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

#include <ActionWithMatrix.h>

Inheritance diagram for PLMD::ActionWithMatrix:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 ActionWithMatrix (const ActionOptions &)
 
virtual ~ActionWithMatrix ()
 
virtual bool actionHasForces ()
 
bool actionInChain () const
 Are we running this command in a chain. More...
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with a name like label.name. More...
 
virtual void addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
 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 addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f)
 Add force to an atom. More...
 
void addForcesOnArguments (const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)
 Add forces to arguments (used in apply) More...
 
void addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with the name label. More...
 
virtual void addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with the name label that has derivatives. More...
 
virtual void apply ()
 Apply the forces on this data. More...
 
virtual void areAllTasksRequired (std::vector< ActionWithVector * > &task_reducing_actions)
 Do we always need to do all the tasks for this action. More...
 
virtual void beforeUpdate ()
 Before Update. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. More...
 
virtual void calculate () override
 Run the calculation. More...
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
virtual bool calculateConstantValues (const bool &have_atoms)
 Used to calculate constant values in startup. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
void calculateNumericalDerivatives (ActionWithValue *av) override
 N.B. More...
 
virtual bool calculateOnUpdate ()
 This is used to check if we run calculate during the update step. More...
 
virtual bool canBeAfterInChain (ActionWithVector *av)
 Check if we can be after another ActionWithVector. More...
 
ActionAtomisticcastToActionAtomistic () noexcept final
 
virtual ActionForInterfacecastToActionForInterface () noexcept
 
virtual ActionShortcutcastToActionShortcut () noexcept
 
virtual ActionToGetDatacastToActionToGetData () noexcept
 
virtual ActionToPutDatacastToActionToPutData () noexcept
 
virtual ActionWithArgumentscastToActionWithArguments () noexcept
 
ActionWithArgumentscastToActionWithArguments () noexcept final
 
virtual ActionWithValuecastToActionWithValue () noexcept
 Specialized casts, to make PlumedMain run faster. More...
 
ActionWithValuecastToActionWithValue () noexcept final
 Specialized casts, to make PlumedMain run faster. More...
 
virtual ActionWithVirtualAtomcastToActionWithVirtualAtom () noexcept
 
virtual DomainDecompositioncastToDomainDecomposition () noexcept
 
virtual PbcActioncastToPbcAction () noexcept
 
void changeBox (const Tensor &newbox)
 Change the box shape. More...
 
virtual void checkFieldsAllowed ()
 
bool checkForDependency (Action *)
 Check that this action does not depend on the action in the argument. More...
 
bool checkForTaskForce (const unsigned &itask, const Value *myval) const override
 Check if there are forces we need to account for on this task. More...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
virtual int checkTaskStatus (const unsigned &taskno, int &flag) const
 Check the status of the ith task. 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 (const bool &force=false) override
 We override clearDerivatives here to prevent data in streams from being deleted. More...
 
void clearInputForces (const bool &force=false) override
 We override clearInputForces here to ensure that forces are deleted from all values. More...
 
virtual void clearOptions ()
 
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...
 
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...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. 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...
 
void finishChainBuild (ActionWithVector *act)
 This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions. More...
 
void finishComputations (const std::vector< double > &buf)
 This is to transfer data from the buffer to the final value. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
void gatherForcesOnStoredValue (const Value *myval, const unsigned &itask, const MultiValue &myvals, std::vector< double > &forces) const override
 This gathers the force on a particular value. More...
 
void gatherProcesses (std::vector< double > &buffer) override
 Gather all the data from the MPI processes. More...
 
void gatherStoredValue (const unsigned &valindex, const unsigned &code, const MultiValue &myvals, const unsigned &bufstart, std::vector< double > &buffer) const override
 Gather a row of the matrix. More...
 
void gatherThreads (const unsigned &nt, const unsigned &bufsize, const std::vector< double > &omp_buffer, std::vector< double > &buffer, MultiValue &myvals) override
 Gather all the data from the threads. More...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. More...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes () const
 Get the vector of absolute indexes. More...
 
virtual void getAdditionalTasksRequired (ActionWithVector *action, std::vector< unsigned > &atasks)
 Get the additional tasks that are required here. More...
 
void getAllActionLabelsInChain (std::vector< std::string > &mylabels) const
 Get every the label of every value that is calculated in this chain. More...
 
void getAllActionLabelsInMatrixChain (std::vector< std::string > &mylabels) const override
 This is overridden in ActionWithMatrix. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
virtual const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. More...
 
const TensorgetBox () const
 Get box shape. 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...
 
std::string getDefaultString () const
 Get the defaults. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
const double & getEnergy () const
 Get energy. More...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
ActionWithVectorgetFirstActionInChain ()
 
const ActionWithVectorgetFirstActionInChain () const
 Return a pointer to the first action in the chain. More...
 
const ActionWithMatrixgetFirstMatrixInChain () const
 Get the first matrix in this chain. More...
 
Vector getForce (const std::pair< std::size_t, std::size_t > &a) const
 Get the force acting on a particular atom. More...
 
Vector getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const
 Get position of i-th atom (access by absolute AtomNumber). More...
 
void getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const
 Transfer the gradients. More...
 
double getkBT ()
 Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. 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...
 
virtual void getMatrixColumnTitles (std::vector< std::string > &argnames) const
 Get the titles to use for the columns of the matrix. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
virtual unsigned getNumberOfColumns () const =0
 This should return the number of columns to help with sparse storage of matrices. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
virtual unsigned getNumberOfDerivatives ()=0
 
void getNumberOfStreamedDerivatives (unsigned &nderivatives, Value *stopat)
 Get the number of derivatives in the stream. More...
 
virtual void getNumberOfTasks (unsigned &ntasks)
 Find out how many tasks we need to perform in this loop. More...
 
virtual std::string getOutputComponentDescription (const std::string &cname, const Keywords &keys) const
 Get the description of this component. More...
 
double getOutputQuantity (const std::string &name) const
 Get the value with a specific name (N.B. if there is no such value this returns zero) More...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
ValuegetPntrToArgument (const unsigned n) const
 Return a pointer to specific argument. More...
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) More...
 
const std::vector< Vector > & getPositions () const
 Get the array of all positions. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
unsigned getTotAtoms () const
 Get total number of atoms, including virtual ones. More...
 
const std::vector< AtomNumber > & getUnique () const
 
const std::vector< AtomNumber > & getUniqueLocal () const
 
Tensor getVirial () const
 Get the virial that is acting. More...
 
bool hasStoredArguments () const
 Check if there are any stored values in arguments. More...
 
void interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
 Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this. More...
 
bool isActive () const
 Check if action is active. More...
 
virtual bool isAdjacencyMatrix () const
 
virtual bool isInSubChain (unsigned &nder)
 Check if we are in a subchain. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
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...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
 Parse a numbered list of arguments. More...
 
void parseArgumentList (const std::string &key, std::vector< Value * > &args)
 Parse a list of arguments. More...
 
void parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
 Parse an list of atom with a numbred keyword. More...
 
void parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
 Parse a list of atoms without a numbered keyword. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
virtual void performTask (const std::string &controller, const unsigned &index1, const unsigned &index2, MultiValue &myvals) const =0
 This is the virtual that will do the calculation of the task for a particular matrix element. More...
 
void performTask (const unsigned &task_index, MultiValue &myvals) const override
 Run over one row of the matrix. More...
 
virtual void prepare () override
 Prepare an Action for calculation This can be used by Action if they need some special preparation before 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 requestArguments (const std::vector< Value * > &arg)
 Setup the dependencies. More...
 
void requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
 Request an array of atoms. More...
 
void requestExtraDependencies (const std::vector< Value * > &extra)
 
void resetStoredTimestep ()
 Set the timestep that is stored in the action to the correct value. More...
 
void retrieveAtoms (const bool &force=false) override
 
virtual void runEndOfRowJobs (const unsigned &ival, const std::vector< unsigned > &indices, MultiValue &myvals) const =0
 This is the jobs that need to be done when we have run all the jobs in a row of the matrix. 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)
 Add the forces to the atoms. More...
 
void setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind)
 Add the virial forces (span-like syntax) More...
 
void setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind)
 Add the virial forces. More...
 
void setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos)
 Modify position of i-th atom (access by absolute AtomNumber). More...
 
void setGradients (Value *myval, unsigned &start) const
 Get the gradient for this action. More...
 
virtual void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setupConstantValues (const bool &have_atoms)
 This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...
 
virtual void setupForTask (const unsigned &task_index, std::vector< unsigned > &indices, MultiValue &myvals) const =0
 
void setupStreamedComponents (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping) override
 This requires some thought. More...
 
void setValue (Value *, double)
 Set the value. More...
 
virtual void switchTaskReduction (const bool &task_reduction, ActionWithVector *aselect)
 Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere. More...
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void unlockRequests () override
 
virtual void update ()
 Update. More...
 
virtual void updateAdditionalIndices (const unsigned &ostrn, MultiValue &myvals) const
 This is used to ensure that all indices are updated when you do local average. More...
 
virtual void updateForceTasksFromValue (const Value *myval, std::vector< unsigned > &force_tasks) const
 Get the force tasks that are active for this action. More...
 
virtual void updateNeighbourList ()
 This is overwritten in Adjacency matrix where we have a neighbour list. More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
virtual std::string writeInGraph () const
 Get the info on what to calculate. More...
 

Static Public Member Functions

static void getAtomValuesFromPlumedObject (const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev)
 This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges. More...
 
static void interpretArgumentList (const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg)
 Convert a list of argument names into a list of pointers to the values. More...
 
static void interpretAtomList (std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t)
 Convert a set of read in strings into an atom list (this is used in parseAtomList) 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 addDerivativeOnMatrixArgument (const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &irow, const unsigned &jcol, const double &der, MultiValue &myvals) const
 Add derivatives given the derative wrt to the input matrix element as input. More...
 
void addDerivativeOnVectorArgument (const bool &inchain, const unsigned &ival, const unsigned &jarg, const unsigned &jelem, const double &der, MultiValue &myvals) const
 Add derivatives given the derivative wrt to the input vector element as input. More...
 
bool argumentDependsOn (const std::string &headstr, ActionWithVector *faction, Value *thearg)
 Check if the arguments of this action depend on thearg. More...
 
unsigned buildArgumentStore (const unsigned &argstart)
 This sets up the arguments at the start of the calculation. More...
 
bool checkForForces ()
 Accumulate the forces from the Values. More...
 
void expandArgKeywordInPDB (const PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
double getArgumentElement (const unsigned &ic, const unsigned &jelem, const MultiValue &myvals) const
 This returns the jelem th element of argument ic. More...
 
const ValuegetConstPntrToComponent (int i) const
 Get a const pointer to the ith component. More...
 
double getElementOfMatrixArgument (const unsigned &imat, const unsigned &irow, const unsigned &jcol, const MultiValue &myvals) const
 This returns an element of a matrix that is passed an argument. More...
 
const std::vector< double > & getForcesToApply () const
 Get the forces to apply. More...
 
double getKBoltzmann () const
 Get the value of Boltzmann's constant. More...
 
std::vector< unsigned > & getListOfActiveTasks (ActionWithVector *action)
 Get the list of tasks that are active. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
const UnitsgetUnits () const
 Get the units that we are operating in. More...
 
std::pair< std::size_t, std::size_t > getValueIndices (const AtomNumber &i) const
 Used to interpret whether this index is a virtual atom or a real atom. More...
 
bool matrixChainContinues () const
 Does the matrix chain continue on from this action. More...
 
void runAllTasks ()
 Run all the tasks in the list. More...
 
bool runInSerial () const
 Run all calculations in serial. More...
 
void setExtraCV (const std::string &name)
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
void updateTaskListReductionStatus ()
 This updates whether or not we are using all the task reduction stuff. More...
 
bool usingNaturalUnits () const
 Are we using natural units. More...
 

Protected Attributes

std::vector< unsigned > arg_deriv_starts
 A vector that contains the start point for the argument derivatives. More...
 
bool chargesWereSet
 
bool clearOnEachCycle
 This turns off derivative clearing for contact matrix if we are not storing derivatives. More...
 
bool done_in_chain
 Assert if this action is part of a chain. More...
 
bool massesWereSet
 

Private Member Functions

bool addActionToChain (const std::vector< std::string > &alabels, ActionWithVector *act)
 Add this action to the recursive chain. More...
 
void addForcesToInput (const std::vector< double > &forcesToApply, unsigned &ind)
 Add the gathered forces to the inputs across the whole chain. More...
 
void broadcastThatTasksAreReduced (ActionWithVector *aselect)
 Send information to arguments that tasks are reduced in depedent actions. More...
 
void canReduceTasks (std::vector< ActionWithVector * > &task_reducing_actions)
 Check if this ation can reduce the number of tasks we perform. More...
 
bool checkChainForNonScalarForces () const
 Check the chain for non scalar forces. More...
 
bool checkComponentsForForce () const
 Check if a force has been added on one of the components of this action. More...
 
bool checkForGrids (unsigned &nder) const
 Check if there are any grids in the stream. More...
 
void clearMatrixElements (MultiValue &myvals) const
 This is used to clear up the matrix elements. More...
 
void gatherAccumulators (const unsigned &taskCode, const MultiValue &myvals, std::vector< double > &buffer) const
 Gather the values that we intend to store in the buffer. More...
 
void gatherForces (const unsigned &i, const MultiValue &myvals, std::vector< double > &forces) const
 Gather the forces on non-scalar quantities. More...
 
ActionWithVectorgetActionWithDerivatives (ActionWithVector *depaction)
 Work backwards through the chain to find an action that has either stored arguments or derivatives. More...
 
int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 
void getForceTasks (std::vector< unsigned > &force_tasks) const
 Get the tasks that we need for forces. More...
 
bool getNumberOfStoredValues (Value *startat, unsigned &nvals, const unsigned &astart, const std::vector< Value * > &stopat)
 Get the number of stored values in the stream. More...
 
void getNumberOfStreamedQuantities (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping)
 Get the number of quantities in the stream. More...
 
void getSizeOfBuffer (const unsigned &nactive_tasks, unsigned &bufsize)
 Get the size of the buffer array that holds the data we are gathering over the MPI loop. More...
 
void getTotalMatrixBookeeping (unsigned &stashsize)
 This is used to find the total amount of space we need for storing matrix elements. More...
 
unsigned reallyBuildArgumentStore (const unsigned &argstart)
 This is used to build the argument store when we cannot use the chain. More...
 
void runTask (const std::string &controller, const unsigned &current, const unsigned colno, MultiValue &myvals) const
 This does the calculation of a particular matrix element. More...
 
void taskIsActive (const unsigned &current, int &flag) const
 Check if a particular task is active at this time. More...
 
void transferNonZeroMatrixElementsToValues (unsigned &nval, const std::vector< unsigned > &matbook)
 This transfers the non-zero elements to the Value. More...
 
void updateAllNeighbourLists ()
 Update all the neighbour lists in the chain. More...
 
void updateTaskReductionFlag (bool &head_reduce_tasks)
 Turn on task reduction flag in dependent actions. More...
 
void updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)
 

Private Attributes

ActionWithVectoraction_to_do_after
 Actions that must be done after this one. More...
 
ActionWithVectoraction_to_do_before
 Action that must be done before this one. More...
 
bool active
 Switch to activate Action on this step. More...
 
std::vector< unsigned > active_tasks
 The list of active tasks. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
std::vector< Value * > arguments
 
std::vector< std::pair< std::size_t, std::size_t > > atom_value_ind
 
std::vector< std::pair< std::size_t, std::vector< std::size_t > > > atom_value_ind_grouped
 
bool atomsWereRetrieved
 Were the atoms retrieved in some earlier action. More...
 
ValueboxValue
 
std::vector< double > buffer
 The buffer that we use (we keep a copy here to avoid resizing) More...
 
std::vector< double > charges
 
std::vector< Value * > chargev
 
std::string defaults
 The set of default arguments that we are using. More...
 
bool doCheckPoint
 
bool donotforce
 
bool donotretrieve
 
double energy
 
bool firststep
 This finishes setup on first step to check if actions are calculated during update. More...
 
double forceOnEnergy
 
double forceOnExtraCV
 
std::vector< Vectorforces
 
std::vector< double > forcesForApply
 A vector that is used to hold the forces that we will apply on the input quantities. More...
 
std::vector< AtomNumberindexes
 
std::string label
 Label of the Action, as set with LABEL= in the plumed.dat file. More...
 
std::vector< std::string > line
 Directive line. More...
 
bool lockRequestArguments
 
bool lockRequestAtoms
 
std::vector< double > masses
 
std::vector< Value * > masv
 
std::vector< unsigned > matrix_bookeeping
 This holds the bookeeping arrays for sparse matrices. More...
 
ActionWithMatrixmatrix_to_do_after
 
ActionWithMatrixmatrix_to_do_before
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
bool never_activate
 
bool never_reduce_tasks
 This is turned on if there is some action that needs all the tasks. More...
 
ActionWithMatrixnext_action_in_chain
 
bool noderiv
 Are we skipping the calculation of the derivatives. More...
 
bool numericalDerivatives
 Are we using numerical derivatives to differentiate. More...
 
std::set< std::string > options
 Option that you might have enabled. More...
 
Pbcpbc =*pbc_fwd
 
ForwardDecl< Pbcpbc_fwd
 
std::vector< Vectorpositions
 
bool reduce_tasks
 Are we allowed to reduce the number of tasks being performed. More...
 
int replica_index
 
bool restart
 
bool serial
 Is the calculation to be done in serial. More...
 
std::vector< ActionWithVector * > task_control_list
 This is the list of actions that control the tasks that we do here. More...
 
double timestep
 Save the timestep here. More...
 
std::vector< AtomNumberunique
 unique should be an ordered set since we later create a vector containing the corresponding indexes More...
 
std::vector< AtomNumberunique_local
 
bool unique_local_needs_update
 unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
std::vector< unsigned > valsToForce
 
std::vector< std::size_t > value_depends
 
std::vector< std::unique_ptr< Value > > values
 An array containing the values for this action. More...
 
std::vector< Value * > xpos
 Values that hold information about atom positions and charges. More...
 
std::vector< Value * > ypos
 
std::vector< Value * > zpos
 

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ ActionWithMatrix()

PLMD::ActionWithMatrix::ActionWithMatrix ( const ActionOptions ao)
explicit

◆ ~ActionWithMatrix()

PLMD::ActionWithMatrix::~ActionWithMatrix ( )
virtual

Member Function Documentation

◆ actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )
virtualinherited

◆ actionInChain()

bool PLMD::ActionWithVector::actionInChain ( ) const
inlineinherited

Are we running this command in a chain.

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addActionToChain()

bool PLMD::ActionWithVector::addActionToChain ( const std::vector< std::string > &  alabels,
ActionWithVector act 
)
privateinherited

Add this action to the recursive chain.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name,
const std::vector< unsigned > &  shape = std::vector<unsigned>() 
)
inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name,
const std::vector< unsigned > &  shape = std::vector<unsigned>() 
)
virtualinherited

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

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addDerivativeOnMatrixArgument()

void PLMD::ActionWithMatrix::addDerivativeOnMatrixArgument ( const bool &  inchain,
const unsigned &  ival,
const unsigned &  jarg,
const unsigned &  irow,
const unsigned &  jcol,
const double &  der,
MultiValue myvals 
) const
inlineprotected

Add derivatives given the derative wrt to the input matrix element as input.

◆ addDerivativeOnVectorArgument()

void PLMD::ActionWithMatrix::addDerivativeOnVectorArgument ( const bool &  inchain,
const unsigned &  ival,
const unsigned &  jarg,
const unsigned &  jelem,
const double &  der,
MultiValue myvals 
) const
inlineprotected

Add derivatives given the derivative wrt to the input vector element as input.

◆ addForce()

void PLMD::ActionAtomistic::addForce ( const std::pair< std::size_t, std::size_t > &  a,
const Vector f 
)
inlineinherited

Add force to an atom.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const unsigned &  argstart,
const std::vector< double > &  forces,
unsigned &  ind,
const std::string &  c 
)
inherited

Add forces to arguments (used in apply)

◆ addForcesToInput()

void PLMD::ActionWithVector::addForcesToInput ( const std::vector< double > &  forcesToApply,
unsigned &  ind 
)
privateinherited

Add the gathered forces to the inputs across the whole chain.

◆ addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > &  shape = std::vector<unsigned>())
inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > &  shape = std::vector<unsigned>())
virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ apply()

void PLMD::ActionWithVector::apply ( )
virtualinherited

Apply the forces on this data.

Implements PLMD::Action.

Reimplemented in PLMD::dimred::ProjectPoints, PLMD::gridtools::FunctionOfGrid< T >, and PLMD::colvar::RMSDVector.

◆ areAllTasksRequired()

virtual void PLMD::ActionWithVector::areAllTasksRequired ( std::vector< ActionWithVector * > &  task_reducing_actions)
inlinevirtualinherited

◆ argumentDependsOn()

bool PLMD::ActionWithVector::argumentDependsOn ( const std::string &  headstr,
ActionWithVector faction,
Value thearg 
)
protectedinherited

Check if the arguments of this action depend on thearg.

◆ 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.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc ( int  i,
double  d1 
) const
inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ broadcastThatTasksAreReduced()

void PLMD::ActionWithVector::broadcastThatTasksAreReduced ( ActionWithVector aselect)
privateinherited

Send information to arguments that tasks are reduced in depedent actions.

◆ buildArgumentStore()

unsigned PLMD::ActionWithVector::buildArgumentStore ( const unsigned &  argstart)
protectedinherited

This sets up the arguments at the start of the calculation.

◆ calculate()

void PLMD::ActionWithMatrix::calculate ( )
overridevirtual

Run the calculation.

Implements PLMD::Action.

◆ 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.

◆ calculateConstantValues()

bool PLMD::ActionWithArguments::calculateConstantValues ( const bool &  have_atoms)
virtualinherited

Used to calculate constant values in startup.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB pdb)
inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives()

void PLMD::ActionWithVector::calculateNumericalDerivatives ( ActionWithValue a)
overridevirtualinherited

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::ActionAtomistic.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )
virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ canBeAfterInChain()

virtual bool PLMD::ActionWithVector::canBeAfterInChain ( ActionWithVector av)
inlinevirtualinherited

Check if we can be after another ActionWithVector.

Reimplemented in PLMD::adjmat::Neighbors.

◆ canReduceTasks()

void PLMD::ActionWithVector::canReduceTasks ( std::vector< ActionWithVector * > &  task_reducing_actions)
privateinherited

Check if this ation can reduce the number of tasks we perform.

◆ castToActionAtomistic()

ActionAtomistic* PLMD::ActionAtomistic::castToActionAtomistic ( )
inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments() [1/2]

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithArguments() [2/2]

ActionWithArguments* PLMD::ActionWithArguments::castToActionWithArguments ( )
inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )
inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )
inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ changeBox()

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

Change the box shape.

◆ checkChainForNonScalarForces()

bool PLMD::ActionWithVector::checkChainForNonScalarForces ( ) const
privateinherited

Check the chain for non scalar forces.

◆ checkComponentsForForce()

bool PLMD::ActionWithVector::checkComponentsForForce ( ) const
privateinherited

Check if a force has been added on one of the components of this action.

◆ checkFieldsAllowed()

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

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

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action action)
inherited

Check that this action does not depend on the action in the argument.

◆ checkForForces()

bool PLMD::ActionWithVector::checkForForces ( )
protectedinherited

Accumulate the forces from the Values.

◆ checkForGrids()

bool PLMD::ActionWithVector::checkForGrids ( unsigned &  nder) const
privateinherited

Check if there are any grids in the stream.

◆ checkForTaskForce()

bool PLMD::ActionWithMatrix::checkForTaskForce ( const unsigned &  itask,
const Value myval 
) const
overridevirtual

Check if there are forces we need to account for on this task.

Reimplemented from PLMD::ActionWithVector.

◆ checkNeedsGradients()

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

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkTaskStatus()

virtual int PLMD::ActionWithVector::checkTaskStatus ( const unsigned &  taskno,
int &  flag 
) const
inlinevirtualinherited

◆ 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::ActionWithVector::clearDerivatives ( const bool &  force = false)
overridevirtualinherited

We override clearDerivatives here to prevent data in streams from being deleted.

Reimplemented from PLMD::ActionWithValue.

◆ clearInputForces()

void PLMD::ActionWithVector::clearInputForces ( const bool &  force = false)
overridevirtualinherited

We override clearInputForces here to ensure that forces are deleted from all values.

Reimplemented from PLMD::ActionWithValue.

◆ clearMatrixElements()

void PLMD::ActionWithMatrix::clearMatrixElements ( MultiValue myvals) const
private

This is used to clear up the matrix elements.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ 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.

◆ 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.

◆ difference()

double PLMD::ActionWithArguments::difference ( int  i,
double  d1,
double  d2 
) const
inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doNotCalculateDerivatives()

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

Are we not calculating derivatives.

◆ 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.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( const PDB pdb)
protectedinherited

This changes the arg keyword in the pdb file.

◆ 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.

◆ finishChainBuild()

void PLMD::ActionWithMatrix::finishChainBuild ( ActionWithVector act)
virtual

This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions.

Reimplemented from PLMD::ActionWithVector.

◆ finishComputations()

void PLMD::ActionWithVector::finishComputations ( const std::vector< double > &  buf)
inherited

This is to transfer data from the buffer to the final value.

◆ 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)

◆ gatherAccumulators()

void PLMD::ActionWithVector::gatherAccumulators ( const unsigned &  taskCode,
const MultiValue myvals,
std::vector< double > &  buffer 
) const
privateinherited

Gather the values that we intend to store in the buffer.

◆ gatherForces()

void PLMD::ActionWithVector::gatherForces ( const unsigned &  i,
const MultiValue myvals,
std::vector< double > &  forces 
) const
privateinherited

Gather the forces on non-scalar quantities.

◆ gatherForcesOnStoredValue()

void PLMD::ActionWithMatrix::gatherForcesOnStoredValue ( const Value myval,
const unsigned &  itask,
const MultiValue myvals,
std::vector< double > &  forces 
) const
overridevirtual

This gathers the force on a particular value.

Reimplemented from PLMD::ActionWithVector.

◆ gatherProcesses()

void PLMD::ActionWithMatrix::gatherProcesses ( std::vector< double > &  buffer)
overridevirtual

Gather all the data from the MPI processes.

Reimplemented from PLMD::ActionWithVector.

◆ gatherStoredValue()

void PLMD::ActionWithMatrix::gatherStoredValue ( const unsigned &  valindex,
const unsigned &  code,
const MultiValue myvals,
const unsigned &  bufstart,
std::vector< double > &  buffer 
) const
overridevirtual

Gather a row of the matrix.

Reimplemented from PLMD::ActionWithVector.

Reimplemented in PLMD::matrixtools::Voronoi.

◆ gatherThreads()

void PLMD::ActionWithMatrix::gatherThreads ( const unsigned &  nt,
const unsigned &  bufsize,
const std::vector< double > &  omp_buffer,
std::vector< double > &  buffer,
MultiValue myvals 
)
overridevirtual

Gather all the data from the threads.

Reimplemented from PLMD::ActionWithVector.

◆ getAbsoluteIndex()

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int  i) const
inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

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

Get the vector of absolute indexes.

◆ getActionWithDerivatives()

ActionWithVector * PLMD::ActionWithVector::getActionWithDerivatives ( ActionWithVector depaction)
privateinherited

Work backwards through the chain to find an action that has either stored arguments or derivatives.

◆ getAdditionalTasksRequired()

void PLMD::ActionWithVector::getAdditionalTasksRequired ( ActionWithVector action,
std::vector< unsigned > &  atasks 
)
virtualinherited

Get the additional tasks that are required here.

Reimplemented in PLMD::adjmat::AdjacencyMatrixBase, and PLMD::matrixtools::MatrixTimesMatrix.

◆ getAllActionLabelsInChain()

void PLMD::ActionWithVector::getAllActionLabelsInChain ( std::vector< std::string > &  mylabels) const
inherited

Get every the label of every value that is calculated in this chain.

◆ getAllActionLabelsInMatrixChain()

void PLMD::ActionWithMatrix::getAllActionLabelsInMatrixChain ( std::vector< std::string > &  matchain) const
overridevirtual

This is overridden in ActionWithMatrix.

Reimplemented from PLMD::ActionWithVector.

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned  n) const
inlineinherited

Returns the value of an argument.

◆ getArgumentElement()

double PLMD::ActionWithMatrix::getArgumentElement ( const unsigned &  ic,
const unsigned &  jelem,
const MultiValue myvals 
) const
inlineprotected

This returns the jelem th element of argument ic.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const
inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getAtomValuesFromPlumedObject()

void PLMD::ActionAtomistic::getAtomValuesFromPlumedObject ( const PlumedMain plumed,
std::vector< Value * > &  xpos,
std::vector< Value * > &  ypos,
std::vector< Value * > &  zpos,
std::vector< Value * > &  masv,
std::vector< Value * > &  chargev 
)
staticinherited

This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges.

◆ getBox()

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

Get box shape.

◆ getCharge()

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

Get charge of i-th atom.

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string &  name) const
privateinherited

Return the index for the component named name.

◆ getComponentsList()

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

get a string that contains all the available components

◆ getComponentsVector()

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

get a vector that contains the label for all the components

◆ getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int  i) const
protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

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

Return true if we are doing at a checkpoint step.

◆ getDefaultString()

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

Get the defaults.

◆ getDependencies()

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

Return dependencies.

◆ getElementOfMatrixArgument()

double PLMD::ActionWithMatrix::getElementOfMatrixArgument ( const unsigned &  imat,
const unsigned &  irow,
const unsigned &  jcol,
const MultiValue myvals 
) const
inlineprotected

This returns an element of a matrix that is passed an argument.

◆ 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.

◆ getFirstActionInChain() [1/2]

ActionWithVector* PLMD::ActionWithVector::getFirstActionInChain ( )
inherited

◆ getFirstActionInChain() [2/2]

ActionWithVector * PLMD::ActionWithVector::getFirstActionInChain ( ) const
inherited

Return a pointer to the first action in the chain.

◆ getFirstMatrixInChain()

const ActionWithMatrix * PLMD::ActionWithMatrix::getFirstMatrixInChain ( ) const

Get the first matrix in this chain.

◆ getForce()

Vector PLMD::ActionAtomistic::getForce ( const std::pair< std::size_t, std::size_t > &  a) const
inlineinherited

Get the force acting on a particular atom.

◆ getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const
inlineprotectedinherited

Get the forces to apply.

◆ getForceTasks()

void PLMD::ActionWithVector::getForceTasks ( std::vector< unsigned > &  force_tasks) const
privateinherited

Get the tasks that we need for forces.

◆ getGlobalPosition()

Vector PLMD::ActionAtomistic::getGlobalPosition ( const std::pair< std::size_t, std::size_t > &  a) 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.

◆ getGradient()

void PLMD::ActionAtomistic::getGradient ( const unsigned &  ind,
Vector deriv,
std::map< AtomNumber, Vector > &  gradients 
) const
inherited

Transfer the gradients.

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const
protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )
inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

◆ 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.

◆ getListOfActiveTasks()

std::vector< unsigned > & PLMD::ActionWithVector::getListOfActiveTasks ( ActionWithVector action)
protectedinherited

Get the list of tasks that are active.

◆ getMass()

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

Get mass of i-th atom.

◆ getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > &  argnames) const
virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

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

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const
inlinevirtualinherited

Returns the number of arguments.

◆ getNumberOfAtoms()

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

Get number of available atoms.

◆ getNumberOfColumns()

virtual unsigned PLMD::ActionWithMatrix::getNumberOfColumns ( ) const
pure virtual

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

virtual unsigned PLMD::ActionWithValue::getNumberOfDerivatives ( )
pure virtualinherited

Implemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::ves::Optimizer, PLMD::generic::Plumed, PLMD::metatensor::MetatensorPlumedAction, PLMD::contour::FindSphericalContour, PLMD::generic::Read, PLMD::contour::FindContourSurface, PLMD::clusters::ClusterDistribution, PLMD::gridtools::KDE, PLMD::fourier::FourierTransform, PLMD::Colvar, PLMD::generic::Constant, PLMD::gridtools::InterpolateGrid, PLMD::gridtools::ReadGridInSetup, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::dimred::ArrangePoints, PLMD::bias::Bias, PLMD::function::FunctionOfVector< T >, PLMD::contour::DistanceFromContourBase, PLMD::function::FunctionOfMatrix< T >, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::opes::ExpansionCVs, PLMD::adjmat::AdjacencyMatrixBase, PLMD::vatom::ArgsToVatom, PLMD::ActionForInterface, PLMD::function::Function, PLMD::generic::Time, PLMD::valtools::Concatenate, PLMD::valtools::SelectWithMask, PLMD::clusters::ClusteringBase, PLMD::generic::CreateMask, PLMD::matrixtools::DiagonalizeMatrix, PLMD::matrixtools::InvertMatrix, PLMD::symfunc::ThreeBodyGFunctions, PLMD::valtools::Flatten, PLMD::landmarks::FarthestPointSampling, PLMD::mapping::GeometricPath, PLMD::valtools::VStack, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::RMSDVector, PLMD::adjmat::Neighbors, PLMD::gridtools::FunctionOfGrid< T >, PLMD::matrixtools::TransposeMatrix, PLMD::matrixtools::Voronoi, PLMD::refdist::MatrixProductDiagonal, PLMD::bias::ReweightBase, PLMD::contour::FindContour, PLMD::wham::Wham, PLMD::ActionWithVirtualAtom, PLMD::matrixtools::MatrixTimesMatrix, PLMD::volumes::ActionVolume, PLMD::dimred::ProjectPoints, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::mapping::PathDisplacements, PLMD::crystdistrib::QuaternionBondProductMatrix, PLMD::generic::GatherReplicas, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::adjmat::TorsionsMatrix, and PLMD::crystdistrib::QuaternionProductMatrix.

◆ getNumberOfStoredValues()

bool PLMD::ActionWithVector::getNumberOfStoredValues ( Value startat,
unsigned &  nvals,
const unsigned &  astart,
const std::vector< Value * > &  stopat 
)
privateinherited

Get the number of stored values in the stream.

◆ getNumberOfStreamedDerivatives()

void PLMD::ActionWithVector::getNumberOfStreamedDerivatives ( unsigned &  nderivatives,
Value stopat 
)
inherited

Get the number of derivatives in the stream.

◆ getNumberOfStreamedQuantities()

void PLMD::ActionWithVector::getNumberOfStreamedQuantities ( const std::string &  headstr,
unsigned &  nquants,
unsigned &  nmat,
unsigned &  maxcol,
unsigned &  nbookeeping 
)
privateinherited

Get the number of quantities in the stream.

◆ getNumberOfTasks()

void PLMD::ActionWithVector::getNumberOfTasks ( unsigned &  ntasks)
virtualinherited

Find out how many tasks we need to perform in this loop.

Reimplemented in PLMD::gridtools::KDE, PLMD::volumes::ActionVolume, and PLMD::contour::FindContour.

◆ getOutputComponentDescription()

std::string PLMD::ActionWithValue::getOutputComponentDescription ( const std::string &  cname,
const Keywords keys 
) const
virtualinherited

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string &  name) const
inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

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

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

◆ getPbc()

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

Get reference to Pbc.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned  n) const
inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the component by index.

◆ getPntrToValue()

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

Get a pointer to the default value.

◆ getPosition()

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

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

◆ getPositions()

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

Get the array of all positions.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection ( unsigned  i,
unsigned  j 
) const
inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

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

Return true if we are doing a restart.

◆ getSizeOfBuffer()

void PLMD::ActionWithVector::getSizeOfBuffer ( const unsigned &  nactive_tasks,
unsigned &  bufsize 
)
privateinherited

Get the size of the buffer array that holds the data we are gathering over the MPI loop.

◆ getStep()

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

Return the present timestep.

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getTotalMatrixBookeeping()

void PLMD::ActionWithMatrix::getTotalMatrixBookeeping ( unsigned &  stashsize)
private

This is used to find the total amount of space we need for storing matrix elements.

◆ getTotAtoms()

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

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.

◆ getUnique()

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

◆ getUniqueLocal()

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

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const
protectedinherited

Get the units that we are operating in.

◆ getValueIndices()

std::pair< std::size_t, std::size_t > PLMD::ActionAtomistic::getValueIndices ( const AtomNumber i) const
protectedinherited

Used to interpret whether this index is a virtual atom or a real atom.

◆ getVirial()

Tensor PLMD::ActionAtomistic::getVirial ( ) const
inherited

Get the virial that is acting.

◆ hasStoredArguments()

bool PLMD::ActionWithVector::hasStoredArguments ( ) const
inherited

Check if there are any stored values in arguments.

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList ( const std::vector< std::string > &  c,
const ActionSet as,
Action action,
std::vector< Value * > &  arg 
)
staticinherited

Convert a list of argument names into a list of pointers to the values.

◆ interpretAtomList() [1/2]

void PLMD::ActionAtomistic::interpretAtomList ( std::vector< std::string > &  strings,
const std::vector< Value * > &  xpos,
Action action,
std::vector< AtomNumber > &  t 
)
staticinherited

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

◆ interpretAtomList() [2/2]

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

Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this.

◆ isActive()

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

Check if action is active.

◆ isAdjacencyMatrix()

virtual bool PLMD::ActionWithMatrix::isAdjacencyMatrix ( ) const
inlinevirtual

◆ isInSubChain()

virtual bool PLMD::ActionWithVector::isInSubChain ( unsigned &  nder)
inlinevirtualinherited

Check if we are in a subchain.

