Changeset 3ccea3 for src/Potentials

Timestamp:

Dec 19, 2012, 3:25:31 PM (12 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:

1dca9a

Parents:

dac89b1

git-author:

Frederik Heber <heber@…> (10/03/12 19:08:38)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:31)

Message:

EmpiricalPotential and FunctionModel are now inherited virtually, have overlapping function definitions.

• EmpiricalPotential and FunctionModel differ only in the way of the derivative. The simple function evaluation is the same. EmpiricalPotential however desires the derivative with respect to the arguments, while FunctionModel requires the derivative with respect to the parameters.
• therefore, we shifted some of the function definitions in between the two and had to some typedefs in PairPotential_Harmonic and ManyBodyPotential_Tersoff to clarify ambiguities.

Location:

src/Potentials

Files:

• EmpiricalPotential.hpp (modified) (2 diffs)
• Specifics/ManyBodyPotential_Tersoff.hpp (modified) (2 diffs)
• Specifics/PairPotential_Harmonic.hpp (modified) (2 diffs)

src/Potentials/EmpiricalPotential.hpp

@@ -31 +31 @@
 {
 public:
+  //!> typedef for the argument vector as input to the function
+  typedef std::vector<argument_t> arguments_t;
+  //!> typedef for a single result degree of freedom
+  typedef double result_t;
+  //!> typedef for the result vector as returned by the function
+  typedef std::vector<result_t> results_t;
+  //!> typedef for the components of the derivative
+  typedef std::vector<result_t> derivative_components_t;
+
   /** Default constructor for class EmpiricalPotential.
    *
@@ -40 +49 @@
    */
   virtual ~EmpiricalPotential() {}
+
+  /** Evaluates the function with the given \a arguments and the current set of
+   * parameters.
+   *
+   * \param arguments set of arguments as input variables to the function
+   * \return result of the function
+   */
+  virtual results_t operator()(const arguments_t &arguments) const=0;
+
+  /** Evaluates the derivative of the function with the given \a arguments
+   * for each component.
+   *
+   * \param arguments set of arguments as input variables to the function
+   * \return result vector containing the derivative with respect to each
+   *         input comonent of the function
+   */
+  virtual derivative_components_t derivative(const arguments_t &arguments) const=0;
 };
 

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -27 +27 @@
  *
  */
-class ManyBodyPotential_Tersoff : public EmpiricalPotential, public FunctionModel
+class ManyBodyPotential_Tersoff : virtual public EmpiricalPotential, virtual public FunctionModel
 {
+  // some repeated typedefs to avoid ambiguities
+  typedef FunctionModel::arguments_t arguments_t;
+  typedef FunctionModel::result_t result_t;
+  typedef FunctionModel::results_t results_t;
+  typedef EmpiricalPotential::derivative_components_t derivative_components_t;
 private:
   //!> cutoff_offset offset for cutoff parameter
@@ -113 +118 @@
   derivative_components_t derivative(const arguments_t &arguments) const;
 
+  /** Evaluates the derivative of the function with the given \a arguments
+   * with respect to a specific parameter indicated by \a index.
+   *
+   * \param arguments set of arguments as input variables to the function
+   * \param index derivative of which parameter
+   * \return result vector containing the derivative with respect to the given
+   *         input
+   */
+  virtual results_t paramter_derivative(const arguments_t &arguments, const size_t index) const=0;
+
 private:
   /** This function represents the cutoff \f$ f_C \f$.

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -24 +24 @@
  *
  */
-class PairPotential_Harmonic : public EmpiricalPotential, public FunctionModel
+class PairPotential_Harmonic : virtual public EmpiricalPotential, virtual public FunctionModel
 {
+  // some repeated typedefs to avoid ambiguities
+  typedef FunctionModel::arguments_t arguments_t;
+  typedef FunctionModel::result_t result_t;
+  typedef FunctionModel::results_t results_t;
+  typedef EmpiricalPotential::derivative_components_t derivative_components_t;
 public:
   PairPotential_Harmonic();
@@ -73 +78 @@
   derivative_components_t derivative(const arguments_t &arguments) const;
 
+  /** Evaluates the derivative of the function with the given \a arguments
+   * with respect to a specific parameter indicated by \a index.
+   *
+   * \param arguments set of arguments as input variables to the function
+   * \param index derivative of which parameter
+   * \return result vector containing the derivative with respect to the given
+   *         input
+   */
+//  results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
+
 private:
   //!> the spring constant for the harmonic potential