Provides the keyword LOCALENSEMBLE More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
LocalEnsemble (const ActionOptions &) | |
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 | 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... | |
void | apply () override |
Apply an 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... | |
void | calculate () override |
Calculate an Action. 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... | |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Perform calculation using numerical derivatives N.B. More... | |
void | calculateNumericalDerivatives (ActionWithValue *a=NULL) override |
Calculate the numerical derivatives N.B. More... | |
virtual bool | calculateOnUpdate () |
This is used to check if we run calculate during the update step. More... | |
virtual ActionAtomistic * | castToActionAtomistic () noexcept |
virtual ActionForInterface * | castToActionForInterface () noexcept |
virtual ActionShortcut * | castToActionShortcut () noexcept |
virtual ActionToGetData * | castToActionToGetData () noexcept |
virtual ActionToPutData * | castToActionToPutData () noexcept |
virtual ActionWithArguments * | castToActionWithArguments () noexcept |
ActionWithArguments * | castToActionWithArguments () noexcept final |
ActionWithValue * | castToActionWithValue () noexcept final |
Specialized casts, to make PlumedMain run faster. More... | |
virtual ActionWithVirtualAtom * | castToActionWithVirtualAtom () noexcept |
virtual DomainDecomposition * | castToDomainDecomposition () noexcept |
virtual PbcAction * | castToPbcAction () noexcept |
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... | |
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... | |
Value * | copyOutput (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... | |
Value * | copyOutput (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 | 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... | |
double | getArgument (const unsigned &iarg) |
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... | |
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 Dependencies & | getDependencies () const |
Return dependencies. More... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. 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... | |
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... | |
int | getNumberOfComponents () const |
Returns the number of values defined. More... | |
unsigned | getNumberOfDerivatives () override |
std::string | getOutputComponentDescription (const std::string &cname, const Keywords &keys) const override |
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... | |
Value * | getPntrToArgument (const unsigned n) const |
Return a pointer to specific argument. 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... | |
bool | isActive () const |
Check if action is active. More... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
virtual void | lockRequests () |
void | lockRequests () override |
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 | 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... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
virtual void | readAtomsFromPDB (const PDB &) |
This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More... | |
void | requestArguments (const std::vector< Value * > &arg) |
Setup the dependencies. More... | |
void | requestExtraDependencies (const std::vector< Value * > &extra) |
void | resetStoredTimestep () |
Set the timestep that is stored in the action to the correct value. More... | |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. 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... | |
void | setValue (Value *, double) |
Set the value. More... | |
virtual void | turnOnDerivatives () |
Activate the calculation of derivatives. More... | |
virtual void | unlockRequests () |
void | unlockRequests () override |
virtual void | update () |
Update. 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 | 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 | 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 | |
Communicator & | comm |
std::set< FILE * > | files |
const Keywords & | keywords |
Log & | log |
Reference to the log stream. More... | |
Communicator & | multi_sim_comm |
PlumedMain & | plumed |
Reference to main plumed object. More... | |
Protected Member Functions | |
void | addComponentWithDerivatives (const std::string &name) |
void | addValueWithDerivatives () |
bool | checkForForces () |
Accumulate the forces from the Values. More... | |
void | expandArgKeywordInPDB (const PDB &pdb) |
This changes the arg keyword in the pdb file. More... | |
const Value * | getConstPntrToComponent (int i) const |
Get a const pointer to the ith component. More... | |
const std::vector< double > & | getForcesToApply () const |
Get the forces to apply. More... | |
double | getKBoltzmann () const |
Get the value of Boltzmann's constant. More... | |
Value * | getPntrToComponent (const std::string &name) |
Return a pointer to the value by name. More... | |
Value * | getPntrToComponent (int i) |
Return a pointer to the component by index. More... | |
Value * | getPntrToValue () |
Get a pointer to the default value. More... | |
const Units & | getUnits () const |
Get the units that we are operating in. More... | |
void | setDerivative (int, double) |
void | setDerivative (Value *, int, double) |
void | setValue (const double &d) |
Set the default value (the one without name) More... | |
bool | usingNaturalUnits () const |
Are we using natural units. More... | |
Private Member Functions | |
int | getComponent (const std::string &name) const |
Return the index for the component named name. More... | |
Private Attributes | |
bool | active |
Switch to activate Action on this step. More... | |
Dependencies | after |
Actions on which this Action depends. More... | |
std::vector< Value * > | arguments |
std::string | defaults |
The set of default arguments that we are using. More... | |
bool | doCheckPoint |
unsigned | ens_dim |
bool | firststep |
This finishes setup on first step to check if actions are calculated during update. More... | |
std::vector< double > | forcesForApply |
A vector that is used to hold the forces that we will apply on the input quantities. More... | |
std::string | label |
Label of the Action, as set with LABEL= in the plumed.dat file. More... | |
std::vector< std::string > | line |
Directive line. More... | |
bool | lockRequestArguments |
const std::string | name |
Name of the directive in the plumed.dat file. More... | |
unsigned | narg |
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... | |
int | replica_index |
bool | restart |
double | timestep |
Save the timestep here. 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::unique_ptr< Value > > | values |
An array containing the values for this action. More... | |
Provides the keyword LOCALENSEMBLE
|
inherited |
|
explicit |
|
virtualinherited |
Set action to active.
|
inherited |
Add a value with a name like label.name.
|
protectedinherited |
|
virtualinherited |
Add a value with a name like label.name that has derivatives.
Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.
|
inherited |
Specify that this Action depends on another one.
|
inherited |
Add forces to arguments (used in apply)
|
inherited |
Add a value with the name label.
|
protectedinherited |
|
virtualinherited |
Add a value with the name label that has derivatives.
Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.
|
overridevirtualinherited |
Apply an Action.
This method is called one time per step. The set of all Actions is applied in backward order.
Implements PLMD::Action.
|
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.
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inlineinherited |
Takes one value and brings it back into the pbc of argument i.
|
overridevirtual |
Calculate an Action.
This method is called one or more times per step. The set of all Actions is calculated in forward order.
Implements PLMD::Action.
|
virtualinherited |
Used to calculate constant values in startup.
Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.
|
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
|
virtualinherited |
Perform calculation using numerical derivatives N.B.
only pass an ActionWithValue to this routine if you know exactly what you are doing.
Reimplemented in PLMD::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.
|
overridevirtualinherited |
Calculate the numerical derivatives 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.
|
virtualinherited |
This is used to check if we run calculate during the update step.
Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionAtomistic.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionForInterface.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionShortcut.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionToGetData.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionToPutData.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionWithArguments.
|
inlinefinalvirtualnoexceptinherited |
Reimplemented from PLMD::Action.
|
inlinefinalvirtualnoexceptinherited |
Specialized casts, to make PlumedMain run faster.
Reimplemented from PLMD::Action.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionWithVirtualAtom.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::DomainDecomposition.
|
inlinevirtualnoexceptinherited |
Reimplemented in PLMD::PbcAction.
|
inlinevirtualinherited |
Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.
|
inherited |
Check that this action does not depend on the action in the argument.
|
protectedinherited |
Accumulate the forces from the Values.
|
inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.
|
inlineoverridevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
|
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
|
inherited |
Check if action should be updated.
|
inherited |
Cite a paper see PlumedMain::cite.
|
inherited |
Clear the dependence list for this Action.
|
virtualinherited |
Clear the derivatives of values wrt parameters.
Reimplemented in PLMD::ActionWithVector, PLMD::ActionForInterface, PLMD::generic::Constant, and PLMD::mapping::PathDisplacements.
|
virtualinherited |
Clear the forces on the values.
Reimplemented in PLMD::ActionWithVector.
|
virtualinherited |
|
inherited |
Set your value component to have no periodicity.
|
inherited |
Set the value to be periodic with a particular domain.
|
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.
|
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.
|
inlinevirtualinherited |
Set action to inactive.
|
inlineinherited |
Takes the difference taking into account pbc for arg i.
|
inlinevirtualinherited |
Are we not calculating derivatives.
|
inherited |
Crash calculation and print documentation.
|
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.
|
inherited |
Exit with error code c.
|
protectedinherited |
This changes the arg keyword in the pdb file.
|
inherited |
Closes a file opened with Action::fclose().
|
inherited |
Tell to the Action to flush open files.
|
inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
|
inlineinherited |
|
inlineinherited |
Returns the value of an argument.
|
inlinevirtualinherited |
Returns an array of pointers to the arguments.
|
privateinherited |
Return the index for the component named name.
|
inherited |
get a string that contains all the available components
|
inherited |
get a vector that contains the label for all the components
|
protectedinherited |
Get a const pointer to the ith component.
|
inherited |
Return true if we are doing at a checkpoint step.
|
inlineinherited |
Get the defaults.
|
inlineinherited |
Return dependencies.
|
inherited |
Check if we are on an exchange step.
|
inlineprotectedinherited |
Get the forces to apply.
|
protectedinherited |
Get the value of Boltzmann's constant.
|
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.
|
inherited |
Just read one of the keywords and return the whole thing as a string.
|
inlineinherited |
Returns the label.
|
virtualinherited |
Get the titles to use for the columns of the matrix.
Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.
|
inlineinherited |
Returns the name.
|
inlinevirtualinherited |
Returns the number of arguments.
|
inlineinherited |
Returns the number of values defined.
|
inlineoverridevirtualinherited |
Implements PLMD::ActionWithValue.
|
overridevirtual |
Get the description of this component.
Reimplemented from PLMD::ActionWithValue.
|
inlineinherited |
Get the value with a specific name (N.B. if there is no such value this returns zero)
|
inlineinherited |
Get the value of one of the components of the PLMD::Action.
|
inlineinherited |
Return a pointer to specific argument.
|
protectedinherited |
Return a pointer to the value by name.
|
protectedinherited |
Return a pointer to the component by index.
|
inlineprotectedinherited |
Get a pointer to the default value.
|
inherited |
Get the scalar product between the gradients of two variables.
|
inlineinherited |
Return true if we are doing a restart.
|
inherited |
Return the present timestep.
|
inherited |
Return the present time.
|
inherited |
Return the timestep.
|
protectedinherited |
Get the units that we are operating in.
|
staticinherited |
Convert a list of argument names into a list of pointers to the values.
|
inlineinherited |
Check if action is active.
|
inlineinherited |
Check if an option is on.
|
inlinevirtualinherited |
|
inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.
|
staticinherited |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.
|
inherited |
Parse one keyword as generic type.
|
inherited |
Parse a numbered list of arguments.
|
inherited |
Parse a list of arguments.
|
inherited |
Parse one keyword as boolean flag.
|
inherited |
Parse one numbered keyword as generic type.
|
inherited |
Parse a vector with a number.
|
inherited |
Parse one keyword as std::vector.
|
virtualinherited |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::dimred::ArrangePoints, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::matrixtools::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::generic::CreateMask, PLMD::matrixtools::DiagonalizeMatrix, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::valtools::VStack, PLMD::landmarks::FarthestPointSampling, PLMD::colvar::CoordinationBase, PLMD::matrixtools::TransposeMatrix, PLMD::matrixtools::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.
|
inlinevirtualinherited |
This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.
Reimplemented in PLMD::ActionAtomistic.
|
static |
|
inherited |
Setup the dependencies.
|
inherited |
|
inherited |
Set the timestep that is stored in the action to the correct value.
|
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.
|
inlineprotectedinherited |
|
inlineprotectedinherited |
|
inherited |
Get the gradient for this action.
|
virtualinherited |
Calculate the gradients and store them for all the values (need for projections)
Reimplemented in PLMD::ActionForInterface.
|
inherited |
Set your default value to have no periodicity.
|
virtualinherited |
|
inherited |
Set the value to be periodic with a particular domain.
|
inherited |
This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.
|
inlineprotectedinherited |
Set the default value (the one without name)
|
inherited |
Set the value.
|
virtualinherited |
Activate the calculation of derivatives.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::Read, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::function::FunctionOfScalar< T >, PLMD::adjmat::Neighbors, PLMD::eds::EDS, and PLMD::fisst::FISST.
|
inlinevirtualinherited |
|
inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.
|
inlinevirtualinherited |
Update.
This method is called one time per step. The set of all Actions is updated in forward order.
Reimplemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::generic::PrintNDX, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.
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staticinherited |
The components in the action will depend on the user.
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inlineinherited |
This forces the class to use numerical derivatives.
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protectedinherited |
Are we using natural units.
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inherited |
Issue a warning.
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virtualinherited |
Get the info on what to calculate.
Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.
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privateinherited |
Switch to activate Action on this step.
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privateinherited |
Actions on which this Action depends.
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privateinherited |
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inherited |
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privateinherited |
The set of default arguments that we are using.
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privateinherited |
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private |
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inherited |
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privateinherited |
This finishes setup on first step to check if actions are calculated during update.
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privateinherited |
A vector that is used to hold the forces that we will apply on the input quantities.
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inherited |
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privateinherited |
Label of the Action, as set with LABEL= in the plumed.dat file.
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privateinherited |
Directive line.
This line is progressively erased during Action construction so as to check if all the present keywords are correct.
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privateinherited |
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inherited |
Reference to the log stream.
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inherited |
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privateinherited |
Name of the directive in the plumed.dat file.
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private |
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privateinherited |
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privateinherited |
Are we skipping the calculation of the derivatives.
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privateinherited |
Are we using numerical derivatives to differentiate.
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privateinherited |
Option that you might have enabled.
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inherited |
Reference to main plumed object.
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privateinherited |
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privateinherited |
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privateinherited |
Save the timestep here.
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privateinherited |
Update only after this time.
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privateinherited |
Update only until this time.
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privateinherited |
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privateinherited |
An array containing the values for this action.
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