Reimplemented in PLMD::volumes::ActionVolume, and PLMD::matrixtools::MatrixTimesVector.

◆ isOptionOn()

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

Check if an option is on.

◆ lockRequests()

void PLMD::ActionWithVector::lockRequests ( )
overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )
inherited

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

◆ matrixChainContinues()

bool PLMD::ActionWithMatrix::matrixChainContinues ( ) const
inlineprotected

Does the matrix chain continue on from this action.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )
inlineinherited

Get a reference to force on energy.

◆ 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.

◆ parse()

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

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

bool PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
int  i,
std::vector< Value * > &  args 
)
inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

void PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
std::vector< Value * > &  args 
)
inherited

Parse a list of arguments.

◆ parseAtomList() [1/2]

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

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

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

Parse a list of atoms without a numbered keyword.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseNumbered()

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

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

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

Parse a vector with a number.

◆ parseVector()

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

Parse one keyword as std::vector.

◆ pbcApply()

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

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

Vector PLMD::ActionAtomistic::pbcDistance ( const Vector v1,
const Vector v2 
) const
inlineinherited

Compute the pbc distance between two positions.

◆ performTask() [1/2]

virtual void PLMD::ActionWithMatrix::performTask ( const std::string &  controller,
const unsigned &  index1,
const unsigned &  index2,
MultiValue myvals 
) const
pure virtual

◆ performTask() [2/2]

void PLMD::ActionWithMatrix::performTask ( const unsigned &  task_index,
MultiValue myvals 
) const
overridevirtual

Run over one row of the matrix.

Implements PLMD::ActionWithVector.

◆ prepare()

void PLMD::ActionWithVector::prepare ( )
overridevirtualinherited

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 from PLMD::Action.

Reimplemented in PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::matrixtools::MatrixTimesMatrix, PLMD::dimred::ProjectPoints, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::valtools::VStack, and PLMD::matrixtools::Voronoi.

◆ 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.

◆ reallyBuildArgumentStore()

unsigned PLMD::ActionWithVector::reallyBuildArgumentStore ( const unsigned &  argstart)
privateinherited

This is used to build the argument store when we cannot use the chain.

◆ registerKeywords()

void PLMD::ActionWithMatrix::registerKeywords ( Keywords keys)
static

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > &  arg)
inherited

Setup the dependencies.

◆ requestAtoms()

void PLMD::ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a,
const bool  clearDep = true 
)
inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > &  extra)
inherited

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )
inherited

Set the timestep that is stored in the action to the correct value.

◆ retrieveAtoms()

void PLMD::ActionWithVector::retrieveAtoms ( const bool &  force = false)
overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ runAllTasks()

void PLMD::ActionWithVector::runAllTasks ( )
protectedinherited

Run all the tasks in the list.

◆ runEndOfRowJobs()

virtual void PLMD::ActionWithMatrix::runEndOfRowJobs ( const unsigned &  ival,
const std::vector< unsigned > &  indices,
MultiValue myvals 
) const
pure virtual

◆ 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.

◆ runInSerial()

bool PLMD::ActionWithVector::runInSerial ( ) const
inlineprotectedinherited

Run all calculations in serial.

◆ runTask()

void PLMD::ActionWithMatrix::runTask ( const std::string &  controller,
const unsigned &  current,
const unsigned  colno,
MultiValue myvals 
) const
private

This does the calculation of a particular matrix element.

◆ setExtraCV()

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

◆ setForcesOnAtoms()

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

Add the forces to the atoms.

◆ setForcesOnCell() [1/2]

void PLMD::ActionAtomistic::setForcesOnCell ( const double *  forcesToApply,
std::size_t  size,
unsigned &  ind 
)
inherited

Add the virial forces (span-like syntax)

◆ setForcesOnCell() [2/2]

void PLMD::ActionAtomistic::setForcesOnCell ( const std::vector< double > &  forcesToApply,
unsigned &  ind 
)
inherited

Add the virial forces.

◆ setGlobalPosition()

void PLMD::ActionAtomistic::setGlobalPosition ( const std::pair< std::size_t, std::size_t > &  a,
const Vector pos 
)
inlineinherited

Modify 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.

◆ setGradients()

void PLMD::ActionWithArguments::setGradients ( Value myval,
unsigned &  start 
) const
inherited

Get the gradient for this action.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
virtualinherited

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

Reimplemented in PLMD::ActionForInterface.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool &  have_atoms)
inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setupForTask()

virtual void PLMD::ActionWithMatrix::setupForTask ( const unsigned &  task_index,
std::vector< unsigned > &  indices,
MultiValue myvals 
) const
pure virtual

◆ setupStreamedComponents()

void PLMD::ActionWithMatrix::setupStreamedComponents ( const std::string &  headstr,
unsigned &  nquants,
unsigned &  nmat,
unsigned &  maxcol,
unsigned &  nbookeeping 
)
overridevirtual

This requires some thought.

Reimplemented from PLMD::ActionWithVector.

Reimplemented in PLMD::function::FunctionOfMatrix< T >.

◆ 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.

◆ switchTaskReduction()

virtual void PLMD::ActionWithVector::switchTaskReduction ( const bool &  task_reduction,
ActionWithVector aselect 
)
inlinevirtualinherited

Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere.

◆ taskIsActive()

void PLMD::ActionWithVector::taskIsActive ( const unsigned &  current,
int &  flag 
) const
privateinherited

Check if a particular task is active at this time.

◆ transferNonZeroMatrixElementsToValues()

void PLMD::ActionWithMatrix::transferNonZeroMatrixElementsToValues ( unsigned &  nval,
const std::vector< unsigned > &  matbook 
)
private

This transfers the non-zero elements to the Value.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests()

void PLMD::ActionWithVector::unlockRequests ( )
overridevirtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ update()

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

◆ updateAdditionalIndices()

virtual void PLMD::ActionWithVector::updateAdditionalIndices ( const unsigned &  ostrn,
MultiValue myvals 
) const
inlinevirtualinherited

This is used to ensure that all indices are updated when you do local average.

Reimplemented in PLMD::matrixtools::MatrixTimesVector.

◆ updateAllNeighbourLists()

void PLMD::ActionWithMatrix::updateAllNeighbourLists ( )
private

Update all the neighbour lists in the chain.

◆ updateForceTasksFromValue()

void PLMD::ActionWithVector::updateForceTasksFromValue ( const Value myval,
std::vector< unsigned > &  force_tasks 
) const
virtualinherited

Get the force tasks that are active for this action.

Reimplemented in PLMD::gridtools::KDE.

◆ updateNeighbourList()

virtual void PLMD::ActionWithMatrix::updateNeighbourList ( )
inlinevirtual

This is overwritten in Adjacency matrix where we have a neighbour list.

Reimplemented in PLMD::adjmat::AdjacencyMatrixBase.

◆ updateTaskListReductionStatus()

void PLMD::ActionWithVector::updateTaskListReductionStatus ( )
protectedinherited

This updates whether or not we are using all the task reduction stuff.

◆ updateTaskReductionFlag()

void PLMD::ActionWithVector::updateTaskReductionFlag ( bool &  head_reduce_tasks)
privateinherited

Turn on task reduction flag in dependent actions.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( const bool &  useunique,
const std::vector< int > &  g2l 
)
privateinherited

◆ 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.

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const
protectedinherited

Are we using natural units.

◆ warning()

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

Issue a warning.

◆ writeInGraph()

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

Member Data Documentation

◆ action_to_do_after

ActionWithVector* PLMD::ActionWithVector::action_to_do_after
privateinherited

Actions that must be done after this one.

◆ action_to_do_before

ActionWithVector* PLMD::ActionWithVector::action_to_do_before
privateinherited

Action that must be done before this one.

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ active_tasks

std::vector<unsigned> PLMD::ActionWithVector::active_tasks
privateinherited

The list of active tasks.

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ arg_deriv_starts

std::vector<unsigned> PLMD::ActionWithVector::arg_deriv_starts
protectedinherited

A vector that contains the start point for the argument derivatives.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments
privateinherited

◆ atom_value_ind

std::vector<std::pair<std::size_t, std::size_t > > PLMD::ActionAtomistic::atom_value_ind
privateinherited

◆ atom_value_ind_grouped

std::vector<std::pair<std::size_t,std::vector<std::size_t> > > PLMD::ActionAtomistic::atom_value_ind_grouped
privateinherited

◆ atomsWereRetrieved

bool PLMD::ActionWithVector::atomsWereRetrieved
privateinherited

Were the atoms retrieved in some earlier action.

◆ boxValue

Value* PLMD::ActionAtomistic::boxValue
privateinherited

◆ buffer

std::vector<double> PLMD::ActionWithVector::buffer
privateinherited

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

◆ charges

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

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet
protectedinherited

◆ chargev

std::vector<Value*> PLMD::ActionAtomistic::chargev
privateinherited

◆ clearOnEachCycle

bool PLMD::ActionWithMatrix::clearOnEachCycle
protected

This turns off derivative clearing for contact matrix if we are not storing derivatives.

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ defaults

std::string PLMD::Action::defaults
privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ done_in_chain

bool PLMD::ActionWithVector::done_in_chain
protectedinherited

Assert if this action is part of a chain.

◆ donotforce

bool PLMD::ActionAtomistic::donotforce
privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve
privateinherited

◆ energy

double PLMD::ActionAtomistic::energy
privateinherited

◆ files

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

◆ firststep

bool PLMD::ActionWithValue::firststep
privateinherited

This finishes setup on first step to check if actions are calculated during update.

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy
privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV
privateinherited

◆ forces

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

◆ forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply
privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

◆ indexes

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

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ label

std::string PLMD::Action::label
privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line
privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments
privateinherited

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms
privateinherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ masses

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

◆ massesWereSet

bool PLMD::ActionAtomistic::massesWereSet
protectedinherited

◆ masv

std::vector<Value*> PLMD::ActionAtomistic::masv
privateinherited

◆ matrix_bookeeping

std::vector<unsigned> PLMD::ActionWithMatrix::matrix_bookeeping
private

This holds the bookeeping arrays for sparse matrices.

◆ matrix_to_do_after

ActionWithMatrix* PLMD::ActionWithMatrix::matrix_to_do_after
private

◆ matrix_to_do_before

ActionWithMatrix* PLMD::ActionWithMatrix::matrix_to_do_before
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ name

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

Name of the directive in the plumed.dat file.

◆ never_activate

bool PLMD::Action::never_activate
privateinherited

◆ never_reduce_tasks

bool PLMD::ActionWithVector::never_reduce_tasks
privateinherited

This is turned on if there is some action that needs all the tasks.

◆ next_action_in_chain

ActionWithMatrix* PLMD::ActionWithMatrix::next_action_in_chain
private

◆ noderiv

bool PLMD::ActionWithValue::noderiv
privateinherited

Are we skipping the calculation of the derivatives.

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives
privateinherited

Are we using numerical derivatives to differentiate.

◆ options

std::set<std::string> PLMD::Action::options
privateinherited

Option that you might have enabled.

◆ pbc

Pbc& PLMD::ActionAtomistic::pbc =*pbc_fwd
privateinherited

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd
privateinherited

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ positions

std::vector<Vector> PLMD::ActionAtomistic::positions
privateinherited

◆ reduce_tasks

bool PLMD::ActionWithVector::reduce_tasks
privateinherited

Are we allowed to reduce the number of tasks being performed.

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ serial

bool PLMD::ActionWithVector::serial
privateinherited

Is the calculation to be done in serial.

◆ task_control_list

std::vector<ActionWithVector*> PLMD::ActionWithVector::task_control_list
privateinherited

This is the list of actions that control the tasks that we do here.

◆ timestep

double PLMD::Action::timestep
privateinherited

Save the timestep here.

◆ unique

std::vector<AtomNumber> PLMD::ActionAtomistic::unique
privateinherited

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

◆ unique_local

std::vector<AtomNumber> PLMD::ActionAtomistic::unique_local
privateinherited

◆ unique_local_needs_update

bool PLMD::ActionAtomistic::unique_local_needs_update
privateinherited

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

◆ update_from

double PLMD::Action::update_from
privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until
privateinherited

Update only until this time.

◆ valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce
privateinherited

◆ value_depends

std::vector<std::size_t> PLMD::ActionAtomistic::value_depends
privateinherited

◆ values

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

An array containing the values for this action.

◆ xpos

std::vector<Value*> PLMD::ActionAtomistic::xpos
privateinherited

Values that hold information about atom positions and charges.

◆ ypos

std::vector<Value*> PLMD::ActionAtomistic::ypos
privateinherited

◆ zpos

std::vector<Value*> PLMD::ActionAtomistic::zpos
privateinherited

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