Changeset bbab87

Timestamp:

Jan 2, 2012, 1:34:29 PM (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, 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:

db8960

Parents:

7afb77

git-author:

Frederik Heber <heber@…> (12/19/11 21:57:06)

git-committer:

Frederik Heber <heber@…> (01/02/12 13:34:29)

Message:

Added test for new descriptor AtomsWithinDistanceOf to AtomDescriptorUnitTest.

• in AtomDescriptorTest::AtomsWithinDistanceOfTest(): ids must not necessarily be in order, added functions that make comparison based on simple N^{2 search and helper functions.}

Location:

src/Descriptors/unittests

Files:

• AtomDescriptorUnitTest.cpp (modified) (8 diffs)
• AtomDescriptorUnitTest.hpp (modified) (2 diffs)

src/Descriptors/unittests/AtomDescriptorUnitTest.cpp

@@ -28 +28 @@
 #include <Descriptors/AtomIdDescriptor.hpp>
 #include <Descriptors/AtomOfMoleculeDescriptor.hpp>
+#include <Descriptors/AtomsWithinDistanceOfDescriptor.hpp>
 
 #include "World.hpp"
 #include "Atom/atom.hpp"
 #include "molecule.hpp"
+#include "LinearAlgebra/Vector.hpp"
 
 #ifdef HAVE_TESTRUNNER
@@ -42 +44 @@
 
 // set up and tear down
-void AtomDescriptorTest::setUp(){
+void AtomDescriptorTest::setUp()
+{
   World::getInstance();
   for(int i=0;i<ATOM_COUNT;++i){
@@ -50 +53 @@
 }
 
-void AtomDescriptorTest::tearDown(){
+void AtomDescriptorTest::tearDown()
+{
   World::purgeInstance();
 }
 
 // some helper functions
-static bool hasAllAtoms(std::vector<atom*> atoms,atomId_t ids[ATOM_COUNT], std::set<atomId_t> excluded = std::set<atomId_t>()){
+static bool hasAllAtoms(std::vector<atom*> atoms,atomId_t ids[ATOM_COUNT], std::set<atomId_t> excluded = std::set<atomId_t>())
+{
   for(int i=0;i<ATOM_COUNT;++i){
     atomId_t id = ids[i];
@@ -73 +78 @@
 }
 
-static bool hasNoDuplicateAtoms(std::vector<atom*> atoms){
+static bool hasNoDuplicateAtoms(std::vector<atom*> atoms)
+{
   std::set<atomId_t> found;
   std::vector<atom*>::iterator iter;
@@ -86 +92 @@
 
 
-void AtomDescriptorTest::AtomBaseSetsTest(){
+void AtomDescriptorTest::AtomBaseSetsTest()
+{
   std::vector<atom*> allAtoms = World::getInstance().getAllAtoms(AllAtoms());
   CPPUNIT_ASSERT_EQUAL( true , hasAllAtoms(allAtoms,atomIds));
@@ -94 +101 @@
   CPPUNIT_ASSERT_EQUAL( true , noAtoms.empty());
 }
-void AtomDescriptorTest::AtomIdTest(){
+
+void AtomDescriptorTest::AtomIdTest()
+{
   // test Atoms from boundaries and middle of the set
   atom* testAtom;
@@ -120 +129 @@
   CPPUNIT_ASSERT(!testAtom);
 }
-void AtomDescriptorTest::AtomOfMoleculeTest(){
+
+void AtomDescriptorTest::AtomOfMoleculeTest()
+{
   // test Atoms from boundaries and middle of the set
   atom* testAtom;
@@ -141 +152 @@
   World::getInstance().destroyMolecule(newmol);
 }
-void AtomDescriptorTest::AtomCalcTest(){
+
+std::set<atomId_t> getDistanceList(const double distance, const Vector &position, atom **list)
+{
+  const double distanceSquared = distance*distance;
+  std::set<atomId_t> reflist;
+  for (size_t i=0; i<ATOM_COUNT;++i)
+    if (list[i]->getPosition().DistanceSquared(position) < distanceSquared)
+      reflist.insert ( list[i]->getId() );
+  return reflist;
+}
+
+
+std::set<atomId_t> getIdList(const World::AtomComposite &list)
+{
+  std::set<atomId_t> testlist;
+  for (World::AtomComposite::const_iterator iter = list.begin();
+      iter != list.end(); ++iter)
+    testlist.insert( (*iter)->getId() );
+  return testlist;
+}
+
+void AtomDescriptorTest::AtomsWithinDistanceOfTest()
+{
+  // align atoms along an axis
+  for(int i=0;i<ATOM_COUNT;++i) {
+    atoms[i]->setPosition(Vector((double)i, 0., 0.));
+    //std::cout << "atoms[" << i << "]: " << atoms[i]->getId() << " at " << atoms[i]->getPosition() << std::endl;
+  }
+
+  // get atom by descriptor ...
+  // ... from origin up to 2.5
+  {
+    const double distance = 1.5;
+    Vector position(0.,0.,0.);
+    World::AtomComposite atomlist = World::getInstance().getAllAtoms(AtomsWithinDistanceOf(distance, position));
+    CPPUNIT_ASSERT_EQUAL( (size_t)2, atomlist.size() );
+    std::set<atomId_t> reflist = getDistanceList(distance, position, atoms);
+    std::set<atomId_t> testlist = getIdList(atomlist);
+    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+  }
+  // ... from (4,0,0) up to 2.9 (i.e. more shells or different view)
+  {
+    const double distance = 2.9;
+    World::AtomComposite atomlist = World::getInstance().getAllAtoms(AtomsWithinDistanceOf(distance, Vector(4.,0.,0.)));
+    CPPUNIT_ASSERT_EQUAL( (size_t)5, atomlist.size() );
+    std::set<atomId_t> reflist = getDistanceList(distance, Vector(4.,0.,0.), atoms);
+    std::set<atomId_t> testlist = getIdList(atomlist);
+    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+  }
+  // ... from (10,0,0) up to 1.5
+  {
+    const double distance = 1.5;
+    Vector *position = new Vector(10.,0.,0.);
+    World::AtomComposite atomlist = World::getInstance().getAllAtoms(AtomsWithinDistanceOf(distance, *position));
+    CPPUNIT_ASSERT_EQUAL( (size_t)1, atomlist.size() );
+    std::set<atomId_t> reflist = getDistanceList(distance, *position, atoms);
+    std::set<atomId_t> testlist = getIdList(atomlist);
+    CPPUNIT_ASSERT_EQUAL( reflist, testlist );
+    delete position;
+  }
+}
+
+void AtomDescriptorTest::AtomCalcTest()
+{
   // test some elementary set operations
   {

src/Descriptors/unittests/AtomDescriptorUnitTest.hpp

@@ -30 +30 @@
   CPPUNIT_TEST ( AtomIdTest );
   CPPUNIT_TEST ( AtomOfMoleculeTest );
+  CPPUNIT_TEST ( AtomsWithinDistanceOfTest );
   CPPUNIT_TEST ( AtomCalcTest );
   CPPUNIT_TEST_SUITE_END();
@@ -40 +41 @@
   void AtomOfMoleculeTest();
   void AtomIdTest();
+  void AtomsWithinDistanceOfTest();
   void AtomCalcTest();