Changeset 67db80 for src/Fragmentation/Homology

Timestamp:

Dec 13, 2012, 9:32:50 AM (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:

12a24c

Parents:

e15ffe

git-author:

Frederik Heber <heber@…> (09/27/12 13:23:40)

git-committer:

Frederik Heber <heber@…> (12/13/12 09:32:50)

Message:

Added serialization capabilities to FragmentEdge, FragmentNode, and HomologyGraph.

• also added unit test function for each.

Location:

src/Fragmentation/Homology

Files:

• FragmentEdge.cpp (modified) (2 diffs)
• FragmentEdge.hpp (modified) (2 diffs)
• FragmentNode.cpp (modified) (2 diffs)
• FragmentNode.hpp (modified) (2 diffs)
• HomologyGraph.cpp (modified) (2 diffs)
• HomologyGraph.hpp (modified) (2 diffs)
• HomologyGraph_getFromKeyset.cpp (modified) (1 diff)
• unittests/FragmentEdgeUnitTest.cpp (modified) (2 diffs)
• unittests/FragmentEdgeUnitTest.hpp (modified) (2 diffs)
• unittests/FragmentNodeUnitTest.cpp (modified) (2 diffs)
• unittests/FragmentNodeUnitTest.hpp (modified) (2 diffs)
• unittests/HomologyGraphUnitTest.cpp (modified) (2 diffs)
• unittests/HomologyGraphUnitTest.hpp (modified) (2 diffs)
• unittests/Makefile.am (modified) (2 diffs)

src/Fragmentation/Homology/FragmentEdge.cpp

@@ -34 +34 @@
 #include <config.h>
 #endif
+
+// include headers that implement a archive in simple text format
+// otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
+#include <boost/archive/text_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
 
 #include "CodePatterns/MemDebug.hpp"
@@ -118 +123 @@
   return out;
 }
+
+
+// we need to explicitly instantiate the serialization functions
+BOOST_CLASS_EXPORT_IMPLEMENT(FragmentEdge)

src/Fragmentation/Homology/FragmentEdge.hpp

@@ -13 +13 @@
 #include <config.h>
 #endif
+
+#include <boost/serialization/export.hpp>
+#include <boost/serialization/utility.hpp>
 
 #include <iosfwd>
@@ -42 +45 @@
   //!> stores the atomic number of either FragmentNode making up the edge
   const AtomicNumberPair_t AtomicNumberPair;
+
+private:
+  friend class boost::serialization::access;
+  // serialization
+  template <typename Archive>
+  void serialize(Archive& ar, const unsigned int version)
+  {
+    ar & const_cast<AtomicNumberPair_t &>(AtomicNumberPair);
+  }
 };
+
+// we need to give this class a unique key for serialization
+BOOST_CLASS_EXPORT_KEY(FragmentEdge)
 
 std::ostream& operator<<(std::ostream &out, const FragmentEdge &node);

src/Fragmentation/Homology/FragmentNode.cpp

@@ -34 +34 @@
 #include <config.h>
 #endif
+
+// include headers that implement a archive in simple text format
+// otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
+#include <boost/archive/text_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
 
 #include "CodePatterns/MemDebug.hpp"
@@ -102 +107 @@
   return out;
 }
+
+
+// we need to explicitly instantiate the serialization functions
+BOOST_CLASS_EXPORT_IMPLEMENT(FragmentNode)

src/Fragmentation/Homology/FragmentNode.hpp

@@ -13 +13 @@
 #include <config.h>
 #endif
+
+#include <boost/serialization/export.hpp>
 
 #include <iosfwd>
@@ -71 +73 @@
   //!> number of connecting edges
   const size_t ConnectedEdges;
+
+private:
+  friend class boost::serialization::access;
+  // serialization
+  template <typename Archive>
+  void serialize(Archive& ar, const unsigned int version)
+  {
+    ar & const_cast<size_t &>(AtomicNumber);
+    ar & const_cast<size_t &>(ConnectedEdges);
+  }
 };
+
+// we need to give this class a unique key for serialization
+BOOST_CLASS_EXPORT_KEY(FragmentNode)
 
 std::ostream& operator<<(std::ostream &out, const FragmentNode &node);

src/Fragmentation/Homology/HomologyGraph.cpp

@@ -34 +34 @@
 #include <config.h>
 #endif
+
+// include headers that implement a archive in simple text format
+// otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
+#include <boost/archive/text_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
 
 #include "CodePatterns/MemDebug.hpp"
@@ -106 +111 @@
 }
 
+// we need to explicitly instantiate the serialization functions
+BOOST_CLASS_EXPORT_IMPLEMENT(HomologyGraph)
+

