Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
PLMD::crystallization::LocalSteinhardt< T > Class Template Reference

#include <LocalSteinhardt.h>

Inheritance diagram for PLMD::crystallization::LocalSteinhardt< T >:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 
typedef std::set< FILE * >::iterator files_iterator
 

Public Member Functions

 LocalSteinhardt (const ActionOptions &ao)
 
double compute (const unsigned &tindex, multicolvar::AtomValuePack &myatoms) const
 This is replaced once we have a function to calculate the cv. More...
 
virtual double transformDotProduct (const double &dot, double &df) const
 
virtual double calculateCoordinationPrefactor (const double &coord, double &df) const
 
bool isPeriodic ()
 Are the base quantities periodic. More...
 
virtual void updateActiveAtoms (AtomValuePack &myatoms) const
 Update the atoms that are active. More...
 
void calculate ()
 Regular calculate. More...
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Calculate the numerical derivatives for this action. More...
 
Vector getPositionOfAtomForLinkCells (const unsigned &iatom) const
 This is used in MultiColvarBase only - it is used to setup the link cells. More...
 
virtual bool isCurrentlyActive (const unsigned &bno, const unsigned &code)
 Some things can be inactive in functions. More...
 
virtual void turnOnDerivatives ()
 Turn on the derivatives. More...
 
bool usesPbc () const
 Do we use pbc to calculate this quantity. More...
 
void applyPbc (std::vector< Vector > &dlist, unsigned max_index=0) const
 Apply PBCs over a set of distance vectors. More...
 
virtual void performTask (const unsigned &, const unsigned &, MultiValue &) const
 Prepare for the calculation Perform one of the tasks. More...
 
virtual double doCalculation (const unsigned &tindex, AtomValuePack &myatoms) const
 And a virtual function which actually computes the colvar. More...
 
virtual void apply ()
 Apply the forces from this action. More...
 
virtual unsigned getNumberOfDerivatives ()
 Get the number of derivatives for this action. More...
 
virtual CatomPack getCentralAtomPack (const unsigned &basn, const unsigned &curr)
 
virtual Vector getCentralAtomPos (const unsigned &curr)
 Get the index where the central atom is stored. More...
 
virtual void calculateWeight (AtomValuePack &myatoms) const
 You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations. More...
 
virtual bool isDensity () const
 Get the list of indices that have derivatives. More...
 
bool storedValueIsActive (const unsigned &iatom)
 Store central atoms so that this can be used in a function. More...
 
virtual bool hasDifferentiableOrientation () const
 This is true if multicolvar is calculating a vector or if the multicolvar is the density. More...
 
virtual void doNotCalculateDirector ()
 This makes sure we are not calculating the director when we do LocalAverage. More...
 
void requestAtoms (const std::vector< AtomNumber > &a)
 Request an array of atoms. More...
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) More...
 
const VectorgetPosition (AtomNumber) const
 Get position of i-th atom (access by absolute AtomNumber). More...
 
VectormodifyPosition (AtomNumber)
 Get modifiable position of i-th atom (access by absolute AtomNumber). More...
 
unsigned getTotAtoms () const
 Get total number of atoms, including virtual ones. More...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force 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...
 
const TensorgetBox () const
 Get box shape. More...
 
const std::vector< Vector > & getPositions () const
 Get the array of all positions. More...
 
const double & getEnergy () const
 Get energy. More...
 
double getMass (int i) const
 Get mass of i-th atom. More...
 
double getCharge (int i) const
 Get charge of i-th atom. More...
 
std::vector< Vector > & modifyForces ()
 Get a reference to forces array. More...
 
TensormodifyVirial ()
 Get a reference to virial array. More...
 
double & modifyForceOnEnergy ()
 Get a reference to force on energy. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
const std::vector< AtomNumber > & getAbsoluteIndexes () const
 Get the vector of absolute indexes. More...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. 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 changeBox (const Tensor &newbox)
 Change the box shape. More...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
void setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
 Add the forces to the atoms. More...
 
void doNotRetrieve ()
 Skip atom retrieval - use with care. More...
 
void doNotForce ()
 Skip atom forces - use with care. More...
 
void makeWhole ()
 Make atoms whole, assuming they are in the proper order. More...
 
void allowToAccessGlobalForces ()
 Allow calls to modifyGlobalForce() More...
 
void clearOutputForces ()
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
void retrieveAtoms ()
 
void applyForces ()
 
void lockRequests ()
 
void unlockRequests ()
 
const std::set< AtomNumber > & getUnique () const
 
void readAtomsFromPDB (const PDB &pdb)
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. 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 >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
virtual void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
virtual void update ()
 Update. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
virtual std::string getDocumentation () const
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual void activate ()
 Set action to active. More...
 
virtual void setOption (const std::string &s)
 
virtual void clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. 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 setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setValue (Value *, double)
 Set the value. 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 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...
 
bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. 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...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. 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...
 
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...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
virtual void checkFieldsAllowed ()
 
void unlockContributors ()
 
void lockContributors ()
 
virtual void finishTaskListUpdate ()
 
virtual void deactivate_task (const unsigned &task_index)
 Activate the jth colvar Deactivate the current task in future loops. More...
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
virtual void finishComputations (const std::vector< double > &buffer)
 Finish running all the calculations. More...
 
virtual void retrieveDomain (std::string &min, std::string &max)
 What are the domains of the base quantities. More...
 
virtual unsigned getNumberOfQuantities ()
 Get the number of quantities that are calculated during each task. More...
 
void activateTheseTasks (std::vector< unsigned > &addtionalTasks)
 Get the list of indices that have derivatives. More...
 
virtual void doJobsRequiredBeforeTaskList ()
 Do any jobs that are required before the task list is undertaken. More...
 
unsigned getFullNumberOfTasks () const
 Get the full size of the taskList dynamic list. More...
 
unsigned getPositionInFullTaskList (const unsigned &ii) const
 Get the position of the ith active task in the full list. More...
 
unsigned getTaskCode (const unsigned &ii) const
 Get the code for the ii th task in the list. More...
 
virtual void transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const
 Do the task if we have a bridge. More...
 
StoreDataVesselbuildDataStashes (const bool &allow_wcutoff, const double &wtol)
 Ensure that data required in other vessels is stored. More...
 
virtual void applyBridgeForces (const std::vector< double > &bb)
 Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...
 
VesselgetVesselWithName (const std::string &mynam)
 These are overwritten in MultiColvarFunction. More...
 
bool weightWithDerivatives () const
 Does the weight have derivatives. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 
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 componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

PlumedMainplumed
 Reference to main plumed object. More...
 
Loglog
 Reference to the log stream. More...
 
std::set< FILE * > files
 
Communicatorcomm
 
Communicatormulti_sim_comm
 
const Keywordskeywords
 

Protected Member Functions

unsigned getFullNumberOfBaseTasks () const
 Get the total number of tasks that this calculation is based on. More...
 
CatomPack getCentralAtomPackFromInput (const unsigned &ind) const
 Get the derivatives for the central atom with index ind. More...
 
void getVectorForTask (const unsigned &ind, const bool &normed, std::vector< double > &orient0) const
 
void getVectorDerivatives (const unsigned &ind, const bool &normed, MultiValue &myder0) const
 
void mergeVectorDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const
 
unsigned convertToLocalIndex (const unsigned &index, const unsigned &mcv_code) const
 Convert an index in the global array to an index in the individual base colvars. More...
 
void buildSets ()
 Build sets by taking one multicolvar from each base. More...
 
void buildSymmetryFunctionLists ()
 Build colvars for atoms as if they were symmetry functions. More...
 
void buildAtomListWithPairs (const bool &allow_intra_group)
 Build a colvar for each pair of atoms. More...
 
unsigned getNumberOfBaseMultiColvars () const
 Get the number of base multicolvars. More...
 
MultiColvarBasegetBaseMultiColvar (const unsigned &icolv) const
 Get an example of the underlying multicolvar. More...
 
unsigned getBaseColvarNumber (const unsigned &iatom) const
 Return the base multicolvar index that this colvar is a part of. More...
 
void addTaskToList (const unsigned &taskCode)
 Add a task to the list of tasks. More...
 
void setupMultiColvarBase ()
 Finish setting up the multicolvar base. More...
 
void setAtomsForCentralAtom (const std::vector< bool > &catom_ind)
 Set which atoms are to be used to calculate the central atom position. More...
 
void setLinkCellCutoff (const double &lcut)
 Set the value of the cutoff for the link cells. More...
 
void setupLinkCells ()
 Setup link cells in order to make this calculation faster. More...
 
Vector getSeparation (const Vector &vec1, const Vector &vec2) const
 Get the separation between a pair of vectors. More...
 
bool setupCurrentAtomList (const unsigned &taskCode, AtomValuePack &myatoms) const
 This sets up the list of atoms that are involved in this colvar. More...
 
void decodeIndexToAtoms (const unsigned &taskCode, std::vector< unsigned > &atoms) const
 Decode indices if there are 2 or 3 atoms involved. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void setValue (const double &d)
 Set the default value (the one without name) 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...
 
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 (Vessel *vv)
 
BridgeVesseladdBridgingVessel (ActionWithVessel *tome)
 Add a bridging vessel to the list of vessels. More...
 
void readVesselKeywords ()
 Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...
 
void needsDerivatives ()
 Turn on the derivatives in the vessel. More...
 
double getTolerance () const
 Return the value of the tolerance. More...
 
double getNLTolerance () const
 Return the value for the neighbor list tolerance. More...
 
unsigned getNumberOfVessels () const
 Get the number of vessels. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
void runAllTasks ()
 Calculate the values of all the vessels. More...
 
void resizeFunctions ()
 Resize all the functions when the number of derivatives change. More...
 
bool 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...
 
bool getForcesFromVessels (std::vector< double > &forcesToApply)
 Retrieve the forces from all the vessels (used in apply) More...
 
bool serialCalculation () const
 Is the calculation being done in serial. More...
 
bool usingLowMem () const
 Are we using low memory. More...
 
void setLowMemOption (const bool &)
 Set that we are using low memory. More...
 
unsigned getCurrentNumberOfActiveTasks () const
 Get the number of tasks that are currently active. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
void deactivateAllTasks ()
 Deactivate all the tasks in the task list. More...
 
void deactivateTasksInRange (const unsigned &lower, const unsigned &upper)
 Deactivate all tasks with i in lower \(\le\) i < upper. More...
 
unsigned getSizeOfBuffer (unsigned &bufsize)
 Get the size of the buffer. More...
 

Protected Attributes

bool usespecies
 Using the species keyword to read in atoms. More...
 
unsigned nblock
 Number of atoms in each block. More...
 
std::vector< unsigned > decoder
 This is used when turning cvcodes into atom numbers. More...
 
std::vector< std::vector< unsigned > > ablocks
 Blocks of atom numbers. More...
 
Atomsatoms
 
bool contributorsAreUnlocked
 The terms in the series are locked. More...
 
bool weightHasDerivatives
 Does the weight have derivatives. More...
 
unsigned bridgeVariable
 This is used for numerical derivatives of bridge variables. More...
 

Member Typedef Documentation

typedef std::vector<Action*> PLMD::Action::Dependencies
inherited
typedef std::set<FILE*>::iterator PLMD::Action::files_iterator
inherited

Constructor & Destructor Documentation

template<class T >
PLMD::crystallization::LocalSteinhardt< T >::LocalSteinhardt ( const ActionOptions ao)
inlineexplicit

Member Function Documentation

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

void PLMD::vesselbase::ActionWithVessel::activateTheseTasks ( std::vector< unsigned > &  addtionalTasks)
inherited

Get the list of indices that have derivatives.

Switch on additional tasks

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

Add a bridging vessel to the list of vessels.

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

Add a value with a name like label.name.

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

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

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

Specify that this Action depends on another one.

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

Add a task to the list of tasks.

void PLMD::ActionWithValue::addValue ( )
inherited

Add a value with the name label.

void PLMD::ActionWithValue::addValueWithDerivatives ( )
inherited

Add a value with the name label that has derivatives.

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.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel vv)
protectedinherited
void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )
inlineinherited

Allow calls to modifyGlobalForce()

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

Apply the forces from this action.

Implements PLMD::Action.

Reimplemented in PLMD::multicolvar::Sprint, and PLMD::multicolvar::BridgedMultiColvarFunction.

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.

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

Apply PBCs over a set of distance vectors.

void PLMD::multicolvar::MultiColvarFunction::buildAtomListWithPairs ( const bool &  allow_intra_group)
protectedinherited

Build a colvar for each pair of atoms.

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( const bool &  allow_wcutoff,
const double &  wtol 
)
inherited

Ensure that data required in other vessels is stored.

void PLMD::multicolvar::MultiColvarFunction::buildSets ( )
protectedinherited

Build sets by taking one multicolvar from each base.

void PLMD::multicolvar::MultiColvarFunction::buildSymmetryFunctionLists ( )
protectedinherited

Build colvars for atoms as if they were symmetry functions.

void PLMD::multicolvar::MultiColvarFunction::calculate ( )
virtualinherited

Regular calculate.

Implements PLMD::Action.

bool 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.

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

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

double PLMD::crystallization::OrientationSphere::calculateCoordinationPrefactor ( const double &  coord,
double &  df 
) const
inlinevirtualinherited

Reimplemented in PLMD::crystallization::SMAC.

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

void PLMD::multicolvar::MultiColvarFunction::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

Calculate the numerical derivatives for this action.

Reimplemented from PLMD::ActionAtomistic.

void PLMD::multicolvar::MultiColvarBase::calculateWeight ( AtomValuePack myatoms) const
virtualinherited

You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations.

Reimplemented in PLMD::multicolvar::Angles, PLMD::multicolvar::NumberOfLinks, PLMD::multicolvar::Bridge, and PLMD::multicolvar::AdjacencyMatrixAction.

void ActionAtomistic::changeBox ( const Tensor newbox)
inherited

Change the box shape.

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )
inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

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

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, and PLMD::generic::DumpProjections.

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

bool PLMD::Action::checkUpdate ( ) const
inherited

Check if action should be updated.

std::string PLMD::Action::cite ( const std::string &  s)
inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

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

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

void PLMD::Action::clearOptions ( )
virtualinherited
void ActionAtomistic::clearOutputForces ( )
inherited
void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name)
inherited

Set your value component to have no periodicity.

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.

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords keys)
staticinherited

Puts a message into the manual that the components always output.

double PLMD::crystallization::OrientationSphere::compute ( const unsigned &  tindex,
multicolvar::AtomValuePack myatoms 
) const
virtualinherited

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

Implements PLMD::multicolvar::MultiColvarBase.

unsigned PLMD::multicolvar::MultiColvarFunction::convertToLocalIndex ( const unsigned &  index,
const unsigned &  mcv_code 
) const
inlineprotectedinherited

Convert an index in the global array to an index in the individual base colvars.

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.

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.

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( const unsigned &  task_index)
virtualinherited

Activate the jth colvar Deactivate the current task in future loops.

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

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

Deactivate all the tasks in the task list.

void PLMD::vesselbase::ActionWithVessel::deactivateTasksInRange ( const unsigned &  lower,
const unsigned &  upper 
)
protectedinherited

Deactivate all tasks with i in lower \(\le\) i < upper.

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

Decode indices if there are 2 or 3 atoms involved.

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

Are derivatives required for this quantity.

double PLMD::multicolvar::MultiColvarBase::doCalculation ( const unsigned &  tindex,
AtomValuePack myatoms 
) const
virtualinherited

And a virtual function which actually computes the colvar.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )
virtualinherited
bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const
inlineinherited

Are we not calculating derivatives.

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.

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.

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.

void PLMD::Action::error ( const std::string &  msg) const
inherited

Crash calculation and print documentation.

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.

void PLMD::Action::exit ( int  c = 0)
inherited

Exit with error code c.

int PLMD::Action::fclose ( FILE *  fp)
inherited

Closes a file opened with Action::fclose().

void PLMD::Action::fflush ( )
inherited

Tell to the Action to flush open files.

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

Finish running all the calculations.

virtual void PLMD::vesselbase::ActionWithVessel::finishTaskListUpdate ( )
inlinevirtualinherited
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)
AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int  i) const
inlineinherited

Get the absolute index of an atom.

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

Get the vector of absolute indexes.

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

Get the ith of the currently active tasks.

unsigned PLMD::multicolvar::MultiColvarFunction::getBaseColvarNumber ( const unsigned &  iatom) const
inlineprotectedinherited

Return the base multicolvar index that this colvar is a part of.

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

Get an example of the underlying multicolvar.

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

Get box shape.

CatomPack PLMD::multicolvar::MultiColvarBase::getCentralAtomPack ( const unsigned &  basn,
const unsigned &  curr 
)
virtualinherited
CatomPack PLMD::multicolvar::MultiColvarFunction::getCentralAtomPackFromInput ( const unsigned &  ind) const
inlineprotectedinherited

Get the derivatives for the central atom with index ind.

