Changeset 0f5d38 for src

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

Files:

• FunctionApproximation/FunctionModel.hpp (modified) (3 diffs)
• Potentials/CompoundPotential.cpp (modified) (3 diffs)
• Potentials/CompoundPotential.hpp (modified) (1 diff)
• Potentials/Specifics/ConstantPotential.cpp (modified) (1 diff)
• Potentials/Specifics/ConstantPotential.hpp (modified) (1 diff)
• Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Angle.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Angle.hpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.hpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Morse.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Morse.hpp (modified) (1 diff)
• Potentials/helpers.hpp (modified) (1 diff)

src/FunctionApproximation/FunctionModel.hpp

@@ -29 +29 @@
  * as possible.
  *
+ * We always work in distances, i.e. pairs of atoms and the distance in between.
+ * As fragments do not contain these distances directly but the atomic positions
+ * (and charges) instead, we need to extract these from the fragment. For this
+ * purpose we need a bound function, termed an 'Extractor'. However, this is only
+ * required when one wants to use a FunctionModel directly on a given fragment.
+ * In FunctionApproximation we instead have TrainingData generate automatically
+ * a list of all pair-wise distances. The FunctionModel's Extractor may however
+ * create a more specific (and tighter) list of arguments, which however can
+ * then only be used with this specific FunctionModel.
+ *
+ * Furthermore, the underlying function to fit may require these distances, or
+ * arguments (termed so if paired with charges and atomic indices), to be in a
+ * certain order or does need only a subset. For this purpose we need another
+ * bound function, called a 'Filter'.
+ *
+ * As a fragment may contain multiple sets of arguments or distances that serve
+ * as valid function arguments, we need to split these sets up, such that they
+ * can be served one by one to the function. For this purpose we need a function
+ * that gives the number of arguments per set. (note that the Filter is supposed
+ * to place related arguments consecutively.
+ *
  */
 class FunctionModel
@@ -45 +66 @@
   //!> typedef for a function containing how to extract required information from a Fragment.
   typedef boost::function< arguments_t (const Fragment &, const size_t)> extractor_t;
+  //!> typedef for a function containing how to filter required distances from a full argument list.
+  typedef boost::function< arguments_t (const arguments_t &)> filter_t;
   //!> typedef for the magic triple function that gets the other two distances for a given argument
   typedef boost::function< std::vector<arguments_t>(const argument_t &, const double)> triplefunction_t;
@@ -130 +153 @@
    */
   virtual extractor_t getSpecificExtractor() const=0;
+
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  virtual filter_t getSpecificFilter() const=0;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * \return number of arguments of the function
+   */
+  virtual size_t getSpecificArgumentCount() const=0;
 };
 

src/Potentials/CompoundPotential.cpp

@@ -53 +53 @@
 #include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/EmpiricalPotential.hpp"
+#include "Potentials/helpers.hpp"
 #include "Potentials/PotentialRegistry.hpp"
 
@@ -433 +434 @@
 {
   // create initial returnfunction
-  particletypes_per_model_t::const_iterator typesiter = particletypes_per_model.begin();
-  Fragment::charges_t charges;
-  {
-    charges.resize((*typesiter).size());
-    std::transform((*typesiter).begin(), (*typesiter).end(),
-        charges.begin(), boost::lambda::_1);
-  }
   FunctionModel::extractor_t returnfunction =
-    boost::bind(&Extractors::gatherAllDistancesFromFragment,
-        boost::bind(&Fragment::getPositions, _1),
-        boost::bind(&Fragment::getCharges, _1),
-        charges,  // no crefs here as are temporaries!
-        _2);
+      boost::bind(&Helpers::returnEmptyArguments);
 
   // every following fragments combines its arguments with the initial function
-  for (; typesiter != particletypes_per_model.end(); ++typesiter) {
+  for (particletypes_per_model_t::const_iterator typesiter = particletypes_per_model.begin();
+      typesiter != particletypes_per_model.end(); ++typesiter) {
     Fragment::charges_t charges;
     {
@@ -468 +459 @@
   return returnfunction;
 }
+
+FunctionModel::filter_t CompoundPotential::getSpecificFilter() const
+{
+  // we must concatenate all filtered arguments here
+  // create initial returnfunction
+  FunctionModel::filter_t returnfunction =
+      boost::bind(&Helpers::returnEmptyArguments);
+
+  // every following fragments combines its arguments with the initial function
+  for (models_t::const_iterator modeliter = models.begin();
+      modeliter != models.end(); ++modeliter) {
+    returnfunction =
+          boost::bind(&Extractors::concatenateArguments,
+              boost::bind(returnfunction, _1),
+              boost::bind((*modeliter)->getSpecificFilter(), _1)
+        );
+  }
+  return returnfunction;
+}
+
+size_t CompoundPotential::getSpecificArgumentCount() const
+{
+  std::vector<size_t> argument_counts(models.size(), 0);
+  std::transform(models.begin(), models.end(), argument_counts.begin(),
+      boost::bind(&FunctionModel::getSpecificArgumentCount, _1));
+  return std::accumulate(argument_counts.begin(), argument_counts.end(), 0,
+      std::plus<size_t>());
+}
+

src/Potentials/CompoundPotential.hpp

@@ -127 +127 @@
    * from a Fragment.
    *
+   * Here, we simply concatenate the arguments delivered by the extractors of each model.
+   *
    * \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.
+   *
+   * \note CompoundPotential has only default filter, as filter needs to be
+   * model-specific.
+   *
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::filter_t getSpecificFilter() const;
+
+  /** Returns the number of arguments the underlying function requires.
+   *
+   * We give the total sum over the argument counts of all models.
+   *
+   * \return number of arguments of the function
+   */
+  size_t getSpecificArgumentCount() const;
 
 private:

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,

src/Potentials/helpers.hpp

@@ -94 +94 @@
   }
 
+  inline FunctionModel::arguments_t
+  NoOp_Filterfunction(
+      const FunctionModel::arguments_t &args
+      )
+  {
+    return args;
+  }
+
+  inline FunctionModel::arguments_t
+  returnEmptyArguments()
+  {
+    return FunctionModel::arguments_t();
+  }
+
 }; /* namespace Helpers */