Changeset 919c8a for src/Potentials/Specifics/PairPotential_Morse.cpp

Timestamp:

Jul 8, 2013, 2:22:02 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:

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.

File:

• src/Potentials/Specifics/PairPotential_Morse.cpp (modified) (7 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;