Provides the keyword PROPERTYMAP More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
PropertyMap (const ActionOptions &) | |
virtual bool | actionHasForces () |
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 | addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f) |
Add force to an atom. 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... | |
virtual void | beforeUpdate () |
Before Update. More... | |
void | calculate () override |
Calculate an Action. More... | |
void | calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum) |
Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More... | |
void | calculateFromPDB (const PDB &) |
Calculate the action given a pdb file as input. More... | |
void | calculateNumericalDerivatives (ActionWithValue *a=NULL) override |
N.B. More... | |
virtual bool | calculateOnUpdate () |
This is used to check if we run calculate during the update step. More... | |
ActionAtomistic * | castToActionAtomistic () noexcept final |
virtual ActionForInterface * | castToActionForInterface () noexcept |
virtual ActionShortcut * | castToActionShortcut () noexcept |
virtual ActionToGetData * | castToActionToGetData () noexcept |
virtual ActionToPutData * | castToActionToPutData () noexcept |
virtual ActionWithArguments * | castToActionWithArguments () noexcept |
virtual ActionWithValue * | castToActionWithValue () noexcept |
Specialized casts, to make PlumedMain run faster. More... | |
ActionWithValue * | castToActionWithValue () noexcept final |
Specialized casts, to make PlumedMain run faster. More... | |
virtual ActionWithVirtualAtom * | castToActionWithVirtualAtom () noexcept |
virtual DomainDecomposition * | castToDomainDecomposition () noexcept |
virtual PbcAction * | castToPbcAction () noexcept |
void | changeBox (const Tensor &newbox) |
Change the box shape. More... | |
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... | |
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 (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... | |
virtual bool | doNotCalculateDerivatives () const |
Are we not calculating derivatives. More... | |
void | doNotForce () |
Skip atom forces - use with care. More... | |
void | doNotRetrieve () |
Skip atom retrieval - use with care. 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... | |
AtomNumber | getAbsoluteIndex (int i) const |
Get the absolute index of an atom. More... | |
virtual const std::vector< AtomNumber > & | getAbsoluteIndexes () const |
Get the vector of absolute indexes. More... | |
const Tensor & | getBox () const |
Get box shape. More... | |
double | getCharge (int i) const |
Get charge of i-th atom. 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... | |
const double & | getEnergy () const |
Get energy. More... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. More... | |
Vector | getForce (const std::pair< std::size_t, std::size_t > &a) const |
Get the force acting on a particular atom. More... | |
Vector | getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const |
Get position of i-th atom (access by absolute AtomNumber). More... | |
void | getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const |
Transfer the gradients. 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... | |
double | getMass (int i) const |
Get mass of i-th atom. 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... | |
unsigned | getNumberOfAtoms () const |
Get number of available atoms. 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... | |
const Pbc & | getPbc () const |
Get reference to Pbc. More... | |
const Vector & | getPosition (int) const |
Get position of i-th atom (access by relative index) More... | |
const std::vector< Vector > & | getPositions () const |
Get the array of all positions. 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... | |
unsigned | getTotAtoms () const |
Get total number of atoms, including virtual ones. More... | |
const std::vector< AtomNumber > & | getUnique () const |
const std::vector< AtomNumber > & | getUniqueLocal () const |
Tensor | getVirial () const |
Get the virial that is acting. More... | |
void | interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t) |
Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this. More... | |
bool | isActive () const |
Check if action is active. More... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
void | lockRequests () override |
void | makeWhole () |
Make atoms whole, assuming they are in the proper order. More... | |
double & | modifyForceOnEnergy () |
Get a reference to force on energy. More... | |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. More... | |
void | parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t) |
Parse an list of atom with a numbred keyword. More... | |
void | parseAtomList (const std::string &key, std::vector< AtomNumber > &t) |
Parse a list of atoms without a numbered keyword. 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... | |
void | pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const |
Applies PBCs to a seriens of positions or distances. More... | |
Vector | pbcDistance (const Vector &, const Vector &) const |
Compute the pbc distance between two positions. More... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
void | readAtomsFromPDB (const PDB &pdb) override |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More... | |
void | requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true) |
Request an array of atoms. More... | |
void | resetStoredTimestep () |
Set the timestep that is stored in the action to the correct value. More... | |
virtual void | retrieveAtoms (const bool &force=false) |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. More... | |
void | setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned &ind) |
Add the forces to the atoms. More... | |
void | setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind) |
Add the virial forces (span-like syntax) More... | |
void | setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind) |
Add the virial forces. More... | |
void | setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos) |
Modify position of i-th atom (access by absolute AtomNumber). 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... | |
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 | getAtomValuesFromPlumedObject (const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev) |
This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges. More... | |
static void | interpretAtomList (std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t) |
Convert a set of read in strings into an atom list (this is used in parseAtomList) 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 | setBoxDerivativesNoPbc (const std::vector< Vector > &pos, std::vector< std::vector< Vector > > &derivs, std::vector< Tensor > &virial) |
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 | apply () override |
Apply an Action. More... | |
bool | checkForForces () |
Accumulate the forces from the Values. More... | |
const Tensor & | getBoxDerivatives () const |
const Value * | getConstPntrToComponent (int i) const |
Get a const pointer to the ith component. More... | |
const double & | getForce () const |
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... | |
std::pair< std::size_t, std::size_t > | getValueIndices (const AtomNumber &i) const |
Used to interpret whether this index is a virtual atom or a real atom. More... | |
void | requestAtoms (const std::vector< AtomNumber > &a) |
void | setAtomsDerivatives (int, const Vector &) |
void | setAtomsDerivatives (Value *, int, const Vector &) |
void | setBoxDerivatives (const Tensor &) |
void | setBoxDerivatives (Value *, const Tensor &) |
void | setBoxDerivativesNoPbc () |
Set box derivatives automatically. More... | |
void | setBoxDerivativesNoPbc (Value *) |
void | setExtraCV (const std::string &name) |
void | setValue (const double &d) |
Set the default value (the one without name) More... | |
bool | usingNaturalUnits () const |
Are we using natural units. More... | |
Protected Attributes | |
bool | chargesWereSet |
std::vector< std::vector< double > > | indexvec |
std::vector< std::string > | labels |
bool | massesWereSet |
unsigned | nframes |
std::vector< PDB > | pdbv |
Private Member Functions | |
int | getComponent (const std::string &name) const |
Return the index for the component named name. More... | |
void | updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l) |
Private Attributes | |
bool | active |
Switch to activate Action on this step. More... | |
Dependencies | after |
Actions on which this Action depends. More... | |
std::vector< std::pair< std::size_t, std::size_t > > | atom_value_ind |
std::vector< std::pair< std::size_t, std::vector< std::size_t > > > | atom_value_ind_grouped |
Value * | boxValue |
std::vector< double > | charges |
std::vector< Value * > | chargev |
bool | computeRefClose |
int | debugClose |
std::string | defaults |
The set of default arguments that we are using. More... | |
std::vector< Vector > | derivs_s |
std::vector< Vector > | derivs_z |
bool | doCheckPoint |
bool | donotforce |
bool | donotretrieve |
std::array< std::array< Tensor, 3 >, 3 > | drotationPosCloseDrr01 |
double | energy |
double | epsilonClose |
bool | firstPosClose |
bool | firststep |
This finishes setup on first step to check if actions are calculated during update. More... | |
double | forceOnEnergy |
double | forceOnExtraCV |
std::vector< Vector > | forces |
std::vector< double > | forcesForApply |
A vector that is used to hold the forces that we will apply on the input quantities. More... | |
std::vector< ImagePath > | imgVec |
std::vector< AtomNumber > | indexes |
std::string | label |
Label of the Action, as set with LABEL= in the plumed.dat file. More... | |
double | lambda |
std::vector< std::string > | line |
Directive line. More... | |
bool | lockRequestAtoms |
int | logClose |
std::vector< double > | masses |
std::vector< Value * > | masv |
std::vector< RMSD > | msdv |
const std::string | name |
Name of the directive in the plumed.dat file. More... | |
int | neigh_size |
int | neigh_stride |
bool | never_activate |
bool | noderiv |
Are we skipping the calculation of the derivatives. More... | |
bool | nopbc |
bool | numericalDerivatives |
Are we using numerical derivatives to differentiate. More... | |
std::set< std::string > | options |
Option that you might have enabled. More... | |
Pbc & | pbc =*pbc_fwd |
ForwardDecl< Pbc > | pbc_fwd |
std::vector< Vector > | positions |
std::string | reference |
int | replica_index |
bool | restart |
RMSD | rmsdPosClose |
Tensor | rotationPosClose |
std::vector< Tensor > | rotationRefClose |
std::vector< unsigned > | savedIndices |
double | timestep |
Save the timestep here. More... | |
std::vector< AtomNumber > | unique |
unique should be an ordered set since we later create a vector containing the corresponding indexes More... | |
std::vector< AtomNumber > | unique_local |
bool | unique_local_needs_update |
unique_local should be an ordered set since we later create a vector containing the corresponding indexes 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::size_t > | value_depends |
std::vector< std::unique_ptr< Value > > | values |
An array containing the values for this action. More... | |
std::vector< Value * > | xpos |
Values that hold information about atom positions and charges. More... | |
std::vector< Value * > | ypos |
std::vector< Value * > | zpos |
Provides the keyword PROPERTYMAP
|
inherited |
|
explicit |
|
virtualinherited |
|
virtualinherited |
Set action to active.
|
inherited |
Add a value with a name like label.name.
|
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.
|
inlineinherited |
Add force to an atom.
|
inherited |
Add a value with the name label.
|
virtualinherited |
Add a value with the name label that has derivatives.
Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.
|
overrideprotectedvirtualinherited |
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.
|
overridevirtualinherited |
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.
|
inherited |
Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.
|
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
|
overridevirtualinherited |
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.
|
inlinefinalvirtualnoexceptinherited |
Reimplemented from PLMD::Action.
|
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.
|
inlinevirtualnoexceptinherited |
Specialized casts, to make PlumedMain run faster.
Reimplemented in PLMD::ActionWithValue.
|
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.
|
inherited |
Change the box shape.
|
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.
|
inlinevirtualinherited |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
|
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.
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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.
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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.
|
inlinevirtualinherited |
Set action to inactive.
|
inlinevirtualinherited |
Are we not calculating derivatives.
|
inlineinherited |
Skip atom forces - use with care.
If this function is called during initialization, then forces are not going to be propagated. Can be used for optimization.
|
inlineinherited |
Skip atom retrieval - use with care.
If this function is called during initialization, then atoms are not going to be retrieved. Can be used for optimization. Notice that calling getPosition(int) in an Action where DoNotRetrieve() was called might lead to undefined behavior.
|
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.
|
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 |
Get the absolute index of an atom.
|
inlinevirtualinherited |
Get the vector of absolute indexes.
|
staticinherited |
This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges.
|
inlineinherited |
Get box shape.
|
protectedinherited |
|
inlineinherited |
Get charge of i-th atom.
|
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.
|
inlineinherited |
Get energy.
|
inherited |
Check if we are on an exchange step.
|
protectedinherited |
|
inlineinherited |
Get the force acting on a particular atom.
|
inlineprotectedinherited |
Get the forces to apply.
|
inlineinherited |
Get position of i-th atom (access by absolute AtomNumber).
With direct access to the global atom array.
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inherited |
Transfer the gradients.
|
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.
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inherited |
Just read one of the keywords and return the whole thing as a string.
|
inlineinherited |
Returns the label.
|
inlineinherited |
Get mass of i-th atom.
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virtualinherited |
Get the titles to use for the columns of the matrix.
Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.
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inlineinherited |
Returns the name.
|
inlineinherited |
Get number of available atoms.
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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)
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inlineinherited |
Get the value of one of the components of the PLMD::Action.
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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.
|
inlineprotectedinherited |
Get a pointer to the default value.
|
inlineinherited |
Get position of i-th atom (access by relative index)
|
inlineinherited |
Get the array of all positions.
|
inlineinherited |
Return true if we are doing a restart.
|
inherited |
Return the present timestep.
|
inherited |
Return the present time.
|
inherited |
Return the timestep.
|
inherited |
Get total number of atoms, including virtual ones.
Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.
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inlineinherited |
|
inlineinherited |
|
protectedinherited |
Get the units that we are operating in.
|
protectedinherited |
Used to interpret whether this index is a virtual atom or a real atom.
|
inherited |
Get the virial that is acting.
|
staticinherited |
Convert a set of read in strings into an atom list (this is used in parseAtomList)
|
inherited |
Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this.
|
inlineinherited |
Check if action is active.
|
inlineinherited |
Check if an option is on.
|
inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.
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inherited |
Make atoms whole, assuming they are in the proper order.
|
inlineinherited |
Get a reference to force on energy.
|
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 an list of atom with a numbred keyword.
|
inherited |
Parse a list of atoms without a numbered keyword.
|
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.
|
inherited |
Applies PBCs to a seriens of positions or distances.
|
inlineinherited |
Compute the pbc distance between two positions.
|
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.
|
overridevirtualinherited |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin.
Reimplemented from PLMD::Action.
|
static |
|
protectedinherited |
|
inherited |
Request an array of atoms.
This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS
|
inherited |
Set the timestep that is stored in the action to the correct value.
|
virtualinherited |
Reimplemented in PLMD::ActionWithVector.
|
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 |
|
inlineprotectedinherited |
|
inlineprotectedinherited |
Set box derivatives automatically.
It should be called after the setAtomsDerivatives has been used for all single atoms.
|
staticinherited |
|
protectedinherited |
|
protectedinherited |
|
inherited |
Add the forces to the atoms.
|
inherited |
Add the virial forces (span-like syntax)
|
inherited |
Add the virial forces.
|
inlineinherited |
Modify position of i-th atom (access by absolute AtomNumber).
|
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.
|
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.
|
privateinherited |
|
staticinherited |
The components in the action will depend on the user.
|
inlineinherited |
This forces the class to use numerical derivatives.
|
protectedinherited |
Are we using natural units.
|
inherited |
Issue a warning.
|
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 >.
|
privateinherited |
Switch to activate Action on this step.
|
privateinherited |
Actions on which this Action depends.
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
protectedinherited |
|
privateinherited |
|
inherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
The set of default arguments that we are using.
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
inherited |
|
privateinherited |
|
privateinherited |
This finishes setup on first step to check if actions are calculated during update.
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
A vector that is used to hold the forces that we will apply on the input quantities.
|
privateinherited |
|
privateinherited |
|
protectedinherited |
|
inherited |
|
privateinherited |
Label of the Action, as set with LABEL= in the plumed.dat file.
|
protectedinherited |
|
privateinherited |
|
privateinherited |
Directive line.
This line is progressively erased during Action construction so as to check if all the present keywords are correct.
|
privateinherited |
|
inherited |
Reference to the log stream.
|
privateinherited |
|
privateinherited |
|
protectedinherited |
|
privateinherited |
|
privateinherited |
|
inherited |
|
privateinherited |
Name of the directive in the plumed.dat file.
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
protectedinherited |
|
privateinherited |
Are we skipping the calculation of the derivatives.
|
privateinherited |
|
privateinherited |
Are we using numerical derivatives to differentiate.
|
privateinherited |
Option that you might have enabled.
|
privateinherited |
|
protectedinherited |
|
inherited |
Reference to main plumed object.
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
|
privateinherited |
Save the timestep here.
|
privateinherited |
unique should be an ordered set since we later create a vector containing the corresponding indexes
|
privateinherited |
|
privateinherited |
unique_local should be an ordered set since we later create a vector containing the corresponding indexes
|
privateinherited |
Update only after this time.
|
privateinherited |
Update only until this time.
|
privateinherited |
|
privateinherited |
|
privateinherited |
An array containing the values for this action.
|
privateinherited |
Values that hold information about atom positions and charges.
|
privateinherited |
|
privateinherited |
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