Changeset 31bd9c

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:

37ef6d

Parents:

9b68fc

git-author:

Frederik Heber <heber@…> (03/20/14 17:28:44)

git-committer:

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

Message:

Added ion class, derived from element.

Location:

src/Element

Files:

• Makefile.am (modified) (2 diffs)
• element.hpp (modified) (4 diffs)
• ion.cpp (added)
• ion.hpp (added)
• unittests/IonUnitTest.cpp (added)
• unittests/IonUnitTest.hpp (added)
• unittests/Makefile.am (modified) (2 diffs)

src/Element/Makefile.am

@@ -4 +4 @@
 ELEMENTSOURCE = \
         Element/element.cpp \
+        Element/ion.cpp \
         Element/periodentafel.cpp \
         Element/elements_db.cpp
@@ -9 +10 @@
 ELEMENTHEADER = \
         Element/element.hpp \
+        Element/ion.hpp \
         Element/periodentafel.hpp \
         Element/elements_db.hpp

src/Element/element.hpp

@@ -25 +25 @@
 
 class periodentafel;
+class IonTest;
 
 /********************************************** declarations *******************************/
@@ -33 +34 @@
 class element {
   friend class periodentafel;
+  friend class IonTest;
   public:
     element();
     element(const element&);
-    ~element();
+    virtual ~element();
 
     element &operator=(const element&);
@@ -47 +49 @@
     double getVanDerWaalsRadius() const;
     atomicNumber_t getAtomicNumber() const;
-    double getValence() const;
-    int getNoValenceOrbitals() const;
+    virtual double getCharge() const
+        { return 0.; }
+    virtual double getValence() const;
+    virtual int getNoValenceOrbitals() const;
     double getHBondDistance(const size_t i) const;
     double getHBondAngle(const size_t i) const;
@@ -87 +91 @@
     }
 
+  protected:
+
     double mass;    //!< mass in g/mol
     double CovalentRadius;  //!< covalent radius

src/Element/unittests/Makefile.am

@@ -4 +4 @@
 ELEMENTTESTSSOURCES = \
   ../Element/unittests/ElementUnitTest.cpp \
-        ../Element/unittests/PeriodentafelUnitTest.cpp
+  ../Element/unittests/IonUnitTest.cpp \
+  ../Element/unittests/PeriodentafelUnitTest.cpp
 
 ELEMENTTESTSHEADERS = \
-        ../Element/unittests/ElementUnitTest.hpp \
-        ../Element/unittests/PeriodentafelUnitTest.hpp
+  ../Element/unittests/ElementUnitTest.hpp \
+  ../Element/unittests/IonUnitTest.hpp \
+  ../Element/unittests/PeriodentafelUnitTest.hpp
 
 ELEMENTTESTS = \
   ElementUnitTest \
+  IonUnitTest \
   PeriodentafelUnitTest
 
@@ -24 +27 @@
         ${CodePatterns_LIBS}
 
-ElementUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
-        ../Element/unittests/ElementUnitTest.cpp \
-        ../Element/unittests/ElementUnitTest.hpp
+ElementUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+  ../Element/unittests/ElementUnitTest.cpp \
+  ../Element/unittests/ElementUnitTest.hpp
 ElementUnitTest_LDADD = $(ELEMENTLIBS)
+
+IonUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+  ../Element/unittests/IonUnitTest.cpp \
+  ../Element/unittests/IonUnitTest.hpp
+IonUnitTest_LDADD = $(ELEMENTLIBS)
 
 PeriodentafelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \