Changeset 7b019a for src/Potentials/Specifics

Timestamp:

Feb 27, 2013, 12:39:03 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:

d52819

Parents:

69fcba

git-author:

Frederik Heber <heber@…> (11/30/12 15:33:58)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:39:03)

Message:

Extended FunctionModel by getFragmentSpecificExtractor() definition.

• shifted extractor_t from TrainingData to FunctionModel.
• implemented function for every specific potential.
• this is preparatory for generalizing function approximation in LevMartester.
• we make use of the newly introduced extractors in the potentials and the required number of charges is ASSERT'd.

Location:

src/Potentials/Specifics

Files:

• ManyBodyPotential_Tersoff.cpp (modified) (2 diffs)
• ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• PairPotential_Angle.cpp (modified) (2 diffs)
• PairPotential_Angle.hpp (modified) (1 diff)
• PairPotential_Harmonic.cpp (modified) (2 diffs)
• PairPotential_Harmonic.hpp (modified) (1 diff)
• PairPotential_Morse.cpp (modified) (3 diffs)
• PairPotential_Morse.hpp (modified) (1 diff)
• SaturationPotential.cpp (modified) (4 diffs)
• SaturationPotential.hpp (modified) (1 diff)
• unittests/Makefile.am (modified) (1 diff)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -48 +48 @@
 #include "CodePatterns/Log.hpp"
 
+#include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+
+class Fragment;
 
 // static definitions
@@ -680 +683 @@
 }
 
+FunctionModel::extractor_t
+ManyBodyPotential_Tersoff::getFragmentSpecificExtractor(
+    const charges_t &charges) const
+{
+  ASSERT(charges.size() <= (size_t)2,
+      "ManyBodyPotential_Tersoff::getFragmentSpecificExtractor() - requires 1 charge.");
+  FunctionModel::extractor_t returnfunction =
+      boost::bind(&Extractors::gatherAllDistances,
+          boost::bind(&Fragment::getPositions, _1),
+          boost::bind(&Fragment::getCharges, _1),
+          _2);
+  return returnfunction;
+}
+

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -178 +178 @@
   }
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
+
 private:
   /** Prohibit private default constructor.

src/Potentials/Specifics/PairPotential_Angle.cpp

@@ -40 +40 @@
 
 #include <boost/assign/list_of.hpp> // for 'map_list_of()'
+#include <boost/bind.hpp>
 #include <string>
 
 #include "CodePatterns/Assert.hpp"
 
+#include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+
+class Fragment;
 
 // static definitions
@@ -199 +203 @@
   }
 }
+
+FunctionModel::extractor_t
+PairPotential_Angle::getFragmentSpecificExtractor(
+    const charges_t &charges) const
+{
+  ASSERT(charges.size() == (size_t)3,
+      "PairPotential_Angle::getFragmentSpecificExtractor() - requires 3 charges.");
+  FunctionModel::extractor_t returnfunction =
+      boost::bind(&Extractors::gatherDistancesFromFragment,
+          boost::bind(&Fragment::getPositions, _1),
+          boost::bind(&Fragment::getCharges, _1),
+          boost::cref(charges),
+          _2);
+  return returnfunction;
+}
+

src/Potentials/Specifics/PairPotential_Angle.hpp

@@ -145 +145 @@
   }
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
+
   enum parameter_enum_t {
     spring_constant=0,

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -40 +40 @@
 
 #include <boost/assign/list_of.hpp> // for 'map_list_of()'
+#include <boost/bind.hpp>
 #include <string>
 
 #include "CodePatterns/Assert.hpp"
 
+#include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+
+class Fragment;
 
 // static definitions
@@ -176 +180 @@
 }
 
+FunctionModel::extractor_t
+PairPotential_Harmonic::getFragmentSpecificExtractor(
+    const charges_t &charges) const
+{
+  ASSERT(charges.size() == (size_t)2,
+      "PairPotential_Harmonic::getFragmentSpecificExtractor() - requires 2 charges.");
+  FunctionModel::extractor_t returnfunction =
+      boost::bind(&Extractors::gatherDistancesFromFragment,
+          boost::bind(&Fragment::getPositions, _1),
+          boost::bind(&Fragment::getCharges, _1),
+          boost::cref(charges),
+          _2);
+  return returnfunction;
+}
+

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -127 +127 @@
   }
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
+
   /** Return the token name of this specific potential.
    *

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -40 +40 @@
 
 #include <boost/assign/list_of.hpp> // for 'map_list_of()'
+#include <boost/bind.hpp>
 #include <cmath>
 #include <string>
@@ -45 +46 @@
 #include "CodePatterns/Assert.hpp"
 
+#include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+
+class Fragment;
 
 // static definitions
@@ -204 +208 @@
   return std::vector<result_t>(1, 0.);
 }
+
+FunctionModel::extractor_t
+PairPotential_Morse::getFragmentSpecificExtractor(
+    const charges_t &charges) const
+{
+  ASSERT(charges.size() == (size_t)2,
+      "PairPotential_Morse::getFragmentSpecificExtractor() - requires 2 charges.");
+  FunctionModel::extractor_t returnfunction =
+      boost::bind(&Extractors::gatherDistancesFromFragment,
+          boost::bind(&Fragment::getPositions, _1),
+          boost::bind(&Fragment::getCharges, _1),
+          boost::cref(charges),
+          _2);
+  return returnfunction;
+}
+

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -144 +144 @@
   }
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
+
   enum parameter_enum_t {
     spring_constant=0,

src/Potentials/Specifics/SaturationPotential.cpp

@@ -47 +47 @@
 #include "CodePatterns/Log.hpp"
 
+#include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+
+class Fragment;
 
 using namespace boost::assign;
@@ -75 +78 @@
   triplefunction(_triplefunction),
   saturation_cutoff(_saturation_cutoff)
-{}
+{
+  // have some decent defaults for parameter_derivative checking
+  // Morse and Angle have their own defaults, offset is set
+  ASSERT( _ParticleTypes.size() == (size_t)2,
+      "SaturationPotential::SaturationPotential() - exactly two types must be given.");
+  ASSERT( _ParticleTypes[1] == 1,
+      "SaturationPotential::SaturationPotential() - second type must be hydrogen.");
+}
 
 SaturationPotential::SaturationPotential(
@@ -94 +104 @@
   saturation_cutoff(_saturation_cutoff)
 {
+  ASSERT( _ParticleTypes.size() == (size_t)2,
+      "SaturationPotential::SaturationPotential() - exactly two types must be given.");
+  ASSERT( _ParticleTypes[1] == 1,
+      "SaturationPotential::SaturationPotential() - second type must be hydrogen.");
   parameters_t morse_params(morse.getParameterDimension());
   morse_params[PairPotential_Morse::spring_constant] = _morse_spring_constant;
@@ -303 +317 @@
   return ist;
 }
+
+FunctionModel::extractor_t
+SaturationPotential::getFragmentSpecificExtractor(
+    const charges_t &charges) const
+{
+  ASSERT(charges.size() == (size_t)2,
+      "SaturationPotential::getFragmentSpecificExtractor() - requires 2 charges.");
+  FunctionModel::extractor_t returnfunction;
+  if (charges[0] == charges[1]) {
+    // In case both types are equal there is only a single pair of possible
+    // type combinations.
+     returnfunction =
+        boost::bind(&Extractors::gatherAllDistancesFromFragment,
+            boost::bind(&Fragment::getPositions, _1),
+            boost::bind(&Fragment::getCharges, _1),
+            boost::cref(charges),
+            _2);
+  } else {
+    // we have to chain here a rather complex "tree" of functions
+    // as we only have a couple of ParticleTypes but need to get
+    // all possible three pairs of the set of the two types.
+    // Finally, we also need to arrange them in correct order
+    // (for PairPotentiale_Angle).
+    charges_t firstpair(2, boost::cref(charges[0]));
+    charges_t secondpair(2, boost::cref(charges[1]));
+    const charges_t &thirdpair = charges;
+    returnfunction =
+        boost::bind(&Extractors::reorderArgumentsByParticleTypes,
+          boost::bind(&Extractors::combineArguments,
+            boost::bind(&Extractors::combineArguments,
+              boost::bind(&Extractors::gatherAllDistancesFromFragment,
+                  boost::bind(&Fragment::getPositions, _1),
+                  boost::bind(&Fragment::getCharges, _1),
+                  firstpair,  // no crefs here as are temporaries!
+                  _2),
+              boost::bind(&Extractors::gatherAllDistancesFromFragment,
+                  boost::bind(&Fragment::getPositions, _1),
+                  boost::bind(&Fragment::getCharges, _1),
+                  secondpair,  // no crefs here as are temporaries!
+                  _2)
+            ),
+            boost::bind(&Extractors::gatherAllDistancesFromFragment,
+                boost::bind(&Fragment::getPositions, _1),
+                boost::bind(&Fragment::getCharges, _1),
+                boost::cref(thirdpair), // only the last one is no temporary
+                _2)
+          ),
+          boost::cref(angle.getParticleTypes())
+        );
+}
+  return returnfunction;
+}

src/Potentials/Specifics/SaturationPotential.hpp

@@ -156 +156 @@
   }
 
+  /** Returns a bound function to be used with TrainingData, extracting distances
+   * from a Fragment.
+   *
+   * \param charges vector of charges to be extracted
+   * \return bound function extracting distances from a fragment
+   */
+  FunctionModel::extractor_t getFragmentSpecificExtractor(const charges_t &charges) const;
+
   enum parameter_enum_t {
     all_energy_offset,

src/Potentials/Specifics/unittests/Makefile.am

@@ -26 +26 @@
 POTENTIALSSPECIFICSLIBS = \
         ../libMolecuilderPotentials.la \
+        ../libMolecuilderFragmentationSetValues.la \
+        ../libMolecuilderFunctionApproximation.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \
-  $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
+        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
         $(BOOST_LIB)