Changeset 24a5e0

Timestamp:

Feb 26, 2010, 12:40:52 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, 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:

1f2217

Parents:

7042f45

Message:

Added -Wall flag and fixed several small hickups

Location:

src

Files:

• Actions/MakroAction.cpp (modified) (1 diff)
• Actions/ManipulateAtomsProcess.cpp (modified) (1 diff)
• Actions/Process.cpp (modified) (1 diff)
• Descriptors/AtomDescriptor.cpp (modified) (5 diffs)
• Descriptors/AtomDescriptor_impl.hpp (modified) (6 diffs)
• Descriptors/AtomIdDescriptor.cpp (modified) (1 diff)
• Descriptors/AtomIdDescriptor_impl.hpp (modified) (1 diff)
• Descriptors/AtomTypeDescriptor.cpp (modified) (1 diff)
• Descriptors/AtomTypeDescriptor_impl.hpp (modified) (1 diff)
• Legacy/oldmenu.cpp (modified) (1 diff)
• Makefile.am (modified) (1 diff)
• Menu/DisplayMenuItem.cpp (modified) (1 diff)
• Menu/TextMenu.cpp (modified) (1 diff)
• Patterns/Cacheable.hpp (modified) (1 diff)
• UIElements/Dialog.cpp (modified) (2 diffs)
• UIElements/TextDialog.cpp (modified) (1 diff)
• Views/MethodStringView.cpp (modified) (1 diff)
• Views/MethodStringView.hpp (modified) (1 diff)
• Views/StreamStringView.cpp (modified) (1 diff)
• Views/StreamStringView.hpp (modified) (2 diffs)
• Views/StringView.hpp (modified) (2 diffs)
• World.cpp (modified) (2 diffs)
• World.hpp (modified) (1 diff)
• WorldIterators.cpp (modified) (1 diff)
• atom_particleinfo.cpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• molecule_dynamics.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)
• tesselationhelpers.cpp (modified) (1 diff)

src/Actions/MakroAction.cpp

@@ -23 +23 @@
 {
   Action* action;
-  while(action=actions->removeLastAction()){
+  while((action=actions->removeLastAction())){
     delete action;
   }

src/Actions/ManipulateAtomsProcess.cpp

@@ -14 +14 @@
 ManipulateAtomsProcess::ManipulateAtomsProcess(boost::function<void(atom*)> _operation, AtomDescriptor _descr,
                                                std::string _name,bool _doRegister) :
-  operation(_operation),
+  Process(0,_name,_doRegister),
   descr(_descr),
-  Process(0,_name,_doRegister)
+  operation(_operation)
 {}
 

src/Actions/Process.cpp

@@ -13 +13 @@
   Action(_name,_doRegister),
   maxSteps(_maxSteps),
+  active(false),
   starts(false),
-  stops(false),
-  active(false)
+  stops(false)
 {}
 

src/Descriptors/AtomDescriptor.cpp

@@ -97 +97 @@
 {}
 
-bool AtomAllDescriptor_impl::predicate(std::pair<int,atom*>){
+bool AtomAllDescriptor_impl::predicate(std::pair<atomId_t,atom*>){
   return true;
 }
@@ -111 +111 @@
 {}
 
-bool AtomNoneDescriptor_impl::predicate(std::pair<int,atom*>){
+bool AtomNoneDescriptor_impl::predicate(std::pair<atomId_t,atom*>){
   return false;
 }
@@ -129 +129 @@
 {}
 
-bool AtomAndDescriptor_impl::predicate(std::pair<int,atom*> atom){
+bool AtomAndDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
   return lhs->predicate(atom) && rhs->predicate(atom);
 }
@@ -145 +145 @@
 }
 
-bool AtomOrDescriptor_impl::predicate(std::pair<int,atom*> atom){
+bool AtomOrDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
   return lhs->predicate(atom) || rhs->predicate(atom);
 }
@@ -165 +165 @@
 }
 
