Changeset 5f612ee for src/atom_bondedparticle.cpp

Timestamp:

Apr 27, 2010, 2:25:42 PM (16 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, 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:

632bc3

Parents:

13d5a9 (diff), c695c9 (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 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

• new molecule() replaced by World::getInstance().createMolecule()
• new atom() replaced by World::getInstance().createAtom() where appropriate.
• Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
• DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
• ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/atom_bondedparticle.cpp (modified) (4 diffs)

src/atom_bondedparticle.cpp

@@ -44 +44 @@
 void BondedParticle::OutputBondOfAtom() const
 {
-  Log() << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: " << endl;
+  DoLog(4) && (Log() << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: " << endl);
   int TotalDegree = 0;
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
-    Log() << Verbose(4) << **Runner << endl;
+    DoLog(4) && (Log() << Verbose(4) << **Runner << endl);
     TotalDegree += (*Runner)->BondDegree;
   }
-  Log() << Verbose(4) << " -- TotalDegree: " << TotalDegree << endl;
+  DoLog(4) && (Log() << Verbose(4) << " -- TotalDegree: " << TotalDegree << endl);
 };
 
@@ -86 +86 @@
       status = true;
     } else {
-      eLog() << Verbose(1) << *Binder << " does not contain " << *this << "." << endl;
+      DoeLog(1) && (eLog()<< Verbose(1) << *Binder << " does not contain " << *this << "." << endl);
     }
   } else {
-    eLog() << Verbose(1) << "Binder is " << Binder << "." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Binder is " << Binder << "." << endl);
   }
   return status;
@@ -105 +105 @@
       status = true;
     } else {
-      eLog() << Verbose(1) << *Binder << " does not contain " << *this << "." << endl;
+      DoeLog(1) && (eLog()<< Verbose(1) << *Binder << " does not contain " << *this << "." << endl);
     }
   } else {
-    eLog() << Verbose(1) << "Binder is " << Binder << "." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Binder is " << Binder << "." << endl);
   }
   return status;
@@ -150 +150 @@
       //Log() << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
     } else {
-      eLog() << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
+      DoeLog(2) && (eLog()<< Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl);
       FalseBondDegree++;
     }