Changeset b9b604 for src

Timestamp:

May 8, 2010, 12:17:30 PM (15 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:

efc3cb

Parents:

bdedb1 (diff), b8d4a3 (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 'StateAndFormatParser' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/Makefile.am

The following conflicts had to be resolved:

• molecuilder/src/Makefile.am had an old version of the HEADER definition which would not be merged automatically. ${PARSERHEADER} was missing.
• molecuilder/src/unittests/Makefile.am had an blank line too much
• TesselPoint::TesselPoint() had an older version where TesselPoint::Name was initialized to "-" instead of NULL. The latter should be correct due to missing delete(Name) in destructor.
• compilation errors arose due to the private nature of Vector::x[] introduced in the branch VectorRefactoring. This has been fixed in XyzParser, TremoloParser and the ParserUnitTest.
• ParserUnitTest runs fine.

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

Location:

src

Files:

• Makefile.am (modified) (3 diffs)
• Parser/ChangeTracker.cpp (added)
• Parser/ChangeTracker.hpp (added)
• Parser/FormatParser.cpp (added)
• Parser/FormatParser.hpp (added)
• Parser/TremoloParser.cpp (added)
• Parser/TremoloParser.hpp (added)
• Parser/XyzParser.cpp (added)
• Parser/XyzParser.hpp (added)
• atom_bondedparticle.cpp (modified) (1 diff)
• atom_bondedparticle.hpp (modified) (1 diff)
• atom_particleinfo.cpp (modified) (1 diff)
• bond.cpp (modified) (2 diffs)
• unittests/Makefile.am (modified) (3 diffs)
• unittests/ParserUnitTest.cpp (added)
• unittests/ParserUnitTest.hpp (added)
• unittests/SingletonTest.cpp (modified) (1 diff)

src/Makefile.am

@@ -50 +50 @@
                             
 
+PARSERSOURCE = Parser/ChangeTracker.cpp Parser/FormatParser.cpp Parser/TremoloParser.cpp Parser/XyzParser.cpp
+PARSERHEADER = Parser/ChangeTracker.hpp Parser/FormatParser.hpp Parser/TremoloParser.hpp Parser/XyzParser.hpp
+
 PATTERNSOURCE = Patterns/Observer.cpp
 PATTERNHEADER = Patterns/Cacheable.hpp \
@@ -98 +101 @@
                  ${ATOMSOURCE} \
                  ${PATTERNSOURCE} \
+                 ${PARSERSOURCE} \
                  ${UISOURCE} \
                  ${DESCRIPTORSOURCE} \
@@ -140 +144 @@
           ${ANALYSISHEADER} \
           ${ATOMHEADER} \
+          ${PARSERHEADER} \
           ${PATTERNHEADER} \
           ${UIHEADER} \

src/atom_bondedparticle.cpp

@@ -74 +74 @@
       *BondFile << nr << "\t" << (*Runner)->GetOtherAtom(this)->nr << "\n";
 };
+
+/**
+ * Adds a bond between this bonded particle and another. Does nothing if this
+ * bond already exists.
+ *
+ * \param bonding partner
+ */
+void BondedParticle::addBond(BondedParticle* Partner) {
+  if (IsBondedTo(Partner)) {
+    return;
+  }
+
+  bond* newBond = new bond((atom*) this, (atom*) Partner, 1, 0);
+  RegisterBond(newBond);
+  Partner->RegisterBond(newBond);
+}
 
 /** Puts a given bond into atom::ListOfBonds.

src/atom_bondedparticle.hpp

@@ -37 +37 @@
   virtual ~BondedParticle();
 
+  void addBond(BondedParticle* Partner);
   bool RegisterBond(bond *Binder);
   bool UnregisterBond(bond *Binder);

src/atom_particleinfo.cpp

@@ -16 +16 @@
     nr(pointer->nr),
     Name(pointer->Name)
-    {}
+    {
+      if (Name == NULL)
+        Name = " ";
+    }
 
 

src/bond.cpp

@@ -15 +15 @@
 /** Empty Constructor for class bond.
  */
-bond::bond() : leftatom(NULL), rightatom(NULL), previous(NULL), next(NULL), HydrogenBond(0), BondDegree(0), nr(-1), Cyclic(false), Type(Undetermined), Used(white)
+bond::bond()
+  : leftatom(NULL), rightatom(NULL), previous(NULL), next(NULL), HydrogenBond(0),
+    BondDegree(0), nr(-1), Cyclic(false), Type(Undetermined), Used(white)
 {
 };
@@ -25 +27 @@
  * \param number increasing index
  */
-bond::bond(atom *left, atom *right, const int degree, const int number) : leftatom(left), rightatom(right), previous(NULL), next(NULL), HydrogenBond(0), BondDegree(degree), nr(number), Cyclic(false), Type(Undetermined), Used(white)
+bond::bond(atom *left, atom *right, const int degree, const int number)
+  : leftatom(left), rightatom(right), previous(NULL), next(NULL), HydrogenBond(0),
+    BondDegree(degree), nr(number), Cyclic(false), Type(Undetermined), Used(white)
 {
   if ((left != NULL) && (right != NULL)) {

src/unittests/Makefile.am

@@ -32 +32 @@
   PlaneUnittest \
   ObserverTest \
+  ParserUnitTest \
   SingletonTest \
   StackClassUnitTest \
@@ -73 +74 @@
   PlaneUnittest.cpp \
   ObserverTest.cpp \
+  ParserUnitTest.cpp \
   SingletonTest.cpp \
   stackclassunittest.cpp \
@@ -204 +206 @@
 AtomDescriptorTest_LDADD = ${ALLLIBS}
 
+ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp
+ParserUnitTest_LDADD = ${ALLLIBS}
+
 manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp
 manipulateAtomsTest_LDADD = ${ALLLIBS}

src/unittests/SingletonTest.cpp

@@ -52 +52 @@
     count1++;
   }
-  // explicit copy constructor to catch if thsi is ever called
+  // explicit copy constructor to catch if this is ever called
   SingletonStub2(const SingletonStub2&){
     CPPUNIT_FAIL    ( "Copy constructor of Singleton called" );