Provides the keyword TOPOLOGY_MATRIX More...

Inheritance diagram for PLMD::adjmat::TopologyMatrix:

[legend]

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

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

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

void	addAtomDerivatives (const int &, const unsigned &, const Vector &, multicolvar::AtomValuePack &) const
	Add some derivatives to a particular component of a particular atom. More...

void	addComponent (const std::string &name)
	Add a value with a name like label.name. More...

void	addComponentWithDerivatives (const std::string &name)
	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 ()
	Add a value with the name label. More...

void	addValueWithDerivatives ()
	Add a value with the name label that has derivatives. More...

void	allowToAccessGlobalForces ()
	Allow calls to modifyGlobalForce() More...

void	apply () override
	Apply the forces from this action. More...

virtual void	applyBridgeForces (const std::vector< double > &bb)
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...

void	applyForces ()

void	applyPbc (std::vector< Vector > &dlist, unsigned max_index=0) const
	Apply PBCs over a set of distance vectors. More...

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

StoreDataVessel *	buildDataStashes (ActionWithVessel *actionThatUses)
	Ensure that data required in other vessels is stored. More...

void	calculate () override
	Do 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...

void	calculateForThreeAtoms (const unsigned &iat, const Vector &d1, const double &d1_len, HistogramBead &bead, multicolvar::AtomValuePack &myatoms) const
	Calculate the contribution from one of the atoms in the third element of the pack. More...

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

void	calculateNumericalDerivatives (ActionWithValue *a=NULL) override
	Calculate numerical derivatives. More...

double	calculateWeight (const unsigned &taskCode, const double &weight, multicolvar::AtomValuePack &myatoms) const override
	This actually calculates the value of the contact function. More...

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

virtual void	checkFieldsAllowed ()

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...

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...

virtual void	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

void	clearInputForces ()
	Clear the forces on the values. More...

virtual void	clearOptions ()

void	clearOutputForces ()

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...

double	compute (const unsigned &tindex, multicolvar::AtomValuePack &myatoms) const override
	This does nothing. 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...

bool	derivativesAreRequired () const
	Are derivatives required for this quantity. More...

virtual void	doJobsRequiredBeforeTaskList ()
	Do any jobs that are required before the task list is undertaken. More...

bool	doNotCalculateDerivatives () const override
	Ensure that derivatives are only calculated when needed. More...

virtual void	doNotCalculateDirector ()
	This makes sure we are not calculating the director when we do LocalAverage. 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...

virtual void	finishComputations (const std::vector< double > &buffer)
	Finish running all the calculations. More...

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

AtomNumber	getAbsoluteIndexOfCentralAtom (const unsigned &i) const
	Get the atom number. More...

unsigned	getActiveTask (const unsigned &ii) const
	Get the ith of the currently active tasks. More...

MultiColvarBase *	getBaseMultiColvar (const unsigned &icolv) const
	Get the icolv th base multicolvar. More...

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

Vector	getCentralAtom ()

virtual void	getCentralAtomPack (const unsigned &basn, const unsigned &curr, CatomPack &mypack)

virtual Vector	getCentralAtomPos (const unsigned &curr)
	Get the index where the central atom is stored. 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...

unsigned	getCurrentNumberOfActiveTasks () const
	Get the number of tasks that are currently active. 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...

unsigned	getFullNumberOfTasks () const
	Get the full size of the taskList dynamic list. More...

const Vector &	getGlobalPosition (AtomNumber) const
	Get position of i-th atom (access by absolute AtomNumber). More...

virtual void	getInputData (const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient) const
	Get an input data. More...

virtual MultiValue &	getInputDerivatives (const unsigned &iatom, const bool &normed, const multicolvar::AtomValuePack &myatoms) const
	Retrieve the input derivatives. 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...

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

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

unsigned	getNumberOfBaseMultiColvars () const
	Get the number of base multicolvars. More...

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

unsigned	getNumberOfDerivatives () override
	Get the number of derivatives for this action. More...

unsigned	getNumberOfQuantities () const override
	Get the number of quantities that we must compute. More...

unsigned	getNumberOfVessels () const
	Get the number of vessels. 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...

Vessel *	getPntrToVessel (const unsigned &i)
	Get a pointer to the ith vessel. More...

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

unsigned	getPositionInCurrentTaskList (const unsigned &myind) const
	Return the position in the current task list. More...

unsigned	getPositionInFullTaskList (const unsigned &ii) const
	Get the position of the ith active task in the full list. More...

virtual Vector	getPositionOfAtomForLinkCells (const unsigned &iatom) const
	This gets the position of an atom for the link cell setup. More...

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

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

Vector	getSeparation (const Vector &vec1, const Vector &vec2) const
	Get the separation between a pair of vectors. More...

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

unsigned	getTaskCode (const unsigned &ii) const
	Get the code for the ii th task in the list. 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

Vessel *	getVesselWithName (const std::string &mynam)
	These are overwritten in MultiColvarFunction. More...

virtual bool	hasDifferentiableOrientation () const
	This is true if multicolvar is calculating a vector or if the multicolvar is the density. More...

void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) More...

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

virtual bool	isCurrentlyActive (const unsigned &code)
	Checks if an task is being performed at the present time. More...

virtual bool	isDensity () const
	Is this a density? More...

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

bool	isPeriodic ()
	None of these things are allowed. More...

void	lockContributors ()

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...

double &	modifyForceOnExtraCV ()
	Get a reference to force on extraCV. More...

std::vector< Vector > &	modifyForces ()
	Get a reference to forces array. More...

Vector &	modifyGlobalForce (AtomNumber)
	Get modifiable force of i-th atom (access by absolute AtomNumber). More...

Pbc &	modifyGlobalPbc ()
	Get modifiable PBC Should be used by action that need to modify the stored box. More...

Vector &	modifyGlobalPosition (AtomNumber)
	Get modifiable position of i-th atom (access by absolute AtomNumber). More...

Tensor &	modifyGlobalVirial ()
	Get modifiable virial Should be used by action that need to modify the stored virial. More...

Tensor &	modifyVirial ()
	Get a reference to virial array. More...

virtual void	normalizeVector (std::vector< double > &vals) const
	These normalizes vectors and is used in StoreDataVessel. More...

virtual void	normalizeVectorDerivatives (MultiValue &myvals) const

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. 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 unsigned &, const unsigned &, MultiValue &) const override
	Perform one of the tasks. More...

void	prepare () override
	Do some setup before the 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	requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
	Request an array of atoms. More...

void	retrieveAtoms () override
	This is overwritten here in order to make sure that we do not retrieve atoms multiple times. More...

virtual void	retrieveDomain (std::string &min, std::string &max)
	What are the domains of the base quantities. 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=0)
	Add the forces to the atoms. More...

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	setupConnector (const unsigned &id, const unsigned &i, const unsigned &j, const std::vector< std::string > &desc) override
	Create the ith, ith switching function. More...

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

bool	storedValueIsActive (const unsigned &iatom)
	Is the iatom'th stored value currently active. More...

bool	taskIsCurrentlyActive (const unsigned &index) const
	Check whether or not a particular task is currently active. More...

bool	threadSafe () const override
	Is it safe to use multithreading. More...

virtual void	transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const
	Do the task if we have a bridge. More...

void	turnOnDerivatives () override
	Turn on the derivatives. More...

void	unlockRequests () override

virtual void	update ()
	Update. More...

virtual void	updateActiveAtoms (AtomValuePack &myatoms) const
	Update the active atoms. More...

void	updateUniqueLocal ()
	updates local unique atoms More...

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

bool	usesPbc () const
	Do we use pbc to calculate this quantity. More...

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

bool	weightWithDerivatives () const
	Does the weight have derivatives. 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)
	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	accumulateSymmetryFunction (const int &ival, const unsigned &iatom, const double &val, const Vector &der, const Tensor &vir, multicolvar::AtomValuePack &myatoms) const
	This is used to accumulate functions of the coordination sphere. Ensures weights are taken into account. More...

BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels. More...

void	addDerivativesOnMatrixElement (const unsigned &ielem, const unsigned &jrow, const double &df, Matrix< double > &der)
	Add derivatives to a matrix element. More...

void	addTaskToList (const unsigned &taskCode)
	Add a task to the list of tasks. More...

void	addVessel (const std::string &name, const std::string &input, const int numlab=0)
	Add a vessel to the list of vessels. More...

void	addVessel (std::unique_ptr< Vessel > vv)

void	buildSets ()
	Build sets by taking one multicolvar from each base. More...

void	calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

void	deactivateAllTasks ()
	Deactivate all the tasks in the task list. More...

void	decodeIndexToAtoms (const unsigned &taskCode, std::vector< unsigned > &atoms) const
	Decode indices if there are 2 or 3 atoms involved. More...

bool	filtersUsedAsInput ()
	Function that recursively checks if filters have been used in the input to a multicolvar we need this to ensure that setupLinkCells is run in calculate with some actions. More...

AdjacencyMatrixVessel *	getAdjacencyVessel ()
	Retrieve the vessel that holds the adjacency matrix. More...

unsigned	getBaseColvarNumber (const unsigned &) const
	Return the group this atom is a part of. More...

bool	getForcesFromVessels (std::vector< double > &forcesToApply)
	Retrieve the forces from all the vessels (used in apply) More...

double	getLinkCellCutoff () const
	Get the cutoff for the link cells. More...

double	getNLTolerance () const
	Return the value for the neighbor list tolerance. More...

unsigned	getNumberOfNodeTypes () const
	Get the number of nodes of different types. 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...

unsigned	getSizeOfBuffer (unsigned &bufsize)
	Get the size of the buffer. More...

unsigned	getSizeOfInputVectors () const
	Get the size of the vectors that were stored in the base colvars. More...

double	getTolerance () const
	Return the value of the tolerance. More...

void	mergeInputDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const
	This routine take the vector of input derivatives and adds all the vectors to ivalth output derivatives In other words end-start sets of derivatives come in and one set of derivatives come out. More...

void	needsDerivatives ()
	Turn on the derivatives in the vessel. More...

void	parseConnectionDescriptions (const std::string &key, const bool &multiple, const unsigned &nrow_t)
	Read in the information on the connectors. More...

bool	parseMultiColvarAtomList (const std::string &key, const int &num, std::vector< AtomNumber > &t)
	Read in some atoms. More...

void	readAtomsLikeKeyword (const std::string &key, const int &natoms, std::vector< AtomNumber > &all_atoms)
	Read in ATOMS keyword. More...

void	readGroupKeywords (const std::string &key0, const std::string &key1, const std::string &key2, const std::string &key3, const bool &no_third_dim_accum, const bool &symmetric, std::vector< AtomNumber > &all_atoms)
	Read in three groups of atoms. More...

void	readMaxThreeSpeciesMatrix (const std::string &key0, const std::string &key1, const std::string &key2, const std::string &keym, const bool &symmetric)
	Read in a matrix involving a maximum of three species. More...

void	readMaxTwoSpeciesMatrix (const std::string &key0, const std::string &key1, const std::string &key2, const bool &symmetric)
	Read in a matrix involving a maximum of two species. More...

void	readThreeGroups (const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2, const bool &no_third_dim_accum, std::vector< AtomNumber > &all_atoms)
	Read in three groups of atoms and construct CVs involving at least one. More...

void	readTwoGroups (const std::string &key0, const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms)
	Read in two groups of atoms and setup multicolvars to calculate. More...

void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...

void	resizeBookeepingArray (const unsigned &num1, const unsigned &num2)
	This resizes the arrays that are used for link cell update. More...

void	resizeFunctions ()
	Resize all the functions when the number of derivatives change. More...

void	retrieveTypeDimensions (unsigned &nrows, unsigned &ncols, unsigned &ntype) const
	Get the dimensions of the matrix of types. More...

void	runAllTasks ()
	Calculate the values of all the vessels. More...

bool	serialCalculation () const
	Is the calculation being done in serial. More...

void	setAtomsForCentralAtom (const std::vector< bool > &catom_ind)
	Set which atoms are to be used to calculate the central atom position. More...

void	setExtraCV (const std::string &name)

void	setLinkCellCutoff (const double &lcut, double tcut=-1.0)
	Set the value of the cutoff for the link cells. More...

void	setLowMemOption (const bool &)
	Set that we are using low memory. More...

void	setMatrixIndexesForTask (const unsigned &ii)
	Put the indices of the matrix elements in current atoms. More...

void	setupActiveTaskSet (std::vector< unsigned > &active_tasks, const std::string &input_label)
	Setup the link cells and neighbour list stuff. More...

bool	setupCurrentAtomList (const unsigned &taskCode, AtomValuePack &myatoms) const
	This sets up the list of atoms that are involved in this colvar. More...

void	setupLinkCells ()
	Setup link cells in order to make this calculation faster. More...

void	setupMultiColvarBase (const std::vector< AtomNumber > &atoms)
	Finish setting up the multicolvar base. More...

void	setupNonUseSpeciesLinkCells (const unsigned &)
	This does setup of link cell stuff that is specific to the non-use of the usespecies keyword. More...

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

void	splitInputDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const
	This routine take the ith set of input derivatives and adds it to each of the (end-start) output derivatives In other words one set of derivatives comes in and end-start sets of derivatives come out. More...

bool	usingLowMem () const
	Are we using low memory. More...

Protected Attributes
std::vector< std::vector< unsigned > >	ablocks
	Blocks of atom numbers. More...

std::vector< std::pair< unsigned, unsigned > >	atom_lab
	This is used to keep track of what is calculated where. More...

