Changeset 8f6e2a for src

Timestamp:

Mar 30, 2012, 9:16:32 AM (13 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:

dd3f4f

Parents:

9e5a306

git-author:

Frederik Heber <heber@…> (01/17/12 21:06:35)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:16:32)

Message:

Added new class Cluster as atomIdset with a Shape.

• inherits ClusterInterface.
• its clone() requires CopyAtomsInterface ref.
• implements getShape(), transform(), and translate().
• added unit test.

Location:

src

Files:

• Filling/Cluster.cpp (added)
• Filling/Cluster.hpp (added)
• Filling/Makefile.am (modified) (3 diffs)
• Filling/unittests/ClusterUnitTest.cpp (added)
• Filling/unittests/ClusterUnitTest.hpp (added)
• Filling/unittests/Makefile.am (modified) (4 diffs)
• LinkedCell/unittests/Makefile.am (modified) (1 diff)
• unittests/stubs/AtomStub.cpp (moved) (moved from src/LinkedCell/unittests/stubs/AtomStub.cpp )
• unittests/stubs/WorldStub.cpp (moved) (moved from src/LinkedCell/unittests/stubs/WorldStub.cpp ) (2 diffs)

src/Filling/Makefile.am

@@ -3 +3 @@
 
 FILLINGSOURCE = \
+        Filling/Cluster.cpp \
         Filling/Predicates/AnyFillPredicate.cpp \
         Filling/Predicates/FillPredicate.cpp \
@@ -12 +13 @@
         
 FILLINGHEADER = \
+        Filling/Cluster.hpp \
         Filling/NodeTypes.hpp \
         Filling/Predicates/AnyFillPredicate.hpp \
@@ -23 +25 @@
         Filling/Predicates/Ops_FillPredicate.hpp \
         Filling/Predicates/Ops_FillPredicate_impl.hpp
-
+                                  
 
 noinst_LTLIBRARIES += libMolecuilderFilling.la

src/Filling/unittests/Makefile.am

@@ -3 +3 @@
 
 FILLINGTESTSSOURCES = \
+  ../Filling/unittests/ClusterUnitTest.cpp \
   ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp \
   ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp \
@@ -10 +11 @@
 
 FILLINGTESTSHEADERS = \
+  ../Filling/unittests/ClusterUnitTest.hpp \
   ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.hpp \
   ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.hpp \
@@ -17 +19 @@
 
 FILLINGTESTS = \
+  ClusterUnitTest \
   IsInsideDomain_FillPredicateUnitTest \
   IsInsideSurface_FillPredicateUnitTest \
@@ -28 +31 @@
 
 FILLINGLIBS =
+
+ClusterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        ../Filling/unittests/ClusterUnitTest.cpp \
+        ../Filling/unittests/ClusterUnitTest.hpp
+ClusterUnitTest_LDADD = \
+        ../libMolecuilderFilling.la \
+        ../libMolecuilderUI.la \
+        ../libMolecuilder.la \
+        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
+        ${CodePatterns_LIBS} \
+        $(BOOST_LIBS)
 
 IsInsideDomain_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

src/LinkedCell/unittests/Makefile.am

@@ -53 +53 @@
         ../LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp \
         ../LinkedCell/unittests/defs.hpp \
-        ../LinkedCell/unittests/stubs/AtomStub.cpp \
+        stubs/AtomStub.cpp \
         ../LinkedCell/unittests/stubs/AtomObserverStub.cpp \
         ../LinkedCell/unittests/stubs/ObserverBoxStub.cpp \
         ../LinkedCell/unittests/stubs/TesselPointStub.cpp \
-        ../LinkedCell/unittests/stubs/WorldStub.cpp \
         ../LinkedCell/unittests/stubs/WorldTimeStub.cpp \
+        stubs/WorldStub.cpp \
         ../LinkedCell/PointCloudAdaptor.hpp \
         ../Box_BoundaryConditions.cpp \

src/unittests/stubs/WorldStub.cpp

@@ -26 +26 @@
 #include "CodePatterns/Observer/ObservedContainer_impl.hpp"
 #include "CodePatterns/Singleton_impl.hpp"
+#include "Descriptors/AtomDescriptor.hpp"
+#include "Descriptors/AtomIdDescriptor_impl.hpp"
 
 #include "IdPool_impl.hpp"
 
 atom* World::_lastchangedatom = NULL;
+
+AtomDescriptor::AtomDescriptor(impl_ptr ptr)
+{}
+
+AtomDescriptor::~AtomDescriptor()
+{}
+
+atom * AtomById(unsigned int i)
+{
+  return NULL;
+}
 
 World::World() :
@@ -56 +69 @@
 }
 
+atom* World::getAtom(AtomDescriptor descr)
+{
+  return NULL;
+}
+
 CONSTRUCT_SINGLETON(World);