Provides the keyword GYRATION More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
Gyration (const ActionOptions &) | |
virtual void | activate () |
Set action to active. More... | |
void | addComponent (const std::string &name) |
Add a value with a name like label.name. More... | |
void | addComponentWithDerivatives (const std::string &name) |
Add a value with a name like label.name that has derivatives. More... | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | addValue () |
Add a value with the name label. More... | |
void | addValueWithDerivatives () |
Add a value with the name label that has derivatives. More... | |
void | allowToAccessGlobalForces () |
Allow calls to modifyGlobalForce() More... | |
void | applyForces () |
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... | |
void | changeBox (const Tensor &newbox) |
Change the box shape. More... | |
virtual void | checkFieldsAllowed () |
bool | checkIsEnergy () |
virtual bool | checkNeedsGradients () const |
Check if the action needs gradient. More... | |
bool | checkNumericalDerivatives () const override |
Check if numerical derivatives should be used. 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 | clearDerivatives () |
Clear the derivatives of values wrt parameters. More... | |
void | clearInputForces () |
Clear the forces on the values. More... | |
virtual void | clearOptions () |
void | clearOutputForces () |
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... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual std::string | getDocumentation () const |
const double & | getEnergy () const |
Get energy. More... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. More... | |
const Vector & | getGlobalPosition (AtomNumber) const |
Get position of i-th atom (access by absolute AtomNumber). 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... | |
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 |
double | getOutputQuantity (const unsigned j) const |
Get the value of one of the components of the PLMD::Action. 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... | |
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 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::set< AtomNumber > & | getUnique () const |
const std::set< AtomNumber > & | getUniqueLocal () const |
void | interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t) |
Convert a set of read in strings into an atom list (this is used in parseAtomList) 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... | |
double & | modifyForceOnExtraCV () |
Get a reference to force on extraCV. More... | |
std::vector< Vector > & | modifyForces () |
Get a reference to forces array. More... | |
Vector & | modifyGlobalForce (AtomNumber) |
Get modifiable force of i-th atom (access by absolute AtomNumber). More... | |
Pbc & | modifyGlobalPbc () |
Get modifiable PBC Should be used by action that need to modify the stored box. More... | |
Vector & | modifyGlobalPosition (AtomNumber) |
Get modifiable position of i-th atom (access by absolute AtomNumber). More... | |
Tensor & | modifyGlobalVirial () |
Get modifiable virial Should be used by action that need to modify the stored virial. More... | |
Tensor & | modifyVirial () |
Get a reference to virial array. 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, std::vector< AtomNumber > &t) |
Parse a list of atoms without a numbered keyword. 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 | 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... | |
virtual void | retrieveAtoms () |
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=0) |
Add the forces to the atoms. More... | |
void | setGradientsIfNeeded () |
Calculate the gradients and store them for all the values (need for projections) More... | |
void | setNotPeriodic () |
Set your default value to have no periodicity. More... | |
virtual void | setOption (const std::string &s) |
void | setPeriodic (const std::string &min, const std::string &max) |
Set the value to be periodic with a particular domain. More... | |
void | 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 | updateUniqueLocal () |
updates local unique atoms More... | |
void | useNumericalDerivatives () |
This forces the class to use numerical derivatives. More... | |
void | warning (const std::string &msg) |
Issue a warning. More... | |
Static Public Member Functions | |
static void | componentsAreNotOptional (Keywords &keys) |
Puts a message into the manual that the components always output. More... | |
static void | noAnalyticalDerivatives (Keywords &keys) |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More... | |
static void | registerKeywords (Keywords &keys) |
static void | useCustomisableComponents (Keywords &keys) |
The components in the action will depend on the user. More... | |
Public Attributes | |
Communicator & | comm |
std::set< FILE * > | files |
const Keywords & | keywords |
Log & | log |
Reference to the log stream. More... | |
Communicator & | multi_sim_comm |
PlumedMain & | plumed |
Reference to main plumed object. More... | |
Protected Member Functions | |
void | apply () override |
Apply an Action. More... | |
const Tensor & | getBoxDerivatives () const |
const double & | getForce () const |
Value * | getPntrToComponent (int i) |
Return a pointer to the component by index. More... | |
Value * | getPntrToComponent (const std::string &name) |
Return a pointer to the value by name. More... | |
Value * | getPntrToValue () |
Get a pointer to the default value. 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... | |
Protected Attributes | |
Atoms & | atoms |
bool | isEnergy |
bool | isExtraCV |
Private Types | |
enum | CV_TYPE { RADIUS, TRACE, GTPC_1, GTPC_2, GTPC_3, ASPHERICITY, ACYLINDRICITY, KAPPA2, GYRATION_3, GYRATION_2, GYRATION_1, TOT } |
Private Attributes | |
bool | nopbc |
int | rg_type |
bool | use_masses |
Provides the keyword GYRATION
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inherited |
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private |
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explicit |
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virtualinherited |
Set action to active.
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inherited |
Add a value with a name like label.name.
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inherited |
Add a value with a name like label.name that has derivatives.
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inherited |
Specify that this Action depends on another one.
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inherited |
Add a value with the name label.
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inherited |
Add a value with the name label that has derivatives.
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inlineinherited |
Allow calls to modifyGlobalForce()
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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.
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inherited |
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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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overridevirtual |
Calculate an Action.
This method is called one or more times per step. The set of all Actions is calculated in forward order.
Implements PLMD::Action.
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inherited |
Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.
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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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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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::multicolvar::MultiColvarBase, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::multicolvar::DumpMultiColvar, and PLMD::multicolvar::BridgedMultiColvarFunction.
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inherited |
Change the box shape.
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inlinevirtualinherited |
Reimplemented in PLMD::piv::PIV, and PLMD::colvar::ContactMap.
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inlineinherited |
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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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inlineoverridevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
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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 |
Clear the derivatives of values wrt parameters.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
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inherited |
Clear the forces on the values.
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virtualinherited |
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inherited |
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inherited |
Set your value component to have no periodicity.
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inherited |
Set the value to be periodic with a particular domain.
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staticinherited |
Puts a message into the manual that the components always output.
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inherited |
Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.
Use getPntrToComponent instead.
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inherited |
Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.
Use getPntrToComponent instead.
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inlinevirtualinherited |
Set action to inactive.
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inlinevirtualinherited |
Are we not calculating derivatives.
Reimplemented in PLMD::multicolvar::MultiColvarBase.
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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.
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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.
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inherited |
Crash calculation and print documentation.
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inherited |
Check if a value with a particular name is present.
This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.
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inherited |
Exit with error code c.
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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 |
Get the absolute index of an atom.
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inlinevirtualinherited |
Get the vector of absolute indexes.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
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inlineinherited |
Get box shape.
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protectedinherited |
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inlineinherited |
Get charge of i-th atom.
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inherited |
get a string that contains all the available components
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inherited |
get a vector that contains the label for all the components
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inherited |
Return true if we are doing at a checkpoint step.
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inlineinherited |
Return dependencies.
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virtualinherited |
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inlineinherited |
Get energy.
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inherited |
Check if we are on an exchange step.
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protectedinherited |
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inlineinherited |
Get position of i-th atom (access by absolute AtomNumber).
With direct access to the global atom array.
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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 |
Get mass of i-th atom.
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inlineinherited |
Returns the name.
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inlineinherited |
Get number of available atoms.
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inlineinherited |
Returns the number of values defined.
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inlineoverridevirtualinherited |
Implements PLMD::ActionWithValue.
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inlineinherited |
Get the value of one of the components of the PLMD::Action.
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inlineinherited |
Get the value with a specific name (N.B. if there is no such value this returns zero)
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protectedinherited |
Return a pointer to the component by index.
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protectedinherited |
Return a pointer to the value by name.
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protectedinherited |
Get a pointer to the default value.
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inlineinherited |
Get position of i-th atom (access by relative index)
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inlineinherited |
Get the array of all positions.
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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 |
Get total number of atoms, including virtual ones.
Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.
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inlineinherited |
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inlineinherited |
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inherited |
Convert a set of read in strings into an atom list (this is used in parseAtomList)
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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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inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
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inherited |
Make atoms whole, assuming they are in the proper order.
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inlineinherited |
Get a reference to force on energy.
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inlineinherited |
Get a reference to force on extraCV.
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inlineinherited |
Get a reference to forces array.
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inlineinherited |
Get modifiable force of i-th atom (access by absolute AtomNumber).
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inlineinherited |
Get modifiable PBC Should be used by action that need to modify the stored box.
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inlineinherited |
Get modifiable position of i-th atom (access by absolute AtomNumber).
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inlineinherited |
Get modifiable virial Should be used by action that need to modify the stored virial.
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inlineinherited |
Get a reference to virial array.
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staticinherited |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.
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inherited |
Parse one keyword as generic type.
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inherited |
Parse a list of atoms without a numbered keyword.
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inherited |
Parse an list of atom with a numbred keyword.
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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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inherited |
Applies PBCs to a seriens of positions or distances.
Compute the pbc distance between two positions.
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virtualinherited |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::colvar::Energy, PLMD::SetupMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.
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overridevirtualinherited |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin.
Reimplemented from PLMD::Action.
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static |
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protectedinherited |
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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
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virtualinherited |
Reimplemented in PLMD::multicolvar::MultiColvarBase.
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inlinevirtualinherited |
RunFinalJobs This method is called once at the very end of the calculation.
The set of all Actions in run for the final time in forward order.
Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.
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inlineprotectedinherited |
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inlineprotectedinherited |
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inlineprotectedinherited |
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inlineprotectedinherited |
Set box derivatives automatically.
It should be called after the setAtomsDerivatives has been used for all single atoms.
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protectedinherited |
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inlineprotectedinherited |
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inherited |
Add the forces to the atoms.
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inherited |
Calculate the gradients and store them for all the values (need for projections)
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inherited |
Set your default value to have no periodicity.
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virtualinherited |
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inherited |
Set the value to be periodic with a particular domain.
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inlineprotectedinherited |
Set the default value (the one without name)
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inherited |
Set the value.
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virtualinherited |
Activate the calculation of derivatives.
Reimplemented in PLMD::eds::EDS, PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, and PLMD::gridtools::ActionWithIntegral.
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inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
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inlinevirtualinherited |
Update.
This method is called one time per step. The set of all Actions is updated in forward order.
Reimplemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, and PLMD::gridtools::GridPrintingBase.
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inherited |
updates local unique atoms
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staticinherited |
The components in the action will depend on the user.
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inlineinherited |
This forces the class to use numerical derivatives.
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inherited |
Issue a warning.
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protectedinherited |
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inherited |
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inherited |
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protectedinherited |
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protectedinherited |
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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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private |
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private |
Hosted by GitHub | 1.8.14 |