Provides the keyword ABMD More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
ABMD (const ActionOptions &) | |
virtual void | activate () |
Set action to active. More... | |
void | addComponent (const std::string &name) |
Add a value with a name like label.name. More... | |
void | addComponentWithDerivatives (const std::string &name) |
Add a value with a name like label.name that has derivatives. More... | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | addForcesOnArguments (const std::vector< double > &forces) |
Add forces to arguments (used in apply) More... | |
void | addValue () |
Add a value with the name label. More... | |
void | addValueWithDerivatives () |
Add a value with the name label that has derivatives. More... | |
void | 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... | |
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 void | checkFieldsAllowed () |
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 () |
Clear the derivatives of values wrt parameters. More... | |
void | clearInputForces () |
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 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... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual std::string | getDocumentation () const |
bool | getExchangeStep () const |
Check if we are on an exchange step. 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... | |
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 |
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) |
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 int | getStep () const |
Return the present timestep. More... | |
int | getStride () const |
Get the stride. More... | |
double | getTime () const |
Return the present time. More... | |
double | getTimeStep () const |
Return the timestep. More... | |
void | interpretArgumentList (const std::vector< std::string > &c, std::vector< Value * > &arg) |
Convert a list of argument names into a list of pointers to the values. 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 |
virtual bool | onStep () const |
Check if the action is active on this step. 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 | 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) |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. More... | |
void | setGradientsIfNeeded () |
Calculate the gradients and store them for all the values (need for projections) More... | |
void | setNotPeriodic () |
Set your default value to have no periodicity. More... | |
virtual void | setOption (const std::string &s) |
void | setPeriodic (const std::string &min, const std::string &max) |
Set the value to be periodic with a particular domain. More... | |
void | setStride (const int &n) |
Set the value of the stride. 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... | |
Static Public Member Functions | |
static void | componentsAreNotOptional (Keywords &keys) |
Puts a message into the manual that the components always output. More... | |
static void | noAnalyticalDerivatives (Keywords &keys) |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More... | |
static void | registerKeywords (Keywords &keys) |
static void | useCustomisableComponents (Keywords &keys) |
The components in the action will depend on the user. More... | |
Public Attributes | |
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 | expandArgKeywordInPDB (const PDB &pdb) |
This changes the arg keyword in the pdb file. 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... | |
void | setBias (double bias) |
set the value of the bias More... | |
void | setOutputForce (int i, double f) |
set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More... | |
void | setValue (const double &d) |
Set the default value (the one without name) 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 |
bool | doCheckPoint |
std::vector< double > | kappa |
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 |
std::vector< double > | min |
const std::string | name |
Name of the directive in the plumed.dat file. More... | |
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... | |
std::vector< double > | outputForces |
the vector of the forces More... | |
std::vector< Random > | random |
int | replica_index |
bool | restart |
std::vector< int > | seed |
int | stride |
std::vector< double > | temp |
std::vector< double > | to |
double | update_from |
Update only after this time. More... | |
double | update_until |
Update only until this time. More... | |
Value * | valueBias |
the pointer to the bias component More... | |
std::vector< std::unique_ptr< Value > > | values |
An array containing the values for this action. More... | |
Provides the keyword ABMD
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inherited |
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explicit |
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virtualinherited |
Set action to active.
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inherited |
Add a value with a name like label.name.
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inherited |
Add a value with a name like label.name that has derivatives.
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inherited |
Specify that this Action depends on another one.
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inherited |
Add forces to arguments (used in apply)
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inherited |
Add a value with the name label.
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inherited |
Add a value with the name label that has derivatives.
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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.
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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.
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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.
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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
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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::vesselbase::ActionWithAveraging, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::ActionWithArguments, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithInputVessel, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.
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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::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.
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inlinevirtualinherited |
Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.
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inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.
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inlinevirtualinherited |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
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inlineoverridevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
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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
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inherited |
Check if action should be updated.
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inherited |
Cite a paper see PlumedMain::cite.
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inherited |
Clear the dependence list for this Action.
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virtualinherited |
Clear the derivatives of values wrt parameters.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
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inherited |
Clear the forces on the values.
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virtualinherited |
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inherited |
Set your value component to have no periodicity.
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inherited |
Set the value to be periodic with a particular domain.
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staticinherited |
Puts a message into the manual that the components always output.
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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.
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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.
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inlinevirtualinherited |
Set action to inactive.
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inlineinherited |
Takes the difference taking into account pbc for arg i.
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inlinevirtualinherited |
Are we not calculating derivatives.
Reimplemented in PLMD::multicolvar::MultiColvarBase.
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inherited |
Crash calculation and print documentation.
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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.
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inherited |
Exit with error code c.
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protectedinherited |
This changes the arg keyword in the pdb file.
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inherited |
Closes a file opened with Action::fclose().
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inherited |
Tell to the Action to flush open files.
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inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
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inlineinherited |
Returns the value of an argument.
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inlinevirtualinherited |
Returns an array of pointers to the arguments.
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privateinherited |
Return the index for the component named name.
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inherited |
get a string that contains all the available components
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inherited |
get a vector that contains the label for all the components
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inherited |
Return true if we are doing at a checkpoint step.
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inlineinherited |
Return dependencies.
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virtualinherited |
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inherited |
Check if we are on an exchange step.
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inherited |
Just read one of the keywords and return the whole thing as a string.
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inlineinherited |
Returns the label.
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inlineinherited |
Returns the name.
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inlinevirtualinherited |
Returns the number of arguments.
Reimplemented in PLMD::vesselbase::ActionWithAveraging.
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inlineinherited |
Returns the number of values defined.
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inlineoverridevirtualinherited |
Implements PLMD::ActionWithValue.
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inlineinherited |
Get the value with a specific name (N.B. if there is no such value this returns zero)
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inlineinherited |
Get the value of one of the components of the PLMD::Action.
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inlineinherited |
Return a pointer to specific argument.
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protectedinherited |
Return a pointer to the value by name.
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protectedinherited |
Return a pointer to the component by index.
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protectedinherited |
Get a pointer to the default value.
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inherited |
Get the scalar product between the gradients of two variables.
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inlineinherited |
Return true if we are doing a restart.
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inherited |
Return the present timestep.
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inherited |
Get the stride.
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inherited |
Return the present time.
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inherited |
Return the timestep.
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inherited |
Convert a list of argument names into a list of pointers to the values.
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inlineinherited |
Check if action is active.
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inlineinherited |
Check if an option is on.
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inlinevirtualinherited |
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inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
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staticinherited |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.
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virtualinherited |
Check if the action is active on this step.
Reimplemented in PLMD::gridtools::ConvertToFES.
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inherited |
Parse one keyword as generic type.
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inherited |
Parse a numbered list of arguments.
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inherited |
Parse a list of arguments.
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inherited |
Parse one keyword as boolean flag.
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inherited |
Parse one numbered keyword as generic type.
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inherited |
Parse a vector with a number.
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inherited |
Parse one keyword as std::vector.
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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::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.
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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.
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static |
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inherited |
Setup the dependencies.
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inherited |
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inlinevirtualinherited |
RunFinalJobs This method is called once at the very end of the calculation.
The set of all Actions in run for the final time in forward order.
Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.
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inlineprotectedinherited |
set the value of the bias
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inherited |
Calculate the gradients and store them for all the values (need for projections)
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inherited |
Set your default value to have no periodicity.
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virtualinherited |
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inlineprotectedinherited |
set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f
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inherited |
Set the value to be periodic with a particular domain.
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inherited |
Set the value of the stride.
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inlineprotectedinherited |
Set the default value (the one without name)
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inherited |
Set the value.
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virtualinherited |
Activate the calculation of derivatives.
Reimplemented in PLMD::isdb::EMMI, PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::gridtools::ActionWithIntegral, PLMD::eds::EDS, and PLMD::fisst::FISST.
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inlinevirtualinherited |
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inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
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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::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::PRE, PLMD::multicolvar::DumpMultiColvar, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, PLMD::gridtools::GridPrintingBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, and PLMD::fisst::FISST.
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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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inherited |
Issue a warning.
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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 |
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inherited |
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private |
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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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private |
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inherited |
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privateinherited |
Name of the directive in the plumed.dat file.
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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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privateinherited |
the vector of the forces
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inherited |
Reference to main plumed object.
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private |
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privateinherited |
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privateinherited |
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private |
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privateinherited |
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private |
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private |
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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 |
the pointer to the bias component
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privateinherited |
An array containing the values for this action.
Hosted by GitHub | 1.8.17 |