Changeset 61745cc

Timestamp:

Jun 10, 2010, 4:17:22 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:

198494

Parents:

7e6b00

Message:

BUGFIX: LoadPeriodentafel() did not close files and elements have to be replaced in-place.

• LoadPeriodentafel() - input file was never closed or cleared.
• LoadPeriodentafel() - new element in case of presence of same-Z, deleted the old one and installed a new one. However, atoms::type knows nothing about this change! Has to be done in-place.
• LoadPeriodentafel() - insertion is now tested with ASSERT
• periodentafel::RemoveElement() now return number of removed elements (good for ASSERT checks)

Location:

src

Files:

• periodentafel.cpp (modified) (10 diffs)
• periodentafel.hpp (modified) (1 diff)

src/periodentafel.cpp

@@ -70 +70 @@
  * \param *pointer element to be removed
  */
-void periodentafel::RemoveElement(element * const pointer)
-{
-  RemoveElement(pointer->getNumber());
+size_t periodentafel::RemoveElement(element * const pointer)
+{
+  return RemoveElement(pointer->getNumber());
 };
 
@@ -78 +78 @@
  * \param Z element to be removed
  */
-void periodentafel::RemoveElement(atomicNumber_t Z)
-{
-  elements.erase(Z);
+size_t periodentafel::RemoveElement(atomicNumber_t Z)
+{
+  return elements.erase(Z);
 };
 
@@ -233 +233 @@
   strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
   input.open(filename);
+  if (!input.fail())
+    DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as elements database." << endl);
   status = status && LoadElementsDatabase(&input);
+  input.close();
+  input.clear();
 
   // fill valence DB per element
@@ -240 +244 @@
   strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
   input.open(filename);
+  if (!input.fail())
+    DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as valence database." << endl);
   otherstatus = otherstatus && LoadValenceDatabase(&input);
+  input.close();
+  input.clear();
 
   // fill orbitals DB per element
@@ -247 +255 @@
   strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
   input.open(filename);
+  if (!input.fail())
+    DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as orbitals database." << endl);
   otherstatus = otherstatus && LoadOrbitalsDatabase(&input);
+  input.close();
+  input.clear();
 
   // fill H-BondAngle DB per element
@@ -254 +266 @@
   strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
   input.open(filename);
+  if (!input.fail())
+    DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as H bond angle database." << endl);
   otherstatus = otherstatus && LoadHBondAngleDatabase(&input);
+  input.close();
+  input.clear();
 
   // fill H-BondDistance DB per element
@@ -261 +277 @@
   strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
   input.open(filename);
+  if (!input.fail())
+    DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as H bond length database." << endl);
   otherstatus = otherstatus && LoadHBondLengthsDatabase(&input);
+  input.close();
+  input.clear();
 
   if (!otherstatus){
@@ -278 +298 @@
   bool status = true;
   int counter = 0;
+  pair< std::map<atomicNumber_t,element*>::iterator, bool > InserterTest;
   if (!(*input).fail()) {
     (*input).getline(header1, MAXSTRINGSIZE);
@@ -303 +324 @@
       //(*input) >> ws;
       (*input) >> ws;
-      if (elements.count(neues->Z)) {// if element already present, remove and delete it
-        element * const Elemental = FindElement(neues->Z);
-        ASSERT(Elemental != NULL, "element should be present but is not??");
-        RemoveElement(Elemental);
-        delete(Elemental);
-      }
       //neues->Output((ofstream *)&cout);
-      if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS)) {
-        DoLog(0) && (Log() << Verbose(0) << " " << neues->symbol);
-        elements[neues->getNumber()] = neues;
+      if ((neues->getNumber() > 0) && (neues->getNumber() < MAX_ELEMENTS)) {
+        if (elements.count(neues->getNumber())) {// if element already present, remove and delete old one (i.e. replace it)
+          //cout << neues->symbol << " is present already." << endl;
+          element * const Elemental = FindElement(neues->getNumber());
+          ASSERT(Elemental != NULL, "element should be present but is not??");
+          *Elemental = *neues;
+        } else {
+          InserterTest = elements.insert(pair <atomicNumber_t,element*> (neues->getNumber(), neues));
+          ASSERT(InserterTest.second, "Could not insert new element into periodentafel on LoadElementsDatabase().");
+        }
+        DoLog(0) && (Log() << Verbose(0) << " " << elements[neues->getNumber()]->symbol);
         counter++;
       } else {
@@ -321 +344 @@
     }
     DoLog(0) && (Log() << Verbose(0) << endl);
-  } else
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Could not open the database." << endl);
     status = false;
+  }
 
   if (counter == 0)

src/periodentafel.hpp

@@ -44 +44 @@
 
   iterator AddElement(element * const pointer);
-  void RemoveElement(element * const pointer);
-  void RemoveElement(atomicNumber_t);
+  size_t RemoveElement(element * const pointer);
+  size_t RemoveElement(atomicNumber_t);
   void CleanupPeriodtable();
   element * const FindElement(atomicNumber_t) const;