-bool AtomNotDescriptor_impl::predicate(std::pair<int,atom*> atom){
+bool AtomNotDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom){
  return !(arg->predicate(atom));
 }

src/Descriptors/AtomDescriptor_impl.hpp

@@ -14 +14 @@
   virtual ~AtomDescriptor_impl();
 
-  virtual bool predicate(std::pair<int,atom*>)=0;
+  virtual bool predicate(std::pair<atomId_t,atom*>)=0;
 
 protected:
@@ -28 +28 @@
   AtomAllDescriptor_impl();
   virtual ~AtomAllDescriptor_impl();
-  virtual bool predicate(std::pair<int,atom*>);
+  virtual bool predicate(std::pair<atomId_t,atom*>);
 };
 
@@ -35 +35 @@
   AtomNoneDescriptor_impl();
   virtual ~AtomNoneDescriptor_impl();
-  virtual bool predicate(std::pair<int,atom*>);
+  virtual bool predicate(std::pair<atomId_t,atom*>);
 };
 
@@ -45 +45 @@
   AtomAndDescriptor_impl(AtomDescriptor::impl_ptr _lhs, AtomDescriptor::impl_ptr _rhs);
   ~AtomAndDescriptor_impl();
-  virtual bool predicate(std::pair<int,atom*>);
+  virtual bool predicate(std::pair<atomId_t,atom*>);
 
 private:
@@ -57 +57 @@
   AtomOrDescriptor_impl(AtomDescriptor::impl_ptr _lhs, AtomDescriptor::impl_ptr _rhs);
   virtual ~AtomOrDescriptor_impl();
-  virtual bool predicate(std::pair<int,atom*>);
+  virtual bool predicate(std::pair<atomId_t,atom*>);
 
 private:
@@ -70 +70 @@
   virtual ~AtomNotDescriptor_impl();
 
-  virtual bool predicate(std::pair<int,atom*>);
+  virtual bool predicate(std::pair<atomId_t,atom*>);
 
 private:

src/Descriptors/AtomIdDescriptor.cpp

@@ -21 +21 @@
 {}
 
-bool AtomIdDescriptor_impl::predicate(std::pair<int,atom*> atom) {
+bool AtomIdDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom) {
   return atom.first==id;
 }

src/Descriptors/AtomIdDescriptor_impl.hpp

@@ -10 +10 @@
   virtual ~AtomIdDescriptor_impl();
 
-  bool predicate(std::pair<int,atom*> atom);
+  bool predicate(std::pair<atomId_t,atom*> atom);
 
 protected:

src/Descriptors/AtomTypeDescriptor.cpp

@@ -20 +20 @@
 {}
 
-bool AtomTypeDescriptor_impl::predicate(std::pair<int,atom*> atom) {
+bool AtomTypeDescriptor_impl::predicate(std::pair<atomId_t,atom*> atom) {
   return (atom.second->getType()==type);
 }

src/Descriptors/AtomTypeDescriptor_impl.hpp

@@ -17 +17 @@
   virtual ~AtomTypeDescriptor_impl();
 
-  bool predicate(std::pair<int,atom*> atom);
+  bool predicate(std::pair<atomId_t,atom*> atom);
 private:
   element *type;

src/Legacy/oldmenu.cpp

@@ -812 +812 @@
 void oldmenu::ManipulateMolecules(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
 {
-  atom *first = NULL;
   Vector x,y,z,n; // coordinates for absolute point in cell volume
-  int j, axis, count, faktor;
   char choice;  // menu choice char
   molecule *mol = NULL;
-  element **Elements;
-  Vector **vectors;
   MoleculeLeafClass *Subgraphs = NULL;
 

src/Makefile.am

@@ -41 +41 @@
 bin_PROGRAMS = molecuilder joiner analyzer
 molecuilderdir = ${bindir}
-#libmolecuilder_a_CXXFLAGS = -DNO_CACHING
+libmolecuilder_a_CXXFLAGS = -Wall
+#libmolecuilder_a_CXXFLAGS += -DNO_CACHING
 libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
 libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
 molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
 molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
-molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
+molecuilder_CXXFLAGS = -Wall $(BOOST_CPPFLAGS)
 #molecuilder_CXXFLAGS += -DNO_CACHING
 molecuilder_SOURCES = builder.cpp

src/Menu/DisplayMenuItem.cpp

@@ -21 +21 @@
 
 DisplayMenuItem::DisplayMenuItem(Menu* _menu, StringView *_view, string _title, char _spacer, int _length ):
-MenuItem('\0',"",_menu),
-view(_view),
-title(_title),
-spacer(_spacer),
-length(_length)
+  MenuItem('\0',"",_menu),
+  view(_view),
+  title(_title),
+  length(_length),
+  spacer(_spacer)
 {
 }
 
 DisplayMenuItem::~DisplayMenuItem()
-{
-  // TODO Auto-generated destructor stub
-}
+{}
 
 

src/Menu/TextMenu.cpp

@@ -18 +18 @@
  */
 TextMenu::TextMenu(ostream& _outputter, string _title, char _spacer,int _length) :
-outputter(_outputter),
-title(_title),
-spacer(_spacer),
-length(_length),
-quit(false),
-defaultItem(0)
+  defaultItem(0),
+  outputter(_outputter),
+  title(_title),
+  spacer(_spacer),
+  length(_length),
+  quit(false)
 {
 }

src/Patterns/Cacheable.hpp

@@ -43 +43 @@
   Cacheable<T>::Cacheable(Observable *_owner, boost::function<T()> _recalcMethod) :
     owner(_owner),
-    recalcMethod(_recalcMethod),
     valid(false),
-    canBeUsed(true)
+    canBeUsed(true),
+    recalcMethod(_recalcMethod)
   {
     // we sign on with the best(=lowest) priority, so cached values are recalculated before

src/UIElements/Dialog.cpp

@@ -102 +102 @@
 Dialog::MoleculeQuery::MoleculeQuery(string title, molecule **_target, MoleculeListClass *_molecules) :
     Query(title),
-    target(_target),
+    tmp(0),
     molecules(_molecules),
-    tmp(0)
+    target(_target)
+
 {}
 
@@ -116 +117 @@
 
 Dialog::VectorQuery::VectorQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check) :
-  Query(title), target(_target), cellSize(_cellSize), check(_check)
+  Query(title),
+  cellSize(_cellSize),
+  check(_check),
+  target(_target)
 {
 tmp = new Vector();

src/UIElements/TextDialog.cpp

@@ -114 +114 @@
 bool TextDialog::VectorTextQuery::handle() {
  tmp->AskPosition(cellSize,check);
+ return true;
 }

src/Views/MethodStringView.cpp

@@ -7 +7 @@
 
 #include "MethodStringView.hpp"
+
+using namespace std;
 
 MethodStringView::MethodStringView(boost::function<string()> _displayMethod) :

src/Views/MethodStringView.hpp

@@ -19 +19 @@
 {
 public:
-  MethodStringView(boost::function<string()>);
+  MethodStringView(boost::function<std::string()>);
   virtual ~MethodStringView();
 
-  virtual const string toString();
+  virtual const std::string toString();
 
 private:
-  boost::function<string()> displayMethod;
+  boost::function<std::string()> displayMethod;
 };
 

src/Views/StreamStringView.cpp

@@ -7 +7 @@
 
 #include <sstream>
+#include <iostream>
 
 #include "StreamStringView.hpp"
 
-StreamStringView::StreamStringView(boost::function<void(ofstream *)> _displayMethod) :
+using namespace std;
+
+StreamStringView::StreamStringView(boost::function<void(ostream *)> _displayMethod) :
 StringView(),
 displayMethod(_displayMethod)
-{
-  // TODO Auto-generated constructor stub
-
-}
+{}
 
 StreamStringView::~StreamStringView()
-{
-  // TODO Auto-generated destructor stub
-}
+{}
 
 const string StreamStringView::toString() {
   stringstream s;
-  displayMethod((ofstream *)&s);
+  displayMethod(dynamic_cast<ostream *>(&s));
   return s.str();
 }

src/Views/StreamStringView.hpp

@@ -10 +10 @@
 
 #include <boost/function.hpp>
+#include <iostream>
 
 #include "Views/StringView.hpp"
@@ -24 +25 @@
 {
 public:
-  StreamStringView(boost::function<void(ofstream *)>);
+  StreamStringView(boost::function<void(std::ostream *)>);
   virtual ~StreamStringView();
 
-  virtual const string toString();
+  virtual const std::string toString();
 
 private:
-  boost::function<void(ofstream *)> displayMethod;
+  boost::function<void(std::ostream *)> displayMethod;
 };
 

src/Views/StringView.hpp

@@ -12 +12 @@
 #include "Views/View.hpp"
 
-using namespace std;
-
 /**
  * View to show something as a string
@@ -26 +24 @@
   virtual ~StringView();
 
-  virtual const string toString()=0;
+  virtual const std::string toString()=0;
 };
 

src/World.cpp

@@ -144 +144 @@
 
 World::World() :
+    periode(new periodentafel),
+    atoms(),
     currAtomId(0),
+    molecules(),
     currMoleculeId(0),
-    periode(new periodentafel),
-    molecules_deprecated(new MoleculeListClass(this)),
-    atoms(),
-    molecules()
+    molecules_deprecated(new MoleculeListClass(this))
 {
   molecules_deprecated->signOn(this);
@@ -206 +206 @@
   // should see that it gets the updated new world
   delete oldWorld;
+  return theWorld;
 }
 

src/World.hpp

@@ -142 +142 @@
   protected:
     void advanceState();
-    World* world;
     AtomSet::iterator state;
     boost::shared_ptr<AtomDescriptor_impl>  descr;
     int index;
+
+    World* world;
   };
 

src/WorldIterators.cpp

@@ -17 +17 @@
 World::AtomIterator::AtomIterator(AtomDescriptor _descr, World* _world) :
     descr(_descr.get_impl()),
-    world(_world),
-    index(0)
+    index(0),
+    world(_world)
 {
   state = world->atoms.begin();

src/atom_particleinfo.cpp

@@ -14 +14 @@
 
 ParticleInfo::ParticleInfo(ParticleInfo *pointer) :
-    Name(pointer->Name),
-    nr(pointer->nr)
+    nr(pointer->nr),
+    Name(pointer->Name)
     {}
 

src/boundary.cpp

@@ -965 +965 @@
   bool freeLC = false;
   bool status = false;
-  CandidateForTesselation *baseline;
+  CandidateForTesselation *baseline=0;
   LineMap::iterator testline;
   bool OneLoopWithoutSuccessFlag = true;  // marks whether we went once through all baselines without finding any without two triangles

src/molecule.cpp

@@ -34 +34 @@
   first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0), 
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
-  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start),
-  formula(this,boost::bind(&molecule::calcFormula,this))
+  ActiveFlag(false), IndexNr(-1),
+  formula(this,boost::bind(&molecule::calcFormula,this)),
+  last_atom(0),
+  InternalPointer(start)
 {
   // init atom chain list

src/molecule.hpp

@@ -350 +350 @@
   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
   int NumberOfActiveMolecules();
-  void Enumerate(ofstream *out);
+  void Enumerate(ostream *out);
   void Output(ofstream *out);
   void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);

src/molecule_dynamics.cpp

@@ -163 +163 @@
 double molecule::ConstrainedPotential(struct EvaluatePotential &Params)
 {
-  double tmp, result;
+  double tmp, result=0;
 
   // go through every atom

src/moleculelist.cpp

@@ -139 +139 @@
  * \param *out output stream
  */
-void MoleculeListClass::Enumerate(ofstream *out)
+void MoleculeListClass::Enumerate(ostream *out)
 {
   element* Elemental = NULL;

src/tesselationhelpers.cpp

@@ -27 +27 @@
   int signum;
   gsl_permutation *p = gsl_permutation_alloc(A->size1);
-  gsl_matrix *tmpA;
+  gsl_matrix *tmpA=0;
 
   if (inPlace)