Changeset 37ef6d for src

Timestamp:

Jun 27, 2014, 9:32:55 PM (11 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:

a42fee

Parents:

31bd9c

git-author:

Frederik Heber <heber@…> (03/20/14 17:29:00)

git-committer:

Frederik Heber <heber@…> (06/27/14 21:32:55)

Message:

Changed element class and periodentafel to have and use functions from ion.

• If ionization is zero, fall back to other function.

Location:

src

Files:

• Actions/CommandAction/ElementDbAction.cpp (modified) (1 diff)
• Element/periodentafel.cpp (modified) (2 diffs)
• Element/periodentafel.hpp (modified) (5 diffs)
• Element/unittests/ElementUnitTest.cpp (modified) (2 diffs)
• Element/unittests/PeriodentafelUnitTest.cpp (modified) (1 diff)

src/Actions/CommandAction/ElementDbAction.cpp

@@ -41 +41 @@
 #include "config.hpp"
 #include "Element/element.hpp"    // we need element because of serialization!
+#include "Element/ion.hpp"    // we need element because of serialization!
 #include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"

src/Element/periodentafel.cpp

@@ -45 +45 @@
 #include "elements_db.hpp"
 #include "Helpers/defs.hpp"
+#include "ion.hpp"
 #include "periodentafel.hpp"
 
@@ -120 +121 @@
   return res!=elements.end()?((*res).second):0;
 };
+
+/** Returns the desired ion to a specific element.
+ *
+ * If the respective element is not in the list, we return
+ * NULL.
+ * \return pointer to an element or NULL if not found
+ */
+const element * periodentafel::FindElement(atomicNumber_t Z, const int ionization)
+{
+  // if not ionization given, fall back to other function
+  if (ionization == 0) {
+    return FindElement(Z);
+  }
+  // element present?
+  const_iterator elementiter = elements.find(Z);
+  if (elementiter == elements.end())
+    return NULL;
+  const element & element_base = *(elementiter->second);
+        
+  // element has already got ions?
+  IonsPerElement::iterator setiter =
+      ions.find(Z);
+  if (setiter != ions.end()) {
+    // yes, found ion list
+    ionSet::const_iterator res = setiter->second.find(ionization);
+        
+        if (res != setiter->second.end()) {
+          // ion present already
+          element * const _ion = res->second;
+          return _ion;
+        } else {
+          // ion not present yet
+          ion * const _ion = new ion(element_base, ionization);
+          // insert ion
+          setiter->second.insert( std::make_pair( ionization, _ion) );
+          return _ion;
+        }
+  } else {
+    // no ions yet, create map
+    ion * const _ion = new ion(element_base, ionization);
+    std::pair<IonsPerElement::iterator,bool> inserter =
+        ions.insert( std::make_pair(Z, ionSet()) );
+    // insert ion
+    ASSERT( inserter.second,
+        "periodentafel::FindElement() - could not insert new ionSet to element.");
+    inserter.first->second.insert( std::make_pair( ionization, _ion) );
+    return _ion;
+  }
+  return NULL;
+}
 
 /** Finds an element by its atomic number.

src/Element/periodentafel.hpp

@@ -22 +22 @@
 
 class element;
+class ion;
 
 /********************************************** declarations *******************************/
@@ -33 +34 @@
 private:
   typedef std::map<atomicNumber_t,element*> elementSet;
+  typedef std::map<int,ion*> ionSet;
+  typedef std::map<atomicNumber_t,ionSet> IonsPerElement;
 public:
   typedef elementSet::iterator iterator;
@@ -48 +51 @@
   void CleanupPeriodtable();
   const element * FindElement(atomicNumber_t) const;
+  const element * FindElement(atomicNumber_t, const int);
   const element * FindElement(const std::string &shorthand) const;
   const element * AskElement() const;
@@ -76 +80 @@
     ar & boost::serialization::make_array<char>(header2, MAXSTRINGSIZE);
     ar & elements;
+    ar & ions;
   }
 
@@ -93 +98 @@
 
   elementSet elements;
+  IonsPerElement ions;
 };
 

src/Element/unittests/ElementUnitTest.cpp

@@ -105 +105 @@
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getElectronegativity() );
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getVanDerWaalsRadius() );
+  CPPUNIT_ASSERT_EQUAL( 0., testelement->getCharge() );
   CPPUNIT_ASSERT_EQUAL( 0., testelement->getValence() );
   CPPUNIT_ASSERT_EQUAL( 0, testelement->getNoValenceOrbitals() );
@@ -172 +173 @@
   boost::archive::text_iarchive ia(stream);
   // read class state from archive
-  element * newelement;
+  element * newelement = NULL;
 
   ia >> newelement;

src/Element/unittests/PeriodentafelUnitTest.cpp

@@ -45 +45 @@
 
 #include "Element/element.hpp"
+#include "Element/ion.hpp"
 #include "Element/elements_db.hpp"
 #include "Element/periodentafel.hpp"