Changeset c26f44

Timestamp:

Oct 5, 2009, 5:21:58 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, 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:

fa861b

Parents:

a33931

git-author:

Frederik Heber <heber@…> (10/05/09 17:14:58)

git-committer:

Frederik Heber <heber@…> (10/05/09 17:21:58)

Message:

Fixed testsuite, removed some minor bugs.

• TesselationUnitTest_SOURCES lacked memoryallocator stuff
• Free does not give a message anymore, as there can be no error.
• testsuite was fixed for suite 2 and 3, mostly due to changed options that were not accomodated for in the testsuite

Files:

• src/Makefile.am (modified) (1 diff)
• src/atom.cpp (modified) (1 diff)
• src/builder.cpp (modified) (1 diff)
• src/memoryallocator.hpp (modified) (1 diff)
• src/memoryusageobserver.cpp (modified) (1 diff)
• src/memoryusageobserver.hpp (modified) (1 diff)
• src/molecules.cpp (modified) (1 diff)
• src/tesselation.cpp (modified) (1 diff)
• src/tesselationunittest.cpp (modified) (2 diffs)
• tests/testsuite.at (modified) (2 diffs)

src/Makefile.am ¶

@@ -16 +16 @@
 VectorUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
 VectorUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
-TesselationUnitTest_SOURCES = defs.hpp helpers.cpp helpers.hpp leastsquaremin.cpp leastsquaremin.hpp linkedcell.cpp linkedcell.hpp tesselation.cpp tesselation.hpp tesselationhelpers.cpp tesselationhelpers.hpp tesselationunittest.cpp tesselationunittest.hpp vector.cpp vector.hpp verbose.cpp verbose.hpp
+TesselationUnitTest_SOURCES = defs.hpp helpers.cpp helpers.hpp leastsquaremin.cpp leastsquaremin.hpp linkedcell.cpp linkedcell.hpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp tesselation.cpp tesselation.hpp tesselationhelpers.cpp tesselationhelpers.hpp tesselationunittest.cpp tesselationunittest.hpp vector.cpp vector.hpp verbose.cpp verbose.hpp
 TesselationUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
 TesselationUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl

src/atom.cpp ¶

@@ -63 +63 @@
 {
   Free<int>(&ComponentNr, "atom::~atom: *ComponentNr");
-  Free<char *>(&Name, "atom::~atom: *Name");
+  Free<char>(&Name, "atom::~atom: *Name");
 };
 

src/builder.cpp ¶

@@ -2057 +2057 @@
       return 0;
       break;
+    case 2:  // just for -f option
+      delete(molecules); // also free's all molecules contained
+      delete(periode);
+      cout << Verbose(0) <<  "Maximum of allocated memory: "
+        << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
+      cout << Verbose(0) <<  "Remaining non-freed memory: "
+        << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
+      return 2;
+      break;
     default:
       break;

src/memoryallocator.hpp ¶

@@ -110 +110 @@
  *
  * \param pointer to the allocated memory range to free; may be NULL, this function is a no-op then
+ * \param *msg optional error message
  */
-template <typename X> void Free(X** buffer)
+template <typename X> void Free(X** buffer, const char *msg = NULL)
 {
   if ((buffer == NULL) || (*buffer == NULL))

src/memoryusageobserver.cpp ¶

@@ -77 +77 @@
  *
  * \param pointer to the allocated piece of memory
+ * \param *msg optional error message
  */
-void MemoryUsageObserver::removeMemory(void* pointer) {
+void MemoryUsageObserver::removeMemory(void* pointer, const char *msg) {
   map<void*, size_t>::iterator current = memoryUsers.find(pointer);
 
   if (current == memoryUsers.end()) {
     cout << "WARNING: There is non-tracked memory to be freed. Pointer "
-      << pointer << " is not registered by MemoryUsageObserver." << endl;
+      << pointer << " is not registered by MemoryUsageObserver: ";
+    if (msg != NULL)
+      cout << *msg;
+    cout << endl;
     return;
   }

src/memoryusageobserver.hpp ¶

@@ -28 +28 @@
   static void purgeInstance();
   void addMemory(void* pointer, size_t size);
-  void removeMemory(void* pointer);
+  void removeMemory(void* pointer, const char *msg = NULL);
   size_t getUsedMemorySize();
   size_t getMaximumUsedMemory();

src/molecules.cpp ¶

@@ -1606 +1606 @@
     MinimiseConstrainedPotential(out, PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
   else {
-    PermutationMap = (atom **) Malloc(AtomCount*sizeof(atom *), "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    PermutationMap = Malloc<atom *>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
     Walker = start;
     while (Walker->next != end) {

src/tesselation.cpp ¶

@@ -552 +552 @@
 TesselPoint::~TesselPoint()
 {
-  Free<char *>(&Name, "~TesselPoint - *Name");
 };
 

src/tesselationunittest.cpp ¶

@@ -84 +84 @@
   delete(TesselStruct);
   for (LinkedNodes::iterator Runner = Corners.begin(); Runner != Corners.end(); Runner++) {
-    delete((*Runner)->Name);
+    delete[]((*Runner)->Name);
     delete((*Runner)->node);
     delete(*Runner);
@@ -178 +178 @@
     for (set<BoundaryTriangleSet*>::iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); TriangleRunner++)
       CPPUNIT_ASSERT_EQUAL( true, (*TriangleRunner)->ContainsBoundaryPoint(Walker) );
+    delete(triangles);
   }
 }

tests/testsuite.at ¶

@@ -33 +33 @@
 AT_DATA([test.conf], [])
 AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
-AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1       10.000000000    10.000000000    10.000000000    0 # Number in molecule 0
+AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1       10.000000000    10.000000000    10.000000000    0 # molecule nr 0
 ], [ignore])
-AT_CHECK([cp test.conf main_pcp_linux], 0, [ignore], [ignore])
-AT_DATA([input], [aa 10. 10. 10. 1
+AT_CHECK([mv test.conf main_pcp_linux], 0, [ignore], [ignore])
+AT_DATA([input], [maa 10. 10. 10. 1
 s
 q
 ])
-AT_CHECK([../../molecuilder -e ./ <input], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder test.conf -e ./ <input], 0, [ignore], [ignore])
 AT_CHECK([diff main_pcp_linux test.conf], 0, [ignore], [ignore])
 # 4. test some more configuration
-AT_CHECK([../../molecuilder test.conf -e ./ -t -s -b -F -E -c -b -a -U -T -u], 0, [ignore], [stderr])
-AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [10
+AT_CHECK([../../molecuilder test.conf -e ./ -t -s -b -E -c -b -a -U -T -u], 0, [ignore], [stderr])
+AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [9
 ], [ignore])
 AT_CLEANUP
@@ -75 +75 @@
 # 4. create the config and check it
 AT_CHECK([../../molecuilder test.conf -e ./ -p test.xyz], 0, [ignore], [ignore])
-AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4       8.532785963     4.787886018     2.645886050     0 # Number in molecule 6
+AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4       8.532785963     4.787886018     2.645886050     0 # molecule nr 6
 ], [ignore])
 AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])