Changeset 155cc2 for src

Timestamp:

Dec 19, 2012, 3:25:43 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:

b70b53

Parents:

9e903b

git-author:

Frederik Heber <heber@…> (10/03/12 20:23:20)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:43)

Message:

Added PairPotential_Morse with derivatives, used by LevMartester.

• we can now succesfully fit the stretched CC bond in C2H6 to a Morse potential.

Location:

src

Files:

• LevMartester.cpp (modified) (3 diffs)
• Potentials/Makefile.am (modified) (2 diffs)
• Potentials/Specifics/PairPotential_Morse.cpp (added)
• Potentials/Specifics/PairPotential_Morse.hpp (added)

src/LevMartester.cpp

@@ -57 +57 @@
 #include "FunctionApproximation/FunctionApproximation.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
-#include "Potentials/Specifics/PairPotential_Harmonic.hpp"
+#include "Potentials/Specifics/PairPotential_Morse.hpp"
 
 namespace po = boost::program_options;
@@ -177 +177 @@
 
   // now perform the function approximation by optimizing the model function
-  PairPotential_Harmonic harmonic(1., 2.9, -80.);
-  FunctionModel &model = harmonic;
+  PairPotential_Morse morse(1., 2.9, 0.5, -80.);
+  FunctionModel &model = morse;
   FunctionApproximation approximator(1, 1, model);
   approximator.setTrainingData(DistanceEnergyVector.first,DistanceEnergyVector.second);
@@ -185 +185 @@
 
   LOG(0, "RESULT: Best parameters are " << params[0] << ","
-      << params[1] << " and " << params[2] << ".");
+      << params[1] << "," << params[2] << " and " << params[3] << ".");
 
   return 0;

src/Potentials/Makefile.am

@@ -4 +4 @@
 POTENTIALSSOURCE = \
   Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
-  Potentials/Specifics/PairPotential_Harmonic.cpp
+  Potentials/Specifics/PairPotential_Harmonic.cpp \
+  Potentials/Specifics/PairPotential_Morse.cpp
 
 POTENTIALSHEADER = \
@@ -10 +11 @@
   Potentials/helpers.hpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.hpp \
-  Potentials/Specifics/PairPotential_Harmonic.hpp
+  Potentials/Specifics/PairPotential_Harmonic.hpp \
+  Potentials/Specifics/PairPotential_Morse.hpp
+  
 
 noinst_LTLIBRARIES += libMolecuilderPotentials.la