Atoms &	atoms

Matrix< std::pair< unsigned, unsigned > >	bookeeping
	This remembers where the boundaries are for the tasks. It makes link cells work fast. More...

unsigned	bridgeVariable
	This is used for numerical derivatives of bridge variables. More...

bool	contributorsAreUnlocked
	The terms in the series are locked. More...

std::vector< unsigned >	decoder
	This is used when turning cvcodes into atom numbers. More...

bool	dertime
	This is also used to minimise computational expense in complex functions. More...

bool	matsums
	Are we doing sums of matrix rows. More...

std::vector< vesselbase::StoreDataVessel * >	mybasedata
	The vessels in these multicolvars in which the data is stored. More...

std::vector< MultiColvarBase * >	mybasemulticolvars
	The multicolvars from which we construct these quantities. More...

StoreDataVessel *	mydata
	A pointer to the object that stores data. More...

unsigned	nblock
	Number of atoms in each block. More...

std::vector< unsigned >	taskFlags
	This list is used to update the neighbor list. More...

bool	usespecies
	Using the species keyword to read in atoms. More...

bool	weightHasDerivatives
	Does the weight have derivatives. More...

Private Member Functions
void	addComDerivatives (const int &ival, const unsigned &iatom, const Vector &der, multicolvar::AtomValuePack &myatoms) const
	Add derivatives of center of mass position. More...

void	finishMatrixSetup (const bool &symmetric, const std::vector< AtomNumber > &all_atoms)
	Finish the setup of the matrix. More...

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

void	recalculateMatrixElement (const unsigned &myelem, MultiValue &myvals)
	This is used within AdjacencyMatrixVessel to recalculate matrix elements which is useful when we are operating with lowmem. More...

Private Attributes
bool	actionIsBridged
	This tells plumed that this is used in a bridge. More...

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

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

bool	allthirdblockintasks
	We use this to say that all the atoms in the third block should are in the tasks. More...

bool	atomsWereRetrieved
	Ensures that retrieving of atoms is only done once per calculation loop. More...

double	beadrad

Matrix< double >	binw_mat

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

Matrix< double >	cell_volume
	The volume of the cells. More...

std::vector< double >	charges

bool	chargesWereSet

unsigned	connect_id
	Used for read in of multiple connection descriptors. More...

Matrix< SwitchingFunction >	cylinder_sw

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

std::vector< unsigned >	der_list
	The list of atoms involved in derivatives (we keep a copy here to avoid resizing) More...

bool	dertime_can_be_off
	These are used to minmise computational expense in complex functions. More...

bool	doCheckPoint

bool	donotforce

bool	donotretrieve

double	energy

std::string	extraCV

double	forceOnEnergy

double	forceOnExtraCV

std::vector< Vector >	forces

std::vector< double >	forcesToApply
	The forces we are going to apply to things. More...

std::vector< unsigned >	fullTaskList
	Ths full list of tasks we have to perform. More...

std::vector< std::unique_ptr< Vessel > >	functions
	Pointers to the functions we are using on each value. More...

std::vector< AtomNumber >	indexes

std::vector< unsigned >	indexOfTaskInFullList
	The indices of the tasks in the full list of tasks. More...

std::string	kerneltype

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
	Stuff for link cells - this is used to make coordination number like variables faster. More...

bool	lockRequestAtoms

Matrix< SwitchingFunction >	low_sf

bool	lowmem
	Lower memory requirements. More...

double	lsfmax

std::vector< double >	masses

AdjacencyMatrixVessel *	mat
	This is the vessel that stores the adjacency matrix. More...

unsigned	maxbins
	The maximum number of bins that will be used This is calculated based on the dmax of the switching functions. More...

unsigned	maxderivatives
	The maximum number of derivatives we can use before we need to invoke lowmem. More...

std::vector< CatomPack >	my_tmp_capacks
	Vector of tempory holders for central atom values. More...

unsigned	nactive_atoms
	Number of atoms that are active on this step. More...

unsigned	nactive_tasks
	The current number of active tasks. More...

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

unsigned	ncentral
	Number of atoms that are being used for central atom position. More...

double	nl_tolerance
	Tolerance for quantities being put in neighbor lists. More...

bool	no_third_dim_accum
	Do we need to separate out the tasks for the third atoms. More...

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

double	numberForCentralAtom
	1/number of atoms involved in central atoms More...

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

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

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

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

int	replica_index

bool	restart

bool	serial
	Do all calculations in serial. More...

bool	setup_completed
	Ensures that setup is only performed once per loop. More...

double	sigma
	The width to use for the kernel density estimation and the sizes of the bins to be used in kernel density estimation. More...

Stopwatch &	stopwatch =*stopwatch_fwd
	The stopwatch that times the different parts of the calculation. More...

ForwardDecl< Stopwatch >	stopwatch_fwd

Matrix< SwitchingFunction >	switchingFunction
	switching function More...

LinkCells	threecells
	Link cells for third block of atoms. More...

SwitchingFunction	threshold_switch

bool	timers
	Do we want to output information on the timings of different parts of the calculation. More...

std::vector< double >	tmpforces
	Tempory storage for forces. More...

double	tolerance
	The tolerance on the accumulators. 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
	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< bool >	use_for_central_atom
	Bool vector telling us which atoms are required to calculate central atom position. More...

bool	uselinkforthree
	In certain cases we can make three atom link cells faster. More...

bool	usepbc
	Use periodic boundary conditions. More...

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

Tensor	virial

Detailed Description

Provides the keyword TOPOLOGY_MATRIX

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ TopologyMatrix()

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

explicit

Constructor.

Member Function Documentation

◆ accumulateSymmetryFunction()

void PLMD::multicolvar::MultiColvarBase::accumulateSymmetryFunction	(	const int &	ival,
		const unsigned &	iatom,
		const double &	val,
		const Vector &	der,
		const Tensor &	vir,
		multicolvar::AtomValuePack &	myatoms
	)		const

protectedinherited

This is used to accumulate functions of the coordination sphere. Ensures weights are taken into account.

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addAtomDerivatives()

void PLMD::multicolvar::MultiColvarBase::addAtomDerivatives	(	const int &	ival,
		const unsigned &	iatom,
		const Vector &	der,
		multicolvar::AtomValuePack &	myatoms
	)		const

inherited

Add some derivatives to a particular component of a particular atom.

◆ addBridgingVessel()

BridgeVessel * PLMD::vesselbase::ActionWithVessel::addBridgingVessel ( ActionWithVessel * tome )

protectedinherited

Add a bridging vessel to the list of vessels.

◆ addComDerivatives()

void PLMD::multicolvar::MultiColvarBase::addComDerivatives	(	const int &	ival,
		const unsigned &	iatom,
		const Vector &	der,
		multicolvar::AtomValuePack &	myatoms
	)		const

privateinherited

Add derivatives of center of mass position.

◆ addComponent()

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

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

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

inherited

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

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addDerivativesOnMatrixElement()

void PLMD::adjmat::AdjacencyMatrixBase::addDerivativesOnMatrixElement	(	const unsigned &	ielem,
		const unsigned &	jrow,
		const double &	df,
		Matrix< double > &	der
	)

protectedinherited

Add derivatives to a matrix element.

◆ addTaskToList()

void PLMD::multicolvar::MultiColvarBase::addTaskToList ( const unsigned & taskCode )

protectedinherited

Add a task to the list of tasks.

◆ addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

◆ addVessel() [1/2]

void PLMD::vesselbase::ActionWithVessel::addVessel	(	const std::string &	name,
		const std::string &	input,
		const int	numlab = `0`
	)

protectedinherited

Add a vessel to the list of vessels.

◆ addVessel() [2/2]

void PLMD::vesselbase::ActionWithVessel::addVessel ( std::unique_ptr< Vessel > vv )

protectedinherited

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::multicolvar::MultiColvarBase::apply ( )

overridevirtualinherited

Apply the forces from this action.

Implements PLMD::Action.

◆ applyBridgeForces()

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > & bb )

inlinevirtualinherited

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )

inherited

◆ applyPbc()

void PLMD::multicolvar::MultiColvarBase::applyPbc	(	std::vector< Vector > &	dlist,
		unsigned	max_index = `0`
	)		const

inherited

Apply PBCs over a set of distance vectors.

◆ 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.

◆ buildDataStashes()

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( ActionWithVessel * actionThatUses )

inherited

Ensure that data required in other vessels is stored.

◆ buildSets()

void PLMD::multicolvar::MultiColvarBase::buildSets ( )

protectedinherited

Build sets by taking one multicolvar from each base.

◆ calculate()

void PLMD::multicolvar::MultiColvarBase::calculate ( )

overridevirtualinherited

Do the calculation.

Implements PLMD::Action.

◆ calculateAllVessels()

void PLMD::vesselbase::ActionWithVessel::calculateAllVessels	(	const unsigned &	taskCode,
		MultiValue &	myvals,
		MultiValue &	bvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)

protectedinherited

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

◆ 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.

◆ calculateForThreeAtoms()

void PLMD::adjmat::TopologyMatrix::calculateForThreeAtoms	(	const unsigned &	iat,
		const Vector &	d1,
		const double &	d1_len,
		HistogramBead &	bead,
		multicolvar::AtomValuePack &	myatoms
	)		const

Calculate the contribution from one of the atoms in the third element of the pack.

◆ 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::multicolvar::MultiColvarBase::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

overridevirtualinherited

Calculate numerical derivatives.

Reimplemented from PLMD::ActionAtomistic.

◆ calculateWeight()

double PLMD::adjmat::TopologyMatrix::calculateWeight	(	const unsigned &	taskCode,
		const double &	weight,
		multicolvar::AtomValuePack &	myatoms
	)		const

overridevirtual

This actually calculates the value of the contact function.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ changeBox()

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

inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

◆ 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

◆ 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::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )

inherited

◆ 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.

◆ compute()

double PLMD::adjmat::TopologyMatrix::compute	(	const unsigned &	tindex,
		multicolvar::AtomValuePack &	myatoms
	)		const

overridevirtual

This does nothing.

Implements PLMD::multicolvar::MultiColvarBase.

◆ 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.

◆ deactivateAllTasks()

void PLMD::vesselbase::ActionWithVessel::deactivateAllTasks ( )

protectedinherited

Deactivate all the tasks in the task list.

◆ decodeIndexToAtoms()

void PLMD::multicolvar::MultiColvarBase::decodeIndexToAtoms	(	const unsigned &	taskCode,
		std::vector< unsigned > &	atoms
	)		const

protectedinherited

Decode indices if there are 2 or 3 atoms involved.

◆ derivativesAreRequired()

bool PLMD::vesselbase::ActionWithVessel::derivativesAreRequired ( ) const

inlineinherited

Are derivatives required for this quantity.

◆ doJobsRequiredBeforeTaskList()

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )

virtualinherited

Do any jobs that are required before the task list is undertaken.

Reimplemented in PLMD::manyrestraints::ManyRestraintsBase, PLMD::multicolvar::VolumeGradientBase, and PLMD::multicolvar::MultiColvarFilter.

◆ doNotCalculateDerivatives()

bool PLMD::multicolvar::MultiColvarBase::doNotCalculateDerivatives ( ) const

inlineoverridevirtualinherited

Ensure that derivatives are only calculated when needed.

Reimplemented from PLMD::ActionWithValue.

◆ doNotCalculateDirector()

virtual void PLMD::multicolvar::MultiColvarBase::doNotCalculateDirector ( )

inlinevirtualinherited

This makes sure we are not calculating the director when we do LocalAverage.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

◆ 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.

◆ 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.

◆ filtersUsedAsInput()

bool PLMD::multicolvar::MultiColvarBase::filtersUsedAsInput ( )

protectedinherited

Function that recursively checks if filters have been used in the input to a multicolvar we need this to ensure that setupLinkCells is run in calculate with some actions.

◆ finishComputations()

void PLMD::vesselbase::ActionWithVessel::finishComputations ( const std::vector< double > & buffer )

virtualinherited

Finish running all the calculations.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ finishMatrixSetup()

void PLMD::adjmat::AdjacencyMatrixBase::finishMatrixSetup	(	const bool &	symmetric,
		const std::vector< AtomNumber > &	all_atoms
	)

privateinherited

Finish the setup of the matrix.

◆ 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)

◆ 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.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getAbsoluteIndexOfCentralAtom()

AtomNumber PLMD::adjmat::AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom ( const unsigned & i ) const

inlinevirtualinherited

Get the atom number.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ getActiveTask()

unsigned PLMD::vesselbase::ActionWithVessel::getActiveTask ( const unsigned & ii ) const

inlineinherited

Get the ith of the currently active tasks.

◆ getAdjacencyVessel()

AdjacencyMatrixVessel * PLMD::adjmat::AdjacencyMatrixBase::getAdjacencyVessel ( )

inlineprotectedinherited

Retrieve the vessel that holds the adjacency matrix.

◆ getBaseColvarNumber()

unsigned PLMD::adjmat::AdjacencyMatrixBase::getBaseColvarNumber ( const unsigned & inum ) const

inlineprotectedinherited

Return the group this atom is a part of.

◆ getBaseMultiColvar()

MultiColvarBase * PLMD::multicolvar::MultiColvarBase::getBaseMultiColvar ( const unsigned & icolv ) const

inlineinherited

Get the icolv th base multicolvar.

◆ getBox()

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

inlineinherited

Get box shape.

◆ getCentralAtom()

Vector PLMD::adjmat::AdjacencyMatrixBase::getCentralAtom ( )

inlineinherited

◆ getCentralAtomPack()

void PLMD::multicolvar::MultiColvarBase::getCentralAtomPack	(	const unsigned &	basn,
		const unsigned &	curr,
		CatomPack &	mypack
	)

virtualinherited

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getCentralAtomPos()

Vector PLMD::multicolvar::MultiColvarBase::getCentralAtomPos ( const unsigned & curr )

virtualinherited

Get the index where the central atom is stored.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ 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

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentNumberOfActiveTasks ( ) const

inlineinherited

Get the number of tasks that are currently active.

◆ getDefaultString()

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

inlineinherited

Get the defaults.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ 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.

◆ getForcesFromVessels()

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > & forcesToApply )

protectedinherited

Retrieve the forces from all the vessels (used in apply)

◆ getFullNumberOfTasks()

unsigned PLMD::vesselbase::ActionWithVessel::getFullNumberOfTasks ( ) const

inlineinherited

Get the full size of the taskList dynamic list.

◆ getGlobalPosition()

const Vector & PLMD::ActionAtomistic::getGlobalPosition ( AtomNumber i ) 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.

◆ getInputData()

void PLMD::multicolvar::MultiColvarBase::getInputData	(	const unsigned &	ind,
		const bool &	normed,
		const multicolvar::AtomValuePack &	myatoms,
		std::vector< double > &	orient
	)		const

virtualinherited

Get an input data.

Reimplemented in PLMD::adjmat::ClusterWithSurface, and PLMD::adjmat::ActionWithInputMatrix.

◆ getInputDerivatives()

MultiValue & PLMD::multicolvar::MultiColvarBase::getInputDerivatives	(	const unsigned &	iatom,
		const bool &	normed,
		const multicolvar::AtomValuePack &	myatoms
	)		const

virtualinherited

Retrieve the input derivatives.

Reimplemented in PLMD::adjmat::ClusterWithSurface, and PLMD::adjmat::ActionWithInputMatrix.

◆ 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.

◆ getLinkCellCutoff()

double PLMD::multicolvar::MultiColvarBase::getLinkCellCutoff ( ) const

protectedinherited

Get the cutoff for the link cells.

◆ getMass()

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

inlineinherited

Get mass of i-th atom.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNLTolerance()

double PLMD::vesselbase::ActionWithVessel::getNLTolerance ( ) const

inlineprotectedinherited

Return the value for the neighbor list tolerance.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfBaseMultiColvars()

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfBaseMultiColvars ( ) const

inlineinherited

Get the number of base multicolvars.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

◆ getNumberOfNodeTypes()

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

protectedinherited

Get the number of nodes of different types.

◆ getNumberOfQuantities()

unsigned PLMD::adjmat::TopologyMatrix::getNumberOfQuantities ( ) const

overridevirtual

Get the number of quantities that we must compute.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ getNumberOfVessels()

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const

inlineinherited

Get the number of vessels.

◆ 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.

◆ 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 ( )

protectedinherited

Get a pointer to the default value.

◆ getPntrToVessel()

Vessel * PLMD::vesselbase::ActionWithVessel::getPntrToVessel ( const unsigned & i )

inlineinherited

Get a pointer to the ith vessel.

◆ getPosition()

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

inlineinherited

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

◆ getPositionInCurrentTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInCurrentTaskList ( const unsigned & myind ) const

inlineinherited

Return the position in the current task list.

◆ getPositionInFullTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInFullTaskList ( const unsigned & ii ) const

inlineinherited

Get the position of the ith active task in the full list.

◆ getPositionOfAtomForLinkCells()

Vector PLMD::multicolvar::MultiColvarBase::getPositionOfAtomForLinkCells ( const unsigned & iatom ) const

inlinevirtualinherited

This gets the position of an atom for the link cell setup.

Reimplemented in PLMD::adjmat::ClusterWithSurface, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, and PLMD::adjmat::ClusterAnalysisBase.

◆ getPositions()

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

inlineinherited

Get the array of all positions.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSeparation()

Vector PLMD::multicolvar::MultiColvarBase::getSeparation	(	const Vector &	vec1,
		const Vector &	vec2
	)		const

inherited

Get the separation between a pair of vectors.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::ActionWithVessel::getSizeOfBuffer ( unsigned & bufsize )

protectedinherited

Get the size of the buffer.

◆ getSizeOfInputVectors()

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

protectedinherited

Get the size of the vectors that were stored in the base colvars.

◆ getStep()

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

inherited

Return the present timestep.

◆ getTaskCode()

unsigned PLMD::vesselbase::ActionWithVessel::getTaskCode ( const unsigned & ii ) const

inlineinherited

Get the code for the ii th task in the list.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTolerance()

double PLMD::vesselbase::ActionWithVessel::getTolerance ( ) const

inlineprotectedinherited

Return the value of the tolerance.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

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

◆ getVesselWithName()

Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string & mynam )

inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ hasDifferentiableOrientation()

virtual bool PLMD::multicolvar::MultiColvarBase::hasDifferentiableOrientation ( ) const

inlinevirtualinherited

This is true if multicolvar is calculating a vector or if the multicolvar is the density.

Reimplemented in PLMD::multicolvar::Density, and PLMD::crystallization::VectorMultiColvar.

◆ interpretAtomList()

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

inherited

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

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isCurrentlyActive()

bool PLMD::multicolvar::MultiColvarBase::isCurrentlyActive ( const unsigned & code )

inlinevirtualinherited

Checks if an task is being performed at the present time.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ isDensity()

virtual bool PLMD::multicolvar::MultiColvarBase::isDensity ( ) const

inlinevirtualinherited

Is this a density?

Reimplemented in PLMD::multicolvar::DistanceFromContour, and PLMD::multicolvar::Density.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ isPeriodic()

bool PLMD::adjmat::AdjacencyMatrixBase::isPeriodic ( )

inlinevirtualinherited

None of these things are allowed.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )

inherited

◆ lockRequests()

void PLMD::ActionAtomistic::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

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

◆ mergeInputDerivatives()

void PLMD::multicolvar::MultiColvarBase::mergeInputDerivatives	(	const unsigned &	ival,
		const unsigned &	start,
		const unsigned &	end,
		const unsigned &	jatom,
		const std::vector< double > &	der,
		MultiValue &	myder,
		AtomValuePack &	myatoms
	)		const

protectedinherited

This routine take the vector of input derivatives and adds all the vectors to ivalth output derivatives In other words end-start sets of derivatives come in and one set of derivatives come out.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

◆ modifyForceOnExtraCV()

double & PLMD::ActionAtomistic::modifyForceOnExtraCV ( )

inlineinherited

Get a reference to force on extraCV.

◆ modifyForces()

std::vector< Vector > & PLMD::ActionAtomistic::modifyForces ( )

inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

Vector & PLMD::ActionAtomistic::modifyGlobalForce ( AtomNumber i )

inlineinherited

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

Warning: Should be used by action that need to modify the stored atomic forces. This should be used with great care since the plumed core does not usually keep all these forces up to date. In particular, if an action require this, one should during constructor call allowToAccessGlobalForces(). Notice that for efficiency reason plumed does not check if this is done!

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )

inlineinherited

Get modifiable PBC Should be used by action that need to modify the stored box.

◆ modifyGlobalPosition()

Vector & PLMD::ActionAtomistic::modifyGlobalPosition ( AtomNumber i )

inlineinherited

Get modifiable 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.

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

Get modifiable virial Should be used by action that need to modify the stored virial.

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ needsDerivatives()

void PLMD::vesselbase::ActionWithVessel::needsDerivatives ( )

protectedinherited

Turn on the derivatives in the vessel.

◆ 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.

◆ normalizeVector()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVector ( std::vector< double > & vals ) const

inlinevirtualinherited

These normalizes vectors and is used in StoreDataVessel.

Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::MoleculeOrientation, and PLMD::crystallization::VectorMultiColvar.

◆ normalizeVectorDerivatives()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVectorDerivatives ( MultiValue & myvals ) const

inlinevirtualinherited

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::MoleculeOrientation, and PLMD::crystallization::VectorMultiColvar.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ 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.

◆ parseConnectionDescriptions()

void PLMD::adjmat::AdjacencyMatrixBase::parseConnectionDescriptions	(	const std::string &	key,
		const bool &	multiple,
		const unsigned &	nrow_t
	)

protectedinherited

Read in the information on the connectors.

◆ parseFlag()

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

inherited

Parse one keyword as boolean flag.

◆ parseMultiColvarAtomList()

bool PLMD::multicolvar::MultiColvarBase::parseMultiColvarAtomList	(	const std::string &	key,
		const int &	num,
		std::vector< AtomNumber > &	t
	)

protectedinherited

Read in some atoms.

◆ 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

inherited

Compute the pbc distance between two positions.

◆ performTask()

void PLMD::multicolvar::MultiColvarBase::performTask	(	const unsigned &	task_index,
		const unsigned &	current,
		MultiValue &	myvals
	)		const

overridevirtualinherited

Perform one of the tasks.

Implements PLMD::vesselbase::ActionWithVessel.

◆ prepare()

void PLMD::multicolvar::MultiColvarBase::prepare ( )

overridevirtualinherited

Do some setup before the calculation.

Reimplemented from PLMD::Action.

◆ 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.

◆ readAtomsLikeKeyword()

void PLMD::multicolvar::MultiColvarBase::readAtomsLikeKeyword	(	const std::string &	key,
		const int &	natoms,
		std::vector< AtomNumber > &	all_atoms
	)

protectedinherited

Read in ATOMS keyword.

◆ readGroupKeywords()

void PLMD::multicolvar::MultiColvarBase::readGroupKeywords	(	const std::string &	key0,
		const std::string &	key1,
		const std::string &	key2,
		const std::string &	key3,
		const bool &	no_third_dim_accum,
		const bool &	symmetric,
		std::vector< AtomNumber > &	all_atoms
	)

protectedinherited

Read in three groups of atoms.

◆ readMaxThreeSpeciesMatrix()

void PLMD::adjmat::AdjacencyMatrixBase::readMaxThreeSpeciesMatrix	(	const std::string &	key0,
		const std::string &	key1,
		const std::string &	key2,
		const std::string &	keym,
		const bool &	symmetric
	)

protectedinherited

Read in a matrix involving a maximum of three species.

◆ readMaxTwoSpeciesMatrix()

void PLMD::adjmat::AdjacencyMatrixBase::readMaxTwoSpeciesMatrix	(	const std::string &	key0,
		const std::string &	key1,
		const std::string &	key2,
		const bool &	symmetric
	)

protectedinherited

Read in a matrix involving a maximum of two species.

◆ readThreeGroups()

void PLMD::multicolvar::MultiColvarBase::readThreeGroups	(	const std::string &	key1,
		const std::string &	key2,
		const std::string &	key3,
		const bool &	allow2,
		const bool &	no_third_dim_accum,
		std::vector< AtomNumber > &	all_atoms
	)

protectedinherited

Read in three groups of atoms and construct CVs involving at least one.

◆ readTwoGroups()

void PLMD::multicolvar::MultiColvarBase::readTwoGroups	(	const std::string &	key0,
		const std::string &	key1,
		const std::string &	key2,
		std::vector< AtomNumber > &	all_atoms
	)

protectedinherited

Read in two groups of atoms and setup multicolvars to calculate.

◆ readVesselKeywords()

void PLMD::vesselbase::ActionWithVessel::readVesselKeywords ( )

protectedinherited

Complete the setup of this object (this routine must be called after construction of ActionWithValue)

◆ recalculateMatrixElement()

void PLMD::adjmat::AdjacencyMatrixBase::recalculateMatrixElement	(	const unsigned &	myelem,
		MultiValue &	myvals
	)

privateinherited

This is used within AdjacencyMatrixVessel to recalculate matrix elements which is useful when we are operating with lowmem.

◆ registerKeywords()

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

static

Create manual.

◆ 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

◆ resizeBookeepingArray()

void PLMD::multicolvar::MultiColvarBase::resizeBookeepingArray	(	const unsigned &	num1,
		const unsigned &	num2
	)

protectedinherited

This resizes the arrays that are used for link cell update.

◆ resizeFunctions()

void PLMD::vesselbase::ActionWithVessel::resizeFunctions ( )

protectedinherited

Resize all the functions when the number of derivatives change.

◆ retrieveAtoms()

void PLMD::multicolvar::MultiColvarBase::retrieveAtoms ( )

overridevirtualinherited

This is overwritten here in order to make sure that we do not retrieve atoms multiple times.

Reimplemented from PLMD::ActionAtomistic.

◆ retrieveDomain()

void PLMD::vesselbase::ActionWithVessel::retrieveDomain	(	std::string &	min,
		std::string &	max
	)

virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::multicolvar::Torsions, and PLMD::crystallization::InterMolecularTorsions.

◆ retrieveTypeDimensions()

void PLMD::adjmat::AdjacencyMatrixBase::retrieveTypeDimensions	(	unsigned &	nrows,
		unsigned &	ncols,
		unsigned &	ntype
	)		const

protectedinherited

Get the dimensions of the matrix of types.

◆ runAllTasks()

void PLMD::vesselbase::ActionWithVessel::runAllTasks ( )

protectedinherited

Calculate the values of all the vessels.

◆ 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.

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

◆ serialCalculation()

bool PLMD::vesselbase::ActionWithVessel::serialCalculation ( ) const

inlineprotectedinherited

Is the calculation being done in serial.

◆ setAtomsForCentralAtom()

void PLMD::multicolvar::MultiColvarBase::setAtomsForCentralAtom ( const std::vector< bool > & catom_ind )

protectedinherited

Set which atoms are to be used to calculate the central atom position.

◆ setExtraCV()

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

inlineprotectedinherited

◆ setForcesOnAtoms()

void PLMD::ActionAtomistic::setForcesOnAtoms	(	const std::vector< double > &	forcesToApply,
		unsigned	ind = `0`
	)

inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ setLinkCellCutoff()

void PLMD::multicolvar::MultiColvarBase::setLinkCellCutoff	(	const double &	lcut,
		double	tcut = `-1.0`
	)

protectedinherited

Set the value of the cutoff for the link cells.

◆ setLowMemOption()

void PLMD::vesselbase::ActionWithVessel::setLowMemOption ( const bool & l )

inlineprotectedinherited

Set that we are using low memory.

◆ setMatrixIndexesForTask()

void PLMD::adjmat::AdjacencyMatrixBase::setMatrixIndexesForTask ( const unsigned & ii )

protectedinherited

Put the indices of the matrix elements in current atoms.

◆ 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.

◆ setupActiveTaskSet()

void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet	(	std::vector< unsigned > &	active_tasks,
		const std::string &	input_label
	)

protectedinherited

Setup the link cells and neighbour list stuff.

