Changeset 065a16 for src/Potentials/Specifics

Timestamp:

Jul 8, 2013, 2:22:02 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:

1e242a

Parents:

919c8a

git-author:

Frederik Heber <heber@…> (05/09/13 13:43:29)

git-committer:

Frederik Heber <heber@…> (07/08/13 14:22:02)

Message:

Removed energy_offset from PairPotential_Harmonic.

Location:

src/Potentials/Specifics

Files:

• PairPotential_Harmonic.cpp (modified) (7 diffs)
• PairPotential_Harmonic.hpp (modified) (3 diffs)
• unittests/PairPotential_HarmonicUnitTest.cpp (modified) (5 diffs)

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -59 +59 @@
       ("spring_constant")
       ("equilibrium_distance")
-      ("") //energy_offset
     ;
 const std::string PairPotential_Harmonic::potential_token("harmonic_bond");
@@ -71 +70 @@
   params[spring_constant] = 1.;
   params[equilibrium_distance] = 1.;
-  params[energy_offset] = 0.1;
 }
 
@@ -77 +75 @@
     const ParticleTypes_t &_ParticleTypes,
     const double _spring_constant,
-    const double _equilibrium_distance,
-    const double _energy_offset) :
+    const double _equilibrium_distance) :
   EmpiricalPotential(_ParticleTypes),
   params(parameters_t(MAXPARAMS, 0.))
@@ -84 +81 @@
   params[spring_constant] = _spring_constant;
   params[equilibrium_distance] = _equilibrium_distance;
-  params[energy_offset] = _energy_offset;
 }
 
@@ -118 +114 @@
   const result_t result =
       params[spring_constant]
-             * Helpers::pow( r_ij.distance - params[equilibrium_distance], 2 )
-            + params[energy_offset];
+             * Helpers::pow( r_ij.distance - params[equilibrium_distance], 2 );
   return std::vector<result_t>(1, result);
 }
@@ -169 +164 @@
       break;
     }
-    case energy_offset:
-    {
-      const result_t result = +1.;
-      return std::vector<result_t>(1, result);
-      break;
-    }
     default:
+      ASSERT(0, "PairPotential_Harmonic::parameter_derivative() - derivative to unknown parameter desired.");
       break;
   }
@@ -202 +192 @@
     const TrainingData &data)
 {
-  params[PairPotential_Harmonic::energy_offset] =
-      data.getTrainingOutputAverage()[0];// -1.;
   params[PairPotential_Harmonic::equilibrium_distance] = 3e+0*rand()/(double)RAND_MAX + .5;// 1.;
   params[PairPotential_Harmonic::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 0.2;

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -42 +42 @@
       const ParticleTypes_t &_ParticleTypes,
       const double _spring_constant,
-      const double _equilibrium_distance,
-      const double _energy_offset);
+      const double _equilibrium_distance);
   virtual ~PairPotential_Harmonic() {}
 
@@ -73 +72 @@
   size_t getParameterDimension() const
   {
-    return 3;
+    return MAXPARAMS;
   }
 
@@ -155 +154 @@
     spring_constant=0,
     equilibrium_distance=1,
-    energy_offset=2,
     MAXPARAMS
   };

src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp

@@ -68 +68 @@
   input += 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.;
   output +=
-      .5*1.+.1,
-      .5*0.+.1,
-      .5*1.+.1,
-      .5*4.+.1,
-      .5*9.+.1,
-      .5*16.+.1,
-      .5*25.+.1,
-      .5*36.+.1,
-      .5*49.+.1,
-      .5*64.+.1;
+      .5*1.,
+      .5*0.,
+      .5*1.,
+      .5*4.,
+      .5*9.,
+      .5*16.,
+      .5*25.,
+      .5*36.,
+      .5*49.,
+      .5*64.;
 
   CPPUNIT_ASSERT_EQUAL( input.size(), output.size() );
@@ -95 +95 @@
         (0)(1)
       ;
-  PairPotential_Harmonic harmonic(types, .5,1.,.1);
+  PairPotential_Harmonic harmonic(types, .5,1.);
   for (size_t index = 0; index < input.size(); ++index) {
     argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), input[index]);
@@ -115 +115 @@
         (0)(1)
       ;
-  PairPotential_Harmonic harmonic(types, .5,1.,.1);
+  PairPotential_Harmonic harmonic(types, .5,1.);
   argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), 1.);
   CPPUNIT_ASSERT(
@@ -136 +136 @@
         (0)(1)
       ;
-  PairPotential_Harmonic harmonic(types, .5,1.,.1);
+  PairPotential_Harmonic harmonic(types, .5,1.);
   argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), 1.);
   CPPUNIT_ASSERT(
@@ -156 +156 @@
       )
   );
-  CPPUNIT_ASSERT(
-      Helpers::isEqual(
-          1.,
-          harmonic.parameter_derivative(
-              FunctionModel::arguments_t(1,arg),
-              2
-          )[0]
-      )
-  );
 }