals) const

void	addDerivativeOnMatrixArgument (const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &irow, const unsigned &jcol, const double &der, MultiValue &myvals) const
	Add derivatives given the derative wrt to the input matrix element as input. More...

void	addDerivativeOnVectorArgument (const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &jelem, const double &der, MultiValue &myvals) const
	Add derivatives given the derivative wrt to the input vector element as input. More...

void	addThirdAtomDerivatives (const unsigned &indno, const Vector &der, MultiValue &myvals) const

bool	argumentDependsOn (const std::string &headstr, ActionWithVector faction, Value thearg)
	Check if the arguments of this action depend on thearg. More...

unsigned	buildArgumentStore (const unsigned &argstart)
	This sets up the arguments at the start of the calculation. More...

bool	checkForForces ()
	Accumulate the forces from the Values. More...

void	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file. More...

double	getArgumentElement (const unsigned &ic, const unsigned &jelem, const MultiValue &myvals) const
	This returns the jelem th element of argument ic. More...

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

double	getElementOfMatrixArgument (const unsigned &imat, const unsigned &irow, const unsigned &jcol, const MultiValue &myvals) const
	This returns an element of a matrix that is passed an argument. More...

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

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

std::vector< unsigned > &	getListOfActiveTasks (ActionWithVector *action)
	Get the list of tasks that are active. 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...

Vector	getPosition (const unsigned &indno, MultiValue &myvals) const

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

std::pair< std::size_t, std::size_t >	getValueIndices (const AtomNumber &i) const
	Used to interpret whether this index is a virtual atom or a real atom. More...

bool	matrixChainContinues () const
	Does the matrix chain continue on from this action. More...

void	runAllTasks ()
	Run all the tasks in the list. More...

bool	runInSerial () const
	Run all calculations in serial. More...

void	setExtraCV (const std::string &name)

void	setLinkCellCutoff (const bool &symmetric, const double &lcut, double tcut=-1.0)

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

void	updateTaskListReductionStatus ()
	This updates whether or not we are using all the task reduction stuff. More...

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

Protected Attributes
std::vector< unsigned >	arg_deriv_starts
	A vector that contains the start point for the argument derivatives. More...

bool	chargesWereSet

bool	clearOnEachCycle
	This turns off derivative clearing for contact matrix if we are not storing derivatives. More...

bool	done_in_chain
	Assert if this action is part of a chain. More...

bool	massesWereSet

Private Member Functions
bool	addActionToChain (const std::vector< std::string > &alabels, ActionWithVector *act)
	Add this action to the recursive chain. More...

void	addForcesToInput (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the gathered forces to the inputs across the whole chain. More...

void	broadcastThatTasksAreReduced (ActionWithVector *aselect)
	Send information to arguments that tasks are reduced in depedent actions. More...

void	canReduceTasks (std::vector< ActionWithVector * > &task_reducing_actions)
	Check if this ation can reduce the number of tasks we perform. More...

bool	checkChainForNonScalarForces () const
	Check the chain for non scalar forces. More...

bool	checkComponentsForForce () const
	Check if a force has been added on one of the components of this action. More...

bool	checkForGrids (unsigned &nder) const
	Check if there are any grids in the stream. More...

void	clearMatrixElements (MultiValue &myvals) const
	This is used to clear up the matrix elements. More...

void	gatherAccumulators (const unsigned &taskCode, const MultiValue &myvals, std::vector< double > &buffer) const
	Gather the values that we intend to store in the buffer. More...

void	gatherForces (const unsigned &i, const MultiValue &myvals, std::vector< double > &forces) const
	Gather the forces on non-scalar quantities. More...

ActionWithVector *	getActionWithDerivatives (ActionWithVector *depaction)
	Work backwards through the chain to find an action that has either stored arguments or derivatives. More...

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

void	getForceTasks (std::vector< unsigned > &force_tasks) const
	Get the tasks that we need for forces. More...

bool	getNumberOfStoredValues (Value startat, unsigned &nvals, const unsigned &astart, const std::vector< Value > &stopat)
	Get the number of stored values in the stream. More...

void	getNumberOfStreamedQuantities (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping)
	Get the number of quantities in the stream. More...

void	getSizeOfBuffer (const unsigned &nactive_tasks, unsigned &bufsize)
	Get the size of the buffer array that holds the data we are gathering over the MPI loop. More...

void	getTotalMatrixBookeeping (unsigned &stashsize)
	This is used to find the total amount of space we need for storing matrix elements. More...

unsigned	reallyBuildArgumentStore (const unsigned &argstart)
	This is used to build the argument store when we cannot use the chain. More...

void	runTask (const std::string &controller, const unsigned &current, const unsigned colno, MultiValue &myvals) const
	This does the calculation of a particular matrix element. More...

void	setupThirdAtomBlock (const std::vector< AtomNumber > &tc, std::vector< AtomNumber > &t)

void	taskIsActive (const unsigned &current, int &flag) const
	Check if a particular task is active at this time. More...

void	transferNonZeroMatrixElementsToValues (unsigned &nval, const std::vector< unsigned > &matbook)
	This transfers the non-zero elements to the Value. More...

void	updateAllNeighbourLists ()
	Update all the neighbour lists in the chain. More...

void	updateTaskReductionFlag (bool &head_reduce_tasks)
	Turn on task reduction flag in dependent actions. More...

void	updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)

Private Attributes
std::vector< unsigned >	ablocks

ActionWithVector *	action_to_do_after
	Actions that must be done after this one. More...

ActionWithVector *	action_to_do_before
	Action that must be done before this one. More...

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

std::vector< unsigned >	active_tasks
	The list of active tasks. More...

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

std::vector< Value * >	arguments

std::vector< std::pair< std::size_t, std::size_t > >	atom_value_ind

std::vector< std::pair< std::size_t, std::vector< std::size_t > > >	atom_value_ind_grouped

bool	atomsWereRetrieved
	Were the atoms retrieved in some earlier action. More...

Value *	boxValue

std::vector< double >	buffer
	The buffer that we use (we keep a copy here to avoid resizing) More...

std::vector< double >	charges

std::vector< Value * >	chargev

bool	components

double	cutoff

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

bool	doCheckPoint

bool	donotforce

bool	donotretrieve

double	energy

bool	firststep
	This finishes setup on first step to check if actions are calculated during update. More...

double	forceOnEnergy

double	forceOnExtraCV

std::vector< Vector >	forces

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

std::vector< AtomNumber >	indexes

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...

LinkCells	linkcells

bool	lockRequestArguments

bool	lockRequestAtoms

std::vector< double >	masses

std::vector< Value * >	masv

std::vector< unsigned >	matrix_bookeeping
	This holds the bookeeping arrays for sparse matrices. More...

ActionWithMatrix *	matrix_to_do_after

ActionWithMatrix *	matrix_to_do_before

unsigned	maxcol

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

unsigned	natoms_per_list

bool	neighbour_list_updated

bool	never_activate

bool	never_reduce_tasks
	This is turned on if there is some action that needs all the tasks. More...

ActionWithMatrix *	next_action_in_chain

double	nl_cut

double	nl_cut2

unsigned	nl_stride

std::vector< unsigned >	nlist

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

bool	nopbc

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

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

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

bool	read_one_group

bool	reduce_tasks
	Are we allowed to reduce the number of tasks being performed. More...

int	replica_index

bool	restart

bool	serial
	Is the calculation to be done in serial. More...

std::vector< ActionWithVector * >	task_control_list
	This is the list of actions that control the tasks that we do here. More...

std::vector< unsigned >	threeblocks

LinkCells	threecells

double	timestep
	Save the timestep here. More...

std::vector< AtomNumber >	unique
	unique should be an ordered set since we later create a vector containing the corresponding indexes More...

std::vector< AtomNumber >	unique_local

bool	unique_local_needs_update
	unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...

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::size_t >	value_depends

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

std::vector< Value * >	xpos
	Values that hold information about atom positions and charges. More...

std::vector< Value * >	ypos

std::vector< Value * >	zpos

Detailed Description

Provides the keyword DISTANCE_MATRIX

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ DistanceMatrix()

PLMD::adjmat::DistanceMatrix::DistanceMatrix ( const ActionOptions & ao )

explicit

Constructor.

Member Function Documentation

◆ actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )

virtualinherited

Reimplemented in PLMD::generic::FitToTemplate, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::DumpAtoms, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, and PLMD::generic::PrintNDX.

◆ actionInChain()

bool PLMD::ActionWithVector::actionInChain ( ) const

inlineinherited

Are we running this command in a chain.

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addActionToChain()

bool PLMD::ActionWithVector::addActionToChain	(	const std::vector< std::string > &	alabels,
		ActionWithVector *	act
	)

privateinherited

Add this action to the recursive chain.

◆ addAtomDerivatives()

void PLMD::adjmat::AdjacencyMatrixBase::addAtomDerivatives	(	const unsigned &	indno,
		const Vector &	der,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

◆ addBoxDerivatives()

void PLMD::adjmat::AdjacencyMatrixBase::addBoxDerivatives	(	const Tensor &	vir,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

◆ 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.

◆ addDerivativeOnMatrixArgument()

void PLMD::ActionWithMatrix::addDerivativeOnMatrixArgument	(	const bool &	inchain,
		const unsigned &	ival,
		const unsigned &	jarg,
		const unsigned &	irow,
		const unsigned &	jcol,
		const double &	der,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

Add derivatives given the derative wrt to the input matrix element as input.

◆ addDerivativeOnVectorArgument()

void PLMD::ActionWithMatrix::addDerivativeOnVectorArgument	(	const bool &	inchain,
		const unsigned &	ival,
		const unsigned &	jarg,
		const unsigned &	jelem,
		const double &	der,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

Add derivatives given the derivative wrt to the input vector element as input.

◆ addForce()

void PLMD::ActionAtomistic::addForce	(	const std::pair< std::size_t, std::size_t > &	a,
		const Vector &	f
	)

inlineinherited

Add force to an atom.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments	(	const unsigned &	argstart,
		const std::vector< double > &	forces,
		unsigned &	ind,
		const std::string &	c
	)

inherited

Add forces to arguments (used in apply)

◆ addForcesToInput()

void PLMD::ActionWithVector::addForcesToInput	(	const std::vector< double > &	forcesToApply,
		unsigned &	ind
	)

privateinherited

Add the gathered forces to the inputs across the whole chain.

◆ addThirdAtomDerivatives()

void PLMD::adjmat::AdjacencyMatrixBase::addThirdAtomDerivatives	(	const unsigned &	indno,
		const Vector &	der,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

◆ 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::ActionWithVector::apply ( )

virtualinherited

Apply the forces on this data.

Implements PLMD::Action.

Reimplemented in PLMD::dimred::ProjectPoints, PLMD::gridtools::FunctionOfGrid< T >, and PLMD::colvar::RMSDVector.

◆ areAllTasksRequired()

virtual void PLMD::ActionWithVector::areAllTasksRequired ( std::vector< ActionWithVector * > & task_reducing_actions )

inlinevirtualinherited

Do we always need to do all the tasks for this action.

Reimplemented in PLMD::gridtools::KDE, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::volumes::ActionVolume, PLMD::contour::FindContour, and PLMD::function::FunctionOfVector< T >.

◆ argumentDependsOn()

bool PLMD::ActionWithVector::argumentDependsOn	(	const std::string &	headstr,
		ActionWithVector *	faction,
		Value *	thearg
	)

protectedinherited

Check if the arguments of this action depend on thearg.

◆ 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.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc	(	int	i,
		double	d1
	)		const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ broadcastThatTasksAreReduced()

void PLMD::ActionWithVector::broadcastThatTasksAreReduced ( ActionWithVector * aselect )

privateinherited

Send information to arguments that tasks are reduced in depedent actions.

◆ buildArgumentStore()

unsigned PLMD::ActionWithVector::buildArgumentStore ( const unsigned & argstart )

protectedinherited

This sets up the arguments at the start of the calculation.

◆ calculate()

void PLMD::ActionWithMatrix::calculate ( )

overridevirtualinherited

Run the calculation.

Implements PLMD::Action.

◆ calculateAtomicNumericalDerivatives()

void PLMD::ActionAtomistic::calculateAtomicNumericalDerivatives	(	ActionWithValue *	a,
		const unsigned &	startnum
	)

inherited

Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.

◆ calculateConstantValues()

bool PLMD::ActionWithArguments::calculateConstantValues ( const bool & have_atoms )

virtualinherited

Used to calculate constant values in startup.

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

◆ 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::ActionWithVector::calculateNumericalDerivatives ( ActionWithValue * a )

overridevirtualinherited

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::ActionAtomistic.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

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

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

◆ calculateWeight()

double PLMD::adjmat::DistanceMatrix::calculateWeight	(	const Vector &	pos1,
		const Vector &	pos2,
		const unsigned &	natoms,
		MultiValue &	myvals
	)		const

virtual

This does nothing.

Implements PLMD::adjmat::AdjacencyMatrixBase.

◆ canBeAfterInChain()

virtual bool PLMD::ActionWithVector::canBeAfterInChain ( ActionWithVector * av )

inlinevirtualinherited

Check if we can be after another ActionWithVector.

Reimplemented in PLMD::adjmat::Neighbors.

◆ canReduceTasks()

void PLMD::ActionWithVector::canReduceTasks ( std::vector< ActionWithVector * > & task_reducing_actions )

privateinherited

Check if this ation can reduce the number of tasks we perform.

◆ castToActionAtomistic()

ActionAtomistic* PLMD::ActionAtomistic::castToActionAtomistic ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ 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() [1/2]

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithArguments() [2/2]

ActionWithArguments* PLMD::ActionWithArguments::castToActionWithArguments ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

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()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ changeBox()

void PLMD::ActionAtomistic::changeBox ( const Tensor & newbox )

inherited

Change the box shape.

◆ checkChainForNonScalarForces()

bool PLMD::ActionWithVector::checkChainForNonScalarForces ( ) const

privateinherited

Check the chain for non scalar forces.

◆ checkComponentsForForce()

bool PLMD::ActionWithVector::checkComponentsForForce ( ) const

privateinherited

Check if a force has been added on one of the components of this action.

◆ 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::ActionWithVector::checkForForces ( )

protectedinherited

Accumulate the forces from the Values.

◆ checkForGrids()

bool PLMD::ActionWithVector::checkForGrids ( unsigned & nder ) const

privateinherited

Check if there are any grids in the stream.

◆ checkForTaskForce()

bool PLMD::ActionWithMatrix::checkForTaskForce	(	const unsigned &	itask,
		const Value *	myval
	)		const

overridevirtualinherited

Check if there are forces we need to account for on this task.

Reimplemented from PLMD::ActionWithVector.

◆ 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() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

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

◆ checkTaskStatus()

virtual int PLMD::ActionWithVector::checkTaskStatus	(	const unsigned &	taskno,
		int &	flag
	)		const

inlinevirtualinherited

Check the status of the ith task.

Reimplemented in PLMD::gridtools::KDE, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::volumes::ActionVolume, and PLMD::contour::FindContour.

◆ 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::ActionWithVector::clearDerivatives ( const bool & force = false )

overridevirtualinherited

We override clearDerivatives here to prevent data in streams from being deleted.

Reimplemented from PLMD::ActionWithValue.

◆ clearInputForces()

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

overridevirtualinherited

We override clearInputForces here to ensure that forces are deleted from all values.

Reimplemented from PLMD::ActionWithValue.

◆ clearMatrixElements()

void PLMD::ActionWithMatrix::clearMatrixElements ( MultiValue & myvals ) const

privateinherited

This is used to clear up the matrix elements.

◆ 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.

◆ 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.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ difference()

double PLMD::ActionWithArguments::difference	(	int	i,
		double	d1,
		double	d2
	)		const

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

If this function is called during initialization, then forces are not going to be propagated. Can be used for optimization.

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

If this function is called during initialization, then atoms are not going to be retrieved. Can be used for optimization. Notice that calling getPosition(int) in an Action where DoNotRetrieve() was called might lead to undefined behavior.

◆ 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.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( const PDB & pdb )

protectedinherited

This changes the arg keyword in the pdb file.

◆ 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.

◆ finishChainBuild()

void PLMD::ActionWithMatrix::finishChainBuild ( ActionWithVector * act )

virtualinherited

This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions.

Reimplemented from PLMD::ActionWithVector.

◆ finishComputations()

void PLMD::ActionWithVector::finishComputations ( const std::vector< double > & buf )

inherited

This is to transfer data from the buffer to the final value.

◆ 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)

◆ gatherAccumulators()

void PLMD::ActionWithVector::gatherAccumulators	(	const unsigned &	taskCode,
		const MultiValue &	myvals,
		std::vector< double > &	buffer
	)		const

privateinherited

Gather the values that we intend to store in the buffer.

◆ gatherForces()

void PLMD::ActionWithVector::gatherForces	(	const unsigned &	i,
		const MultiValue &	myvals,
		std::vector< double > &	forces
	)		const

privateinherited

Gather the forces on non-scalar quantities.

◆ gatherForcesOnStoredValue()

void PLMD::ActionWithMatrix::gatherForcesOnStoredValue	(	const Value *	myval,
		const unsigned &	itask,
		const MultiValue &	myvals,
		std::vector< double > &	forces
	)		const

overridevirtualinherited

This gathers the force on a particular value.

Reimplemented from PLMD::ActionWithVector.

◆ gatherProcesses()

void PLMD::ActionWithMatrix::gatherProcesses ( std::vector< double > & buffer )

overridevirtualinherited

Gather all the data from the MPI processes.

Reimplemented from PLMD::ActionWithVector.

◆ gatherStoredValue()

void PLMD::ActionWithMatrix::gatherStoredValue	(	const unsigned &	valindex,
		const unsigned &	code,
		const MultiValue &	myvals,
		const unsigned &	bufstart,
		std::vector< double > &	buffer
	)		const

overridevirtualinherited

Gather a row of the matrix.

Reimplemented from PLMD::ActionWithVector.

Reimplemented in PLMD::matrixtools::Voronoi.

◆ gatherThreads()

void PLMD::ActionWithMatrix::gatherThreads	(	const unsigned &	nt,
		const unsigned &	bufsize,
		const std::vector< double > &	omp_buffer,
		std::vector< double > &	buffer,
		MultiValue &	myvals
	)

overridevirtualinherited

Gather all the data from the threads.

Reimplemented from PLMD::ActionWithVector.

◆ getAbsoluteIndex()

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int i ) const

inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getAbsoluteIndexes ( ) const

inlinevirtualinherited

Get the vector of absolute indexes.

◆ getActionWithDerivatives()

ActionWithVector * PLMD::ActionWithVector::getActionWithDerivatives ( ActionWithVector * depaction )

privateinherited

Work backwards through the chain to find an action that has either stored arguments or derivatives.

◆ getAdditionalTasksRequired()

void PLMD::adjmat::AdjacencyMatrixBase::getAdditionalTasksRequired	(	ActionWithVector *	action,
		std::vector< unsigned > &	atasks
	)

overridevirtualinherited

Get the additional tasks that are required here.

Reimplemented from PLMD::ActionWithVector.

◆ getAllActionLabelsInChain()

void PLMD::ActionWithVector::getAllActionLabelsInChain ( std::vector< std::string > & mylabels ) const

inherited

Get every the label of every value that is calculated in this chain.

◆ getAllActionLabelsInMatrixChain()

void PLMD::ActionWithMatrix::getAllActionLabelsInMatrixChain ( std::vector< std::string > & matchain ) const

overridevirtualinherited

This is overridden in ActionWithMatrix.

Reimplemented from PLMD::ActionWithVector.

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned n ) const

inlineinherited

Returns the value of an argument.

◆ getArgumentElement()

double PLMD::ActionWithMatrix::getArgumentElement	(	const unsigned &	ic,
		const unsigned &	jelem,
		const MultiValue &	myvals
	)		const

inlineprotectedinherited

This returns the jelem th element of argument ic.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getAtomValuesFromPlumedObject()

void PLMD::ActionAtomistic::getAtomValuesFromPlumedObject	(	const PlumedMain &	plumed,
		std::vector< Value * > &	xpos,
		std::vector< Value * > &	ypos,
		std::vector< Value * > &	zpos,
		std::vector< Value * > &	masv,
		std::vector< Value * > &	chargev
	)

staticinherited

This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges.

◆ getBox()

const Tensor & PLMD::ActionAtomistic::getBox ( ) const

inlineinherited

Get box shape.

◆ getCharge()

double PLMD::ActionAtomistic::getCharge ( int i ) const

inlineinherited

Get charge of i-th atom.

◆ 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.

◆ getDefaultString()

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

inlineinherited

Get the defaults.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getElementOfMatrixArgument()

double PLMD::ActionWithMatrix::getElementOfMatrixArgument	(	const unsigned &	imat,
		const unsigned &	irow,
		const unsigned &	jcol,
		const MultiValue &	myvals
	)		const

inlineprotectedinherited

This returns an element of a matrix that is passed an argument.

◆ getEnergy()

const double & PLMD::ActionAtomistic::getEnergy ( ) const

inlineinherited

Get energy.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getFirstActionInChain() [1/2]

ActionWithVector* PLMD::ActionWithVector::getFirstActionInChain ( )

inherited

◆ getFirstActionInChain() [2/2]

ActionWithVector * PLMD::ActionWithVector::getFirstActionInChain ( ) const

inherited

Return a pointer to the first action in the chain.

◆ getFirstMatrixInChain()

const ActionWithMatrix * PLMD::ActionWithMatrix::getFirstMatrixInChain ( ) const

inherited

Get the first matrix in this chain.

◆ getForce()

Vector PLMD::ActionAtomistic::getForce ( const std::pair< std::size_t, std::size_t > & a ) const

inlineinherited

Get the force acting on a particular atom.

◆ getForcesToApply()

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

inlineprotectedinherited

Get the forces to apply.

◆ getForceTasks()

void PLMD::ActionWithVector::getForceTasks ( std::vector< unsigned > & force_tasks ) const

privateinherited

Get the tasks that we need for forces.

◆ getGlobalPosition()

Vector PLMD::ActionAtomistic::getGlobalPosition ( const std::pair< std::size_t, std::size_t > & a ) const

inlineinherited

Get position of i-th atom (access by absolute AtomNumber).

With direct access to the global atom array.

Warning: Should be only used by actions that need to read the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ getGradient()

void PLMD::ActionAtomistic::getGradient	(	const unsigned &	ind,
		Vector &	deriv,
		std::map< AtomNumber, Vector > &	gradients
	)		const

inherited

Transfer the gradients.

◆ 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.

◆ getListOfActiveTasks()

std::vector< unsigned > & PLMD::ActionWithVector::getListOfActiveTasks ( ActionWithVector * action )

protectedinherited

Get the list of tasks that are active.

◆ getMass()

double PLMD::ActionAtomistic::getMass ( int i ) const

inlineinherited

Get mass of i-th atom.

◆ 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::valtools::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfColumns()

unsigned PLMD::adjmat::AdjacencyMatrixBase::getNumberOfColumns ( ) const

inlineoverridevirtualinherited

This should return the number of columns to help with sparse storage of matrices.

Implements PLMD::ActionWithMatrix.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::adjmat::AdjacencyMatrixBase::getNumberOfDerivatives ( )

overridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getNumberOfStoredValues()

bool PLMD::ActionWithVector::getNumberOfStoredValues	(	Value *	startat,
		unsigned &	nvals,
		const unsigned &	astart,
		const std::vector< Value * > &	stopat
	)

privateinherited

Get the number of stored values in the stream.

◆ getNumberOfStreamedDerivatives()

void PLMD::ActionWithVector::getNumberOfStreamedDerivatives	(	unsigned &	nderivatives,
		Value *	stopat
	)

inherited

Get the number of derivatives in the stream.

◆ getNumberOfStreamedQuantities()

void PLMD::ActionWithVector::getNumberOfStreamedQuantities	(	const std::string &	headstr,
		unsigned &	nquants,
		unsigned &	nmat,
		unsigned &	maxcol,
		unsigned &	nbookeeping
	)

privateinherited

Get the number of quantities in the stream.

◆ getNumberOfTasks()

void PLMD::ActionWithVector::getNumberOfTasks ( unsigned & ntasks )

virtualinherited

Find out how many tasks we need to perform in this loop.

Reimplemented in PLMD::gridtools::KDE, PLMD::volumes::ActionVolume, and PLMD::contour::FindContour.

◆ getOutputComponentDescription()

std::string PLMD::ActionWithValue::getOutputComponentDescription	(	const std::string &	cname,
		const Keywords &	keys
	)		const

virtualinherited

Get the description of this component.

Reimplemented in PLMD::generic::Read, PLMD::colvar::PropertyMap, PLMD::function::LocalEnsemble, PLMD::function::Ensemble, PLMD::function::FunctionOfVector< T >, PLMD::opes::ExpansionCVs, PLMD::function::FunctionOfScalar< T >, PLMD::colvar::ColvarFake, PLMD::matrixtools::MatrixTimesVector, PLMD::symfunc::ThreeBodyGFunctions, and PLMD::contour::FindContour.

◆ 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.

◆ getPbc()

const Pbc & PLMD::ActionAtomistic::getPbc ( ) const

inlineinherited

Get reference to Pbc.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned n ) const

inlineinherited

Return a pointer to specific argument.

◆ 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.

◆ getPosition() [1/2]

Vector PLMD::adjmat::AdjacencyMatrixBase::getPosition	(	const unsigned &	indno,
		MultiValue &	myvals
	)		const

inlineprotectedinherited

◆ getPosition() [2/2]

const Vector & PLMD::ActionAtomistic::getPosition ( int i ) const

inlineinherited

Get position of i-th atom (access by relative index)

◆ getPositions()

const std::vector< Vector > & PLMD::ActionAtomistic::getPositions ( ) const

inlineinherited

Get the array of all positions.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection	(	unsigned	i,
		unsigned	j
	)		const

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSizeOfBuffer()

void PLMD::ActionWithVector::getSizeOfBuffer	(	const unsigned &	nactive_tasks,
		unsigned &	bufsize
	)

privateinherited

Get the size of the buffer array that holds the data we are gathering over the MPI loop.

◆ 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.

◆ getTotalMatrixBookeeping()

void PLMD::ActionWithMatrix::getTotalMatrixBookeeping ( unsigned & stashsize )

privateinherited

This is used to find the total amount of space we need for storing matrix elements.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.

◆ getUnique()

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const

inlineinherited

◆ getUniqueLocal()

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getUniqueLocal ( ) const

inlineinherited

◆ getUnits()

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

protectedinherited

Get the units that we are operating in.

◆ getValueIndices()

std::pair< std::size_t, std::size_t > PLMD::ActionAtomistic::getValueIndices ( const AtomNumber & i ) const

protectedinherited

Used to interpret whether this index is a virtual atom or a real atom.

◆ getVirial()

Tensor PLMD::ActionAtomistic::getVirial ( ) const

inherited

Get the virial that is acting.

◆ hasStoredArguments()

bool PLMD::ActionWithVector::hasStoredArguments ( ) const

inherited

Check if there are any stored values in arguments.

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList	(	const std::vector< std::string > &	c,
		const ActionSet &	as,
		Action *	action,
		std::vector< Value * > &	arg
	)

staticinherited

Convert a list of argument names into a list of pointers to the values.

◆ interpretAtomList() [1/2]

void PLMD::ActionAtomistic::interpretAtomList	(	std::vector< std::string > &	strings,
		const std::vector< Value * > &	xpos,
		Action *	action,
		std::vector< AtomNumber > &	t
	)

staticinherited

Convert a set of read in strings into an atom list (this is used in parseAtomList)

◆ interpretAtomList() [2/2]

void PLMD::ActionAtomistic::interpretAtomList	(	std::vector< std::string > &	strings,
		std::vector< AtomNumber > &	t
	)

inherited

Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isAdjacencyMatrix()

bool PLMD::adjmat::AdjacencyMatrixBase::isAdjacencyMatrix ( ) const

inlineoverridevirtualinherited

Reimplemented from PLMD::ActionWithMatrix.

◆ isInSubChain()

virtual bool PLMD::ActionWithVector::isInSubChain ( unsigned & nder )

inlinevirtualinherited

Check if we are in a subchain.

Reimplemented in PLMD::volumes::ActionVolume, and PLMD::matrixtools::MatrixTimesVector.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ lockRequests()

void PLMD::ActionWithVector::lockRequests ( )

overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

Make atoms whole, assuming they are in the proper order.

◆ matrixChainContinues()

bool PLMD::ActionWithMatrix::matrixChainContinues ( ) const

inlineprotectedinherited

Does the matrix chain continue on from this action.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

◆ 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.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

bool PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		int	i,
		std::vector< Value * > &	args
	)

inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

void PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		std::vector< Value * > &	args
	)

inherited

Parse a list of arguments.

◆ parseAtomList() [1/2]

void PLMD::ActionAtomistic::parseAtomList	(	const std::string &	key,
		const int	num,
		std::vector< AtomNumber > &	t
	)

inherited

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

void PLMD::ActionAtomistic::parseAtomList	(	const std::string &	key,
		std::vector< AtomNumber > &	t
	)

inherited

Parse a list of atoms without a numbered keyword.

◆ 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.

◆ pbcApply()

void PLMD::ActionAtomistic::pbcApply	(	std::vector< Vector > &	dlist,
		unsigned	max_index = `0`
	)		const

inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

Vector PLMD::ActionAtomistic::pbcDistance	(	const Vector &	v1,
		const Vector &	v2
	)		const

inlineinherited

Compute the pbc distance between two positions.

◆ performTask() [1/2]

void PLMD::adjmat::AdjacencyMatrixBase::performTask	(	const std::string &	controller,
		const unsigned &	index1,
		const unsigned &	index2,
		MultiValue &	myvals
	)		const

overridevirtualinherited

This is the virtual that will do the calculation of the task for a particular matrix element.

Implements PLMD::ActionWithMatrix.

◆ performTask() [2/2]

void PLMD::ActionWithMatrix::performTask	(	const unsigned &	task_index,
		MultiValue &	myvals
	)		const

overridevirtualinherited

Run over one row of the matrix.

Implements PLMD::ActionWithVector.

◆ prepare()

void PLMD::adjmat::AdjacencyMatrixBase::prepare ( )

overridevirtualinherited

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 from PLMD::ActionWithVector.

◆ readAtomsFromPDB()

void PLMD::ActionAtomistic::readAtomsFromPDB ( const PDB & pdb )

overridevirtualinherited

Read in an input file containing atom positions and calculate the action for the atomic configuration therin.

Reimplemented from PLMD::Action.

◆ reallyBuildArgumentStore()

unsigned PLMD::ActionWithVector::reallyBuildArgumentStore ( const unsigned & argstart )

privateinherited

This is used to build the argument store when we cannot use the chain.

◆ registerKeywords()

void PLMD::adjmat::DistanceMatrix::registerKeywords ( Keywords & keys )

static

Create manual.

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > & arg )

inherited

Setup the dependencies.

◆ requestAtoms()

void PLMD::ActionAtomistic::requestAtoms	(	const std::vector< AtomNumber > &	a,
		const bool	clearDep = `true`
	)

inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > & extra )

inherited

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )

inherited

Set the timestep that is stored in the action to the correct value.

◆ retrieveAtoms()

void PLMD::ActionWithVector::retrieveAtoms ( const bool & force = false )

overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ retrieveNeighbours()

unsigned PLMD::adjmat::AdjacencyMatrixBase::retrieveNeighbours	(	const unsigned &	current,
		std::vector< unsigned > &	indices
	)		const

inherited

◆ runAllTasks()

void PLMD::ActionWithVector::runAllTasks ( )

protectedinherited

Run all the tasks in the list.

◆ runEndOfRowJobs()

void PLMD::adjmat::AdjacencyMatrixBase::runEndOfRowJobs	(	const unsigned &	ival,
		const std::vector< unsigned > &	indices,
		MultiValue &	myvals
	)		const

overridevirtualinherited

This is the jobs that need to be done when we have run all the jobs in a row of the matrix.

Implements PLMD::ActionWithMatrix.

◆ 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.

◆ runInSerial()

bool PLMD::ActionWithVector::runInSerial ( ) const

inlineprotectedinherited

Run all calculations in serial.

◆ runTask()

void PLMD::ActionWithMatrix::runTask	(	const std::string &	controller,
		const unsigned &	current,
		const unsigned	colno,
		MultiValue &	myvals
	)		const

privateinherited

This does the calculation of a particular matrix element.

◆ setExtraCV()

void PLMD::ActionAtomistic::setExtraCV ( const std::string & name )

protectedinherited

◆ setForcesOnAtoms()

void PLMD::ActionAtomistic::setForcesOnAtoms	(	const std::vector< double > &	forcesToApply,
		unsigned &	ind
	)

inherited

Add the forces to the atoms.

◆ setForcesOnCell() [1/2]

void PLMD::ActionAtomistic::setForcesOnCell	(	const double *	forcesToApply,
		std::size_t	size,
		unsigned &	ind
	)

inherited

Add the virial forces (span-like syntax)

◆ setForcesOnCell() [2/2]

void PLMD::ActionAtomistic::setForcesOnCell	(	const std::vector< double > &	forcesToApply,
		unsigned &	ind
	)

inherited

Add the virial forces.

◆ setGlobalPosition()

void PLMD::ActionAtomistic::setGlobalPosition	(	const std::pair< std::size_t, std::size_t > &	a,
		const Vector &	pos
	)

inlineinherited

Modify position of i-th atom (access by absolute AtomNumber).

Warning: Should be only used by actions that need to modify the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ setGradients()

void PLMD::ActionWithArguments::setGradients	(	Value *	myval,
		unsigned &	start
	)		const

inherited

Get the gradient for this action.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

virtualinherited

Calculate the gradients and store them for all the values (need for projections)

Reimplemented in PLMD::ActionForInterface.

◆ setLinkCellCutoff()

void PLMD::adjmat::AdjacencyMatrixBase::setLinkCellCutoff	(	const bool &	symmetric,
		const double &	lcut,
		double	tcut = `-1.0`
	)

protectedinherited

◆ 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.

◆ 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.

