Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::multicolvar::ActionVolume Class Referenceabstract


This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box. More...

#include <ActionVolume.h>

Inheritance diagram for PLMD::multicolvar::ActionVolume:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 ActionVolume (const ActionOptions &)
 
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 addBridgeForces (const std::vector< double > &bb)
 Forces here are applied through the bridge. 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 an Action. More...
 
void applyBridgeForces (const std::vector< double > &bb) override
 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 calculateAllVolumes (const unsigned &curr, MultiValue &outvals) const override
 Calculate whats in the volume. More...
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
Vector calculateCentralAtomPosition ()
 This should not be called. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual double calculateNumberInside (const Vector &cpos, Vector &derivatives, Tensor &vir, std::vector< Vector > &refders) const =0
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL) override
 We need our own calculate numerical derivatives here. 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...
 
bool checkNumericalDerivatives () const override
 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...
 
void clearDerivatives () override
 Don't actually clear the derivatives when this is called from plumed main. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void clearOutputForces ()
 
void completeTask (const unsigned &curr, MultiValue &invals, MultiValue &outvals) const override
 Actually do what we are asked. More...
 
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, AtomValuePack &myvals) 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...
 
void deactivate_task (const unsigned &taskno)
 Routines that have to be defined so as not to have problems with virtual methods. More...
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
void doJobsRequiredBeforeTaskList () override
 Do jobs required before tasks are 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...
 
const std::vector< AtomNumber > & getAbsoluteIndexes () const override
 Get indicecs involved in this colvar. More...
 
AtomNumber getAbsoluteIndexOfCentralAtom (const unsigned &i) const override
 Get the 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...
 
unsigned getCentralAtomElementIndex ()
 
void getCentralAtomPack (const unsigned &basn, const unsigned &curr, CatomPack &mypack) override
 
Vector getCentralAtomPos (const unsigned &curr) override
 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...
 
void getIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)
 
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 each time. 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...
 
MultiColvarBasegetPntrToMultiColvar () const
 Get a pointer to the base multicolvar. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. 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 &iatom) 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...
 
unsigned getSizeOfAtomsWithDerivatives ()
 Get the size of the atoms with derivatives array. 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 inVolumeOfInterest (const unsigned &curr) const
 This calculates whether or not a particular is inside the box of interest this is used for neighbour list with volumes. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isCurrentlyActive (const unsigned &) override
 Is this atom currently being copied. 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
 Is the output quantity 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...
 
void normalizeVector (std::vector< double > &vals) const override
 These normalizes vectors and is used in StoreDataVessel. More...
 
void normalizeVectorDerivatives (MultiValue &myvals) const override
 
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...
 
void performTask (const unsigned &, const unsigned &, MultiValue &) 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...
 
Vector retrieveCentralAtomPos ()
 Get the central atom position. 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...
 
virtual void setupRegions ()=0
 Setup the regions that this is based on. More...
 
void setValue (Value *, double)
 Set the value. More...
 
bool storedValueIsActive (const unsigned &iatom)
 Is the iatom'th stored value currently active. More...
 
bool taskIsCurrentlyActive (const unsigned &index) const
 Check whether or not a particular task is currently active. More...
 
bool threadSafe () const override
 Is it safe to use multithreading. More...
 
void transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const override
 This does the task. More...
 
void turnOnDerivatives () override
 Check nothing impossible being done with 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)
 
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)
 
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 deactivateAllAtoms ()
 Deactivate all the atoms in the list. 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...
 
const TensorgetBox () const
 Get the cell box. More...
 
bool getForcesFromVessels (std::vector< double > &forcesToApply)
 Retrieve the forces from all the vessels (used in apply) More...
 
std::string getKernelType () const
 
double getLinkCellCutoff () const
 Get the cutoff for the link cells. More...
 
double getNLTolerance () const
 Return the value for the neighbor list tolerance. More...
 
const PbcgetPbc () const
 Get reference to Pbc. 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...
 
Vector getPosition (int iatom) const
 Get position of atom. More...
 
double getSigma () 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 parseMultiColvarAtomList (const std::string &key, const int &num, std::vector< AtomNumber > &t)
 Read in some atoms. More...
 
Vector pbcDistance (const Vector &v1, const Vector &v2) const
 Calculate distance between two points. 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 requestAtoms (const std::vector< AtomNumber > &atoms)
 Request the atoms. 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 runAllTasks ()
 Calculate the values of all the vessels. More...
 
bool serialCalculation () const
 Is the calculation being done in serial. More...
 
void setAtomActive (const unsigned &n)
 Activate the nth atom in the list. 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 setNumberInVolume (const unsigned &, const unsigned &, const double &, const Vector &, const Tensor &, const std::vector< Vector > &, MultiValue &) const
 Set the number in the volume. 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

std::string kerneltype
 The kernel type for this histogram. More...
 
bool not_in
 Are we interested in the area outside the colvar. More...
 
unsigned nquantities
 Number of quantities in use in this colvar. More...
 
double sigma
 The value of sigma. More...
 

Detailed Description


This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box.

You can use this to calculate the number of atoms inside that part or the average value of a quantity like the coordination number inside that part of the cell.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ ActionVolume()

PLMD::multicolvar::ActionVolume::ActionVolume ( const ActionOptions ao)
explicit

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.

◆ addBridgeForces()

void PLMD::multicolvar::VolumeGradientBase::addBridgeForces ( const std::vector< double > &  bb)
inherited

Forces here are applied through the bridge.

◆ 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.

◆ 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::BridgedMultiColvarFunction::apply ( )
inlineoverridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ applyBridgeForces()

void PLMD::multicolvar::BridgedMultiColvarFunction::applyBridgeForces ( const std::vector< double > &  bb)
overridevirtualinherited

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

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ 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::BridgedMultiColvarFunction::calculate ( )
inlineoverridevirtualinherited

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.

◆ calculateAllVolumes()

void PLMD::multicolvar::ActionVolume::calculateAllVolumes ( const unsigned &  curr,
MultiValue outvals 
) const
overridevirtual

Calculate whats in the volume.

Implements PLMD::multicolvar::VolumeGradientBase.

◆ 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.

◆ calculateCentralAtomPosition()

Vector PLMD::multicolvar::BridgedMultiColvarFunction::calculateCentralAtomPosition ( )
inlineinherited

This should not be called.

◆ 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

◆ calculateNumberInside()

virtual double PLMD::multicolvar::ActionVolume::calculateNumberInside ( const Vector cpos,
Vector derivatives,
Tensor vir,
std::vector< Vector > &  refders 
) const
pure virtual

◆ calculateNumericalDerivatives()

void PLMD::multicolvar::BridgedMultiColvarFunction::calculateNumericalDerivatives ( ActionWithValue a = NULL)
overridevirtualinherited

We need our own calculate numerical derivatives here.

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::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
inlineoverridevirtualinherited

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::multicolvar::BridgedMultiColvarFunction::clearDerivatives ( )
inlineoverridevirtualinherited

Don't actually clear the derivatives when this is called from plumed main.

They are calculated inside another action and clearing them would be bad

Reimplemented from PLMD::ActionWithValue.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )
inherited

◆ completeTask()

void PLMD::multicolvar::VolumeGradientBase::completeTask ( const unsigned &  curr,
MultiValue invals,
MultiValue outvals 
) const
overridevirtualinherited

Actually do what we are asked.

Implements PLMD::multicolvar::BridgedMultiColvarFunction.

◆ 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::multicolvar::BridgedMultiColvarFunction::compute ( const unsigned &  tindex,
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.

◆ deactivate_task()

void PLMD::multicolvar::BridgedMultiColvarFunction::deactivate_task ( const unsigned &  taskno)
inherited

Routines that have to be defined so as not to have problems with virtual methods.

◆ deactivateAllAtoms()

void PLMD::multicolvar::BridgedMultiColvarFunction::deactivateAllAtoms ( )
protectedinherited

Deactivate all the atoms in the list.

◆ 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::multicolvar::VolumeGradientBase::doJobsRequiredBeforeTaskList ( )
overridevirtualinherited

Do jobs required before tasks are undertaken.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ 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.

◆ 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::multicolvar::BridgedMultiColvarFunction::getAbsoluteIndexes ( ) const
inlineoverridevirtualinherited

Get indicecs involved in this colvar.

Reimplemented from PLMD::ActionAtomistic.

◆ getAbsoluteIndexOfCentralAtom()

AtomNumber PLMD::multicolvar::BridgedMultiColvarFunction::getAbsoluteIndexOfCentralAtom ( const unsigned &  i) const
inlineoverridevirtualinherited

Get the index of the central atom.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ 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::multicolvar::VolumeGradientBase::getBox ( ) const
inlineprotectedinherited

Get the cell box.

◆ getCentralAtomElementIndex()

unsigned PLMD::multicolvar::ActionVolume::getCentralAtomElementIndex ( )
inline

◆ getCentralAtomPack()

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

◆ getCentralAtomPos()

Vector PLMD::multicolvar::BridgedMultiColvarFunction::getCentralAtomPos ( const unsigned &  curr)
inlineoverridevirtualinherited

Get the index where the central atom is stored.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ 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.

◆ getIndexList()

void PLMD::multicolvar::BridgedMultiColvarFunction::getIndexList ( const unsigned &  ntotal,
const unsigned &  jstore,
const unsigned &  maxder,
std::vector< unsigned > &  indices 
)
inherited

◆ 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.

◆ getKernelType()

std::string PLMD::multicolvar::ActionVolume::getKernelType ( ) const
inlineprotected

◆ 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::BridgedMultiColvarFunction::getNumberOfDerivatives ( )
inlineoverridevirtualinherited

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

◆ getNumberOfQuantities()

unsigned PLMD::multicolvar::ActionVolume::getNumberOfQuantities ( ) const
inlineoverridevirtual

Get the number of quantities that are calculated each time.

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::multicolvar::VolumeGradientBase::getPbc ( ) const
inlineprotectedinherited

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.

◆ getPntrToMultiColvar()

MultiColvarBase * PLMD::multicolvar::BridgedMultiColvarFunction::getPntrToMultiColvar ( ) const
inlineinherited

Get a pointer to the base multicolvar.

◆ 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()

Vector PLMD::multicolvar::VolumeGradientBase::getPosition ( int  iatom) const
inlineprotectedinherited

Get position of atom.

◆ 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::BridgedMultiColvarFunction::getPositionOfAtomForLinkCells ( const unsigned &  iatom) const
inlineoverridevirtualinherited

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.

◆ 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.

◆ getSigma()

double PLMD::multicolvar::ActionVolume::getSigma ( ) const
inlineprotected

◆ getSizeOfAtomsWithDerivatives()

unsigned PLMD::multicolvar::BridgedMultiColvarFunction::getSizeOfAtomsWithDerivatives ( )
inlineinherited

Get the size of the atoms with derivatives array.

◆ 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::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)

◆ inVolumeOfInterest()

bool PLMD::multicolvar::ActionVolume::inVolumeOfInterest ( const unsigned &  curr) const

This calculates whether or not a particular is inside the box of interest this is used for neighbour list with volumes.

◆ isActive()

bool PLMD::Action::isActive ( ) const
inlineinherited

Check if action is active.

◆ isCurrentlyActive()

bool PLMD::multicolvar::BridgedMultiColvarFunction::isCurrentlyActive ( const unsigned &  code)
inlineoverridevirtualinherited

Is this atom currently being copied.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

◆ 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::multicolvar::BridgedMultiColvarFunction::isPeriodic ( )
overridevirtualinherited

Is the output quantity 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.

◆ normalizeVector()

void PLMD::multicolvar::BridgedMultiColvarFunction::normalizeVector ( std::vector< double > &  vals) const
inlineoverridevirtualinherited

These normalizes vectors and is used in StoreDataVessel.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ normalizeVectorDerivatives()

void PLMD::multicolvar::BridgedMultiColvarFunction::normalizeVectorDerivatives ( MultiValue myvals) const
inlineoverridevirtualinherited

◆ 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.

◆ 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::multicolvar::VolumeGradientBase::pbcDistance ( const Vector v1,
const Vector v2 
) const
inlineprotectedinherited

Calculate distance between two points.

◆ performTask()

void PLMD::multicolvar::BridgedMultiColvarFunction::performTask ( const unsigned &  ,
const unsigned &  ,
MultiValue  
) const
overridevirtualinherited

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::multicolvar::ActionVolume::registerKeywords ( Keywords keys)
static

◆ requestAtoms() [1/2]

void PLMD::multicolvar::VolumeGradientBase::requestAtoms ( const std::vector< AtomNumber > &  atoms)
protectedinherited

Request the atoms.

◆ requestAtoms() [2/2]

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.

◆ retrieveCentralAtomPos()

Vector PLMD::multicolvar::BridgedMultiColvarFunction::retrieveCentralAtomPos ( )
inherited

Get the central atom position.

◆ 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.

◆ 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.

◆ setAtomActive()

void PLMD::multicolvar::BridgedMultiColvarFunction::setAtomActive ( const unsigned &  n)
protectedinherited

Activate the nth atom in the list.

◆ 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.

◆ setNumberInVolume()

void PLMD::multicolvar::VolumeGradientBase::setNumberInVolume ( const unsigned &  ivol,
const unsigned &  curr,
const double &  weight,
const Vector wdf,
const Tensor virial,
const std::vector< Vector > &  refders,
MultiValue outvals 
) const
protectedinherited

Set the number in the volume.

◆ 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.

◆ 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.

◆ setupRegions()

virtual void PLMD::multicolvar::VolumeGradientBase::setupRegions ( )
pure virtualinherited

◆ 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::multicolvar::BridgedMultiColvarFunction::transformBridgedDerivatives ( const unsigned &  current,
MultiValue invals,
MultiValue outvals 
) const
overridevirtualinherited

This does the task.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ turnOnDerivatives()

void PLMD::multicolvar::BridgedMultiColvarFunction::turnOnDerivatives ( )
overridevirtualinherited

Check nothing impossible being done with derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ 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.

◆ 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

◆ 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.

◆ 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.

◆ 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::multicolvar::ActionVolume::kerneltype
private

The kernel type for this histogram.

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ matsums

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

Are we doing sums of matrix rows.

◆ 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.

◆ not_in

bool PLMD::multicolvar::ActionVolume::not_in
private

Are we interested in the area outside the colvar.

◆ nquantities

unsigned PLMD::multicolvar::ActionVolume::nquantities
private

Number of quantities in use in this colvar.

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ sigma

double PLMD::multicolvar::ActionVolume::sigma
private

The value of sigma.

◆ taskFlags

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

This list is used to update the neighbor list.

◆ 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 files: