Changeset 5f612ee for src/stackclass.hpp

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/stackclass.hpp (modified) (7 diffs)

src/stackclass.hpp

@@ -72 +72 @@
     return true;
   } else {
-    eLog() << Verbose(1) << "Stack is full, " << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tNextFreeField " << NextFreeField << "\tEntryCount " << EntryCount << "!" << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Stack is full, " << "Stack: CurrentLastEntry " << CurrentLastEntry<< "\tCurrentFirstEntry " << CurrentFirstEntry << "\tNextFreeField " << NextFreeField << "\tEntryCount " << EntryCount << "!" << endl);
     return false;
   }
@@ -87 +87 @@
     Walker = StackList[CurrentFirstEntry];
     if (Walker == NULL)
-      eLog() << Verbose(1) << "Stack's field is empty!" << endl;
+      DoeLog(1) && (eLog()<< Verbose(1) << "Stack's field is empty!" << endl);
     StackList[CurrentFirstEntry] = NULL;
     if (CurrentFirstEntry != CurrentLastEntry) { // hasn't last item been popped as well?
@@ -96 +96 @@
     }
   } else
-    eLog() << Verbose(1) << "Stack is empty!" << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Stack is empty!" << endl);
   return Walker;
 };
@@ -111 +111 @@
     StackList[CurrentLastEntry] = NULL;
     if (Walker == NULL)
-      eLog() << Verbose(1) << "Stack's field is empty!" << endl;
+      DoeLog(1) && (eLog()<< Verbose(1) << "Stack's field is empty!" << endl);
     NextFreeField = CurrentLastEntry;
     if (CurrentLastEntry != CurrentFirstEntry)  // has there been more than one item on stack
       CurrentLastEntry = (CurrentLastEntry + (EntryCount-1)) % EntryCount; // step back from current free field to last (modulo does not work in -1, thus go EntryCount-1 instead)
   } else {
-    eLog() << Verbose(1) << "Stack is empty!" << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Stack is empty!" << endl);
   }
   return Walker;
@@ -130 +130 @@
 {
   bool found = false;
-  Log() << Verbose(5) << "First " << CurrentFirstEntry<< "\tLast " << CurrentLastEntry<< "\tNext " << NextFreeField<< "\tCount " << EntryCount<< "." << endl;
+  DoLog(5) && (Log() << Verbose(5) << "First " << CurrentFirstEntry<< "\tLast " << CurrentLastEntry<< "\tNext " << NextFreeField<< "\tCount " << EntryCount<< "." << endl);
   int i=CurrentFirstEntry;
   if (!IsEmpty())
     do {
       if (StackList[i] == ptr) {  // if item found, remove
-        Log() << Verbose(5) << "Item " << *ptr << " was number " << i << " on stack, removing it." << endl;
+        DoLog(5) && (Log() << Verbose(5) << "Item " << *ptr << " was number " << i << " on stack, removing it." << endl);
         found = true;
         StackList[i] = NULL;
@@ -141 +141 @@
       if ((found) && (StackList[i] != NULL)) {  // means we have to shift (and not the removed item)
         if (i == 0) { // we are down to first item in stack, have to put onto last item
-          Log() << Verbose(5) << "Shifting item 0 to place " << EntryCount-1 << "." << endl;
+          DoLog(5) && (Log() << Verbose(5) << "Shifting item 0 to place " << EntryCount-1 << "." << endl);
           StackList[EntryCount-1] = StackList[0];
         } else {
-          Log() << Verbose(5) << "Shifting item " << i << " to place " << i-1 << "." << endl;
+          DoLog(5) && (Log() << Verbose(5) << "Shifting item " << i << " to place " << i-1 << "." << endl);
           StackList[i-1] = StackList[i];
         }
@@ -151 +151 @@
     } while (i!=NextFreeField);
   else
-    eLog() << Verbose(1) << "Stack is already empty!" << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Stack is already empty!" << endl);
   if (found) {
     NextFreeField = CurrentLastEntry;