Changeset 16227a for src/Potentials/Specifics

Timestamp:

Jun 27, 2014, 9:32:55 PM (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:

e1fe7e

Parents:

f4496d

git-author:

Frederik Heber <heber@…> (02/27/14 21:44:28)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:55)

Message:

Removed FunctionModel::getSpecificExtractor() that is not needed anymore.

• it was only used in FitPotentialAction generating WorstFragmentMap.
• strangely required to change the order of some libraries (libMolecuilderFragmentation_Summation needed further down).

Location:

src/Potentials/Specifics

Files:

• ConstantPotential.cpp (modified) (1 diff)
• ConstantPotential.hpp (modified) (1 diff)
• FourBodyPotential_Torsion.cpp (modified) (1 diff)
• FourBodyPotential_Torsion.hpp (modified) (1 diff)
• ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• PairPotential_Harmonic.cpp (modified) (1 diff)
• PairPotential_Harmonic.hpp (modified) (1 diff)
• PairPotential_LennardJones.cpp (modified) (1 diff)
• PairPotential_LennardJones.hpp (modified) (1 diff)
• PairPotential_Morse.cpp (modified) (1 diff)
• PairPotential_Morse.hpp (modified) (1 diff)
• ThreeBodyPotential_Angle.cpp (modified) (1 diff)
• ThreeBodyPotential_Angle.hpp (modified) (1 diff)
• unittests/Makefile.am (modified) (1 diff)

src/Potentials/Specifics/ConstantPotential.cpp

@@ -163 +163 @@
 }
 
-FunctionModel::extractor_t
-ConstantPotential::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t ConstantPotential::getSpecificFilter() const
 {

src/Potentials/Specifics/ConstantPotential.hpp

@@ -169 +169 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/FourBodyPotential_Torsion.cpp

@@ -223 +223 @@
 }
 
-FunctionModel::extractor_t
-FourBodyPotential_Torsion::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t
 FourBodyPotential_Torsion::getSpecificFilter() const

src/Potentials/Specifics/FourBodyPotential_Torsion.hpp

@@ -175 +175 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -691 +691 @@
 }
 
-FunctionModel::extractor_t
-ManyBodyPotential_Tersoff::getSpecificExtractor() const
-{
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherAllDistances,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t ManyBodyPotential_Tersoff::getSpecificFilter() const
 {

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -194 +194 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -186 +186 @@
 }
 
-FunctionModel::extractor_t
-PairPotential_Harmonic::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t PairPotential_Harmonic::getSpecificFilter() const
 {

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -154 +154 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/PairPotential_LennardJones.cpp

@@ -195 +195 @@
 }
 
-FunctionModel::extractor_t
-PairPotential_LennardJones::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t PairPotential_LennardJones::getSpecificFilter() const
 {

src/Potentials/Specifics/PairPotential_LennardJones.hpp

@@ -171 +171 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -215 +215 @@
 }
 
-FunctionModel::extractor_t
-PairPotential_Morse::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t PairPotential_Morse::getSpecificFilter() const
 {

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -171 +171 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

@@ -210 +210 @@
 }
 
-FunctionModel::extractor_t
-ThreeBodyPotential_Angle::getSpecificExtractor() const
-{
-  Fragment::charges_t charges;
-  charges.resize(getParticleTypes().size());
-  std::transform(getParticleTypes().begin(), getParticleTypes().end(),
-      charges.begin(), boost::lambda::_1);
-  FunctionModel::extractor_t returnfunction =
-      boost::bind(&Extractors::gatherDistancesFromFragment,
-          boost::bind(&Fragment::getPositions, _1),
-          boost::bind(&Fragment::getCharges, _1),
-          charges,
-          _2);
-  return returnfunction;
-}
-
 FunctionModel::filter_t ThreeBodyPotential_Angle::getSpecificFilter() const
 {

src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp

@@ -172 +172 @@
    * \return bound function extracting distances from a fragment
    */
-  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;
 

src/Potentials/Specifics/unittests/Makefile.am

@@ -38 +38 @@
 POTENTIALSSPECIFICSLIBS = \
         ../libMolecuilderPotentials.la \
-        ../libMolecuilderFragmentationSetValues.la \
         ../libMolecuilderFragmentation.la \
         ../libMolecuilderFunctionApproximation.la \
         ../libMolecuilderRandomNumbers.la \
+        ../libMolecuilderFragmentationSummation.la \
+        ../libMolecuilderFragmentation_getFromKeysetStub.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \