Changeset 52ed5b for src

Timestamp:

Feb 17, 2012, 3:24:20 PM (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:

ea7a50

Parents:

cdaae6

git-author:

Frederik Heber <heber@…> (02/08/12 17:36:46)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:20)

Message:

Ids handed out by molecule now start with 1.

• this required some changes because of the shifted molecular indices, especially in:
  • BondedParticle::OutputAdjacency(): removed +1
  • BondedParticle::OutputBonds(): same
  • Fragmentation::StoreFragmentFromKeySet(): increased array size
  • Fragmentation::CreateMappingLabelsToConfigSequence() : same
  • CheckAgainstAdjacencyFile::ParseInExternalMap(): decreased index by one. This is actually broken and only working if World's and molecular indices coincide.
  • molecule::CreateFatherLookupTable(): increased array size
• TESTFIX: CheckAgainstAdjacencyFileUnitTest had its internal file strings' indices decreased by one.

Location:

src

Files:

• Atom/atom_bondedparticle.cpp (modified) (2 diffs)
• Fragmentation/Fragmentation.cpp (modified) (2 diffs)
• Graph/CheckAgainstAdjacencyFile.cpp (modified) (1 diff)
• Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) (3 diffs)
• molecule.cpp (modified) (2 diffs)
• molecule_graph.cpp (modified) (2 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -72 +72 @@
 {
   const BondList& ListOfBonds = getListOfBonds();
-  *AdjacencyFile << getNr()+1 << "\t";
+  *AdjacencyFile << getNr() << "\t";
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
-    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\t";
+    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr() << "\t";
   *AdjacencyFile << endl;
 };
@@ -87 +87 @@
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
     if (getNr() < (*Runner)->GetOtherAtom(this)->getNr())
-      *BondFile << getNr()+1 << "\t" << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\n";
+      *BondFile << getNr() << "\t" << (*Runner)->GetOtherAtom(this)->getNr() << "\n";
 };
 

src/Fragmentation/Fragmentation.cpp

@@ -419 +419 @@
 {
   Info info(__func__);
-  atom **SonList = new atom*[mol->getAtomCount()];
+  atom **SonList = new atom*[mol->getAtomCount()+1];
   molecule *Leaf = World::getInstance().createMolecule();
 
-  for(int i=0;i<mol->getAtomCount();i++)
+  for(int i=0;i<=mol->getAtomCount();i++)
     SonList[i] = NULL;
 
@@ -626 +626 @@
     return false;
   }
-  SortIndex = new int[mol->getAtomCount()];
-  for(int i=mol->getAtomCount();i--;)
+  SortIndex = new int[mol->getAtomCount()+1];
+  for(int i=mol->getAtomCount()+1;i--;)
     SortIndex[i] = -1;
 

src/Graph/CheckAgainstAdjacencyFile.cpp

@@ -72 +72 @@
     line >> AtomNr;
     // parse into structure
-    if (AtomNr >= 0) {
-      const atom *Walker = World::getInstance().getAtom(AtomById(AtomNr));
+    if (AtomNr > 0) {
+      const atom *Walker = World::getInstance().getAtom(AtomById(AtomNr-1));
       ASSERT(Walker != NULL,
-          "CheckAgainstAdjacencyFile::ParseInExternalMap() - there is no atom with id "+toString(AtomNr)+".");
+          "CheckAgainstAdjacencyFile::ParseInExternalMap() - there is no atom with id "+toString(AtomNr-1)+".");
       if (Walker == NULL)
         return false;
       // parse bond partner ids associated to AtomNr
       while (line >> ws >> tmp) {
-        LOG(3, "INFO: Recognized bond partner " << tmp);
-        ExternalAtomBondMap.insert( std::make_pair(AtomNr, tmp) );
+        LOG(3, "INFO: Recognized bond partner " << tmp-1);
+        ExternalAtomBondMap.insert( std::make_pair(Walker->getId(), tmp-1) );
       }
     } else {

src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp

@@ -48 +48 @@
 
 static std::string adjacencyfile ="\
-0 1\n\
-1 0 2\n\
-2 1 3\n\
-3 2 4\n\
-4 3 5\n\
-5 4 6\n\
-6 5 7\n\
-7 6 8\n\
-8 7 9\n\
-9 8\n";
-
-static std::string wrongadjacencyfile1 ="\
-0 1\n\
-1 0 2\n\
-3 2 4\n\
-4 3 5\n\
-5 4 6\n\
-6 5 7\n\
-7 6 8\n\
-8 7 9\n\
-9 8\n";
-
-static std::string wrongadjacencyfile2 ="\
-0 1\n\
-1 0 2\n\
+1 2\n\
 2 1 3\n\
 3 2 4\n\
@@ -81 +57 @@
 8 7 9\n\
 9 8 10\n\
-10 9";
+10 9\n";
+
+static std::string wrongadjacencyfile1 ="\
+1 2\n\
+2 1 3\n\
+4 3 5\n\
+5 4 6\n\
+6 5 7\n\
+7 6 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9\n";
+
+static std::string wrongadjacencyfile2 ="\
+1 2\n\
+2 1 3\n\
+3 2 4\n\
+4 3 5\n\
+5 4 6\n\
+6 5 7\n\
+7 6 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9 11\n\
+11 10";
 
 // set up and tear down
@@ -202 +202 @@
 
   // assert equality after parsing
-  CPPUNIT_ASSERT( fileChecker.InternalAtomBondMap.size() == fileChecker.ExternalAtomBondMap.size() );
-  CPPUNIT_ASSERT( fileChecker.InternalAtomBondMap == fileChecker.ExternalAtomBondMap );
+  CPPUNIT_ASSERT_EQUAL( fileChecker.InternalAtomBondMap.size(), fileChecker.ExternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( fileChecker.InternalAtomBondMap, fileChecker.ExternalAtomBondMap );
   CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
 }

src/molecule.cpp

@@ -66 +66 @@
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"),
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
-  atomIdPool(0, 20, 100),
+  atomIdPool(1, 20, 100),
   last_atom(0)
 {
@@ -246 +246 @@
 {
   std::stringstream sstr;
-  sstr << _atom->getType()->getSymbol() << _atom->getNr()+1;
+  sstr << _atom->getType()->getSymbol() << _atom->getNr();
   _atom->setName(sstr.str());
 }

src/molecule_graph.cpp

@@ -258 +258 @@
 
   // allocate and fill
-  LookupTable = new atom *[count];
+  LookupTable = new atom *[count+1];
   if (LookupTable == NULL) {
     ELOG(0, "LookupTable memory allocation failed!");
@@ -264 +264 @@
     status = false;
   } else {
-    for (int i=0;i<count;i++)
+    for (int i=0;i<=count;i++)
       LookupTable[i] = NULL;
     for (molecule::iterator iter = begin(); iter != end(); ++iter) {
       AtomNo = (*iter)->GetTrueFather()->getNr();
-      if ((AtomNo >= 0) && (AtomNo < count)) {
-        //*out << "Setting LookupTable[" << AtomNo << "] to " << *(*iter) << endl;
+      if ((AtomNo >= 0) && (AtomNo <= count)) {
+        LOG(3, "DEBUG: Setting LookupTable[" << AtomNo << "] to " << *(*iter));
         LookupTable[AtomNo] = (*iter);
       } else {
-        ELOG(1, "Walker " << *(*iter) << " exceeded range of nuclear ids [0, " << count << ").");
+        ELOG(1, "Walker " << *(*iter) << " exceeded range of nuclear ids [0, " << count << "].");
         status = false;
         break;