Changeset f3bc5f for src/Fragmentation/SetValues/Fragment.hpp

Timestamp:

Nov 21, 2012, 10:03:24 AM (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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

a0f8d3

Parents:

184943

git-author:

Frederik Heber <heber@…> (08/10/12 08:21:49)

git-committer:

Frederik Heber <heber@…> (11/21/12 10:03:24)

Message:

Added extensive unit tests and some more functions to Fragment.

File:

• src/Fragmentation/SetValues/Fragment.hpp (modified) (5 diffs)

src/Fragmentation/SetValues/Fragment.hpp

@@ -18 +18 @@
 #include <vector>
 
+class FragmentTest;
+
 class Fragment {
   //!> grant ostream operator access
   friend std::ostream & operator<<(std::ostream &ost, const Fragment &f);
+  //!> grant unit test access
+  friend class FragmentTest;
 public:
-  typedef std::vector< std::vector<double> > positions_t;
+  typedef std::vector<double> position_t;
+  typedef std::vector< position_t > positions_t;
   typedef std::vector< double > charges_t;
-  typedef std::pair< std::vector<double>, double> nucleus_t;
+  typedef std::pair< position_t, double> nucleus_t;
   typedef std::vector< nucleus_t > nuclei_t;
 
@@ -44 +49 @@
    * @param _charges given charges
    */
-  Fragment(const std::vector< std::vector<double> > &_positions, const std::vector< double > &_charges);
+  Fragment(const positions_t &_positions, const charges_t &_charges);
 
   /** Adding another fragment onto this one.
@@ -82 +87 @@
   charges_t getCharges() const;
 
+  /** Equality operator.
+   *
+   * @param other other instance to check against
+   * @return true - both are equal, false - some nucleus_t differ
+   */
+  bool operator==(const Fragment& other) const;
+
+  bool operator!=(const Fragment& other) const
+  {
+    return (!(*this == other));
+  }
+
+  /** Creates type nucleus_t from given \a position and \a charge.
+   *
+   * @param position position of nucleus to create
+   * @param charge charge of nucleus to create
+   * @return nucleus with given \a position and \a charge
+   */
+  static nucleus_t createNucleus(const position_t &position, const double charge);
+
+  /** Helper function to check whether two positions are equal.
+   *
+   * @param a first position
+   * @param b second position
+   * @return a equals b within numerical precision
+   */
+  static bool isPositionEqual(const position_t &a, const position_t &b);
+
 private:
-  /** Helper function that checks whether this nuclei is present.
+  /** Helper function that checks whether this nuclei \b position is present.
    *
    * This operation is \f${\cal O}(n)\f$
@@ -92 +125 @@
   bool containsNuclei(const nucleus_t &n) const;
 
-  /** Seeks through all nuclei and removes matching one if found.
+  /** Seeks through all nuclei and removes one with matching \b position if found.
    *
    * @param n nuclei to remove
@@ -102 +135 @@
 };
 
+/** Equality operator for two nuclei.
+ *
+ * @param a first nuclei
+ * @param b second nuclei
+ * @return true - both have same position and charge, false - either charge or position is different
+ */
+bool operator==(const Fragment::nucleus_t &a, const Fragment::nucleus_t &b);
+
+std::ostream & operator<<(std::ostream &ost, const Fragment::nucleus_t &n);
+
 std::ostream & operator<<(std::ostream &ost, const Fragment &f);