Changeset 65c42c for src/Potentials/Specifics/PairPotential_Harmonic.cpp

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.

File:

• src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) (2 diffs)

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;
 }