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -14 +14 @@
 #include <config.h>
 #endif
+
+#include <boost/serialization/export.hpp>
+#include <boost/serialization/set.hpp>
 
 #include <set>
@@ -95 +98 @@
   //!> information on the edges of the graph
   const edges_t edges;
+
+private:
+  friend class boost::serialization::access;
+  // serialization
+  template <typename Archive>
+  void serialize(Archive& ar, const unsigned int version)
+  {
+    ar & const_cast<nodes_t &>(nodes);
+    ar & const_cast<edges_t &>(edges);
+  }
 };
 
 std::ostream& operator<<(std::ostream& ost, const HomologyGraph &graph);
+
+// we need to give this class a unique key for serialization
+BOOST_CLASS_EXPORT_KEY(HomologyGraph)
 
 // define some helpers outside to allow for light-weight unit testing

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -47 +47 @@
 #include "World.hpp"
 
+// we have placed these functions into an extra module to allow compiling the
+// unit tests which do no require them against dummy units which do not pull
+// in all the cludder of World, atom, molecule, and so on ...
+
 namespace detail {
   const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset)

src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp

@@ -48 +48 @@
 
 #include "CodePatterns/Assert.hpp"
+
+#include <sstream>
 
 #ifdef HAVE_TESTRUNNER
@@ -134 +136 @@
   CPPUNIT_ASSERT( edge == edge);
 }
+
+
+/** UnitTest for serialization
+ */
+void FragmentEdgeTest::serializeTest()
+{
+  FragmentEdge edge(1,1);
+  // serialize
+  std::stringstream outputstream;
+  boost::archive::text_oarchive oa(outputstream);
+  oa << edge;
+
+  // deserialize
+  FragmentEdge sameedge;
+  std::stringstream returnstream(outputstream.str());
+  boost::archive::text_iarchive ia(returnstream);
+  ia >> sameedge;
+
+  CPPUNIT_ASSERT( edge == sameedge );
+}

src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp

@@ -26 +26 @@
     CPPUNIT_TEST ( comparatorTest );
     CPPUNIT_TEST ( assignmentTest );
+    CPPUNIT_TEST ( serializeTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -33 +34 @@
       void comparatorTest();
       void assignmentTest();
+      void serializeTest();
 
 };

src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp

@@ -49 +49 @@
 
 #include "CodePatterns/Assert.hpp"
+#include <sstream>
 
 #ifdef HAVE_TESTRUNNER
@@ -135 +136 @@
   CPPUNIT_ASSERT( node == node);
 }
+
+
+/** UnitTest for serialization
+ */
+void FragmentNodeTest::serializeTest()
+{
+  FragmentNode node(1,1);
+  // serialize
+  std::stringstream outputstream;
+  boost::archive::text_oarchive oa(outputstream);
+  oa << node;
+
+  // deserialize
+  FragmentNode samenode;
+  std::stringstream returnstream(outputstream.str());
+  boost::archive::text_iarchive ia(returnstream);
+  ia >> samenode;
+
+  CPPUNIT_ASSERT( node == samenode );
+}

src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp

@@ -26 +26 @@
     CPPUNIT_TEST ( comparatorTest );
     CPPUNIT_TEST ( assignmentTest );
+    CPPUNIT_TEST ( serializeTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -33 +34 @@
       void comparatorTest();
       void assignmentTest();
+      void serializeTest();
 };
 

src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp

@@ -51 +51 @@
 
 #include <boost/assign.hpp>
+#include <sstream>
 
 using namespace boost::assign;
@@ -147 +148 @@
   CPPUNIT_ASSERT( *graph == *graph);
 }
+
+
+/** UnitTest for serialization
+ */
+void HomologyGraphTest::serializeTest()
+{
+  // serialize
+  std::stringstream outputstream;
+  boost::archive::text_oarchive oa(outputstream);
+  oa << graph;
+
+  // deserialize
+  HomologyGraph *samegraph;
+  std::stringstream returnstream(outputstream.str());
+  boost::archive::text_iarchive ia(returnstream);
+  ia >> samegraph;
+
+  CPPUNIT_ASSERT( *graph == *samegraph );
+
+  delete samegraph;
+}

src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp

@@ -29 +29 @@
     CPPUNIT_TEST ( comparatorTest );
     CPPUNIT_TEST ( assigmentTest );
+    CPPUNIT_TEST ( serializeTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -36 +37 @@
       void comparatorTest();
       void assigmentTest();
+      void serializeTest();
 
 private:

src/Fragmentation/Homology/unittests/Makefile.am

@@ -28 +28 @@
         ../libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
+  $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
         $(BOOST_LIB)
 
@@ -39 +40 @@
         ../Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp
 FragmentNodeUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
-
+        
 HomologyContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ../Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp \