#include <ActionWithInputVessel.h>
Public Types | |
typedef std::vector< Action * > | Dependencies |
typedef std::set< FILE * >::iterator | files_iterator |
Public Member Functions | |
ActionWithInputVessel (const ActionOptions &) | |
virtual | ~ActionWithInputVessel () |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Calculate the numerical derivatives N.B. More... | |
void | applyBridgeForces (const std::vector< double > &bb) |
Apply forces from the bridge. More... | |
virtual void | addBridgeForces (const std::vector< double > &bb) |
Apply forces from the bridge. More... | |
bool | checkUpdate () const |
Check if action should be updated. More... | |
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... | |
bool | getRestart () const |
Return true if we are doing a restart. 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... | |
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... | |
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) |
Registers the list of keywords. 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 |
Protected Member Functions | |
void | readArgument (const std::string &type) |
What type of arguments are we reading in. More... | |
Vessel * | getPntrToArgument () |
Return a pointer to specific argument. More... | |
void | addForcesOnArguments (const std::vector< double > &forces) |
Add forces to arguments (used in apply) More... | |
Private Attributes | |
Vessel * | arguments |
BridgeVessel * | myBridgeVessel |
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inherited |
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inherited |
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explicit |
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inlinevirtual |
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virtualinherited |
Set action to active.
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inlinevirtual |
Apply forces from the bridge.
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inherited |
Specify that this Action depends on another one.
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protected |
Add forces to arguments (used in apply)
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pure virtualinherited |
Apply an Action.
This method is called one time per step. The set of all Actions is applied in backward order.
Implemented in PLMD::mapping::PCAVars, PLMD::generic::WrapAround, PLMD::analysis::Analysis, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::generic::EffectiveEnergyDrift, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, PLMD::generic::FitToTemplate, PLMD::multicolvar::Sprint, PLMD::mapping::Mapping, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarDensity, PLMD::generic::Print, PLMD::multicolvar::BridgedMultiColvarFunction, 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.
void PLMD::vesselbase::ActionWithInputVessel::applyBridgeForces | ( | const std::vector< double > & | bb | ) |
Apply forces from the bridge.
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pure virtualinherited |
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::bias::PBMetaD, PLMD::function::FuncSumHills, PLMD::mapping::PCAVars, PLMD::function::Matheval, PLMD::generic::WrapAround, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::bias::ExtendedLagrangian, PLMD::generic::Group, PLMD::colvar::Distance, PLMD::generic::DumpAtoms, PLMD::bias::MovingRestraint, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::bias::External, PLMD::generic::DumpMassCharge, PLMD::generic::FitToTemplate, PLMD::colvar::Gyration, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::colvar::ContactMap, PLMD::colvar::DRMSD, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::NOE, PLMD::IMD, PLMD::vatom::Center, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::RandomExchanges, PLMD::multicolvar::MultiColvarFunction, PLMD::function::Piecewise, PLMD::colvar::PathMSDBase, PLMD::colvar::Position, PLMD::multicolvar::DumpMultiColvar, PLMD::colvar::Torsion, PLMD::multicolvar::MultiColvarDensity, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::vatom::COM, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::colvar::Energy, PLMD::multicolvar::MultiColvar, PLMD::function::Sort, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::colvar::Dipole, PLMD::colvar::Puckering, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::function::Target, PLMD::colvar::Template, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::PCARMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.
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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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virtual |
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::multicolvar::MultiColvarDensity.
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inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, and PLMD::generic::DumpProjections.
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inlinevirtualinherited |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
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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 |
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inlinevirtualinherited |
Set action to inactive.
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inherited |
Crash calculation and print documentation.
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inherited |
Exit with error code c.
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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 |
Return dependencies.
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virtualinherited |
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inherited |
Check if we are on an exchange step.
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inlineinherited |
Returns the label.
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inlineinherited |
Returns the name.
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inlineprotected |
Return a pointer to specific argument.
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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 |
Return the present time.
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inherited |
Return the timestep.
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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 |
Reimplemented in PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
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inherited |
Parse one keyword as generic type.
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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::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.
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protected |
What type of arguments are we reading in.
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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 |
Registers the list of keywords.
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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::analysis::Analysis.
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virtualinherited |
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inlinevirtualinherited |
Reimplemented in PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
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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::bias::PBMetaD, PLMD::analysis::Analysis, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::DumpAtoms, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarDensity, PLMD::generic::Print, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::multicolvar::VolumeTetrapore, and PLMD::generic::DumpProjections.
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inherited |
Issue a warning.
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private |
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inherited |
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inherited |
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inherited |
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inherited |
Reference to the log stream.
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inherited |
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private |
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inherited |
Reference to main plumed object.
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