Changeset 0f5d38 for src/Potentials/Specifics

Timestamp:

Aug 9, 2013, 2:20:35 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:

51e0e3

Parents:

f0025d

git-author:

Frederik Heber <heber@…> (06/25/13 10:54:50)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:35)

Message:

Added getSpecificFilter() and getSpecificArgumentCount() to FunctionModel.

• implemented getSpecificArgumentCount() in all specific potentials.
• added NoOp_filterfunction to Helpers.
• enhanced Documentation on FunctionModel on new Extractor,Filter,Count system.
• rewrote CompoundPotential::getSpecificExtractor() using Helpers::returnEmptyArguments() such that first model does not have to be treated special anymore.

Location:

src/Potentials/Specifics

Files:

• ConstantPotential.cpp (modified) (1 diff)
• ConstantPotential.hpp (modified) (1 diff)
• ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• PairPotential_Angle.cpp (modified) (1 diff)
• PairPotential_Angle.hpp (modified) (1 diff)
• PairPotential_Harmonic.cpp (modified) (1 diff)
• PairPotential_Harmonic.hpp (modified) (1 diff)
• PairPotential_Morse.cpp (modified) (1 diff)
• PairPotential_Morse.hpp (modified) (1 diff)

src/Potentials/Specifics/ConstantPotential.cpp

@@ -177 +177 @@
 }
 
+FunctionModel::filter_t ConstantPotential::getSpecificFilter() const
+{
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Helpers::NoOp_Filterfunction,
+          _1);
+  return returnfunction;
+}
+
 void
 ConstantPotential::setParametersToRandomInitialValues(

src/Potentials/Specifics/ConstantPotential.hpp

@@ -163 +163 @@
   FunctionModel::extractor_t getSpecificExtractor() const;
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const
+  { return 0; }
+
   enum parameter_enum_t {
     energy_offset=0,

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -698 +698 @@
 }
 
+FunctionModel::filter_t ManyBodyPotential_Tersoff::getSpecificFilter() const
+{
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Helpers::NoOp_Filterfunction,
+          _1);
+  return returnfunction;
+}
+
 void
 ManyBodyPotential_Tersoff::setParametersToRandomInitialValues(

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -188 +188 @@
   FunctionModel::extractor_t getSpecificExtractor() const;
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const
+  { return 1; }
+
   /** Sets the magic triple function that we use for getting angle distances.
    *

src/Potentials/Specifics/PairPotential_Angle.cpp

@@ -221 +221 @@
 }
 
+FunctionModel::filter_t PairPotential_Angle::getSpecificFilter() const
+{
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Extractors::reorderArgumentsByParticleTypes,
+          _1,
+          getParticleTypes()
+      );
+  return returnfunction;
+}
+
 void
 PairPotential_Angle::setParametersToRandomInitialValues(

src/Potentials/Specifics/PairPotential_Angle.hpp

@@ -166 +166 @@
   FunctionModel::extractor_t getSpecificExtractor() const;
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const
+  { return 3; }
+
   enum parameter_enum_t {
     spring_constant=0,

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -198 +198 @@
 }
 
+FunctionModel::filter_t PairPotential_Harmonic::getSpecificFilter() const
+{
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Helpers::NoOp_Filterfunction,
+          _1);
+  return returnfunction;
+}
+
 void
 PairPotential_Harmonic::setParametersToRandomInitialValues(

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -148 +148 @@
   FunctionModel::extractor_t getSpecificExtractor() const;
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const
+  { return 1; }
+
   /** Return the token name of this specific potential.
    *

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -227 +227 @@
 }
 
+FunctionModel::filter_t PairPotential_Morse::getSpecificFilter() const
+{
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Helpers::NoOp_Filterfunction,
+          _1);
+  return returnfunction;
+}
+
 void
 PairPotential_Morse::setParametersToRandomInitialValues(

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -165 +165 @@
   FunctionModel::extractor_t getSpecificExtractor() const;
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const
+  { return 1; }
+
   enum parameter_enum_t {
     spring_constant=0,