Changeset d26fb7 for src/Element

Timestamp:

Jan 31, 2016, 12:47:12 PM (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:

e38750

Parents:

6a922b (diff), 2f429e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Better_HBondDistances' into Candidate_v1.5.1

Location:

src/Element

Files:

• element.cpp (modified) (1 diff)
• elements_db.cpp (modified) (2 diffs)
• unittests/ElementUnitTest.cpp (modified) (1 diff)

src/Element/element.cpp

@@ -64 +64 @@
     color[i] = (unsigned char)0;
   for (size_t i =0; i<3;++i)
-    HBondDistance[i] = 0.;
-  for (size_t i =0; i<3;++i)
-    HBondAngle[i] = 0.;
+    HBondDistance[i] = -1.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = -1.;
 };
 

src/Element/elements_db.cpp

@@ -258 +258 @@
 const char *HbonddistanceDB =\
 "#atomic number bond distances for single, double and triple bond (-1 no bond)\n\
-1       0.74    -1      -1\n\
-2       0.77429209      -1      -1\n\
-5       1.23    1.19    1.18\n\
-6       1.09    1.076   1.06\n\
-7       1.04    1.02    1.01\n\
-8       0.96    0.957   -1\n\
-14      1.48    1.48    1.48\n\
-15      1.42    -1      -1\n\
-16      1.35    -1      -1\n\
-17      1.29    -1      -1\n\
-20      1.09    1.09    -1\n\
-34      1.47    -1      -1\n\
-35      1.44    -1      -1\n\
+1       0.741283  -1. -1.\n\
+2       0  -1. -1.\n\
+3       1.65217  -1. -1.\n\
+4       1.3455  -1. -1.\n\
+5       1.1962  1.19 1.18\n\
+6       1.09234  1.076 1.06\n\
+7       1.00154  1.02 1.01\n\
+8       0.941566  0.957 -1.\n\
+9       0.958865  -1. -1.\n\
+10      0  -1. -1.\n\
+11      1.9426  -1. -1.\n\
+12      1.73705  -1. -1.\n\
+13      1.60991  -1. -1.\n\
+14      1.49796  1.48 1.48\n\
+15      1.39145  -1. -1.\n\
+16      1.32987  -1. -1.\n\
+17      1.31403  -1. -1.\n\
+18      0  -1. -1.\n\
+19      2.38168  -1. -1.\n\
+20      2.39602  -1. -1.\n\
+21      1.69169  -1. -1.\n\
+22      1.69817  -1. -1.\n\
+23      1.75022  -1. -1.\n\
+24      1.79185  -1. -1.\n\
+25      1.49581  -1. -1.\n\
+26      1.76215  -1. -1.\n\
+27      1.4284  -1. -1.\n\
+28      1.56442  -1. -1.\n\
+29      2.00512  -1. -1.\n\
+30      1.55672  -1. -1.\n\
+31      1.58872  -1. -1.\n\
+32      1.5484  -1. -1.\n\
+33      1.47208  -1. -1.\n\
+34      1.43322  -1. -1.\n\
+35      1.45079  -1. -1.\n\
+36      0  -1. -1.\n\
 ";
 
@@ -280 +303 @@
 7       0       110     106.67\n\
 8       0       104.5   -1\n\
+11  0 -1 -1\n\
 14      0       120     109.47\n\
 15      0       -1      -1\n\

src/Element/unittests/ElementUnitTest.cpp

@@ -110 +110 @@
   CPPUNIT_ASSERT_EQUAL( 0, testelement->getNoValenceOrbitals() );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondDistance(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondDistance(i) );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondAngle(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondAngle(i) );
 }