Base class for all the input Actions. More...
#include <Action.h>
Public Types | |
typedef std::vector< Action * > | Dependencies |
typedef std::set< FILE * > ::iterator | files_iterator |
Public Member Functions | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | clearDependencies () |
Clear the dependence list for this Action. More... | |
long int | getStep () const |
Return the present timestep. More... | |
double | getTime () const |
Return the present time. More... | |
double | getTimeStep () const |
Return the timestep. More... | |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. More... | |
template<class T > | |
bool | parseNumbered (const std::string &key, const int no, T &t) |
Parse one numbered keyword as generic type. More... | |
template<class T > | |
void | parseVector (const std::string &key, std::vector< T > &t) |
Parse one keyword as std::vector. More... | |
template<class T > | |
bool | parseNumberedVector (const std::string &key, const int no, std::vector< T > &t) |
Parse a vector with a number. More... | |
void | parseFlag (const std::string &key, bool &t) |
Parse one keyword as boolean flag. More... | |
void | error (const std::string &msg) const |
Crash calculation and print documentation. More... | |
void | warning (const std::string &msg) |
Issue a warning. More... | |
void | exit (int c=0) |
Exit with error code c. More... | |
Action (const ActionOptions &) | |
Standard constructor from ActionOptions. More... | |
virtual | ~Action () |
Destructor. More... | |
void | checkRead () |
Check if Action was properly read. More... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
virtual void | lockRequests () |
virtual void | unlockRequests () |
virtual void | calculate ()=0 |
Calculate an Action. More... | |
virtual void | apply ()=0 |
Apply an Action. More... | |
virtual void | update () |
Update. More... | |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. More... | |
void | fflush () |
Tell to the Action to flush open files. More... | |
virtual std::string | getDocumentation () const |
const std::string & | getLabel () const |
Returns the label. More... | |
const std::string & | getName () const |
Returns the name. More... | |
virtual void | activate () |
Set action to active. More... | |
virtual void | setOption (const std::string &s) |
virtual void | clearOptions () |
virtual void | deactivate () |
Set action to inactive. More... | |
bool | isActive () const |
Check if action is active. More... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual bool | checkNumericalDerivatives () const |
Check if numerical derivatives should be performed. More... | |
virtual bool | checkNeedsGradients () const |
Check if the action needs gradient. More... | |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Perform calculation using numerical derivatives N.B. More... | |
FILE * | fopen (const char *path, const char *mode) |
Opens a file. More... | |
int | fclose (FILE *fp) |
Closes a file opened with Action::fclose(). More... | |
void | calculateFromPDB (const PDB &) |
Calculate the action given a pdb file as input. More... | |
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... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. More... | |
std::string | cite (const std::string &s) |
Cite a paper see PlumedMain::cite. More... | |
Static Public Member Functions | |
static void | registerKeywords (Keywords &keys) |
Register all the relevant keywords for the action. More... | |
Public Attributes | |
PlumedMain & | plumed |
Reference to main plumed object. More... | |
Log & | log |
Reference to the log stream. More... | |
std::set< FILE * > | files |
Communicator & | comm |
Communicator & | multi_sim_comm |
const Keywords & | keywords |
Private Member Functions | |
Action (const Action &a) | |
Copy constructor is disabled (private and unimplemented) More... | |
Action & | operator= (const Action &a) |
Assignment operator is disabled (private and unimplemented) More... | |
Private Attributes | |
const std::string | name |
Name of the directive in the plumed.dat file. 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... | |
Dependencies | after |
Actions on which this Action depends. More... | |
bool | active |
Switch to activate Action on this step. More... | |
std::set< std::string > | options |
Option that you might have enabled. More... | |
Base class for all the input Actions.
The input Actions are more or less corresponding to the directives in the plumed.dat file and are applied in order at each time-step.
typedef std::vector<Action*> PLMD::Action::Dependencies |
typedef std::set<FILE*>::iterator PLMD::Action::files_iterator |
PLMD::Action::Action | ( | const ActionOptions & | ao | ) |
Standard constructor from ActionOptions.
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virtual |
Destructor.
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private |
Copy constructor is disabled (private and unimplemented)
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virtual |
Set action to active.
void PLMD::Action::addDependency | ( | Action * | action | ) |
Specify that this Action depends on another one.
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pure virtual |
Apply an Action.
This method is called one time per step. The set of all Actions is applied in backward order.
Implemented in PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::generic::WholeMolecules, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::multicolvar::Sprint, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::IMD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::Include, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.
