Provides the keyword COLLECT_FRAMES More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
CollectFrames (const ActionOptions &ao) | |
virtual void | activate () |
Set action to active. More... | |
void | addCommentToShortcutOutput (const std::string &input) |
Add a comment to your shortcut output. More... | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | apply () override |
Do nothing. More... | |
virtual void | beforeUpdate () |
Before Update. More... | |
void | calculate () override |
Do nothing. 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... | |
virtual ActionAtomistic * | castToActionAtomistic () noexcept |
virtual ActionForInterface * | castToActionForInterface () noexcept |
ActionShortcut * | castToActionShortcut () noexcept final |
virtual ActionToGetData * | castToActionToGetData () noexcept |
virtual ActionToPutData * | castToActionToPutData () noexcept |
virtual ActionWithArguments * | castToActionWithArguments () noexcept |
virtual ActionWithValue * | castToActionWithValue () noexcept |
Specialized casts, to make PlumedMain run faster. More... | |
virtual ActionWithVirtualAtom * | castToActionWithVirtualAtom () noexcept |
virtual DomainDecomposition * | castToDomainDecomposition () noexcept |
virtual PbcAction * | castToPbcAction () noexcept |
bool | checkForDependency (Action *) |
Check that this action does not depend on the action in the argument. More... | |
virtual bool | checkNeedsGradients () const |
Check if the action needs gradient. More... | |
virtual bool | checkNumericalDerivatives () const |
Check if numerical derivatives should be performed. More... | |
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 | clearOptions () |
std::string | convertInputLineToString () |
Take everything that was input to this action and convert it to a string. More... | |
virtual void | deactivate () |
Set action to inactive. More... | |
void | error (const std::string &msg) const |
Crash calculation and print documentation. 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... | |
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... | |
const std::string & | getName () const |
Returns the name. More... | |
bool | getRestart () const |
Return true if we are doing a restart. More... | |
std::vector< std::string > | getSavedInputLines () const |
Get the lines of the shortcut that were read in. More... | |
std::vector< std::string > | getSavedOutputs () const |
Get the labels of the actions that this creates. More... | |
const std::string & | getShortcutLabel () const |
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... | |
void | interpretDataLabel (const std::string &mystr, Action *myuser, std::vector< Value * > &args) const |
This sorts out the reading of arguments from shortcuts. 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 () |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. 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 | readInputLine (const std::string &input, bool saveline=true) |
Read a line of input and create appropriate actions. More... | |
void | readShortcutKeywords (const Keywords &keys, std::map< std::string, std::string > &keymap) |
Read keywords. More... | |
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... | |
virtual void | setOption (const std::string &s) |
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... | |
virtual void | unlockRequests () |
virtual void | update () |
Update. 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 | registerKeywords (Keywords &keys) |
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 | |
double | getKBoltzmann () const |
Get the value of Boltzmann's constant. More... | |
const Units & | getUnits () const |
Get the units that we are operating in. More... | |
std::string | getUpdateLimits () const |
bool | usingNaturalUnits () const |
Are we using natural units. More... | |
Private Member Functions | |
void | addToSavedInputLines (const std::string &line) |
std::string | fixArgumentName (const std::string &argin) |
Private Attributes | |
bool | active |
Switch to activate Action on this step. More... | |
Dependencies | after |
Actions on which this Action depends. More... | |
std::string | defaults |
The set of default arguments that we are using. More... | |
bool | doCheckPoint |
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... | |
const std::string | name |
Name of the directive in the plumed.dat file. More... | |
bool | never_activate |
std::set< std::string > | options |
Option that you might have enabled. More... | |
int | replica_index |
bool | restart |
std::vector< std::string > | savedInputLines |
std::vector< std::string > | savedOutputs |
std::string | shortcutlabel |
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... | |
Provides the keyword COLLECT_FRAMES
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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 comment to your shortcut output.
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inherited |
Specify that this Action depends on another one.
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privateinherited |
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inlineoverridevirtualinherited |
Do nothing.
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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inlineoverridevirtualinherited |
Do nothing.
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::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionAtomistic.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionForInterface.
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inlinefinalvirtualnoexceptinherited |
Reimplemented from PLMD::Action.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionToGetData.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionToPutData.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionWithArguments.
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inlinevirtualnoexceptinherited |
Specialized casts, to make PlumedMain run faster.
Reimplemented in PLMD::ActionWithValue.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::ActionWithVirtualAtom.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::DomainDecomposition.
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inlinevirtualnoexceptinherited |
Reimplemented in PLMD::PbcAction.
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inherited |
Check that this action does not depend on the action in the argument.
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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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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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inherited |
Take everything that was input to this action and convert it to a string.
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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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private |
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inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
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inherited |
Return true if we are doing at a checkpoint step.
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inlineinherited |
Get the defaults.
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inlineinherited |
Return dependencies.
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inherited |
Check if we are on an exchange step.
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protectedinherited |
Get the value of Boltzmann's constant.
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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.
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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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inlineinherited |
Return true if we are doing a restart.
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inherited |
Get the lines of the shortcut that were read in.
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inherited |
Get the labels of the actions that this creates.
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inherited |
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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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protectedinherited |
Get the units that we are operating in.
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protectedinherited |
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inherited |
This sorts out the reading of arguments from shortcuts.
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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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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::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.
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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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inherited |
Read a line of input and create appropriate actions.
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inherited |
Read keywords.
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static |
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inherited |
Set the timestep that is stored in the action to the correct value.
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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.
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virtualinherited |
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inherited |
This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.
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inlinevirtualinherited |
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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::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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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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inherited |
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privateinherited |
The set of default arguments that we are using.
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privateinherited |
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inherited |
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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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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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privateinherited |
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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 |
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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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