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::maze::Optimizer Class Referenceabstract

Base class for implementing optimizers for ligand unbinding. More...

#include "maze/Optimizer.h"

Inheritance diagram for PLMD::maze::Optimizer:
Inheritance graph
[legend]

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Optimizer (const ActionOptions &)
 PLMD constructor. More...
 
 ~Optimizer ()
 Destructor. More...
 
virtual bool actionHasForces ()
 
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 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 beforeUpdate ()
 Before Update. More...
 
void calculate ()
 Calculate the optimal direction of pulling. More...
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL) override
 N.B. More...
 
virtual bool calculateOnUpdate ()
 This is used to check if we run calculate during the update step. More...
 
ActionAtomisticcastToActionAtomistic () noexcept final
 
virtual ActionForInterfacecastToActionForInterface () noexcept
 
virtual ActionShortcutcastToActionShortcut () noexcept
 
virtual ActionToGetDatacastToActionToGetData () noexcept
 
virtual ActionToPutDatacastToActionToPutData () noexcept
 
virtual ActionWithArgumentscastToActionWithArguments () noexcept
 
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
 
Vector center_of_mass () const
 Calculate the center of mass. More...
 
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...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
virtual void clearDerivatives (const bool &force=false)
 Clear the derivatives of values wrt parameters. More...
 
virtual void clearInputForces (const bool &force=false)
 Clear the forces on the 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...
 
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...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
std::string get_label () const
 Getters and setters. More...
 
unsigned int get_n_iterations () const
 
unsigned int get_n_threads_openmp () const
 
double get_nl_cutofff () const
 
unsigned int get_nl_stride () const
 
Vector get_opt () const
 
double get_opt_value () const
 
unsigned int get_optimizer_stride () const
 
unsigned int get_rank_openmp () const
 
double get_sampling_radius () const
 
unsigned int get_stride_openmp () const
 
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...
 
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...
 
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...
 
const std::string & getName () const
 Returns the name. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned getNumberOfDerivatives () override
 
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...
 
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...
 
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...
 
void interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
 Convert a set of read in strings into an atom list (this is used in parseAtomList) More...
 
bool is_pbc_on () const
 
bool isActive () const
 Check if action is active. 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...
 
virtual void optimize ()=0
 Optimal values needed for biasing are computed by methods overridding the optimize function. More...
 
virtual double pairing (double distance) const
 The pairing function needs to be overridden by a specific optimizer. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
void parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
 Parse an list of atom with a numbred keyword. More...
 
void parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
 Parse a list of atoms without a numbered keyword. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
void pbc_off ()
 
void pbc_on ()
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
void prepare ()
 Prepare the neighbor list. More...
 
void readAtomsFromPDB (const PDB &pdb) override
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
void requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
 Request an array of atoms. More...
 
virtual void retrieveAtoms (const bool &force=false)
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
double sampling_radius ()
 Calculate sampling radius as the minimal distance between two groups in neighbors list. More...
 
double score ()
 Score a ligand-protein configuration. More...
 
void set_label (const std::string &)
 
void set_n_iterations (unsigned int)
 
void set_n_threads_openmp (unsigned int)
 
void set_nl_cutoff (double)
 
void set_nl_stride (unsigned int)
 
void set_opt (Vector)
 
void set_opt_value (double)
 
void set_optimizer_stride (unsigned int)
 
void set_rank_openmp (unsigned int)
 
void set_sampling_radius (double)
 
void set_stride_openmp (unsigned int)
 
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...
 
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...
 
void setValue (Value *, double)
 Set the value. More...
 
void start_step_0 ()
 
void start_step_stride ()
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void unlockRequests () override
 
virtual void update ()
 Update. More...
 
void update_nl ()
 Load new positions of atoms in the neighbor 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 componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &keys)
 Registers PLMD keywords. More...
 
static void setBoxDerivativesNoPbc (const std::vector< Vector > &pos, std::vector< std::vector< Vector > > &derivs, std::vector< Tensor > &virial)
 
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...
 
Valuevalue_action_
 Loss value. More...
 
Valuevalue_sampling_radius_
 Sampling radiues value. More...
 
Valuevalue_x_
 Biased cv. More...
 
Valuevalue_y_
 
Valuevalue_z_
 

Protected Member Functions

void apply () override
 Apply an Action. More...
 
bool checkForForces ()
 Accumulate the forces from the Values. More...
 
const TensorgetBoxDerivatives () const
 
const ValuegetConstPntrToComponent (int i) const
 Get a const pointer to the ith component. More...
 
const double & getForce () const
 
const std::vector< double > & getForcesToApply () const
 Get the forces to apply. More...
 
double getKBoltzmann () const
 Get the value of Boltzmann's constant. 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...
 
void requestAtoms (const std::vector< AtomNumber > &a)
 
void setAtomsDerivatives (int, const Vector &)
 
void setAtomsDerivatives (Value *, int, const Vector &)
 
void setBoxDerivatives (const Tensor &)
 
void setBoxDerivatives (Value *, const Tensor &)
 
void setBoxDerivativesNoPbc ()
 Set box derivatives automatically. More...
 
void setBoxDerivativesNoPbc (Value *)
 
void setExtraCV (const std::string &name)
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
bool usingNaturalUnits () const
 Are we using natural units. More...
 

Protected Attributes

bool chargesWereSet
 
bool first_step_
 Start either at time = 0 or time = optimizer stride. More...
 
std::string label_
 Optimizer label. More...
 
unsigned int n_iter_
 Number of global iterations. More...
 
unsigned int n_threads_
 
std::unique_ptr< NeighborListneighbor_list_
 Neighbor list of ligand-protein atom pairs. More...
 
double nl_cutoff_
 Neighbor list cut-off. More...
 
int nl_stride_
 Neighbor list stride. More...
 
Vector opt_
 Biasing direction. More...
 
double opt_value_
 Current loss function value. More...
 
unsigned int optimizer_stride_
 Optimizer stride. More...
 
bool pbc_
 Periodic boundary conditions. More...
 
unsigned int rank_
 OpenMP. More...
 
double sampling_r_
 Sampling radius. More...
 
unsigned int stride_
 

Private Member Functions

int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 
void updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)
 

Private Attributes

bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
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
 
ValueboxValue
 
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 first_time_
 
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 lockRequestAtoms
 
Lossloss_
 Pointer to the loss function. More...
 
std::vector< double > masses
 
std::vector< Value * > masv
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
bool never_activate
 
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
 
int replica_index
 
bool restart
 
bool serial_
 
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...
 
bool validate_list_
 
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< Loss * > vec_loss_
 
std::vector< Value * > xpos
 Values that hold information about atom positions and charges. More...
 
std::vector< Value * > ypos
 
std::vector< Value * > zpos
 

Detailed Description

Base class for implementing optimizers for ligand unbinding.

An optimizer is defined as a colvar that can be passed to Optimizer_Bias.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Optimizer()

PLMD::maze::Optimizer::Optimizer ( const ActionOptions ao)
explicit

PLMD constructor.

Parameters
[in]aoPLMD::ActionOptions&

◆ ~Optimizer()

PLMD::maze::Optimizer::~Optimizer ( )
inline

Destructor.

Member Function Documentation

◆ actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )
virtualinherited

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ 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.

◆ addForce()

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

Add force to an atom.

◆ 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::Colvar::apply ( )
overrideprotectedvirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ 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.

◆ calculate()

void PLMD::maze::Optimizer::calculate ( )
virtual

Calculate the optimal direction of pulling.

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.

◆ 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::ActionAtomistic::calculateNumericalDerivatives ( ActionWithValue a = NULL)
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::Action.

Reimplemented in PLMD::ActionWithVector, PLMD::generic::DumpAtoms, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, and PLMD::isdb::MetainferenceBase.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )
virtualinherited

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

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::analysis::Accumulate, and PLMD::analysis::Collect.

◆ 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()

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

Reimplemented in PLMD::ActionWithArguments.

◆ 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.

◆ center_of_mass()

Vector PLMD::maze::Optimizer::center_of_mass ( ) const

Calculate the center of mass.

Returns
center of mass

◆ changeBox()

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

Change the box shape.

◆ checkFieldsAllowed()

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

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

◆ checkForDependency()

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

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

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )
protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

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

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

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

◆ checkUpdate()

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

Check if action should be updated.

◆ cite()

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

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( const bool &  force = false)
virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionForInterface, PLMD::generic::Constant, and PLMD::mapping::PathDisplacements.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( const bool &  force = false)
virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ 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.

◆ componentsAreNotOptional()

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

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

◆ 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.

◆ 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.

◆ 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.

◆ 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)

◆ get_label()

std::string PLMD::maze::Optimizer::get_label ( ) const
inline

Getters and setters.

◆ get_n_iterations()

unsigned int PLMD::maze::Optimizer::get_n_iterations ( ) const
inline

◆ get_n_threads_openmp()

unsigned int PLMD::maze::Optimizer::get_n_threads_openmp ( ) const
inline

◆ get_nl_cutofff()

double PLMD::maze::Optimizer::get_nl_cutofff ( ) const
inline

◆ get_nl_stride()

unsigned int PLMD::maze::Optimizer::get_nl_stride ( ) const
inline

◆ get_opt()

Vector PLMD::maze::Optimizer::get_opt ( ) const
inline

◆ get_opt_value()

double PLMD::maze::Optimizer::get_opt_value ( ) const
inline

◆ get_optimizer_stride()

unsigned int PLMD::maze::Optimizer::get_optimizer_stride ( ) const
inline

◆ get_rank_openmp()

unsigned int PLMD::maze::Optimizer::get_rank_openmp ( ) const
inline

◆ get_sampling_radius()

double PLMD::maze::Optimizer::get_sampling_radius ( ) const
inline

◆ get_stride_openmp()

unsigned int PLMD::maze::Optimizer::get_stride_openmp ( ) const
inline

◆ 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.

◆ getBox()

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

Get box shape.

◆ getBoxDerivatives()

const Tensor& PLMD::Colvar::getBoxDerivatives ( ) const
protectedinherited

◆ 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.

◆ 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.

◆ getForce() [1/2]

const double& PLMD::Colvar::getForce ( ) const
protectedinherited

◆ getForce() [2/2]

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.

◆ 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.

◆ getMass()

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

Get mass of i-th atom.

◆ getName()

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

Returns the name.

◆ getNumberOfAtoms()

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

Get number of available atoms.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::Colvar::getNumberOfDerivatives ( )
inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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

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

◆ getOutputQuantity() [2/2]

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

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

◆ getPbc()

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

Get reference to Pbc.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the component by index.

◆ getPntrToValue()

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

◆ getRestart()

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

Return true if we are doing a restart.

◆ 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.

◆ 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.

◆ interpretAtomList()

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

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

◆ is_pbc_on()

bool PLMD::maze::Optimizer::is_pbc_on ( ) const
inline

◆ isActive()

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

Check if action is active.

◆ isOptionOn()

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

Check if an option is on.

◆ lockRequests()

void PLMD::ActionAtomistic::lockRequests ( )
inlineoverridevirtualinherited

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )
inherited

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

◆ 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.

◆ optimize()

virtual void PLMD::maze::Optimizer::optimize ( )
pure virtual

Optimal values needed for biasing are computed by methods overridding the optimize function.

Implemented in PLMD::maze::Simulated_Annealing, PLMD::maze::Random_Walk, PLMD::maze::Random_Acceleration_MD, PLMD::maze::Steered_MD, and PLMD::maze::Memetic.

◆ pairing()

double PLMD::maze::Optimizer::pairing ( double  distance) const
virtual

The pairing function needs to be overridden by a specific optimizer.

Parameters
[in]distancedistance between a pair of atoms

◆ parse()

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

Parse one keyword as generic type.

◆ parseAtomList() [1/2]

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

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

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

Parse a list of atoms without a numbered keyword.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ 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.

◆ pbc_off()

void PLMD::maze::Optimizer::pbc_off ( )
inline

◆ pbc_on()

void PLMD::maze::Optimizer::pbc_on ( )
inline

◆ 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.

◆ prepare()

void PLMD::maze::Optimizer::prepare ( )
virtual

Prepare the neighbor list.

Reimplemented from PLMD::Action.

◆ readAtomsFromPDB()

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

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

Reimplemented from PLMD::Action.

◆ registerKeywords()

void PLMD::maze::Optimizer::registerKeywords ( Keywords keys)
static

Registers PLMD keywords.

Parameters
[in]keysPLMD keywords

◆ requestAtoms() [1/2]

void PLMD::Colvar::requestAtoms ( const std::vector< AtomNumber > &  a)
protectedinherited

◆ requestAtoms() [2/2]

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

Request an array of atoms.

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

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( const bool &  force = false)
virtualinherited

Reimplemented in PLMD::ActionWithVector.

◆ runFinalJobs()

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

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::generic::DumpPDB.

◆ sampling_radius()

double PLMD::maze::Optimizer::sampling_radius ( )

Calculate sampling radius as the minimal distance between two groups in neighbors list.

Returns
minimal distance of ligand-protein atom pairs

◆ score()

double PLMD::maze::Optimizer::score ( )

Score a ligand-protein configuration.

Returns
score

◆ set_label()

void PLMD::maze::Optimizer::set_label ( const std::string &  label)
inline

◆ set_n_iterations()

void PLMD::maze::Optimizer::set_n_iterations ( unsigned int  n_iter)
inline

◆ set_n_threads_openmp()

void PLMD::maze::Optimizer::set_n_threads_openmp ( unsigned int  n_threads)
inline

◆ set_nl_cutoff()

void PLMD::maze::Optimizer::set_nl_cutoff ( double  nl_cutoff)
inline

◆ set_nl_stride()

void PLMD::maze::Optimizer::set_nl_stride ( unsigned int  nl_stride)
inline

◆ set_opt()

void PLMD::maze::Optimizer::set_opt ( Vector  opt)
inline

◆ set_opt_value()

void PLMD::maze::Optimizer::set_opt_value ( double  opt_value)
inline

◆ set_optimizer_stride()

void PLMD::maze::Optimizer::set_optimizer_stride ( unsigned int  optimizer_stride)
inline

◆ set_rank_openmp()

void PLMD::maze::Optimizer::set_rank_openmp ( unsigned int  rank)
inline

◆ set_sampling_radius()

void PLMD::maze::Optimizer::set_sampling_radius ( double  sampling_r)
inline

◆ set_stride_openmp()

void PLMD::maze::Optimizer::set_stride_openmp ( unsigned int  stride)
inline

◆ setAtomsDerivatives() [1/2]

void PLMD::Colvar::setAtomsDerivatives ( int  i,
const Vector d 
)
inlineprotectedinherited

◆ setAtomsDerivatives() [2/2]

void PLMD::Colvar::setAtomsDerivatives ( Value v,
int  i,
const Vector d 
)
inlineprotectedinherited

◆ setBoxDerivatives() [1/2]

void PLMD::Colvar::setBoxDerivatives ( const Tensor d)
inlineprotectedinherited

◆ setBoxDerivatives() [2/2]

void PLMD::Colvar::setBoxDerivatives ( Value v,
const Tensor d 
)
inlineprotectedinherited

◆ setBoxDerivativesNoPbc() [1/3]

void PLMD::Colvar::setBoxDerivativesNoPbc ( )
inlineprotectedinherited

Set box derivatives automatically.

It should be called after the setAtomsDerivatives has been used for all single atoms.

Warning
It only works for collective variable NOT using PBCs!

◆ setBoxDerivativesNoPbc() [2/3]

void PLMD::Colvar::setBoxDerivativesNoPbc ( const std::vector< Vector > &  pos,
std::vector< std::vector< Vector > > &  derivs,
std::vector< Tensor > &  virial 
)
staticinherited

◆ setBoxDerivativesNoPbc() [3/3]

void PLMD::Colvar::setBoxDerivativesNoPbc ( Value v)
protectedinherited

◆ 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.

◆ 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.

◆ 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.

◆ start_step_0()

void PLMD::maze::Optimizer::start_step_0 ( )
inline

◆ start_step_stride()

void PLMD::maze::Optimizer::start_step_stride ( )
inline

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )
inlineoverridevirtualinherited

◆ update()

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

◆ update_nl()

void PLMD::maze::Optimizer::update_nl ( )

Load new positions of atoms in the neighbor list.

◆ 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

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ 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

◆ boxValue

Value* PLMD::ActionAtomistic::boxValue
privateinherited

◆ charges

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

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet
protectedinherited

◆ chargev

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

◆ 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

◆ 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

◆ first_step_

bool PLMD::maze::Optimizer::first_step_
protected

Start either at time = 0 or time = optimizer stride.

◆ first_time_

bool PLMD::maze::Optimizer::first_time_
private

◆ 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.

◆ label_

std::string PLMD::maze::Optimizer::label_
protected

Optimizer label.

◆ 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.

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms
privateinherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ loss_

Loss* PLMD::maze::Optimizer::loss_
private

Pointer to the loss function.

◆ masses

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

◆ masv

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

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ n_iter_

unsigned int PLMD::maze::Optimizer::n_iter_
protected

Number of global iterations.

◆ n_threads_

unsigned int PLMD::maze::Optimizer::n_threads_
protected

◆ name

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

Name of the directive in the plumed.dat file.

◆ neighbor_list_

std::unique_ptr<NeighborList> PLMD::maze::Optimizer::neighbor_list_
protected

Neighbor list of ligand-protein atom pairs.

◆ never_activate

bool PLMD::Action::never_activate
privateinherited

◆ nl_cutoff_

double PLMD::maze::Optimizer::nl_cutoff_
protected

Neighbor list cut-off.

◆ nl_stride_

int PLMD::maze::Optimizer::nl_stride_
protected

Neighbor list stride.

◆ 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.

◆ opt_

Vector PLMD::maze::Optimizer::opt_
protected

Biasing direction.

◆ opt_value_

double PLMD::maze::Optimizer::opt_value_
protected

Current loss function value.

◆ optimizer_stride_

unsigned int PLMD::maze::Optimizer::optimizer_stride_
protected

Optimizer stride.

◆ options

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

Option that you might have enabled.

◆ pbc

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

◆ pbc_

bool PLMD::maze::Optimizer::pbc_
protected

Periodic boundary conditions.

◆ 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

◆ rank_

unsigned int PLMD::maze::Optimizer::rank_
protected

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ sampling_r_

double PLMD::maze::Optimizer::sampling_r_
protected

Sampling radius.

◆ serial_

bool PLMD::maze::Optimizer::serial_
private

◆ stride_

unsigned int PLMD::maze::Optimizer::stride_
protected

◆ 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.

◆ validate_list_

bool PLMD::maze::Optimizer::validate_list_
private

◆ valsToForce

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

◆ value_action_

Value* PLMD::maze::Optimizer::value_action_

Loss value.

◆ value_depends

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

◆ value_sampling_radius_

Value* PLMD::maze::Optimizer::value_sampling_radius_

Sampling radiues value.

◆ value_x_

Value* PLMD::maze::Optimizer::value_x_

Biased cv.

◆ value_y_

Value* PLMD::maze::Optimizer::value_y_

◆ value_z_

Value* PLMD::maze::Optimizer::value_z_

◆ values

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

An array containing the values for this action.

◆ vec_loss_

std::vector<Loss*> PLMD::maze::Optimizer::vec_loss_
private

◆ 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: