Changeset b70b53 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:

76cbd0

Parents:

155cc2

git-author:

Frederik Heber <heber@…> (11/27/12 08:41:58)

git-committer:

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

Message:

FIX: Checked PairPotential_Morse::parameter_derivative with Maple.

• also added maple's results as comments and reformatted code to match.

File:

• src/Potentials/Specifics/PairPotential_Morse.cpp (modified) (6 diffs)

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -70 +70 @@
       "PairPotential_Morse::operator() - requires exactly one argument.");
   const argument_t &r_ij = arguments[0];
+  // Maple: f(r,D,k,R,c) := D * (1 - exp(-k*(r-R)))^(2)+c
   const result_t result =
       params[dissociation_energy] * Helpers::pow( 1.
@@ -86 +87 @@
   derivative_components_t result;
   const argument_t &r_ij = arguments[0];
+  // Maple result: 2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
   result.push_back(
       2. * params[dissociation_energy]
       * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-      * -1. * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-      * (- params[spring_constant])
+      * (- params[spring_constant]) * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
   );
   ASSERT( result.size() == 1,
@@ -109 +110 @@
     case spring_constant:
     {
+      // Maple result: -2*D*(1-exp(-k*(r-R)))*(-r+R)*exp(-k*(r-R))
       const result_t result =
-          2. * params[dissociation_energy]
+          - 2. * params[dissociation_energy]
           * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-          * -1. * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-          * (- ( r_ij.distance - params[equilibrium_distance]))
+          * (- r_ij.distance + params[equilibrium_distance])
+          * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
           ;
       return std::vector<result_t>(1, result);
@@ -120 +122 @@
     case equilibrium_distance:
     {
+      // Maple result: -2*D*(1-exp(-k*(r-R)))*k*exp(-k*(r-R))
       const result_t result =
-          2. * params[dissociation_energy]
+          - 2. * params[dissociation_energy]
           * ( 1. - exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance])))
-          * -1. * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
-          * params[spring_constant]
+          * params[spring_constant] * exp( - params[spring_constant] * ( r_ij.distance - params[equilibrium_distance]))
           ;
       return std::vector<result_t>(1, result);
@@ -131 +133 @@
     case dissociation_energy:
     {
+      // Maple result: (1-exp(-k*(r-R)))^2
       const result_t result =
           Helpers::pow(1.
@@ -139 +142 @@
     case energy_offset:
     {
+      // Maple result: 1
       const result_t result = +1.;
       return std::vector<result_t>(1, result);