Changeset 94453f1

Timestamp:

Oct 6, 2013, 8:45:08 AM (11 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

c76b8b

Parents:

4e6a60

git-author:

Frederik Heber <heber@…> (09/03/13 10:19:31)

git-committer:

Frederik Heber <heber@…> (10/06/13 08:45:08)

Message:

Added getCoordinator() to EmpiricalPotential interface.

• implemented with all specific potentials.

Location:

src/Potentials

Files:

• EmpiricalPotential.hpp (modified) (3 diffs)
• Specifics/ConstantPotential.cpp (modified) (2 diffs)
• Specifics/ConstantPotential.hpp (modified) (2 diffs)
• Specifics/FourBodyPotential_Improper.cpp (modified) (2 diffs)
• Specifics/FourBodyPotential_Improper.hpp (modified) (2 diffs)
• Specifics/FourBodyPotential_Torsion.cpp (modified) (2 diffs)
• Specifics/FourBodyPotential_Torsion.hpp (modified) (2 diffs)
• Specifics/ManyBodyPotential_Tersoff.cpp (modified) (2 diffs)
• Specifics/ManyBodyPotential_Tersoff.hpp (modified) (2 diffs)
• Specifics/PairPotential_Harmonic.cpp (modified) (2 diffs)
• Specifics/PairPotential_Harmonic.hpp (modified) (2 diffs)
• Specifics/PairPotential_LennardJones.cpp (modified) (2 diffs)
• Specifics/PairPotential_LennardJones.hpp (modified) (2 diffs)
• Specifics/PairPotential_Morse.cpp (modified) (2 diffs)
• Specifics/PairPotential_Morse.hpp (modified) (2 diffs)
• Specifics/ThreeBodyPotential_Angle.cpp (modified) (2 diffs)
• Specifics/ThreeBodyPotential_Angle.hpp (modified) (2 diffs)

src/Potentials/EmpiricalPotential.hpp

@@ -20 +20 @@
 #include "FunctionApproximation/FunctionModel.hpp"
 #include "Potentials/SerializablePotential.hpp"
+#include "Potentials/InternalCoordinates/Coordinator.hpp"
 
 /** An EmpiricalPotential is a function that is given a vector of objects as
@@ -73 +74 @@
   virtual derivative_components_t derivative(const arguments_t &arguments) const=0;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  virtual Coordinator::ptr getCoordinator() const=0;
+
 protected:
   /** Default constructor for class EmpiricalPotential.
@@ -81 +89 @@
   EmpiricalPotential()
   {}
-
-
 };
 

src/Potentials/Specifics/ConstantPotential.cpp

@@ -52 +52 @@
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "Potentials/InternalCoordinates/OneBody_Constant.hpp"
 
 class Fragment;
@@ -62 +63 @@
     ;
 const std::string ConstantPotential::potential_token("constant");
+Coordinator::ptr ConstantPotential::coordinator(new OneBody_Constant());
 
 ConstantPotential::ConstantPotential() :

src/Potentials/Specifics/ConstantPotential.hpp

@@ -112 +112 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -191 +199 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/FourBodyPotential_Improper.cpp

@@ -39 +39 @@
 #include <boost/assign/list_of.hpp> // for 'map_list_of()'
 
+#include "Potentials/InternalCoordinates/FourBody_ImproperAngle.hpp"
+
 // static definitions
 const FourBodyPotential_Improper::ParameterNames_t
@@ -47 +49 @@
     ;
 const std::string FourBodyPotential_Improper::improper_token("improper");
-
+Coordinator::ptr FourBodyPotential_Improper::coordinator(new FourBody_ImproperAngle());
 
 FourBodyPotential_Improper::FourBodyPotential_Improper() :

src/Potentials/Specifics/FourBodyPotential_Improper.hpp

@@ -44 +44 @@
   FourBodyPotential_Improper();
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
 public:
   FourBodyPotential_Improper(const ParticleTypes_t &_ParticleTypes);
@@ -80 +88 @@
   //!> static token of this potential type
   static const std::string improper_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/FourBodyPotential_Torsion.cpp

@@ -49 +49 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/FourBody_TorsionAngle.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -61 +62 @@
     ;
 const std::string FourBodyPotential_Torsion::potential_token("torsion");
+Coordinator::ptr FourBodyPotential_Torsion::coordinator(new FourBody_TorsionAngle());
 
 FourBodyPotential_Torsion::FourBodyPotential_Torsion() :

src/Potentials/Specifics/FourBodyPotential_Torsion.hpp

@@ -114 +114 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -207 +215 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -52 +52 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/OneBody_Constant.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -77 +78 @@
     ;
 const std::string ManyBodyPotential_Tersoff::potential_token("tersoff");
+Coordinator::ptr ManyBodyPotential_Tersoff::coordinator(new OneBody_Constant());
 
 ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff() :

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -129 +129 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -358 +366 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -50 +50 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -62 +63 @@
     ;
 const std::string PairPotential_Harmonic::potential_token("harmonic_bond");
+Coordinator::ptr PairPotential_Harmonic::coordinator(new TwoBody_Length());
 
 PairPotential_Harmonic::PairPotential_Harmonic() :

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -112 +112 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** States whether lower and upper boundaries should be used to constraint
    * the parameter search for this function model.
@@ -192 +200 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/PairPotential_LennardJones.cpp

@@ -50 +50 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -62 +63 @@
     ;
 const std::string PairPotential_LennardJones::potential_token("lennardjones");
+Coordinator::ptr PairPotential_LennardJones::coordinator(new TwoBody_Length());
 
 void PairPotential_LennardJones::setDefaultParameters()

src/Potentials/Specifics/PairPotential_LennardJones.hpp

@@ -114 +114 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -200 +208 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -51 +51 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -64 +65 @@
     ;
 const std::string PairPotential_Morse::potential_token("morse");
+Coordinator::ptr PairPotential_Morse::coordinator(new TwoBody_Length());
 
 PairPotential_Morse::PairPotential_Morse() :

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -113 +113 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -195 +203 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };
 

src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

@@ -50 +50 @@
 #include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
+#include "Potentials/InternalCoordinates/ThreeBody_Angle.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
 
@@ -62 +63 @@
     ;
 const std::string ThreeBodyPotential_Angle::potential_token("harmonic_angle");
+Coordinator::ptr ThreeBodyPotential_Angle::coordinator(new ThreeBody_Angle());
 
 ThreeBodyPotential_Angle::ThreeBodyPotential_Angle() :

src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp

@@ -112 +112 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** Returns the functor that converts argument_s into the
+   * internal coordinate described by this potential function.
+   *
+   * \return coordinator functor
+   */
+  Coordinator::ptr getCoordinator() const
+  { return coordinator; }
+
   /** Return the token name of this specific potential.
    *
@@ -202 +210 @@
   //!> static token of this potential type
   static const std::string potential_token;
+
+  //!> internal coordinator object for converting arguments_t
+  static Coordinator::ptr coordinator;
 };