Changeset 5197e5

Timestamp:

Dec 3, 2012, 9:50:01 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:

3aa8a5

Parents:

0fad93

git-author:

Frederik Heber <heber@…> (09/21/12 12:11:23)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

REFACTOR: AdjacencyList's map creations may now create either map.

• this is to allow having either way: Either the info from file as internal map or the info from the World's atoms.

Location:

src/Graph

Files:

• AdjacencyList.cpp (modified) (7 diffs)
• AdjacencyList.hpp (modified) (1 diff)
• unittests/AdjacencyListUnitTest.cpp (modified) (3 diffs)
• unittests/AdjacencyListUnitTest.hpp (modified) (2 diffs)

src/Graph/AdjacencyList.cpp

@@ -58 +58 @@
   NonMatchNumber(0)
 {
-  bool status = ParseInInternalMap(File);
+  bool status = ParseIntoMap(File, InternalAtomBondMap);
   if (!status) // remove map if failed to parse
     InternalAtomBondMap.clear();
@@ -66 +66 @@
 {}
 
-/** Parses the bond partners of each atom from an external file into \a AtomBondMap.
+/** Parses the bond partners of each atom from an external file into \a atombondmap.
  *
  * @param File file to parse
+ * @param &atombondmap map to parse into
  * @return true - everything ok, false - error while parsing
  */
-bool AdjacencyList::ParseInInternalMap(std::istream &File)
+bool AdjacencyList::ParseIntoMap(std::istream &File, AtomBondMap &atombondmap)
 {
   if (File.fail()) {
@@ -78 +79 @@
   }
 
-  InternalAtomBondMap.clear();
+  atombondmap.clear();
   char buffer[MAXSTRINGSIZE];
   int tmp;
@@ -97 +98 @@
       while (line >> ws >> tmp) {
         LOG(3, "INFO: Recognized bond partner " << tmp-1 << " for " << WalkerId << ".");
-        InternalAtomBondMap.insert( std::make_pair(WalkerId, tmp-1) );
+        atombondmap.insert( std::make_pair(WalkerId, tmp-1) );
       }
     } else {
@@ -111 +112 @@
 /** Fills the InternalAtomBondMap from the atoms given by the two iterators.
  *
+ * @param &atombondmap map to create
  * @param atomids set of atomic ids to check (must be global ids, i.e. from atom::getId())
  */
-void AdjacencyList::CreateExternalMap(const atomids_t &atomids)
-{
-  ExternalAtomBondMap.clear();
+void AdjacencyList::CreateMap(const atomids_t &atomids, AtomBondMap &atombondmap)
+{
+  atombondmap.clear();
   // go through each atom in the list
   for (atomids_t::const_iterator iter = atomids.begin(); iter != atomids.end(); ++iter) {
     const atomId_t WalkerId = *iter;
     ASSERT(WalkerId != (size_t)-1,
-        "AdjacencyList::CreateExternalMap() - Walker has no id.");
+        "AdjacencyList::CreateMap() - Walker has no id.");
     const atom *Walker = World::getInstance().getAtom(AtomById(WalkerId));
     ASSERT( Walker != NULL,
-        "AdjacencyList::CreateExternalMap() - Walker id "+toString(*iter)
+        "AdjacencyList::CreateMap() - Walker id "+toString(*iter)
         +" is not associated to any of World's atoms.");
     const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -132 +134 @@
       const atomId_t id = (*Runner)->GetOtherAtom(Walker)->getId();
       ASSERT(id != (size_t)-1,
-          "AdjacencyList::CreateExternalMap() - OtherAtom has not id.");
-      ExternalAtomBondMap.insert( std::make_pair(WalkerId, id) );
+          "AdjacencyList::CreateMap() - OtherAtom has not id.");
+      atombondmap.insert( std::make_pair(WalkerId, id) );
     }
   }
@@ -146 +148 @@
 
   // parse in external map
-  CreateExternalMap(atomids);
+  CreateMap(atomids, ExternalAtomBondMap);
 
   bool status = CompareInternalExternalMap();

src/Graph/AdjacencyList.hpp

@@ -56 +56 @@
   ValuesSet getValues(const AtomBondRange&_range) const;
 
-  void CreateExternalMap(const atomids_t &atoms);
-  bool ParseInInternalMap(std::istream &File);
+  void CreateMap(const atomids_t &atoms, AtomBondMap &atombondmap);
+  bool ParseIntoMap(std::istream &File, AtomBondMap &atombondmap);
   bool CompareInternalExternalMap();
 };

src/Graph/unittests/AdjacencyListUnitTest.cpp

@@ -161 +161 @@
 }
 
-/** Unit tests for AdjacencyList::CreateExternalMap().
- *
- */
-void AdjacencyListTest::CreateExternalMapTest()
+/** Unit tests for AdjacencyList::CreateMap().
+ *
+ */
+void AdjacencyListTest::CreateMapTest()
 {
   std::stringstream input;
   AdjacencyList fileChecker(input);
-  fileChecker.CreateExternalMap(atomIds);
+  fileChecker.CreateMap(atomIds, fileChecker.ExternalAtomBondMap);
 
   // check size (it's 8*2 + 2*1 = 18 keys)
@@ -190 +190 @@
 }
 
-/** Unit tests for AdjacencyList::ParseInInternalMap().
- *
- */
-void AdjacencyListTest::ParseInInternalMapTest()
+/** Unit tests for AdjacencyList::ParseIntoMap().
+ *
+ */
+void AdjacencyListTest::ParseIntoMapTest()
 {
   std::stringstream input(adjacencyfile);
   AdjacencyList fileChecker(input);
   std::vector<atomId_t> noids;
-  fileChecker.CreateExternalMap(noids);
+  fileChecker.CreateMap(noids, fileChecker.ExternalAtomBondMap);
 
   // check size (it's 8*2 + 2*1 = 18 keys)
@@ -232 +232 @@
 
   // parse in external map
-  fileChecker.CreateExternalMap(atomIds);
+  fileChecker.CreateMap(atomIds, fileChecker.ExternalAtomBondMap);
 
   // assert equality after parsing

src/Graph/unittests/AdjacencyListUnitTest.hpp

@@ -30 +30 @@
 {
   CPPUNIT_TEST_SUITE( AdjacencyListTest );
-  CPPUNIT_TEST ( CreateExternalMapTest );
-  CPPUNIT_TEST ( ParseInInternalMapTest );
+  CPPUNIT_TEST ( CreateMapTest );
+  CPPUNIT_TEST ( ParseIntoMapTest );
   CPPUNIT_TEST ( CompareInternalExternalMapTest );
   CPPUNIT_TEST ( CheckAgainstSubsetTest );
@@ -40 +40 @@
   void tearDown();
 
-  void CreateExternalMapTest();
-  void ParseInInternalMapTest();
+  void CreateMapTest();
+  void ParseIntoMapTest();
   void CompareInternalExternalMapTest();
   void CheckAgainstSubsetTest();