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

Provides the keyword CLUSTER_NATOMS More...

Inheritance diagram for PLMD::adjmat::ClusterSize:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 ClusterSize (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...
 
StoreDataVesselbuildDataStashes (ActionWithVessel *actionThatUses)
 Ensure that data required in other vessels is stored. More...
 
void calculate () override
 Calculate an Action. 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 calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL) override
 Calculate numerical derivatives. More...
 
virtual double calculateWeight (const unsigned &taskCode, const double &weight, AtomValuePack &myatoms) const
 You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations. 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 is replaced once we have a function to calculate the cv. 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 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...
 
virtual AtomNumber getAbsoluteIndexOfCentralAtom (const unsigned &i) const
 Get the absolute index of the central atom. 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...
 
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...
 
unsigned getNumberOfDerivatives () override
 Get the number of derivatives for this action. More...
 
unsigned getNumberOfQuantities () const override
 Get the number of quantities that are calculated during each task. 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 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...
 
Vector getPositionOfAtomForLinkCells (const unsigned &) const override
 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 () override
 Are the base quantities periodic. 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...
 
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, 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 &task_index, const unsigned &current, MultiValue &myvals) const override
 Calculate one of the functions in the distribution. 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 setupActiveTaskSet (std::vector< unsigned > &active_tasks, const std::string &input_label)
 
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
 Activate the calculation of 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

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 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)
 
bool areConnected (const unsigned &ind1, const unsigned &ind2) const
 
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...
 
double getCutoffForConnection () const
 
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...
 
void getNodePropertyDerivatives (const unsigned &ind, MultiValue &myvals) const
 
unsigned getNumberOfClusters () const
 
unsigned getNumberOfNodes () const
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void getPropertiesOfNode (const unsigned &ind, std::vector< double > &vals) const
 
unsigned getSizeOfBuffer (unsigned &bufsize)
 Get the size of the buffer. 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...
 
bool nodeIsActive (const unsigned &ind) const
 
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 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 retrieveAtomsInCluster (const unsigned &clust, std::vector< unsigned > &myatoms) const
 
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...
 
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 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...
 
int getComponent (const std::string &name) const
 Return the index for the component named name. 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...
 
std::vector< double > buffer
 The buffer that we use (we keep a copy here to avoid resizing) More...
 
std::vector< double > charges
 
bool chargesWereSet
 
unsigned clustr
 The cluster we are looking for. 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< Vectorforces
 
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< AtomNumberindexes
 
std::vector< unsigned > indexOfTaskInFullList
 The indices of the tasks in the full list of tasks. More...
 
std::string label
 Label of the Action, as set with LABEL= in the plumed.dat file. More...
 
std::vector< std::string > line
 Directive line. More...
 
LinkCells linkcells
 Stuff for link cells - this is used to make coordination number like variables faster. More...
 
bool lockRequestAtoms
 
bool lowmem
 Lower memory requirements. More...
 
std::vector< double > masses
 
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...
 
ClusteringBasemyclusters
 
multicolvar::AtomValuePack myfatoms
 
MultiValue myfvals
 
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 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...
 
Pbcpbc =*pbc_fwd
 
ForwardDecl< Pbcpbc_fwd
 
std::vector< Vectorpositions
 
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...
 
Stopwatchstopwatch =*stopwatch_fwd
 The stopwatch that times the different parts of the calculation. More...
 
ForwardDecl< Stopwatchstopwatch_fwd
 
LinkCells threecells
 Link cells for third block of atoms. More...
 
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::set< AtomNumberunique
 unique should be an ordered set since we later create a vector containing the corresponding indexes More...
 
std::set< AtomNumberunique_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 CLUSTER_NATOMS

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ ClusterSize()

PLMD::adjmat::ClusterSize::ClusterSize ( 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.

◆ 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.

◆ areConnected()

bool PLMD::adjmat::ClusterAnalysisBase::areConnected ( const unsigned &  ind1,
const unsigned &  ind2 
) const
protectedinherited

◆ 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::adjmat::ClusterSize::calculate ( )
overridevirtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

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.

◆ 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::multicolvar::MultiColvarBase::calculateWeight ( const unsigned &  taskCode,
const double &  weight,
AtomValuePack myatoms 
) const
virtualinherited

◆ 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::ClusterAnalysisBase::compute ( const unsigned &  tindex,
multicolvar::AtomValuePack myatoms 
) const
inlineoverridevirtualinherited

This is replaced once we have a function to calculate the cv.

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.

◆ 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::multicolvar::MultiColvarBase::getAbsoluteIndexOfCentralAtom ( const unsigned &  i) const
inlinevirtualinherited

◆ getActiveTask()

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

Get the ith of the currently active tasks.

◆ 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.

◆ 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.

◆ 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.

◆ getCutoffForConnection()

double PLMD::adjmat::ClusterAnalysisBase::getCutoffForConnection ( ) const
protectedinherited

◆ 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.

◆ getNodePropertyDerivatives()

void PLMD::adjmat::ClusterAnalysisBase::getNodePropertyDerivatives ( const unsigned &  ind,
MultiValue myvals 
) const
protectedinherited

◆ 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.

◆ getNumberOfClusters()

unsigned PLMD::adjmat::ClusterAnalysisBase::getNumberOfClusters ( ) const
protectedinherited

◆ 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.

◆ getNumberOfNodes()

unsigned PLMD::adjmat::ClusterAnalysisBase::getNumberOfNodes ( ) const
protectedinherited

◆ getNumberOfQuantities()

unsigned PLMD::adjmat::ClusterAnalysisBase::getNumberOfQuantities ( ) const
overridevirtualinherited

Get the number of quantities that are calculated during each task.

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::adjmat::ClusterAnalysisBase::getPositionOfAtomForLinkCells ( const unsigned &  iatom) const
overridevirtualinherited

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

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ getPositions()

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

Get the array of all positions.

◆ getPropertiesOfNode()

void PLMD::adjmat::ClusterAnalysisBase::getPropertiesOfNode ( const unsigned &  ind,
std::vector< double > &  vals 
) const
protectedinherited

◆ 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.

◆ 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::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::ClusterAnalysisBase::isPeriodic ( )
overridevirtualinherited

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

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

◆ lockRequests()

void PLMD::ActionAtomistic::lockRequests ( )
inlineoverridevirtualinherited

◆ 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.

◆ nodeIsActive()

bool PLMD::adjmat::ClusterAnalysisBase::nodeIsActive ( const unsigned &  ind) const
protectedinherited

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

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

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

Parse a list of atoms without a numbered keyword.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ 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::adjmat::ClusterSize::performTask ( const unsigned &  ,
const unsigned &  ,
MultiValue  
) const
inlineoverridevirtual

Calculate one of the functions in the distribution.

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.

◆ 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::ClusterSize::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.

◆ retrieveAtomsInCluster()

void PLMD::adjmat::ClusterAnalysisBase::retrieveAtomsInCluster ( const unsigned &  clust,
std::vector< unsigned > &  myatoms 
) const
protectedinherited

◆ 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.

◆ 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.

◆ 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::adjmat::ClusterAnalysisBase::setupActiveTaskSet ( std::vector< unsigned > &  active_tasks,
const std::string &  input_label 
)
inlineinherited

◆ 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::adjmat::ClusterSize::turnOnDerivatives ( )
overridevirtual

Activate the calculation of derivatives.

Reimplemented from PLMD::adjmat::ClusterAnalysisBase.

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )
inlineoverridevirtualinherited

◆ 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.

◆ 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.

◆ 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)

◆ charges

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

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet
privateinherited

◆ clustr

unsigned PLMD::adjmat::ClusterSize::clustr
private

The cluster we are looking for.

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

◆ decoder

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

This is used when turning cvcodes into atom numbers.

◆ 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.

◆ 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.

◆ lowmem

bool PLMD::vesselbase::ActionWithVessel::lowmem
privateinherited

Lower memory requirements.

◆ masses

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

◆ matsums

bool PLMD::multicolvar::MultiColvarBase::matsums
protectedinherited

Are we doing sums of matrix rows.

◆ 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.

◆ myclusters

ClusteringBase* PLMD::adjmat::ClusterAnalysisBase::myclusters
privateinherited

◆ mydata

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

A pointer to the object that stores data.

◆ myfatoms

multicolvar::AtomValuePack PLMD::adjmat::ClusterAnalysisBase::myfatoms
privateinherited

◆ myfvals

MultiValue PLMD::adjmat::ClusterAnalysisBase::myfvals
privateinherited

◆ 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.

◆ 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.

◆ 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

◆ 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.

◆ 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::set<AtomNumber> PLMD::ActionAtomistic::unique
privateinherited

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

◆ unique_local

std::set<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: