Changeset 87d6bd

Timestamp:

May 6, 2013, 9:33:49 PM (12 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:

5aaa43

Parents:

40d3ea

Message:

FIX: Fixing several clang errors such that we may safely use the compiler.

Changes:

• clang does not like execeptions as pure forward declarations.
• clang does not like AtomTypes[MaxTypes] with MaxTypes being dynamic.
• clang does not like cppunit to have no operator<<() for std::sets (it though finds the ones for std::vector?), it cannot use one from toString.hpp as it is declared afterwards (although before instantiation site).
• clang does not tolerate inheriting from a protected member class TQuery.
• clang does not tolerate shadowing of a variable inside a for-loop (i.e. declaring variable in loop body with same name as e.g. loop variable).

• clang compilation ran through after these changes without a single failing test.

Location:

src

Files:

• Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) (3 diffs)
• Fragmentation/Mask.hpp (modified) (6 diffs)
• Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) (3 diffs)
• Graph/unittests/AdjacencyListUnitTest.cpp (modified) (2 diffs)
• Parameters/Validators/DiscreteValidator.hpp (modified) (1 diff)
• Parameters/Validators/RangeValidator.hpp (modified) (1 diff)
• Parameters/Validators/RangeValidator_impl.hpp (modified) (1 diff)
• Parser/PcpParser_helper.cpp (modified) (2 diffs)
• Shapes/BaseShapes.cpp (modified) (1 diff)
• UIElements/Dialog.hpp (modified) (1 diff)

src/Descriptors/unittests/AtomDescriptorUnitTest.cpp

@@ -275 +275 @@
     std::set<atomId_t> reflist = getDistanceList(distance, position, atoms);
     std::set<atomId_t> testlist = getIdList(atomlist);
-    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+    CPPUNIT_ASSERT( reflist == testlist );
   }
   // ... from (4,0,0) up to 2.9 (i.e. more shells or different view)
@@ -284 +284 @@
     std::set<atomId_t> reflist = getDistanceList(distance, Vector(4.,0.,0.), atoms);
     std::set<atomId_t> testlist = getIdList(atomlist);
-    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+    CPPUNIT_ASSERT( reflist == testlist );
   }
   // ... from (10,0,0) up to 1.5
@@ -294 +294 @@
     std::set<atomId_t> reflist = getDistanceList(distance, *position, atoms);
     std::set<atomId_t> testlist = getIdList(atomlist);
-    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+    CPPUNIT_ASSERT( reflist == testlist );
     delete position;
   }

src/Fragmentation/Mask.hpp

@@ -35 +35 @@
    * @return true - bit set, false - bit not set
    */
-  bool isTrue(const T id) const {
+  bool isTrue(const T &id) const {
     const typename std::set<T>::const_iterator iter = std::set<T>::find(id);
     return (iter != std::set<T>::end());
@@ -45 +45 @@
    * @return true - bit set, false - bit not set
    */
-  bool isFalse(const T id) const {
+  bool isFalse(const T &id) const {
     return (!isTrue(id));
   }
@@ -53 +53 @@
    * @param id id to set to true
    */
-  void setTrue(const T id)
+  void setTrue(const T &id)
   {
-    insert(id);
+    std::set<T>::insert(id);
   }
 
@@ -62 +62 @@
    * @param id id to set to false
    */
-  void setFalse(const T id)
+  void setFalse(const T &id)
   {
     typename std::set<T>::iterator iter = std::set<T>::find(id);
     if (iter != std::set<T>::end())
-      erase(iter);
+      std::set<T>::erase(iter);
   }
 
@@ -74 +74 @@
    * @param value bit giving whether to set or unset
    */
-  void setValue(const T id, bool value) {
+  void setValue(const T &id, bool value) {
     if (value)
       setTrue(id);
@@ -86 +86 @@
    * @return "t" or "f" whether bit is set or not.
    */
-  const char* printBit(const T id) const
+  const char* printBit(const T &id) const
   {
     const typename std::set<T>::const_iterator iter = std::set<T>::find(id);

src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp

@@ -116 +116 @@
 
   CPPUNIT_ASSERT_EQUAL( (size_t)2, testivectors.vectors.size() );
-  CPPUNIT_ASSERT_EQUAL( ones, testivectors.vectors[1] );
-  CPPUNIT_ASSERT_EQUAL( threes, testivectors.vectors[3] );
+  CPPUNIT_ASSERT( ones == testivectors.vectors[1] );
+  CPPUNIT_ASSERT( threes == testivectors.vectors[3] );
   CPPUNIT_ASSERT( testivectors.vectors.find(-1) == testivectors.vectors.end() );
 }
@@ -145 +145 @@
     CPPUNIT_ASSERT_EQUAL( IndexedVectors::FixedSize, iter->second.size() );
   }
-  CPPUNIT_ASSERT_EQUAL( result, ivectors->vectors[1] );
-  CPPUNIT_ASSERT_EQUAL( twos, ivectors->vectors[2] );
-  CPPUNIT_ASSERT_EQUAL( threes, ivectors->vectors[3] );
+  CPPUNIT_ASSERT( result == ivectors->vectors[1] );
+  CPPUNIT_ASSERT( twos == ivectors->vectors[2] );
+  CPPUNIT_ASSERT( threes == ivectors->vectors[3] );
 }
 
@@ -177 +177 @@
     CPPUNIT_ASSERT_EQUAL( IndexedVectors::FixedSize, iter->second.size() );
   }
-  CPPUNIT_ASSERT_EQUAL( result, ivectors->vectors[1] );
-  CPPUNIT_ASSERT_EQUAL( twos, ivectors->vectors[2] );
-  CPPUNIT_ASSERT_EQUAL( thirdresult, ivectors->vectors[3] );
+  CPPUNIT_ASSERT( result == ivectors->vectors[1] );
+  CPPUNIT_ASSERT( twos == ivectors->vectors[2] );
+  CPPUNIT_ASSERT( thirdresult == ivectors->vectors[3] );
 }
 

src/Graph/unittests/AdjacencyListUnitTest.cpp

@@ -253 +253 @@
   // assert equality after parsing
   CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap.size(), WorldAdjacency.atombondmap.size() );
-  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap, WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap == WorldAdjacency.atombondmap );
   CPPUNIT_ASSERT( WorldAdjacency < FileAdjacency );
   CPPUNIT_ASSERT( WorldAdjacency > FileAdjacency );
@@ -282 +282 @@
   // assert equality after parsing
   CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap.size(), WorldAdjacency.atombondmap.size() );
-  CPPUNIT_ASSERT_EQUAL( FileAdjacency.atombondmap, WorldAdjacency.atombondmap );
+  CPPUNIT_ASSERT( FileAdjacency.atombondmap == WorldAdjacency.atombondmap );
   CPPUNIT_ASSERT( WorldAdjacency == FileAdjacency );
 }

src/Parameters/Validators/DiscreteValidator.hpp

@@ -19 +19 @@
 #include <vector>
 
+#include "Parameters/ParameterExceptions.hpp"
+
 class DiscreteValueTest;
-class ParameterValidatorException;
 
 /** A validator with a discrete list of valid values.

src/Parameters/Validators/RangeValidator.hpp

@@ -18 +18 @@
 #include "CodePatterns/Range.hpp"
 
-class ParameterValueException;
+#include "Parameters/ParameterExceptions.hpp"
+
 
 /** A validator with an interval of valid values.

src/Parameters/Validators/RangeValidator_impl.hpp

@@ -14 +14 @@
 #include <config.h>
 #endif
-
-#include "Parameters/ParameterExceptions.hpp"
 
 template <class T>

src/Parser/PcpParser_helper.cpp

@@ -36 +36 @@
 
 #include <boost/tokenizer.hpp>
+#include <map>
 #include <sstream>
 #include <string>
+#include <vector>
 
 #include "CodePatterns/Log.hpp"
@@ -548 +550 @@
     }
 
-    map<int, atom *> AtomList[MaxTypes];
+    std::vector<map<int, atom *> > AtomList(MaxTypes);
     map<int, atom *> LinearList;
     atom *neues = NULL;

src/Shapes/BaseShapes.cpp

@@ -416 +416 @@
   int x[2]={-1,+1};
   for(int i=NDIM;i--;){
-    for(int p=0;p<2;++p){
+    for(int j=0;j<2;++j){
       if(c==2) goto end; // I know this sucks, but breaking two loops is stupid
       Vector base;
-      base[i]=x[p];
+      base[i]=x[j];
       // base now points to the surface and is normal to it at the same time
       Plane p(base,base);

src/UIElements/Dialog.hpp

@@ -191 +191 @@
   virtual void update(){}
 
-protected:
+public:
   // methodology for handling queries
   // all queries are stored and then performed at appropriate times