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pure virtual |
Calculate an Action.
This method is called one or more times per step. The set of all Actions is calculated in forward order.
Implemented in PLMD::bias::MetaD, PLMD::function::FuncSumHills, PLMD::function::Matheval, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::generic::WholeMolecules, PLMD::multicolvar::ActionVolume, PLMD::generic::Group, PLMD::bias::External, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::multicolvar::MultiColvarFunction, PLMD::colvar::ContactMap, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::colvar::NOE, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::colvar::PathMSDBase, PLMD::function::Piecewise, PLMD::colvar::Position, PLMD::vatom::Center, PLMD::colvar::Torsion, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvar, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::vatom::COM, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::vatom::Ghost, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::function::Target, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.
void PLMD::Action::calculateFromPDB | ( | const PDB & | pdb | ) |
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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virtual |
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::analysis::Analysis, PLMD::ActionAtomistic, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarFunction, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.
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inlinevirtual |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, and PLMD::generic::DumpProjections.
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inlinevirtual |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
void PLMD::Action::checkRead | ( | ) |
Check if Action was properly read.
This checks if Action::line is empty. It must be called after a final Action has been initialized
std::string PLMD::Action::cite | ( | const std::string & | s | ) |
Cite a paper see PlumedMain::cite.
void PLMD::Action::clearDependencies | ( | ) |
Clear the dependence list for this Action.
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virtual |
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inlinevirtual |
Set action to inactive.
void PLMD::Action::error | ( | const std::string & | msg | ) | const |
Crash calculation and print documentation.
void PLMD::Action::exit | ( | int | c = 0 | ) |
Exit with error code c.
int PLMD::Action::fclose | ( | FILE * | fp | ) |
Closes a file opened with Action::fclose().
void PLMD::Action::fflush | ( | ) |
Tell to the Action to flush open files.
FILE * PLMD::Action::fopen | ( | const char * | path, |
const char * | mode | ||
) |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
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inline |
Return dependencies.
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virtual |
bool PLMD::Action::getExchangeStep | ( | ) | const |
Check if we are on an exchange step.
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inline |
Returns the label.
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inline |
Returns the name.
long int PLMD::Action::getStep | ( | ) | const |
Return the present timestep.
double PLMD::Action::getTime | ( | ) | const |
Return the present time.
double PLMD::Action::getTimeStep | ( | ) | const |
Return the timestep.
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inline |
Check if action is active.
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inline |
Check if an option is on.
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inlinevirtual |
Reimplemented in PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
Assignment operator is disabled (private and unimplemented)
void PLMD::Action::parse | ( | const std::string & | key, |
T & | t | ||
) |
Parse one keyword as generic type.
void PLMD::Action::parseFlag | ( | const std::string & | key, |
bool & | t | ||
) |
Parse one keyword as boolean flag.
bool PLMD::Action::parseNumbered | ( | const std::string & | key, |
const int | no, | ||
T & | t | ||
) |
Parse one numbered keyword as generic type.
bool PLMD::Action::parseNumberedVector | ( | const std::string & | key, |
const int | no, | ||
std::vector< T > & | t | ||
) |
Parse a vector with a number.
void PLMD::Action::parseVector | ( | const std::string & | key, |
std::vector< T > & | t | ||
) |
Parse one keyword as std::vector.
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virtual |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.
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inlinevirtual |
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 |
Register all the relevant keywords for the action.
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inlinevirtual |
RunFinalJobs This method is called once at the very end of the calculation.
The set of all Actions in run for the final time in forward order.
Reimplemented in PLMD::analysis::Analysis.
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virtual |
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inlinevirtual |
Reimplemented in PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
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inlinevirtual |
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::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.
void PLMD::Action::warning | ( | const std::string & | msg | ) |
Issue a warning.
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private |
Switch to activate Action on this step.
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private |
Actions on which this Action depends.
Communicator& PLMD::Action::comm |
std::set<FILE*> PLMD::Action::files |
const Keywords& PLMD::Action::keywords |
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private |
Label of the Action, as set with LABEL= in the plumed.dat file.
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private |
Directive line.
This line is progressively erased during Action construction so as to check if all the present keywords are correct.
Log& PLMD::Action::log |
Reference to the log stream.
Communicator& PLMD::Action::multi_sim_comm |
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private |
Name of the directive in the plumed.dat file.
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private |
Option that you might have enabled.
PlumedMain& PLMD::Action::plumed |
Reference to main plumed object.
Hosted by GitHub | 1.8.7 |