Changeset d79ca1

Timestamp:

Oct 11, 2015, 7:11:38 AM (9 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:

6c30ab

Parents:

2a7dbe

git-author:

Frederik Heber <heber@…> (09/30/15 17:54:29)

git-committer:

Frederik Heber <heber@…> (10/11/15 07:11:38)

Message:

FIX: SaturateAction would use double instead of single hydrogen bond length.

Files:

• src/Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) (1 diff)

src/Actions/AtomAction/SaturateAction.cpp

@@ -79 +79 @@
     // add the hydrogens
     const Vector AtomsPosition = _atom->getPosition();
-    double typical_distance = _atom->getType()->getHBondDistance(1);
+    double typical_distance = _atom->getType()->getHBondDistance(0);
     if (typical_distance == -1.)
       typical_distance = 1.;

tests/regression/Atoms/Saturate/post/saturated_carbon.xyz

@@ -1 +1 @@
 5
-        Created by molecuilder on Wed Jan 28 20:57:11 2015, time step 0
+        Created by molecuilder on Wed Sep 30 22:15:20 2015, time step 0
 C       10      10      10
-H       11.076  10      10
-H       9.64133 11.0145 10
-H       9.64133 9.49277 10.8786
-H       9.64133 9.49277 9.12145
+H       11.09   10      10
+H       9.63667 11.0277 10
+H       9.63667 9.48617 10.89
+H       9.63667 9.48617 9.11002

tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz

@@ -1 +1 @@
 4
-        Created by molecuilder on Wed Jan 28 21:41:39 2015, time step 0
+        Created by molecuilder on Wed Sep 30 22:15:20 2015, time step 0
 N       10      10      10
-H       11.02   10      10
-H       9.49    10.866  10
-H       9.49    9.13397 10
+H       11.04   10      10
+H       9.48    10.866  10
+H       9.48    9.13397 10