Changeset 5b5724 for src/Potentials

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:

3c1465

Parents:

1dca9a

git-author:

Frederik Heber <heber@…> (10/03/12 19:58:56)

git-committer:

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

Message:

FunctionApproximation now uses levmar_der, i.e. additionally the derivative of the FunctionModel.

• added LevMarDerivativeCallback as another static function.
• added ::evaluateDerivative that fills the Jacobian matrix as output.
• removed meyer and jacmeyer from FunctionApproximation module.

Location:

src/Potentials/Specifics

Files:

• PairPotential_Harmonic.cpp (modified) (1 diff)
• PairPotential_Harmonic.hpp (modified) (1 diff)

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -88 +88 @@
 }
 
+PairPotential_Harmonic::results_t
+PairPotential_Harmonic::parameter_derivative(
+    const arguments_t &arguments,
+    const size_t index
+    ) const
+{
+  ASSERT( arguments.size() == 1,
+      "PairPotential_Harmonic::parameter_derivative() - requires exactly one argument.");
+  const argument_t &r_ij = arguments[0];
+  switch (index) {
+    case spring_constant:
+    {
+      const result_t result =
+                 Helpers::pow( r_ij.distance - params[equilibrium_distance], 2 );
+      return std::vector<result_t>(1, result);
+      break;
+    }
+    case equilibrium_distance:
+    {
+      const result_t result =
+          -2. * params[spring_constant]
+                 * ( r_ij.distance - params[equilibrium_distance]);
+      return std::vector<result_t>(1, result);
+      break;
+    }
+    case energy_offset:
+    {
+      const result_t result = +1.;
+      return std::vector<result_t>(1, result);
+      break;
+    }
+    default:
+      break;
+  }
+
+  return PairPotential_Harmonic::results_t(1, 0.);
+}
+

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -94 +94 @@
    *         input
    */
-//  results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
+  results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
 private: