Changeset 8203ce8 for src

Timestamp:

Jul 8, 2013, 2:22:01 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:

cf4905

Parents:

060e1e

git-author:

Frederik Heber <heber@…> (05/09/13 11:02:28)

git-committer:

Frederik Heber <heber@…> (07/08/13 14:22:01)

Message:

Added ConstantPotential to fit a non-zero offset in potential energy.

• also added ConstantPotentialUnitTest.

Location:

src

Files:

• FunctionApproximation/Extractors.cpp (modified) (2 diffs)
• Potentials/Makefile.am (modified) (2 diffs)
• Potentials/PotentialFactory.cpp (modified) (1 diff)
• Potentials/Specifics/ConstantPotential.cpp (added)
• Potentials/Specifics/ConstantPotential.hpp (added)
• Potentials/Specifics/PotentialTypes.def (modified) (1 diff)
• Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (added)
• Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp (added)
• Potentials/Specifics/unittests/Makefile.am (modified) (4 diffs)

src/FunctionApproximation/Extractors.cpp

@@ -308 +308 @@
   /// we first have to count same elements, then get different targets
   /// for each and then associated them in correct order back again.
+
+  // 0. if no elements given, we return empty arguments
+  if (elements.empty())
+    return FunctionModel::arguments_t();
 
   // 1. we have to place each charge into a map as unique chargeiter, i.e. map
@@ -416 +420 @@
 {
   // get last element from charges
+  ASSERT( !elements.empty(),
+      "Extractors::_detail::pickLastElementAsTarget() - no elements given to pick targets for.");
   const Fragment::charge_t charge = elements.back();
   elements.pop_back();

src/Potentials/Makefile.am

@@ -8 +8 @@
   Potentials/PotentialRegistry.cpp \
   Potentials/SerializablePotential.cpp \
+  Potentials/Specifics/ConstantPotential.cpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
   Potentials/Specifics/PairPotential_Angle.cpp \
@@ -30 +31 @@
 # add here headers for real potentials (i.e. the PotentialFactory should instantiate)  
 SPECIFICPOTENTIALSHEADER = \
+  Potentials/Specifics/ConstantPotential.hpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.hpp \
   Potentials/Specifics/PairPotential_Angle.hpp \

src/Potentials/PotentialFactory.cpp

@@ -103 +103 @@
       "PotentialFactory::createInstance() - cannot find potential of name "+potentialtype);
   switch (NameToType[potentialtype]) {
+  case constant:
+      return new ConstantPotential(types);
   case tersoff:
       return new ManyBodyPotential_Tersoff(types);

src/Potentials/Specifics/PotentialTypes.def

@@ -1 +1 @@
 //!> preprocessor sequence of all known potential types. Just add new parser here
-#define POTENTIALSEQUENCE (tersoff)(morse)(harmonic)(harmonic_angle)(saturation)
+#define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(saturation)
 //!> Number of enumerations calculate automatically
 #define PotentialTypes_END BOOST_PP_SEQ_SIZE(POTENTIALSEQUENCE)

src/Potentials/Specifics/unittests/Makefile.am

@@ -3 +3 @@
 
 POTENTIALSSPECIFICSTESTSSOURCES = \
+        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
         ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp \
         ../Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp \
@@ -9 +10 @@
 
 POTENTIALSSPECIFICSTESTSHEADERS = \
+        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp \
         ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp \
         ../Potentials/Specifics/unittests/PairPotential_AngleUnitTest.hpp \
@@ -15 +17 @@
 
 POTENTIALSSPECIFICSTESTS = \
+        ConstantPotentialUnitTest \
         ManyBodyPotential_TersoffUnitTest \
         PairPotential_AngleUnitTest \
@@ -33 +36 @@
         $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
         $(BOOST_LIB)
+
+ConstantPotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
+        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp
+ConstantPotentialUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
 
 ManyBodyPotential_TersoffUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \