Changeset 5d5550 for src/Fragmentation/Exporters/SaturatedFragment.cpp

Timestamp:

Aug 16, 2014, 3:52:30 PM (10 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:

343c5a

Parents:

a1d1dd

git-author:

Frederik Heber <heber@…> (07/18/14 17:45:45)

git-committer:

Frederik Heber <heber@…> (08/16/14 15:52:30)

Message:

FragmentationAction now compiles global saturation positions information.

File:

• src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) (2 diffs)

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -269 +269 @@
             +toString(*OtherWalker)+" to atom "+toString(*Walker));
 
-        // get typical bond distance from elements database
-        double BondDistance = Walker->getType()->getHBondDistance(positionsiter->second.size()-1);
-        if (BondDistance < 0.) {
-          ELOG(2, "saturateAtoms() - no typical hydrogen bond distance of degree "
-              +toString(positionsiter->second.size())+" for element "
-              +toString(Walker->getType()->getName()));
-          // try bond degree 1 distance
-          BondDistance = Walker->getType()->getHBondDistance(1-1);
-          if (BondDistance < 0.) {
-            ELOG(1, "saturateAtoms() - no typical hydrogen bond distance for element "
-                +toString(Walker->getType()->getName()));
-            BondDistance = 1.;
-          }
-        }
-        ASSERT( BondDistance > 0.,
-            "SaturatedFragment::saturate() - negative bond distance");
+//        // get typical bond distance from elements database
+//        double BondDistance = Walker->getType()->getHBondDistance(positionsiter->second.size()-1);
+//        if (BondDistance < 0.) {
+//          ELOG(2, "saturateAtoms() - no typical hydrogen bond distance of degree "
+//              +toString(positionsiter->second.size())+" for element "
+//              +toString(Walker->getType()->getName()));
+//          // try bond degree 1 distance
+//          BondDistance = Walker->getType()->getHBondDistance(1-1);
+//          if (BondDistance < 0.) {
+//            ELOG(1, "saturateAtoms() - no typical hydrogen bond distance for element "
+//                +toString(Walker->getType()->getName()));
+//            BondDistance = 1.;
+//          }
+//        }
 
         // place hydrogen at each point
@@ -293 +291 @@
             positer != positionsiter->second.end(); ++positer) {
           const atom& hydrogen =
-              setHydrogenReplacement(Walker, *positer, BondDistance, father);
+              setHydrogenReplacement(Walker, *positer, 1., father);
           FullMolecule.insert(hydrogen.getId());
         }