◆ setupConnector()

void PLMD::adjmat::TopologyMatrix::setupConnector	(	const unsigned &	id,
		const unsigned &	i,
		const unsigned &	j,
		const std::vector< std::string > &	desc
	)

overridevirtual

Create the ith, ith switching function.

Implements PLMD::adjmat::AdjacencyMatrixBase.

◆ setupCurrentAtomList()

bool PLMD::multicolvar::MultiColvarBase::setupCurrentAtomList	(	const unsigned &	taskCode,
		AtomValuePack &	myatoms
	)		const

protectedinherited

This sets up the list of atoms that are involved in this colvar.

◆ setupLinkCells()

void PLMD::multicolvar::MultiColvarBase::setupLinkCells ( )

protectedinherited

Setup link cells in order to make this calculation faster.

◆ setupMultiColvarBase()

void PLMD::multicolvar::MultiColvarBase::setupMultiColvarBase ( const std::vector< AtomNumber > & atoms )

protectedinherited

Finish setting up the multicolvar base.

◆ setupNonUseSpeciesLinkCells()

void PLMD::multicolvar::MultiColvarBase::setupNonUseSpeciesLinkCells ( const unsigned & my_always_active )

protectedinherited

This does setup of link cell stuff that is specific to the non-use of the usespecies keyword.

◆ 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.

◆ splitInputDerivatives()

void PLMD::multicolvar::MultiColvarBase::splitInputDerivatives	(	const unsigned &	ival,
		const unsigned &	start,
		const unsigned &	end,
		const unsigned &	jatom,
		const std::vector< double > &	der,
		MultiValue &	myder,
		AtomValuePack &	myatoms
	)		const

protectedinherited

This routine take the ith set of input derivatives and adds it to each of the (end-start) output derivatives In other words one set of derivatives comes in and end-start sets of derivatives come out.

◆ storedValueIsActive()

bool PLMD::multicolvar::MultiColvarBase::storedValueIsActive ( const unsigned & iatom )

inherited

Is the iatom'th stored value currently active.

◆ taskIsCurrentlyActive()

bool PLMD::vesselbase::ActionWithVessel::taskIsCurrentlyActive ( const unsigned & index ) const

inherited

Check whether or not a particular task is currently active.

◆ threadSafe()

bool PLMD::multicolvar::MultiColvarBase::threadSafe ( ) const

inlineoverridevirtualinherited

Is it safe to use multithreading.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ transformBridgedDerivatives()

void PLMD::vesselbase::ActionWithVessel::transformBridgedDerivatives	(	const unsigned &	current,
		MultiValue &	invals,
		MultiValue &	outvals
	)		const

virtualinherited

Do the task if we have a bridge.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ turnOnDerivatives()

void PLMD::multicolvar::MultiColvarBase::turnOnDerivatives ( )

overridevirtualinherited

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ 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::bias::PBMetaD, PLMD::isdb::SAXS, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::PRE, PLMD::multicolvar::DumpMultiColvar, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, PLMD::gridtools::GridPrintingBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ updateActiveAtoms()

void PLMD::multicolvar::MultiColvarBase::updateActiveAtoms ( AtomValuePack & myatoms ) const

virtualinherited

Update the active atoms.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )

inherited

updates local unique atoms

◆ 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.

◆ usesPbc()

bool PLMD::multicolvar::MultiColvarBase::usesPbc ( ) const

inlineinherited

Do we use pbc to calculate this quantity.

◆ usingLowMem()

bool PLMD::vesselbase::ActionWithVessel::usingLowMem ( ) const

inlineprotectedinherited

Are we using low memory.

◆ warning()

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

inherited

Issue a warning.

◆ weightWithDerivatives()

bool PLMD::vesselbase::ActionWithVessel::weightWithDerivatives ( ) const

inlineinherited

Does the weight have derivatives.

Member Data Documentation

◆ ablocks

std::vector< std::vector<unsigned> > PLMD::multicolvar::MultiColvarBase::ablocks

protectedinherited

Blocks of atom numbers.

◆ actionIsBridged

bool PLMD::vesselbase::ActionWithVessel::actionIsBridged

privateinherited

This tells plumed that this is used in a bridge.

◆ 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.

◆ allthirdblockintasks

bool PLMD::multicolvar::MultiColvarBase::allthirdblockintasks

privateinherited

We use this to say that all the atoms in the third block should are in the tasks.

◆ atom_lab

std::vector< std::pair<unsigned,unsigned> > PLMD::multicolvar::MultiColvarBase::atom_lab

protectedinherited

This is used to keep track of what is calculated where.

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

◆ atomsWereRetrieved

bool PLMD::multicolvar::MultiColvarBase::atomsWereRetrieved

privateinherited

Ensures that retrieving of atoms is only done once per calculation loop.

◆ beadrad

double PLMD::adjmat::TopologyMatrix::beadrad

private

◆ binw_mat

Matrix<double> PLMD::adjmat::TopologyMatrix::binw_mat

private

◆ bookeeping

Matrix<std::pair<unsigned,unsigned> > PLMD::multicolvar::MultiColvarBase::bookeeping

protectedinherited

This remembers where the boundaries are for the tasks. It makes link cells work fast.

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

◆ buffer

std::vector<double> PLMD::vesselbase::ActionWithVessel::buffer

privateinherited

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

◆ cell_volume

Matrix<double> PLMD::adjmat::TopologyMatrix::cell_volume

private

The volume of the cells.

◆ charges

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

privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ connect_id

unsigned PLMD::adjmat::AdjacencyMatrixBase::connect_id

privateinherited

Used for read in of multiple connection descriptors.

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

◆ cylinder_sw

Matrix<SwitchingFunction> PLMD::adjmat::TopologyMatrix::cylinder_sw

private

◆ decoder

std::vector<unsigned> PLMD::multicolvar::MultiColvarBase::decoder

protectedinherited

This is used when turning cvcodes into atom numbers.

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ der_list

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::der_list

privateinherited

The list of atoms involved in derivatives (we keep a copy here to avoid resizing)

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime

protectedinherited

This is also used to minimise computational expense in complex functions.

◆ dertime_can_be_off

bool PLMD::vesselbase::ActionWithVessel::dertime_can_be_off

privateinherited

These are used to minmise computational expense in complex functions.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

◆ energy

double PLMD::ActionAtomistic::energy

privateinherited

◆ extraCV

std::string PLMD::ActionAtomistic::extraCV

privateinherited

◆ files

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

inherited

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

◆ forces

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

privateinherited

◆ forcesToApply

std::vector<double> PLMD::multicolvar::MultiColvarBase::forcesToApply

privateinherited

The forces we are going to apply to things.

◆ fullTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::fullTaskList

privateinherited

Ths full list of tasks we have to perform.

◆ functions

std::vector<std::unique_ptr<Vessel> > PLMD::vesselbase::ActionWithVessel::functions

privateinherited

Pointers to the functions we are using on each value.

◆ indexes

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

privateinherited

◆ indexOfTaskInFullList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::indexOfTaskInFullList

privateinherited

The indices of the tasks in the full list of tasks.

◆ kerneltype

std::string PLMD::adjmat::TopologyMatrix::kerneltype

private

◆ 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::multicolvar::MultiColvarBase::linkcells

privateinherited

Stuff for link cells - this is used to make coordination number like variables faster.

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ low_sf

Matrix<SwitchingFunction> PLMD::adjmat::TopologyMatrix::low_sf

private

◆ lowmem

bool PLMD::vesselbase::ActionWithVessel::lowmem

privateinherited

Lower memory requirements.

◆ lsfmax

double PLMD::adjmat::TopologyMatrix::lsfmax

private

◆ masses

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

privateinherited

◆ mat

AdjacencyMatrixVessel* PLMD::adjmat::AdjacencyMatrixBase::mat

privateinherited

This is the vessel that stores the adjacency matrix.

◆ matsums

bool PLMD::multicolvar::MultiColvarBase::matsums

protectedinherited

Are we doing sums of matrix rows.

◆ maxbins

unsigned PLMD::adjmat::TopologyMatrix::maxbins

private

The maximum number of bins that will be used This is calculated based on the dmax of the switching functions.

◆ maxderivatives

unsigned PLMD::vesselbase::ActionWithVessel::maxderivatives

privateinherited

The maximum number of derivatives we can use before we need to invoke lowmem.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ my_tmp_capacks

std::vector<CatomPack> PLMD::multicolvar::MultiColvarBase::my_tmp_capacks

privateinherited

Vector of tempory holders for central atom values.

◆ mybasedata

std::vector<vesselbase::StoreDataVessel*> PLMD::multicolvar::MultiColvarBase::mybasedata

protectedinherited

The vessels in these multicolvars in which the data is stored.

◆ mybasemulticolvars

std::vector<MultiColvarBase*> PLMD::multicolvar::MultiColvarBase::mybasemulticolvars

protectedinherited

The multicolvars from which we construct these quantities.

◆ mydata

StoreDataVessel* PLMD::vesselbase::ActionWithVessel::mydata

protectedinherited

A pointer to the object that stores data.

◆ nactive_atoms

unsigned PLMD::multicolvar::MultiColvarBase::nactive_atoms

privateinherited

Number of atoms that are active on this step.

◆ nactive_tasks

unsigned PLMD::vesselbase::ActionWithVessel::nactive_tasks

privateinherited

The current number of active tasks.

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ nblock

unsigned PLMD::multicolvar::MultiColvarBase::nblock

protectedinherited

Number of atoms in each block.

◆ ncentral

unsigned PLMD::multicolvar::MultiColvarBase::ncentral

privateinherited

Number of atoms that are being used for central atom position.

◆ nl_tolerance

double PLMD::vesselbase::ActionWithVessel::nl_tolerance

privateinherited

Tolerance for quantities being put in neighbor lists.

◆ no_third_dim_accum

bool PLMD::adjmat::AdjacencyMatrixBase::no_third_dim_accum

privateinherited

Do we need to separate out the tasks for the third atoms.

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ numberForCentralAtom

double PLMD::multicolvar::MultiColvarBase::numberForCentralAtom

privateinherited

1/number of atoms involved in central atoms

◆ 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.

◆ partialTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::partialTaskList

privateinherited

The list of currently active tasks.

◆ 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

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ serial

bool PLMD::vesselbase::ActionWithVessel::serial

privateinherited

Do all calculations in serial.

◆ setup_completed

bool PLMD::multicolvar::MultiColvarBase::setup_completed

privateinherited

Ensures that setup is only performed once per loop.

◆ sigma

double PLMD::adjmat::TopologyMatrix::sigma

private

The width to use for the kernel density estimation and the sizes of the bins to be used in kernel density estimation.

◆ stopwatch

Stopwatch& PLMD::vesselbase::ActionWithVessel::stopwatch =*stopwatch_fwd

privateinherited

The stopwatch that times the different parts of the calculation.

◆ stopwatch_fwd

ForwardDecl<Stopwatch> PLMD::vesselbase::ActionWithVessel::stopwatch_fwd

privateinherited

◆ switchingFunction

Matrix<SwitchingFunction> PLMD::adjmat::TopologyMatrix::switchingFunction

private

switching function

◆ taskFlags

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::taskFlags

protectedinherited

This list is used to update the neighbor list.

◆ threecells

LinkCells PLMD::multicolvar::MultiColvarBase::threecells

privateinherited

Link cells for third block of atoms.

◆ threshold_switch

SwitchingFunction PLMD::adjmat::TopologyMatrix::threshold_switch

private

◆ timers

bool PLMD::vesselbase::ActionWithVessel::timers

privateinherited

Do we want to output information on the timings of different parts of the calculation.

◆ tmpforces

std::vector<double> PLMD::vesselbase::ActionWithVessel::tmpforces

privateinherited

Tempory storage for forces.

◆ tolerance

double PLMD::vesselbase::ActionWithVessel::tolerance

privateinherited

The tolerance on the accumulators.

◆ 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 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.

◆ use_for_central_atom

std::vector<bool> PLMD::multicolvar::MultiColvarBase::use_for_central_atom

privateinherited

Bool vector telling us which atoms are required to calculate central atom position.

◆ uselinkforthree

bool PLMD::multicolvar::MultiColvarBase::uselinkforthree

privateinherited

In certain cases we can make three atom link cells faster.

◆ usepbc

bool PLMD::multicolvar::MultiColvarBase::usepbc

privateinherited

Use periodic boundary conditions.

◆ usespecies

bool PLMD::multicolvar::MultiColvarBase::usespecies

protectedinherited

Using the species keyword to read in atoms.

◆ values

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

privateinherited

An array containing the values for this action.

◆ virial

Tensor PLMD::ActionAtomistic::virial

privateinherited

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

adjmat/TopologyMatrix.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

◆ TopologyMatrix()

Member Function Documentation

◆ accumulateSymmetryFunction()

◆ activate()

◆ addAtomDerivatives()

◆ addBridgingVessel()

◆ addComDerivatives()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addDerivativesOnMatrixElement()

◆ addTaskToList()

◆ addValue()

◆ addValueWithDerivatives()

◆ addVessel() [1/2]

◆ addVessel() [2/2]

◆ allowToAccessGlobalForces()

◆ apply()

◆ applyBridgeForces()

◆ applyForces()

◆ applyPbc()

◆ beforeUpdate()

◆ buildDataStashes()

◆ buildSets()

◆ calculate()

◆ calculateAllVessels()

◆ calculateAtomicNumericalDerivatives()

◆ calculateForThreeAtoms()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateWeight()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ clearOutputForces()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ compute()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ deactivateAllTasks()

◆ decodeIndexToAtoms()

◆ derivativesAreRequired()

◆ doJobsRequiredBeforeTaskList()

◆ doNotCalculateDerivatives()

◆ doNotCalculateDirector()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ filtersUsedAsInput()

◆ finishComputations()

◆ finishMatrixSetup()

◆ fopen()