Changeset 919c8a for src/Potentials

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:

065a16

Parents:

1e565c

git-author:

Frederik Heber <heber@…> (05/09/13 13:40:51)

git-committer:

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

Message:

Removed energy_offset from PairPotential_Morse.

• regression test FitPotential with morse potential marked as XFAIL. This is required until we use new CompoundPotential in FitPotentialAction.

Location:

src/Potentials/Specifics

Files:

• PairPotential_Morse.cpp (modified) (7 diffs)
• PairPotential_Morse.hpp (modified) (3 diffs)
• unittests/PairPotential_MorseUnitTest.cpp (modified) (6 diffs)

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -61 +61 @@
       ("equilibrium_distance")
       ("dissociation_energy")
-      ("") //energy_offset
     ;
 const std::string PairPotential_Morse::potential_token("morse");
@@ -75 +74 @@
   params[equilibrium_distance] = 1.;
   params[dissociation_energy] = 0.1;
-  params[energy_offset] = 0.;
 }
 
@@ -82 +80 @@
     const double _spring_constant,
     const double _equilibrium_distance,
-    const double _dissociation_energy,
-    const double _energy_offset) :
+    const double _dissociation_energy) :
   EmpiricalPotential(_ParticleTypes),
   params(parameters_t(MAXPARAMS, 0.))
@@ -90 +87 @@
   params[equilibrium_distance] = _equilibrium_distance;
   params[dissociation_energy] = _dissociation_energy;
-  params[energy_offset] = _energy_offset;
 }
 
@@ -125 +121 @@
   const result_t result =
       params[dissociation_energy] * Helpers::pow( 1.
-          - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2)
-            + params[energy_offset];
+          - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])),2);
   return std::vector<result_t>(1, result);
 }
@@ -198 +193 @@
       break;
     }
-    case energy_offset:
-    {
-      // Maple result: 1
-      const result_t result = +1.;
-      return std::vector<result_t>(1, result);
-      break;
-    }
     default:
+      ASSERT(0, "PairPotential_Morse::parameter_derivative() - derivative to unknown parameter desired.");
       break;
   }
@@ -232 +221 @@
 {
   params[PairPotential_Morse::dissociation_energy] = 1e+0*rand()/(double)RAND_MAX;// 0.5;
-  params[PairPotential_Morse::energy_offset] =
-      data.getTrainingOutputAverage()[0];// -1.;
   params[PairPotential_Morse::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 1.;
   params[PairPotential_Morse::equilibrium_distance] =  3e+0*rand()/(double)RAND_MAX;//2.9;

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -43 +43 @@
       const double _spring_constant,
       const double _equilibrium_distance,
-      const double _dissociation_energy,
-      const double _energy_offset);
+      const double _dissociation_energy);
   virtual ~PairPotential_Morse() {}
 
@@ -74 +73 @@
   size_t getParameterDimension() const
   {
-    return 4;
+    return MAXPARAMS;
   }
 
@@ -157 +156 @@
     equilibrium_distance=1,
     dissociation_energy=2,
-    energy_offset=3,
     MAXPARAMS
   };

src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp

@@ -66 +66 @@
   ASSERT_DO(Assert::Throw);
 
-  // data is taken from gnuplot via set table "morse.dat" with
+  // data is taken from gnuplot via
   // g(x)=D*(1- exp(-a*(x-c)))**2+d
+  // set table "morse.dat"
+  // plot [1.89012:4.46595] g(x)
   a = 0.897888;
   c = 2.92953;
@@ -84 +86 @@
       4.46595;
   output +=
-      -78.5211,
-      -78.8049,
-      -78.935,
-      -78.9822,
-      -78.9867,
-      -78.971,
-      -78.9475,
-      -78.9225,
-      -78.899,
-      -78.8784;
+                        0.467226,
+                        0.183388,
+                        0.0532649,
+                        0.00609808,
+                        0.00160056,
+                        0.0172506,
+                        0.0407952,
+                        0.0658475,
+                        0.0893157,
+                        0.109914;
 
   CPPUNIT_ASSERT_EQUAL( input.size(), output.size() );
@@ -111 +113 @@
         (0)(1)
       ;
-  PairPotential_Morse Morse(types, a,c,D,d);
+  PairPotential_Morse Morse(types, a,c,D);
   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]);
@@ -132 +134 @@
         (0)(1)
       ;
-  PairPotential_Morse Morse(types, a,c,D,d);
+  PairPotential_Morse Morse(types, a,c,D);
   argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), c);
   CPPUNIT_ASSERT(
@@ -154 +156 @@
         (0)(1)
       ;
-  PairPotential_Morse Morse(types, a,c,D,d);
+  PairPotential_Morse Morse(types, a,c,D);
   argument_t arg(argument_t::indices_t(0,1), argument_t::types_t(0,1), c);
   CPPUNIT_ASSERT(
@@ -186 +188 @@
       )
   );
-  CPPUNIT_ASSERT(
-      Helpers::isEqual(
-          1.,
-          Morse.parameter_derivative(
-              FunctionModel::arguments_t(1,arg),
-              3
-          )[0],
-          1.e+6
-      )
-  );
 }