Changeset 51c3e4 for src/molecule_fragmentation.cpp

Timestamp:

Aug 25, 2010, 12:25:28 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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, Candidate_v1.7.0, 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:

2be37b

Parents:

14c57a (diff), d17f3d (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 'stable' into StructureRefactoring

Conflicts:

src/atom_trajectoryparticle.cpp

File:

• src/molecule_fragmentation.cpp (modified) (6 diffs)

src/molecule_fragmentation.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * molecule_fragmentation.cpp
@@ -456 +463 @@
       for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     #ifdef ADDHYDROGEN
-        if ((*iter)->getType()->Z != 1) // skip hydrogen
+        if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
     #endif
         {
@@ -476 +483 @@
     for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
   #ifdef ADDHYDROGEN
-      if ((*iter)->getType()->Z != 1) // skip hydrogen
+      if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
   #endif
       {
@@ -885 +892 @@
   for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
     Runner = FindAtom((*runner));
-    if (Runner->getType()->Z != 1) { // skip all those added hydrogens when re-filling snake stack
+    if (Runner->getType()->getAtomicNumber() != 1) { // skip all those added hydrogens when re-filling snake stack
       if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
         SP = ShortestPathList[(*runner)];
@@ -974 +981 @@
     ++iter;
 #ifdef ADDHYDROGEN
-    while ((iter != Leaf->end()) && ((*iter)->getType()->Z == 1)){ // skip added hydrogen
+    while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
       iter++;
     }
@@ -1352 +1359 @@
         if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
   #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->Z != 1)
+         && (OtherWalker->getType()->getAtomicNumber() != 1)
   #endif
                                                               ) {  // skip hydrogens and restrict to fragment