Changeset 65c42c for src

Timestamp:

Dec 19, 2012, 3:25:31 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:

dac89b1

Parents:

c62f96

git-author:

Frederik Heber <heber@…> (12/11/12 16:03:40)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:31)

Message:

PairPotential_Harmonic now has additional offset parameter.

• do we need this value in general or not?. A constant should in fact be removed by zero and first order ... but it has to to remove the minimum value. Otherwise the fit cannot converge properly (hence the parameter probably inavoidable for stability).
• With this setup we were able to successfully fit to a C2H6 system where the CC bond length was specifically manipulated. However, the harmonic function is not the best model, a Morse potential seems more adept.

Location:

src

Files:

• LevMartester.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.cpp (modified) (2 diffs)
• Potentials/Specifics/PairPotential_Harmonic.hpp (modified) (3 diffs)

src/LevMartester.cpp

@@ -176 +176 @@
   // NOTICE that distance are in bohrradi as they come from MPQC!
 
-  PairPotential_Harmonic harmonic(1., 1.);
+  PairPotential_Harmonic harmonic(1., 2., 0.);
   FunctionApproximation approximator(1, 1, harmonic);
   approximator();
   const FunctionModel::parameters_t params = harmonic.getParameters();
 
-  LOG(0, "RESULT: Best parameters are " << params[0] << " and " << params[1] << ".");
+  LOG(0, "RESULT: Best parameters are " << params[0] << ","
+      << params[1] << " and " << params[2] << ".");
 
   return 0;

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -51 +51 @@
       "PairPotential_Harmonic::operator() - requires exactly one argument.");
   const argument_t &r_ij = arguments[0];
-  const result_t result = spring_constant * Helpers::pow( r_ij.distance - equilibrium_distance, 2 );
+  const result_t result = spring_constant * Helpers::pow( r_ij.distance - equilibrium_distance, 2 ) - energy_offset;
   return std::vector<result_t>(1, result);
 }
@@ -72 +72 @@
 void PairPotential_Harmonic::setParameters(const parameters_t &_params)
 {
-  ASSERT( _params.size() == 2,
+  ASSERT( _params.size() == 3,
       "PairPotential_Harmonic::setParameters() - we need exactly two parameters.");
   spring_constant = _params[0];
   equilibrium_distance = _params[1];
+  energy_offset = _params[2];
 }
 
 PairPotential_Harmonic::parameters_t PairPotential_Harmonic::getParameters() const
 {
-  parameters_t params(2, 0.);
+  parameters_t params(3, 0.);
   params[0] = spring_constant;
   params[1] = equilibrium_distance;
+  params[2] = energy_offset;
   return params;
 }

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -30 +30 @@
   PairPotential_Harmonic(
       const double _spring_constant,
-      const double _equilibrium_distance) :
+      const double _equilibrium_distance,
+      const double _energy_offset) :
     spring_constant(_spring_constant),
-    equilibrium_distance(_equilibrium_distance)
+    equilibrium_distance(_equilibrium_distance),
+    energy_offset(_energy_offset)
   {}
   virtual ~PairPotential_Harmonic() {}
@@ -54 +56 @@
   size_t getParameterDimension() const
   {
-    return 2;
+    return 3;
   }
 
@@ -76 +78 @@
   //!> the equilibrium distance indicating the potential minimum
   double equilibrium_distance;
+  //!> energy offset
+  double energy_offset;
 };