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

Get the index where the central atom is stored.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

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

Get charge of i-th atom.

std::string PLMD::ActionWithValue::getComponentsList ( ) const
inherited

get a string that contains all the available components

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const
inherited

get a vector that contains the label for all the components

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

Get the number of tasks that are currently active.

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

Return dependencies.

std::string PLMD::Action::getDocumentation ( ) const
virtualinherited
const double & PLMD::ActionAtomistic::getEnergy ( ) const
inlineinherited

Get energy.

bool PLMD::Action::getExchangeStep ( ) const
inherited

Check if we are on an exchange step.

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

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

unsigned PLMD::multicolvar::MultiColvarFunction::getFullNumberOfBaseTasks ( ) const
inlineprotectedinherited

Get the total number of tasks that this calculation is based on.

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

Get the full size of the taskList dynamic list.

const std::string & PLMD::Action::getLabel ( ) const
inlineinherited

Returns the label.

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

Get mass of i-th atom.

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

Returns the name.

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

Return the value for the neighbor list tolerance.

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const
inlineinherited

Get number of available atoms.

unsigned PLMD::multicolvar::MultiColvarFunction::getNumberOfBaseMultiColvars ( ) const
inlineprotectedinherited

Get the number of base multicolvars.

int PLMD::ActionWithValue::getNumberOfComponents ( ) const
inlineinherited

Returns the number of values defined.

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

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfQuantities ( )
inlinevirtualinherited
unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const
inlineprotectedinherited

Get the number of vessels.

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned  j) const
inlineinherited

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

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)

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

Get reference to Pbc.

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

Return a pointer to the component by index.

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

Return a pointer to the value by name.

Value * PLMD::ActionWithValue::getPntrToValue ( )
protectedinherited

Get a pointer to the default value.

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

Get a pointer to the ith vessel.

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

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

const Vector & PLMD::ActionAtomistic::getPosition ( AtomNumber  i) const
inlineinherited

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

With direct access to the global atom array

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

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

Vector PLMD::multicolvar::MultiColvarFunction::getPositionOfAtomForLinkCells ( const unsigned &  iatom) const
inlinevirtualinherited

This is used in MultiColvarBase only - it is used to setup the link cells.

Implements PLMD::multicolvar::MultiColvarBase.

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

Get the array of all positions.

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

Return true if we are doing a restart.

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

Get the separation between a pair of vectors.

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

Get the size of the buffer.

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

Return the present timestep.

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

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

double PLMD::Action::getTime ( ) const
inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const
inherited

Return the timestep.

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

Return the value of the tolerance.

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const
inlineinherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyPosition or getPosition(AtomNumber)

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const
inlineinherited
void PLMD::multicolvar::MultiColvarFunction::getVectorDerivatives ( const unsigned &  ind,
const bool &  normed,
MultiValue myder0 
) const
protectedinherited
void PLMD::multicolvar::MultiColvarFunction::getVectorForTask ( const unsigned &  ind,
const bool &  normed,
std::vector< double > &  orient0 
) const
inlineprotectedinherited
Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string &  mynam)
inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

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.

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

Check if action is active.

bool PLMD::multicolvar::MultiColvarFunction::isCurrentlyActive ( const unsigned &  bno,
const unsigned &  code 
)
inlinevirtualinherited

Some things can be inactive in functions.

Implements PLMD::multicolvar::MultiColvarBase.

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

Get the list of indices that have derivatives.

Is this a density?

Reimplemented in PLMD::multicolvar::Density.

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

Check if an option is on.

bool PLMD::crystallization::OrientationSphere::isPeriodic ( )
inlinevirtualinherited

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )
inherited
void PLMD::ActionAtomistic::lockRequests ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

void ActionAtomistic::makeWhole ( )
inherited

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

void PLMD::multicolvar::MultiColvarFunction::mergeVectorDerivatives ( const unsigned &  ival,
const unsigned &  start,
const unsigned &  end,
const unsigned &  jatom,
const std::vector< double > &  der,
MultiValue myder,
AtomValuePack myatoms 
) const
protectedinherited
double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )
inlineinherited

Get a reference to force on energy.

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

Get a reference to forces array.

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!
Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )
inlineinherited

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

Vector & PLMD::ActionAtomistic::modifyPosition ( AtomNumber  i)
inlineinherited

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

Should be used by action that need to modify the stored atomic coordinates

Tensor & PLMD::ActionAtomistic::modifyVirial ( )
inlineinherited

Get a reference to virial array.

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

Turn on the derivatives in the vessel.

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.

template<class T >
void PLMD::Action::parse ( const std::string &  key,
T &  t 
)
inherited

Parse one keyword as generic type.

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

Parse a list of atoms without a numbered keyword.

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

Parse an list of atom with a numbred keyword.

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

Parse one keyword as boolean flag.

template<class T >
bool PLMD::Action::parseNumbered ( const std::string &  key,
const int  no,
T &  t 
)
inherited

Parse one numbered keyword as generic type.

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.

template<class T >
void PLMD::Action::parseVector ( const std::string &  key,
std::vector< T > &  t 
)
inherited

Parse one keyword as std::vector.

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

Applies PBCs to a seriens of positions or distances.

Vector ActionAtomistic::pbcDistance ( const Vector v1,
const Vector v2 
) const
inherited

Compute the pbc distance between two positions.

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

Prepare for the calculation Perform one of the tasks.

Implements PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

void PLMD::Action::prepare ( )
virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

void ActionAtomistic::readAtomsFromPDB ( const PDB pdb)
virtualinherited

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

Reimplemented from PLMD::Action.

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

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

template<class T >
static void PLMD::crystallization::LocalSteinhardt< T >::registerKeywords ( Keywords keys)
inlinestatic
void ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a)
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

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

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )
inherited
void PLMD::vesselbase::ActionWithVessel::retrieveDomain ( std::string &  min,
std::string &  max 
)
virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

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

Calculate the values of all the vessels.

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::analysis::Analysis.

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

Is the calculation being done in serial.

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.

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

Add the forces to the atoms.

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

void PLMD::multicolvar::MultiColvarBase::setLinkCellCutoff ( const double &  lcut)
protectedinherited

Set the value of the cutoff for the link cells.

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

Set that we are using low memory.

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited
void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

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.

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

Setup link cells in order to make this calculation faster.

void PLMD::multicolvar::MultiColvarBase::setupMultiColvarBase ( )
protectedinherited

Finish setting up the multicolvar base.

void PLMD::ActionWithValue::setValue ( const double &  d)
inlineprotectedinherited

Set the default value (the one without name)

void PLMD::ActionWithValue::setValue ( Value ,
double   
)
inherited

Set the value.

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

Store central atoms so that this can be used in a function.

Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout) Activate the atoms that have derivatives from a storeDataVessel Add central atom derivatives to a multicolvar function Get the value for this task Used to accumulate values Used for calculating weighted averages Add derivatives to the orientations Is the iatom'th stored value currently active

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.

double PLMD::crystallization::OrientationSphere::transformDotProduct ( const double &  dot,
double &  df 
) const
inlinevirtualinherited

Reimplemented in PLMD::crystallization::SMAC.

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

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

Reimplemented in PLMD::crystallization::DFSClustering, and PLMD::crystallization::DFSClusterDiameter.

void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )
inherited
void PLMD::ActionAtomistic::unlockRequests ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

virtual void PLMD::Action::update ( )
inlinevirtualinherited
void PLMD::multicolvar::MultiColvarFunction::updateActiveAtoms ( AtomValuePack myatoms) const
virtualinherited

Update the atoms that are active.

Implements PLMD::multicolvar::MultiColvarBase.

Reimplemented in PLMD::crystallization::DFSClustering.

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords keys)
staticinherited

The components in the action will depend on the user.

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

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

Do we use pbc to calculate this quantity.

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

Are we using low memory.

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

Issue a warning.

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

Does the weight have derivatives.

Member Data Documentation

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

Blocks of atom numbers.

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited
unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable
protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm
inherited
bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

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

This is used when turning cvcodes into atom numbers.

std::set<FILE*> PLMD::Action::files
inherited
const Keywords& PLMD::Action::keywords
inherited
Log& PLMD::Action::log
inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm
inherited
unsigned PLMD::multicolvar::MultiColvarBase::nblock
protectedinherited

Number of atoms in each block.

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

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

Using the species keyword to read in atoms.

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

Does the weight have derivatives.


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