◆ setupForTask()

void PLMD::adjmat::AdjacencyMatrixBase::setupForTask	(	const unsigned &	current,
		std::vector< unsigned > &	indices,
		MultiValue &	myvals
	)		const

overridevirtualinherited

Implements PLMD::ActionWithMatrix.

◆ setupStreamedComponents()

void PLMD::ActionWithMatrix::setupStreamedComponents	(	const std::string &	headstr,
		unsigned &	nquants,
		unsigned &	nmat,
		unsigned &	maxcol,
		unsigned &	nbookeeping
	)

overridevirtualinherited

This requires some thought.

Reimplemented from PLMD::ActionWithVector.

Reimplemented in PLMD::function::FunctionOfMatrix< T >.

◆ setupThirdAtomBlock()

void PLMD::adjmat::AdjacencyMatrixBase::setupThirdAtomBlock	(	const std::vector< AtomNumber > &	tc,
		std::vector< AtomNumber > &	t
	)

privateinherited

◆ 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.

◆ switchTaskReduction()

virtual void PLMD::ActionWithVector::switchTaskReduction	(	const bool &	task_reduction,
		ActionWithVector *	aselect
	)

inlinevirtualinherited

Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere.

◆ taskIsActive()

void PLMD::ActionWithVector::taskIsActive	(	const unsigned &	current,
		int &	flag
	)		const

privateinherited

Check if a particular task is active at this time.

◆ transferNonZeroMatrixElementsToValues()

void PLMD::ActionWithMatrix::transferNonZeroMatrixElementsToValues	(	unsigned &	nval,
		const std::vector< unsigned > &	matbook
	)

privateinherited

This transfers the non-zero elements to the Value.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

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

◆ unlockRequests()

void PLMD::ActionWithVector::unlockRequests ( )

overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ 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::DumpPDB, PLMD::generic::DumpProjections, PLMD::generic::PrintNDX, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

◆ updateAdditionalIndices()

virtual void PLMD::ActionWithVector::updateAdditionalIndices	(	const unsigned &	ostrn,
		MultiValue &	myvals
	)		const

inlinevirtualinherited

This is used to ensure that all indices are updated when you do local average.

Reimplemented in PLMD::matrixtools::MatrixTimesVector.

◆ updateAllNeighbourLists()

void PLMD::ActionWithMatrix::updateAllNeighbourLists ( )

privateinherited

Update all the neighbour lists in the chain.

◆ updateForceTasksFromValue()

void PLMD::ActionWithVector::updateForceTasksFromValue	(	const Value *	myval,
		std::vector< unsigned > &	force_tasks
	)		const

virtualinherited

Get the force tasks that are active for this action.

Reimplemented in PLMD::gridtools::KDE.

◆ updateNeighbourList()

void PLMD::adjmat::AdjacencyMatrixBase::updateNeighbourList ( )

overridevirtualinherited

This is overwritten in Adjacency matrix where we have a neighbour list.

Reimplemented from PLMD::ActionWithMatrix.

◆ updateTaskListReductionStatus()

void PLMD::ActionWithVector::updateTaskListReductionStatus ( )

protectedinherited

This updates whether or not we are using all the task reduction stuff.

◆ updateTaskReductionFlag()

void PLMD::ActionWithVector::updateTaskReductionFlag ( bool & head_reduce_tasks )

privateinherited

Turn on task reduction flag in dependent actions.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal	(	const bool &	useunique,
		const std::vector< int > &	g2l
	)

privateinherited

◆ 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.

◆ warning()

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

inherited

Issue a warning.

◆ 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::function::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Member Data Documentation

◆ ablocks

std::vector<unsigned> PLMD::adjmat::AdjacencyMatrixBase::ablocks

privateinherited

◆ action_to_do_after

ActionWithVector* PLMD::ActionWithVector::action_to_do_after

privateinherited

Actions that must be done after this one.

◆ action_to_do_before

ActionWithVector* PLMD::ActionWithVector::action_to_do_before

privateinherited

Action that must be done before this one.

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ active_tasks

std::vector<unsigned> PLMD::ActionWithVector::active_tasks

privateinherited

The list of active tasks.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ arg_deriv_starts

std::vector<unsigned> PLMD::ActionWithVector::arg_deriv_starts

protectedinherited

A vector that contains the start point for the argument derivatives.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments

privateinherited

◆ atom_value_ind

std::vector<std::pair<std::size_t, std::size_t > > PLMD::ActionAtomistic::atom_value_ind

privateinherited

◆ atom_value_ind_grouped

std::vector<std::pair<std::size_t,std::vector<std::size_t> > > PLMD::ActionAtomistic::atom_value_ind_grouped

privateinherited

◆ atomsWereRetrieved

bool PLMD::ActionWithVector::atomsWereRetrieved

privateinherited

Were the atoms retrieved in some earlier action.

◆ boxValue

Value* PLMD::ActionAtomistic::boxValue

privateinherited

◆ buffer

std::vector<double> PLMD::ActionWithVector::buffer

privateinherited

The buffer that we use (we keep a copy here to avoid resizing)

◆ charges

std::vector<double> PLMD::ActionAtomistic::charges

privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

protectedinherited

◆ chargev

std::vector<Value*> PLMD::ActionAtomistic::chargev

privateinherited

◆ clearOnEachCycle

bool PLMD::ActionWithMatrix::clearOnEachCycle

protectedinherited

This turns off derivative clearing for contact matrix if we are not storing derivatives.

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ components

bool PLMD::adjmat::AdjacencyMatrixBase::components

privateinherited

◆ cutoff

double PLMD::adjmat::DistanceMatrix::cutoff

private

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ done_in_chain

bool PLMD::ActionWithVector::done_in_chain

protectedinherited

Assert if this action is part of a chain.

◆ donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

◆ energy

double PLMD::ActionAtomistic::energy

privateinherited

◆ files

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

inherited

◆ firststep

bool PLMD::ActionWithValue::firststep

privateinherited

This finishes setup on first step to check if actions are calculated during update.

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

◆ forces

std::vector<Vector> PLMD::ActionAtomistic::forces

privateinherited

◆ 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.

◆ indexes

std::vector<AtomNumber> PLMD::ActionAtomistic::indexes

privateinherited

◆ 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.

◆ linkcells

LinkCells PLMD::adjmat::AdjacencyMatrixBase::linkcells

privateinherited

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments

privateinherited

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ masses

std::vector<double> PLMD::ActionAtomistic::masses

privateinherited

◆ massesWereSet

bool PLMD::ActionAtomistic::massesWereSet

protectedinherited

◆ masv

std::vector<Value*> PLMD::ActionAtomistic::masv

privateinherited

◆ matrix_bookeeping

std::vector<unsigned> PLMD::ActionWithMatrix::matrix_bookeeping

privateinherited

This holds the bookeeping arrays for sparse matrices.

◆ matrix_to_do_after

ActionWithMatrix* PLMD::ActionWithMatrix::matrix_to_do_after

privateinherited

◆ matrix_to_do_before

ActionWithMatrix* PLMD::ActionWithMatrix::matrix_to_do_before

privateinherited

◆ maxcol

unsigned PLMD::adjmat::AdjacencyMatrixBase::maxcol

privateinherited

◆ 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.

◆ natoms_per_list

unsigned PLMD::adjmat::AdjacencyMatrixBase::natoms_per_list

privateinherited

◆ neighbour_list_updated

bool PLMD::adjmat::AdjacencyMatrixBase::neighbour_list_updated

privateinherited

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ never_reduce_tasks

bool PLMD::ActionWithVector::never_reduce_tasks

privateinherited

This is turned on if there is some action that needs all the tasks.

◆ next_action_in_chain

ActionWithMatrix* PLMD::ActionWithMatrix::next_action_in_chain

privateinherited

◆ nl_cut

double PLMD::adjmat::AdjacencyMatrixBase::nl_cut

privateinherited

◆ nl_cut2

double PLMD::adjmat::AdjacencyMatrixBase::nl_cut2

privateinherited

◆ nl_stride

unsigned PLMD::adjmat::AdjacencyMatrixBase::nl_stride

privateinherited

◆ nlist

std::vector<unsigned> PLMD::adjmat::AdjacencyMatrixBase::nlist

privateinherited

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ nopbc

bool PLMD::adjmat::AdjacencyMatrixBase::nopbc

privateinherited

◆ 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.

◆ pbc

Pbc& PLMD::ActionAtomistic::pbc =*pbc_fwd

privateinherited

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd

privateinherited

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ positions

std::vector<Vector> PLMD::ActionAtomistic::positions

privateinherited

◆ read_one_group

bool PLMD::adjmat::AdjacencyMatrixBase::read_one_group

privateinherited

◆ reduce_tasks

bool PLMD::ActionWithVector::reduce_tasks

privateinherited

Are we allowed to reduce the number of tasks being performed.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ serial

bool PLMD::ActionWithVector::serial

privateinherited

Is the calculation to be done in serial.

◆ task_control_list

std::vector<ActionWithVector*> PLMD::ActionWithVector::task_control_list

privateinherited

This is the list of actions that control the tasks that we do here.

◆ threeblocks

std::vector<unsigned> PLMD::adjmat::AdjacencyMatrixBase::threeblocks

privateinherited

◆ threecells

LinkCells PLMD::adjmat::AdjacencyMatrixBase::threecells

privateinherited

◆ timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

◆ unique

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

privateinherited

unique should be an ordered set since we later create a vector containing the corresponding indexes

◆ unique_local

std::vector<AtomNumber> PLMD::ActionAtomistic::unique_local

privateinherited

◆ unique_local_needs_update

bool PLMD::ActionAtomistic::unique_local_needs_update

privateinherited

unique_local should be an ordered set since we later create a vector containing the corresponding indexes

◆ 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

◆ value_depends

std::vector<std::size_t> PLMD::ActionAtomistic::value_depends

privateinherited

◆ values

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

privateinherited

An array containing the values for this action.

◆ xpos

std::vector<Value*> PLMD::ActionAtomistic::xpos

privateinherited

Values that hold information about atom positions and charges.

◆ ypos

std::vector<Value*> PLMD::ActionAtomistic::ypos

privateinherited

◆ zpos

std::vector<Value*> PLMD::ActionAtomistic::zpos

privateinherited

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

adjmat/DistanceMatrix.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ DistanceMatrix()

Member Function Documentation

◆ actionHasForces()

◆ actionInChain()

◆ activate()

◆ addActionToChain()

◆ addAtomDerivatives()

◆ addBoxDerivatives()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addDerivativeOnMatrixArgument()

◆ addDerivativeOnVectorArgument()

◆ addForce()

◆ addForcesOnArguments()

◆ addForcesToInput()

◆ addThirdAtomDerivatives()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ areAllTasksRequired()

◆ argumentDependsOn()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ broadcastThatTasksAreReduced()

◆ buildArgumentStore()

◆ calculate()

◆ calculateAtomicNumericalDerivatives()

◆ calculateConstantValues()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateOnUpdate()

◆ calculateWeight()

◆ canBeAfterInChain()

◆ canReduceTasks()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments() [1/2]

◆ castToActionWithArguments() [2/2]

◆ castToActionWithValue() [1/2]

◆ castToActionWithValue() [2/2]

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ changeBox()

◆ checkChainForNonScalarForces()

◆ checkComponentsForForce()

◆ checkFieldsAllowed()

◆ checkForDependency()

◆ checkForForces()

◆ checkForGrids()

◆ checkForTaskForce()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkTaskStatus()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearMatrixElements()

◆ clearOptions()

◆ componentIsNotPeriodic()