Changeset f3bc5f

Timestamp:

Nov 21, 2012, 10:03:24 AM (12 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:

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.

Location:

src/Fragmentation/SetValues

Files:

• Fragment.cpp (modified) (6 diffs)
• Fragment.hpp (modified) (5 diffs)
• unittests/FragmentUnitTest.cpp (added)
• unittests/FragmentUnitTest.hpp (added)
• unittests/Makefile.am (modified) (2 diffs)

src/Fragmentation/SetValues/Fragment.cpp ¶

@@ -38 +38 @@
 #include "Fragment.hpp"
 
+#include <algorithm>
+#include <cmath>
 #include <iostream>
+#include <limits>
 
 #include "CodePatterns/Assert.hpp"
@@ -69 +72 @@
 Fragment& Fragment::operator=(const Fragment &other)
 {
-  nuclei.clear();
-  nuclei = other.nuclei;
+  if (this != &other) {
+    nuclei.clear();
+    nuclei = other.nuclei;
+  }
   return *this;
 }
@@ -85 +90 @@
 {
   for (nuclei_t::const_iterator iter = nuclei.begin();
-      iter != nuclei.end(); ++iter) {
-    if (((*iter).first == n.first) && ((*iter).second == n.second))
+      iter != nuclei.end(); ++iter)
+    if (Fragment::isPositionEqual(iter->first, n.first))
       return true;
-  }
   return false;
 }
@@ -95 +99 @@
 {
   for (nuclei_t::iterator iter = nuclei.begin();
-      iter != nuclei.end(); ++iter) {
-    if (((*iter).first == n.first) && ((*iter).second == n.second)) {
+      iter != nuclei.end(); ++iter)
+    if (Fragment::isPositionEqual(iter->first, n.first)) {
       nuclei.erase(iter);
       break;
     }
-  }
 }
 
@@ -121 +124 @@
 }
 
+Fragment::nucleus_t Fragment::createNucleus(const position_t &position, const double charge)
+{
+  return nucleus_t( make_pair( position, charge ) );
+}
+
+bool Fragment::isPositionEqual(const position_t &a, const position_t &b)
+{
+  bool status = true;
+  for (size_t i=0;i<3;++i)
+    status &= fabs(a[i] - b[i]) < std::numeric_limits<double>::epsilon();
+  return status;
+}
+
+bool Fragment::operator==(const Fragment& other) const
+{
+  bool status = true;
+  // compare sizes
+  if (nuclei.size() != other.nuclei.size()) {
+    return false;
+  } else {
+    // if equal, sort, and compare each nuclei
+    Fragment::nuclei_t thisnuclei(nuclei);
+    Fragment::nuclei_t othernuclei(other.nuclei);
+    std::sort(thisnuclei.begin(), thisnuclei.end());
+    std::sort(othernuclei.begin(), othernuclei.end());
+    Fragment::nuclei_t::const_iterator iter = thisnuclei.begin();
+    Fragment::nuclei_t::const_iterator oiter = othernuclei.begin();
+    for (; iter != thisnuclei.end(); ++iter,++oiter)
+      status &= (*iter == *oiter);
+  }
+  return status;
+}
+
 std::ostream & operator<<(std::ostream &ost, const Fragment &f)
 {
@@ -126 +162 @@
   for (Fragment::nuclei_t::const_iterator iter = f.nuclei.begin();
       iter != f.nuclei.end(); ++iter)
-    ost << NucleiCounter++ << "\t" << iter->first << " with charge " << iter->second << std::endl;
+    ost << "[" << NucleiCounter++ << "]:" << *iter << ", ";
   return ost;
+}
+
+std::ostream & operator<<(std::ostream &ost, const Fragment::nucleus_t &n)
+{
+  ost << n.first << " with charge " << n.second;
+  return ost;
+}
+
+bool operator==(const Fragment::nucleus_t &a, const Fragment::nucleus_t &b)
+{
+  bool status = true;
+  // check positions
+  status &= Fragment::isPositionEqual(a.first, b.first);
+  status &= fabs(a.second - b.second) < std::numeric_limits<double>::epsilon();
+  return status;
 }
 

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);
 

src/Fragmentation/SetValues/unittests/Makefile.am ¶

@@ -3 +3 @@
 
 FRAGMENTATIONSETVALUESTESTSSOURCES = \
+        ../Fragmentation/SetValues/unittests/FragmentUnitTest.cpp \
         ../Fragmentation/SetValues/unittests/HistogramUnitTest.cpp \
         ../Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.cpp
 
 FRAGMENTATIONSETVALUESTESTSHEADERS = \
+        ../Fragmentation/SetValues/unittests/FragmentUnitTest.hpp \
         ../Fragmentation/SetValues/unittests/HistogramUnitTest.hpp \
         ../Fragmentation/SetValues/unittests/IndexedVectorsUnitTest.hpp
 
 FRAGMENTATIONSETVALUESTESTS = \
+        FragmentUnitTest \
   HistogramUnitTest \
   IndexedVectorsUnitTest
@@ -23 +26 @@
         $(BOOST_LIB)
 
+FragmentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        ../Fragmentation/SetValues/unittests/FragmentUnitTest.cpp \
+        ../Fragmentation/SetValues/unittests/FragmentUnitTest.hpp
+FragmentUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
 
 HistogramUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \