hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/core/ActionAtomistic.h

@@ -0,0 +1,343 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_core_ActionAtomistic_h
+#define __PLUMED_core_ActionAtomistic_h
+
+#include "Action.h"
+#include "../tools/Tensor.h"
+#include "../tools/Pbc.h"
+#include "../tools/ForwardDecl.h"
+#include "Value.h"
+#include <vector>
+#include <map>
+
+namespace PLMD {
+
+class Pbc;
+class PDB;
+class GenericMolInfo;
+class Tree;
+
+namespace colvar {
+class SelectMassCharge;
+}
+
+/// \ingroup MULTIINHERIT
+/// Action used to create objects that access the positions of the atoms from the MD code
+class ActionAtomistic :
+  virtual public Action {
+  friend class Group;
+  friend class DomainDecomposition;
+  friend class colvar::SelectMassCharge;
+  friend class ActionWithVirtualAtom;
+
+  std::vector<AtomNumber> indexes;         // the set of needed atoms
+  std::vector<std::size_t>   value_depends;   // The list of values that are being used
+  std::vector<std::pair<std::size_t, std::size_t > > atom_value_ind;  // The list of values and indices for the atoms that are being used
+  std::vector<std::pair<std::size_t,std::vector<std::size_t>>> atom_value_ind_grouped;
+/// unique should be an ordered set since we later create a vector containing the corresponding indexes
+  std::vector<AtomNumber>  unique;
+/// unique_local should be an ordered set since we later create a vector containing the corresponding indexes
+  bool unique_local_needs_update;
+  std::vector<AtomNumber>  unique_local;
+  std::vector<Vector>   actionPositions;       // positions of the needed atoms
+  double                energy;
+  Value*                boxValue;
+  ForwardDecl<Pbc>      pbc_fwd;
+  Pbc&                  actionPbc=*pbc_fwd;
+  std::vector<double>   masses;
+  std::vector<double>   charges;
+
+  std::vector<Vector>   forces;          // forces on the needed atoms
+  double                forceOnEnergy;
+
+  double                forceOnExtraCV;
+
+  bool                  lockRequestAtoms; // forbid changes to request atoms
+
+  bool                  donotretrieve;
+  bool                  donotforce;
+
+  // EMST
+  GenericMolInfo* actionMoldat{nullptr};
+  std::unique_ptr<Tree> tree;
+
+/// Values that hold information about atom positions and charges
+  std::vector<Value*>   xpos, ypos, zpos, masv, chargev;
+  void updateUniqueLocal( const bool& useunique, const std::vector<int>& g2l );
+protected:
+  bool                  massesWereSet;
+  bool                  chargesWereSet;
+  void setExtraCV(const std::string &name);
+/// Used to interpret whether this index is a virtual atom or a real atom
+  std::pair<std::size_t, std::size_t> getValueIndices( const AtomNumber& i ) const ;
+public:
+/// 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
+  void requestAtoms(const std::vector<AtomNumber> & a, const bool clearDep=true);
+/// Get position of i-th atom (access by relative index)
+  const Vector & getPosition(int)const;
+/// Get position of i-th atom (access by absolute AtomNumber).
+/// With direct access to the global atom array.
+/// \warning Should be only used by actions that need to read the shared position array.
+///          This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.
+  Vector getGlobalPosition(const std::pair<std::size_t,std::size_t>& ) const ;
+/// Modify position of i-th atom (access by absolute AtomNumber).
+/// \warning Should be only used by actions that need to modify the shared position array.
+///          This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.
+  void setGlobalPosition(const std::pair<std::size_t,std::size_t>&, const Vector& pos);
+/// Get total number of atoms, including virtual ones.
+/// Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.
+  unsigned getTotAtoms()const;
+/// Get box shape
+  const Tensor & getBox()const;
+/// Get the array of all positions
+  const std::vector<Vector> & getPositions()const;
+/// Get the array of all masses
+  const std::vector<double>& getMasses()const;
+/// Get the array of all charges
+  const std::vector<double>& getCharges( const bool allowempty=false )const;
+/// Get the virial that is acting
+  Tensor getVirial() const ;
+/// Get energy
+  const double & getEnergy()const;
+/// Get mass of i-th atom
+  double getMass(int i)const;
+/// Get charge of i-th atom
+  double getCharge(int i)const;
+/// Get the force acting on a particular atom
+  Vector getForce( const std::pair<std::size_t, std::size_t>& a ) const ;
+/// Add force to an atom
+  void addForce( const std::pair<std::size_t, std::size_t>& a, const Vector& f );
+/// Get a reference to force on energy
+  double & modifyForceOnEnergy();
+/// Get number of available atoms
+  unsigned getNumberOfAtoms()const {
+    return indexes.size();
+  }
+/// Compute the pbc distance between two positions
+  Vector pbcDistance(const Vector&,const Vector&)const;
+/// Applies  PBCs to a seriens of positions or distances
+  void pbcApply(std::vector<Vector>& dlist, unsigned max_index=0) const;
+/// Get the vector of absolute indexes
+  virtual const std::vector<AtomNumber> & getAbsoluteIndexes()const;
+/// Get the absolute index of an atom
+  AtomNumber getAbsoluteIndex(int i)const;
+/// Parse a list of atoms without a numbered keyword
+  void parseAtomList(const std::string&key,std::vector<AtomNumber> &t);
+/// Parse an list of atom with a numbred keyword
+  void parseAtomList(const std::string&key,const int num, 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.
+  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)
+  static void interpretAtomList( std::vector<std::string>& strings, const std::vector<Value*>& xpos, Action* action, std::vector<AtomNumber> &t);
+/// This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges
+  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 );
+/// Change the box shape
+  void changeBox( const Tensor& newbox );
+/// Get reference to Pbc
+  const Pbc & getPbc() const;
+/// Add the forces to the atoms
+  void setForcesOnAtoms( const std::vector<double>& forcesToApply, unsigned& ind );
+/// Add the virial forces
+  void setForcesOnCell(const std::vector<double>& forcesToApply, unsigned& ind);
+/// Add the virial forces (span-like syntax)
+  void setForcesOnCell(const double* forcesToApply, std::size_t size, unsigned& ind);
+/// 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.
+  void doNotRetrieve() {
+    donotretrieve=true;
+  }
+/// 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.
+  void doNotForce() {
+    donotforce=true;
+  }
+/// Make atoms whole, assuming they are in the proper order
+  void makeWhole();
+public:
+
+// virtual functions:
+
+  explicit ActionAtomistic(const ActionOptions&ao);
+  ~ActionAtomistic();
+  static void registerKeywords( Keywords& keys );
+
+/// 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
+  void   calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;
+/// Numerical derivative routine to use when using Actions that inherit from BOTH
+/// ActionWithArguments and ActionAtomistic
+  void calculateAtomicNumericalDerivatives( ActionWithValue* a, const unsigned& startnum );
+
+  virtual void retrieveAtoms( const bool& force=false );
+  void lockRequests() override;
+  void unlockRequests() override;
+  const std::vector<AtomNumber> & getUnique()const;
+  const std::vector<AtomNumber> & getUniqueLocal()const;
+/// Read in an input file containing atom positions and calculate the action for the atomic
+/// configuration therin
+  void readAtomsFromPDB( const PDB& pdb ) override;
+/// Transfer the gradients
+  void getGradient( const unsigned& ind, Vector& deriv, std::map<AtomNumber,Vector>& gradients ) const ;
+  ActionAtomistic* castToActionAtomistic() noexcept final {
+    return this;
+  }
+  virtual bool actionHasForces();
+};
+
+inline
+const Vector & ActionAtomistic::getPosition(int i)const {
+  return actionPositions[i];
+}
+
+inline
+double ActionAtomistic::getMass(int i)const {
+  if( !massesWereSet ) {
+    log.printf("WARNING: masses were not passed to plumed\n");
+  }
+  return masses[i];
+}
+
+inline
+double ActionAtomistic::getCharge(int i) const {
+  if( !chargesWereSet ) {
+    error("charges were not passed to plumed");
+  }
+  return charges[i];
+}
+
+inline
+const std::vector<AtomNumber> & ActionAtomistic::getAbsoluteIndexes()const {
+  return indexes;
+}
+
+inline
+AtomNumber ActionAtomistic::getAbsoluteIndex(int i)const {
+  return indexes[i];
+}
+
+inline
+const std::vector<Vector> & ActionAtomistic::getPositions()const {
+  return actionPositions;
+}
+
+inline
+const std::vector<double> & ActionAtomistic::getMasses()const {
+  return masses;
+}
+
+inline
+const std::vector<double> & ActionAtomistic::getCharges( const bool allowempty )const {
+  if( !allowempty && !chargesWereSet ) {
+    error("charges were not passed to plumed");
+  }
+  return charges;
+}
+
+inline
+const double & ActionAtomistic::getEnergy()const {
+  return energy;
+}
+
+inline
+const Tensor & ActionAtomistic::getBox()const {
+  return actionPbc.getBox();
+}
+
+inline
+double & ActionAtomistic::modifyForceOnEnergy() {
+  return forceOnEnergy;
+}
+
+inline
+const Pbc & ActionAtomistic::getPbc() const {
+  return actionPbc;
+}
+
+inline
+void ActionAtomistic::lockRequests() {
+  lockRequestAtoms=true;
+}
+
+inline
+void ActionAtomistic::unlockRequests() {
+  lockRequestAtoms=false;
+}
+
+inline
+const std::vector<AtomNumber> & ActionAtomistic::getUnique()const {
+  return unique;
+}
+
+inline
+const std::vector<AtomNumber> & ActionAtomistic::getUniqueLocal() const {
+  return unique_local;
+}
+
+inline
+Vector ActionAtomistic::getGlobalPosition(const std::pair<std::size_t,std::size_t>& a) const {
+  Vector pos;
+  pos[0]=xpos[a.first]->data[a.second];
+  pos[1]=ypos[a.first]->data[a.second];
+  pos[2]=zpos[a.first]->data[a.second];
+  return pos;
+}
+
+inline
+void ActionAtomistic::setGlobalPosition(const std::pair<std::size_t, std::size_t>& a, const Vector& pos ) {
+  xpos[a.first]->data[a.second]=pos[0];
+  ypos[a.first]->data[a.second]=pos[1];
+  zpos[a.first]->data[a.second]=pos[2];
+}
+
+inline
+Vector ActionAtomistic::getForce( const std::pair<std::size_t, std::size_t>& a ) const {
+  Vector f;
+  f[0]=xpos[a.first]->getForce(a.second);
+  f[1]=ypos[a.first]->getForce(a.second);
+  f[2]=zpos[a.first]->getForce(a.second);
+  return f;
+}
+
+inline
+void ActionAtomistic::addForce( const std::pair<std::size_t, std::size_t>& a, const Vector& f ) {
+  xpos[a.first]->addForce( a.second, f[0] );
+  ypos[a.first]->addForce( a.second, f[1] );
+  zpos[a.first]->addForce( a.second, f[2] );
+}
+
+inline
+Vector ActionAtomistic::pbcDistance(const Vector &v1,const Vector &v2)const {
+  return actionPbc.distance(v1,v2);
+}
+
+}
+#endif

plumed/_lib/include/plumed/core/ActionForInterface.h

@@ -0,0 +1,99 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2017-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_core_ActionForInterface_h
+#define __PLUMED_core_ActionForInterface_h
+
+#include "../tools/TypesafePtr.h"
+#include "ActionWithValue.h"
+
+namespace PLMD {
+
+class ActionForInterface : public ActionWithValue {
+  friend class Atoms;
+  friend class PlumedMain;
+protected:
+// Is this the first step
+  bool firststep;
+/// Have the forces in this action been scaled by another action
+  bool wasscaled;
+/// Action has been set
+  bool wasset;
+/// The role this plays
+  std::string role;
+public:
+  static void registerKeywords(Keywords& keys);
+  explicit ActionForInterface(const ActionOptions&ao);
+/// Override clear the input data
+  void clearDerivatives(const bool& force=false) override {}
+/// Override the need to deal with gradients
+  void setGradientsIfNeeded() override {}
+/// Check if the value has been set
+  bool hasBeenSet() const ;
+/// The number of derivatives
+  unsigned getNumberOfDerivatives() override {
+    return 0;
+  }
+///
+  virtual void resetForStepStart() = 0;
+/// Set the start point for the memory if needed
+  virtual void setStart( const std::string& name, const unsigned& sss) = 0;
+/// Set the stride for the memory if needed
+  virtual void setStride( const std::string& name, const unsigned& sss) = 0;
+/// Set the pointer to the value that contains this data
+  virtual bool setValuePointer( const std::string& name, const TypesafePtr & ) = 0;
+/// Set the force to the value that contains this data
+  virtual bool setForcePointer( const std::string& name, const TypesafePtr & ) = 0;
+/// This get the number of forces that need to be rescaled in rescale forces
+  virtual unsigned getNumberOfForcesToRescale() const {
+    plumed_merror("no method for rescaling forces for this type of input");
+  }
+/// Overriding this method from ActionWithValue ensures that taskLists that are set during share are not updated during calculate loop
+//  void setupForCalculation( const bool& force=false ) override {}
+/// Get the data
+  virtual void share() = 0;
+  virtual void shareAll() = 0;
+/// Get the data to share
+  virtual void wait() = 0;
+/// Actually set the values for the output
+  void calculate() override {
+    firststep=false;
+    wasscaled=false;
+  }
+  virtual void reset() {}
+  virtual void Set_comm(Communicator& comm) = 0;
+/// For replica exchange
+  virtual void writeBinary(std::ostream&o) = 0;
+  virtual void readBinary(std::istream&i) = 0;
+  virtual bool onStep() const = 0;
+  std::string getRole() const ;
+  ActionForInterface* castToActionForInterface() noexcept final {
+    return this;
+  }
+};
+
+inline
+bool ActionForInterface::hasBeenSet() const {
+  return wasset;
+}
+
+}
+#endif

plumed/_lib/include/plumed/core/ActionPilot.h

@@ -0,0 +1,57 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_core_ActionPilot_h
+#define __PLUMED_core_ActionPilot_h
+
+#include "Action.h"
+
+namespace PLMD {
+
+/**
+\ingroup MULTIINHERIT
+This is used to create PLMD::Action objects that are run with some set frequency.
+Any PLMD::Action
+that does not inherit from PLMD::Action is only run when some other Action requires the output from
+it in order to run.  This class is used in PLMD::Bias
+ Action which drives the execution of other Action's.
+ Action's of this kind are executed with a fixed stride
+ which is specified on the directive line with a STRIDE= keyword
+*/
+class ActionPilot:
+  public virtual Action {
+  unsigned actionStride=1; // multiple time step
+public:
+  explicit ActionPilot(const ActionOptions&);
+/// Create the keywords for actionPilot
+  static void registerKeywords(Keywords& keys);
+/// Check if the action is active on this step
+  virtual bool onStep()const;
+/// Set the value of the stride
+  void setStride(unsigned n);
+/// Get the stride
+  unsigned getStride()const;
+};
+
+}
+
+#endif
+

plumed/_lib/include/plumed/core/ActionRegister.h

@@ -0,0 +1,124 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_core_ActionRegister_h
+#define __PLUMED_core_ActionRegister_h
+
+#include "RegisterBase.h"
+
+#include "../tools/Keywords.h"
+
+namespace PLMD {
+
+class Action;
+class ActionOptions;
+
+struct ActionRegisterPointers {
+/// Pointer to a function which, given the options, create an Action
+  typedef std::unique_ptr<Action>(*creator_pointer)(const ActionOptions&);
+/// Pointer to a function which, returns the keywords allowed
+  typedef void(*keywords_pointer)(Keywords&);
+  creator_pointer create;
+  keywords_pointer keys;
+};
+
+/// Register holding all the allowed keywords.
+/// This is a register which holds a map between strings (directives) and function pointers.
+/// The function pointers are pointing to functions which create an object of
+/// the corresponding class given the corresponding options (ActionOptions).
+/// There should be only one of there objects allocated.
+/// Actions should be registered here at the beginning of execution
+///
+class ActionRegister:
+  public RegisterBase<ActionRegisterPointers> {
+
+  typedef ActionRegisterPointers::creator_pointer creator_pointer;
+  typedef ActionRegisterPointers::keywords_pointer keywords_pointer;
+  typedef ActionRegisterPointers Pointers;
+
+public:
+  ID add(std::string key,creator_pointer cp,keywords_pointer kp);
+/// Create an Action of the type indicated in the options
+/// \param ao object containing information for initialization, such as the full input line, a pointer to PlumedMain, etc
+  std::unique_ptr<Action> create(const ActionOptions&ao);
+  std::unique_ptr<Action> create(const std::vector<void*> & images,const ActionOptions&ao);
+/// Print out the keywords for an action in html/vim ready for input into the manual
+  bool printManual(const std::string& action, const bool& vimout, const bool& spellout);
+/// Retrieve a keywords object for a particular action
+  bool getKeywords( const std::string& action, Keywords& keys );
+  void getKeywords(const std::vector<void*> & images, const std::string& action, Keywords& keys);
+/// Print out a template command for an action
+  bool printTemplate(const std::string& action, bool include_optional);
+  std::vector<std::string> getActionNames() const;
+};
+
+/// Function returning a reference to the ActionRegister.
+/// \relates ActionRegister
+/// To avoid problems with order of initialization, this function contains
+/// a static ActionRegister which is built the first time the function is called.
+/// In this manner, it is always initialized before it's used
+ActionRegister& actionRegister();
+
+template<typename T>
+inline constexpr bool isActionType = std::is_base_of<Action, T>::value;
+//in C++20 you we'll make this a concept
+//template<typename T>
+//concept ActionType = std::is_base_of<::PLMD::Action, T>::value;
+//so the template will be template<ActionType ActionType>class ActionRegistration{...}
+//without the explicit need of the static assert
+
+///Each instance of this specialized class represents an action that can be called
+///with  the specified directive.
+///As soon it goes out of scope it will deregister the directive from the singleton ActionRegister
+template<typename ActionClass>
+class ActionRegistration {
+  ActionRegister::ID id;
+  static std::unique_ptr<Action> create(const ActionOptions&ao) {
+    return std::make_unique<ActionClass>(ao);
+  }
+public:
+  ///On construction register the ActionClass with the wanted directive
+  ActionRegistration(std::string_view directive):
+    id(actionRegister().add(directive.data(),create,ActionClass::registerKeywords)) {
+    static_assert(isActionType<ActionClass>,
+                  "ActionRegistration accepts only class that inherit from Action");
+  }
+  ///On destruction deregister the ActionClass (useful when you unload a shared object)
+  ~ActionRegistration() {
+    actionRegister().remove(id);
+  }
+};
+} //PLMD
+
+#define PLUMED_CONCATENATE_DIRECT(s1, s2) s1##s2
+#define PLUMED_CONCATENATE(s1, s2) PLUMED_CONCATENATE_DIRECT(s1, s2)
+
+/// Shortcut for Action registration
+/// \relates PLMD::ActionRegister
+/// For easier registration, this file also provides a macro PLUMED_REGISTER_ACTION.
+/// \param classname the name of the class to be registered
+/// \param directive a string containing the corresponding directive
+/// This macro should be used in the .cpp file of the corresponding class
+#define PLUMED_REGISTER_ACTION(classname,directive) \
+  namespace {::PLMD::ActionRegistration<classname> \
+             PLUMED_CONCATENATE(classname##Registerer,__LINE__)(directive);}
+#endif
+