Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::adjmat::TopologyMatrix Class Reference

Provides the keyword TOPOLOGY_MATRIX More...

Inheritance diagram for PLMD::adjmat::TopologyMatrix:
Inheritance graph
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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...
 
virtual void apply ()
 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...
 
StoreDataVesselbuildDataStashes (ActionWithVessel *actionThatUses)
 Ensure that data required in other vessels is stored. More...
 
virtual void calculate ()
 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...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Calculate numerical derivatives. More...
 
double calculateWeight (const unsigned &taskCode, const double &weight, multicolvar::AtomValuePack &myatoms) const
 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...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. 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
 This does nothing. More...
 
ValuecopyOutput (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...
 
ValuecopyOutput (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
 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...
 
MultiColvarBasegetBaseMultiColvar (const unsigned &icolv) const
 Get the icolv th base multicolvar. More...
 
const TensorgetBox () 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...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual std::string getDocumentation () const
 
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 VectorgetGlobalPosition (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 MultiValuegetInputDerivatives (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...
 
virtual unsigned getNumberOfDerivatives ()
 Get the number of derivatives for this action. More...
 
unsigned getNumberOfQuantities () const
 Get the number of quantities that we must compute. More...
 
unsigned getNumberOfVessels () const
 Get the number of vessels. More...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. 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...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
const VectorgetPosition (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 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::set< AtomNumber > & getUnique () const
 
const std::set< AtomNumber > & getUniqueLocal () const
 
VesselgetVesselWithName (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 ()
 
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...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force of i-th atom (access by absolute AtomNumber). More...
 
PbcmodifyGlobalPbc ()
 Get modifiable PBC Should be used by action that need to modify the stored box. More...
 
VectormodifyGlobalPosition (AtomNumber)
 Get modifiable position of i-th atom (access by absolute AtomNumber). More...
 
TensormodifyGlobalVirial ()
 Get modifiable virial Should be used by action that need to modify the stored virial. More...
 
TensormodifyVirial ()
 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, std::vector< AtomNumber > &t)
 Parse a list of atoms without a numbered keyword. 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 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...
 
virtual void performTask (const unsigned &, const unsigned &, MultiValue &) const
 Perform one of the tasks. More...
 
void prepare ()
 Do some setup before the calculation. More...
 
void readAtomsFromPDB (const PDB &pdb)
 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 ()
 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)
 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
 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 ()
 Turn on the derivatives. More...
 
void unlockRequests ()
 
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

Communicatorcomm
 
std::set< FILE * > files
 
const Keywordskeywords
 
Loglog
 Reference to the log stream. More...
 
Communicatormulti_sim_comm
 
PlumedMainplumed
 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...
 
BridgeVesseladdBridgingVessel (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...
 
AdjacencyMatrixVesselgetAdjacencyVessel ()
 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...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToValue ()
 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...
 
Atomsatoms
 
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...
 
StoreDataVesselmydata
 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 Attributes

double beadrad
 
Matrix< double > binw_mat
 
Matrix< double > cell_volume
 The volume of the cells. More...
 
Matrix< SwitchingFunctioncylinder_sw
 
std::string kerneltype
 
Matrix< SwitchingFunctionlow_sf
 
double lsfmax
 
unsigned maxbins
 The maximum number of bins that will be used This is calculated based on the dmax of the switching functions. 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...
 
Matrix< SwitchingFunctionswitchingFunction
 switching function More...
 
SwitchingFunction threshold_switch
 

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.

◆ 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 ( )
virtualinherited

◆ 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 ( )
virtualinherited

◆ 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)
virtualinherited

Calculate numerical derivatives.

Reimplemented from PLMD::ActionAtomistic.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ calculateWeight()

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

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

◆ 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]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const
inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ 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
virtual

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
inlinevirtualinherited

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.

◆ 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

◆ 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.

◆ 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.

◆ getDependencies()

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

Return dependencies.

◆ getDocumentation()

std::string PLMD::Action::getDocumentation ( ) const
virtualinherited

◆ 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 ( )
inlinevirtualinherited

◆ getNumberOfNodeTypes()

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

Get the number of nodes of different types.

◆ getNumberOfQuantities()

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

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 unsigned  j) const
inlineinherited

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

◆ getOutputQuantity() [2/2]

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)

◆ getPbc()

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

Get reference to Pbc.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the value by name.

◆ 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

◆ 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 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::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const
inlineinherited

◆ getUniqueLocal()

const std::set< 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::crystallization::VectorMultiColvar, and PLMD::multicolvar::Density.

◆ 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 ( )
inlinevirtualinherited

◆ 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

◆ normalizeVectorDerivatives()

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

◆ 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,
std::vector< AtomNumber > &  t 
)
inherited

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

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.

◆ 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
virtualinherited

◆ prepare()

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

Do some setup before the calculation.

Reimplemented from PLMD::Action.

◆ readAtomsFromPDB()

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

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)

◆ 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 ( )
virtualinherited

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::crystallization::InterMolecularTorsions, and PLMD::multicolvar::Torsions.

◆ 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 
)
virtual

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
inlinevirtualinherited

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 ( )
virtualinherited

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )
inlinevirtualinherited

◆ update()

virtual void PLMD::Action::update ( )
inlinevirtualinherited

◆ 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.

◆ 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

◆ 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.

◆ cell_volume

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

The volume of the cells.

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ 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.

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime
protectedinherited

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

◆ files

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

◆ kerneltype

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

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ low_sf

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

◆ lsfmax

double PLMD::adjmat::TopologyMatrix::lsfmax
private

◆ 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.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ 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.

◆ nblock

unsigned PLMD::multicolvar::MultiColvarBase::nblock
protectedinherited

Number of atoms in each block.

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ 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.

◆ 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.

◆ threshold_switch

SwitchingFunction PLMD::adjmat::TopologyMatrix::threshold_switch
private

◆ usespecies

bool PLMD::multicolvar::MultiColvarBase::usespecies
protectedinherited

Using the species keyword to read in atoms.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives
protectedinherited

Does the weight have derivatives.


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