Changeset bbc422

Timestamp:

Jul 8, 2013, 2:22:00 PM (11 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:

5f0c60

Parents:

e352cb

git-author:

Frederik Heber <heber@…> (06/25/13 09:30:44)

git-committer:

Frederik Heber <heber@…> (07/08/13 14:22:00)

Message:

FIX: Renamed arguments in PairPotential_Angle to make proper sense.

• this does/should not change functionality in any way.

File:

• src/Potentials/Specifics/PairPotential_Angle.cpp (modified) (5 diffs)

src/Potentials/Specifics/PairPotential_Angle.cpp

@@ -109 +109 @@
 PairPotential_Angle::function_theta(
     const double &r_ij,
-    const double &r_ik,
-    const double &r_jk
+    const double &r_jk,
+    const double &r_ik
   ) const
 {
 //  Info info(__func__);
-  const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_ik,2) - Helpers::pow(r_jk,2);
-  const double divisor = 2.* r_ij * r_ik;
+  const double angle = Helpers::pow(r_ij,2) + Helpers::pow(r_jk,2) - Helpers::pow(r_ik,2);
+  const double divisor = 2.* r_ij * r_jk;
 
 //  LOG(2, "DEBUG: cos(theta)= " << angle/divisor);
@@ -131 +131 @@
   ASSERT( arguments.size() == 3,
       "PairPotential_Angle::operator() - requires exactly three arguments.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
+  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
       arguments, getParticleTypes()),
       "PairPotential_Angle::operator() - types don't match with ones in arguments.");
   const argument_t &r_ij = arguments[0]; // 01
-  const argument_t &r_ik = arguments[2]; // 12
-  const argument_t &r_jk = arguments[1]; // 02
+  const argument_t &r_jk = arguments[2]; // 12
+  const argument_t &r_ik = arguments[1]; // 02
   const result_t result =
       params[spring_constant]
-             * Helpers::pow( function_theta(r_ij.distance, r_ik.distance, r_jk.distance) - params[equilibrium_distance], 2 )
-            + params[energy_offset];
+             * Helpers::pow( function_theta(r_ij.distance, r_jk.distance, r_ik.distance) - params[equilibrium_distance], 2 )
+      + params[energy_offset];
   return std::vector<result_t>(1, result);
 }
@@ -151 +151 @@
   ASSERT( arguments.size() == 3,
       "PairPotential_Angle::operator() - requires exactly three arguments.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
+  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
       arguments, getParticleTypes()),
       "PairPotential_Angle::operator() - types don't match with ones in arguments.");
   derivative_components_t result;
   const argument_t &r_ij = arguments[0]; //01
-  const argument_t &r_ik = arguments[2]; //12
-  const argument_t &r_jk = arguments[1]; //02
-  result.push_back( 2. * params[spring_constant] * ( function_theta(r_ij.distance, r_ik.distance, r_jk.distance) - params[equilibrium_distance]) );
+  const argument_t &r_jk = arguments[2]; //12
+  const argument_t &r_ik = arguments[1]; //02
+  result.push_back( 2. * params[spring_constant] * ( function_theta(r_ij.distance, r_jk.distance, r_ik.distance) - params[equilibrium_distance]) );
   ASSERT( result.size() == 1,
       "PairPotential_Angle::operator() - we did not create exactly one component.");
@@ -172 +172 @@
   ASSERT( arguments.size() == 3,
       "PairPotential_Angle::parameter_derivative() - requires exactly three arguments.");
-  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypesStrictOrdering(
+  ASSERT( ParticleTypeChecker::checkArgumentsAgainstParticleTypes(
       arguments, getParticleTypes()),
       "PairPotential_Angle::operator() - types don't match with ones in arguments.");
   const argument_t &r_ij = arguments[0]; //01
-  const argument_t &r_ik = arguments[2]; //12
-  const argument_t &r_jk = arguments[1]; //02
+  const argument_t &r_jk = arguments[2]; //12
+  const argument_t &r_ik = arguments[1]; //02
   switch (index) {
     case spring_constant:
     {
       const result_t result =
-                 Helpers::pow( function_theta(r_ij.distance, r_ik.distance, r_jk.distance) - params[equilibrium_distance], 2 );
+                 Helpers::pow( function_theta(r_ij.distance, r_jk.distance, r_ik.distance) - params[equilibrium_distance], 2 );
       return std::vector<result_t>(1, result);
       break;
@@ -190 +190 @@
       const result_t result =
           -2. * params[spring_constant]
-                 * ( function_theta(r_ij.distance, r_ik.distance, r_jk.distance) - params[equilibrium_distance]);
+                 * ( function_theta(r_ij.distance, r_jk.distance, r_ik.distance) - params[equilibrium_distance]);
       return std::vector<result_t>(1, result);
       break;