Changeset 1dca9a

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:

5b5724

Parents:

3ccea3

git-author:

Frederik Heber <heber@…> (10/03/12 19:58:07)

git-committer:

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

Message:

Modified PairPotential_Harmonic to have an internal vector of parameters.

• an enum gives which index in the vector refers to which parameter. This makes the subsequent implementation of the parameter derivative easier.

Location:

src/Potentials/Specifics

Files:

• PairPotential_Harmonic.cpp (modified) (4 diffs)
• PairPotential_Harmonic.hpp (modified) (6 diffs)

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -43 +43 @@
 #include "Potentials/helpers.hpp"
 
+PairPotential_Harmonic::PairPotential_Harmonic() :
+  params(parameters_t(MAXPARAMS, 0.))
+{}
+
+PairPotential_Harmonic::PairPotential_Harmonic(
+    const double _spring_constant,
+    const double _equilibrium_distance,
+    const double _energy_offset) :
+      params(parameters_t(MAXPARAMS, 0.))
+{
+  params[spring_constant] = _spring_constant;
+  params[equilibrium_distance] = _equilibrium_distance;
+  params[energy_offset] = _energy_offset;
+}
+
 PairPotential_Harmonic::results_t
 PairPotential_Harmonic::operator()(
@@ -51 +66 @@
       "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 ) - energy_offset;
+  const result_t result =
+      params[spring_constant]
+             * Helpers::pow( r_ij.distance - params[equilibrium_distance], 2 )
+            + params[energy_offset];
   return std::vector<result_t>(1, result);
 }
@@ -64 +82 @@
   derivative_components_t result;
   const argument_t &r_ij = arguments[0];
-  result.push_back( 2. * spring_constant * ( r_ij.distance - equilibrium_distance) );
+  result.push_back( 2. * params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]) );
   ASSERT( result.size() == 1,
       "PairPotential_Harmonic::operator() - we did not create exactly one component.");
@@ -70 +88 @@
 }
 
-void PairPotential_Harmonic::setParameters(const parameters_t &_params)
-{
-  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(3, 0.);
-  params[0] = spring_constant;
-  params[1] = equilibrium_distance;
-  params[2] = energy_offset;
-  return params;
-}

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -15 +15 @@
 #endif
 
+#include "CodePatterns/Assert.hpp"
 
 #include "Potentials/EmpiricalPotential.hpp"
@@ -31 +32 @@
   typedef FunctionModel::results_t results_t;
   typedef EmpiricalPotential::derivative_components_t derivative_components_t;
+  typedef FunctionModel::parameters_t parameters_t;
 public:
   PairPotential_Harmonic();
@@ -36 +38 @@
       const double _spring_constant,
       const double _equilibrium_distance,
-      const double _energy_offset) :
-    spring_constant(_spring_constant),
-    equilibrium_distance(_equilibrium_distance),
-    energy_offset(_energy_offset)
-  {}
+      const double _energy_offset);
   virtual ~PairPotential_Harmonic() {}
 
@@ -47 +45 @@
    * \param _params given set of parameters
    */
-  void setParameters(const parameters_t &_params);
+  void setParameters(const parameters_t &_params)
+  {
+    ASSERT( _params.size() <= getParameterDimension(),
+        "PairPotential_Harmonic::setParameters() - we need not more than "
+        +toString(getParameterDimension())+" parameters.");
+    for(size_t i=0;i<_params.size();++i)
+      params[i] = _params[i];
+  }
 
   /** Getter for parameters as required by FunctionModel interface.
@@ -53 +58 @@
    * \return set of parameters
    */
-  parameters_t getParameters() const;
+  parameters_t getParameters() const
+  {
+    return params;
+  }
 
   /** Getter for the number of parameters of this model function.
@@ -89 +97 @@
 
 private:
-  //!> the spring constant for the harmonic potential
-  double spring_constant;
-  //!> the equilibrium distance indicating the potential minimum
-  double equilibrium_distance;
-  //!> energy offset
-  double energy_offset;
+  enum parameter_enum_t {
+    spring_constant=0,
+    equilibrium_distance=1,
+    energy_offset=2,
+    MAXPARAMS
+  };
+  //!> parameter vector with parameters as in enum parameter_enum_t
+  parameters_t params;
 };