Changeset 220cf37

Timestamp:

Nov 7, 2009, 12:25:32 PM (15 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:

9a7186

Parents:

b9947d

git-author:

Frederik Heber <heber@…> (11/07/09 12:18:56)

git-committer:

Frederik Heber <heber@…> (11/07/09 12:25:32)

Message:

Two new bond analysis functions.

• GetMaxMinMeanBondCount() - evaluates min, mean and max bond count
• MinMaxBondDistanceBetweenElements() - evaluates min, mean and max bond distance
• Unit tests are in place and working fine.

Location:

src

Files:

• analysis_bonds.cpp (modified) (1 diff)
• analysis_bonds.hpp (modified) (1 diff)
• unittests/analysisbondsunittest.cpp (modified) (7 diffs)
• unittests/analysisbondsunittest.hpp (modified) (3 diffs)

src/analysis_bonds.cpp

@@ -6 +6 @@
  */
 
+#include "analysis_bonds.hpp"
+#include "atom.hpp"
+#include "bond.hpp"
+#include "log.hpp"
+#include "molecule.hpp"
+
+/** Calculates the min, mean and maximum bond counts for the given molecule.
+ * \param *mol molecule with atoms and atom::ListOfBonds
+ * \param &Min minimum count on return
+ * \param &Mean mean count on return
+ * \param &Max maximum count on return
+ */
+void GetMaxMinMeanBondCount(const molecule * const mol, double &Min, double &Mean, double &Max)
+{
+  Min = 2e+6;
+  Max = -2e+5;
+  Mean = 0.;
+
+  atom *Walker = mol->start;
+  int AtomCount = 0;
+  while (Walker->next != mol->end) {
+    Walker = Walker->next;
+    const int count = Walker->ListOfBonds.size();
+    if (Max < count)
+      Max = count;
+    if (Min > count)
+      Min = count;
+    Mean += count;
+    AtomCount++;
+  }
+  if (((int)Mean % 2) != 0)
+    eLog() << Verbose(1) << "Something is wrong with the bond structure, the number of bonds is not even!" << endl;
+  Mean /= (double)AtomCount;
+};
+
+/** Calculates the min and max bond distance of all atoms of two given elements.
+ * \param *mol molecule with atoms
+ * \param *type1 one element
+ * \param *type2 other element
+ * \param &Min minimum distance on return, 0 if no bond between the two elements
+ * \param &Mean mean distance (i.e. sum of distance for matching element pairs, divided by number) on return, 0 if no bond between the two elements
+ * \param &Max maximum distance on return, 0 if no bond between the two elements
+ */
+void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max)
+{
+  Min = 2e+6;
+  Mean = 0.;
+  Max = -2e+6;
+
+  int AtomNo = 0;
+  atom *Walker = mol->start;
+  while (Walker->next != mol->end) {
+    Walker = Walker->next;
+    if (Walker->type == type1)
+      for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++)
+        if ((*BondRunner)->GetOtherAtom(Walker)->type == type2) {
+          const double distance = (*BondRunner)->GetDistanceSquared();
+          if (Min > distance)
+            Min = distance;
+          if (Max < distance)
+            Max = distance;
+          Mean += sqrt(distance);
+          AtomNo++;
+        }
+  }
+  if (Max < 0) {
+    Max = Min = 0.;
+  } else {
+    Max = sqrt(Max);
+    Min = sqrt(Min);
+    Mean = Mean/(double)AtomNo;
+  }
+};

src/analysis_bonds.hpp

@@ -21 +21 @@
 /****************************************** forward declarations *****************************/
 
+class element;
+class molecule;
 
 /********************************************** declarations *******************************/
 
+void GetMaxMinMeanBondCount(const molecule * const mol, double &Min, double &Mean, double &Max);
+void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max);
+
 #endif /* ANALYSIS_BONDS_HPP_ */

src/unittests/analysisbondsunittest.cpp

@@ -15 +15 @@
 #include <stdio.h>
 
+#include "analysis_bonds.hpp"
+#include "analysisbondsunittest.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -21 +23 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
-#include "analysisbondsunittest.hpp"
 
 /********************************************** Test classes **************************************/
@@ -41 +42 @@
   hydrogen = new element;
   hydrogen->Z = 1;
+  hydrogen->Valence = 1;
+  hydrogen->NoValenceOrbitals = 1;
   strcpy(hydrogen->name, "hydrogen");
   strcpy(hydrogen->symbol, "H");
   carbon = new element;
   carbon->Z = 1;
+  carbon->Valence = 4;
+  carbon->NoValenceOrbitals = 4;
   strcpy(carbon->name, "carbon");
   strcpy(carbon->symbol, "C");
@@ -58 +63 @@
   Walker = new atom();
   Walker->type = hydrogen;
-  Walker->node->Init(1., 0., 1. );
+  Walker->node->Init(1.5, 0., 1.5 );
   TestMolecule->AddAtom(Walker);
   Walker = new atom();
   Walker->type = hydrogen;
-  Walker->node->Init(0., 1., 1. );
+  Walker->node->Init(0., 1.5, 1.5 );
   TestMolecule->AddAtom(Walker);
   Walker = new atom();
   Walker->type = hydrogen;
-  Walker->node->Init(1., 1., 0. );
+  Walker->node->Init(1.5, 1.5, 0. );
   TestMolecule->AddAtom(Walker);
   Walker = new atom();
@@ -72 +77 @@
   Walker->node->Init(0., 0., 0. );
   TestMolecule->AddAtom(Walker);
+  Walker = new atom();
+  Walker->type = carbon;
+  Walker->node->Init(0.5, 0.5, 0.5 );
+  TestMolecule->AddAtom(Walker);
 
   // check that TestMolecule was correctly constructed
-  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
+  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 5 );
 
   // create a small file with table
@@ -82 +91 @@
   test << "H\t1.\t1.2\n";
   test << "C\t1.2\t1.5\n";
+  test.close();
   BG = new BondGraph(true);
+
+  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
+  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
+  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
+  CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
+
+  BG->ConstructBondGraph(TestMolecule);
 };
 
@@ -100 +117 @@
 };
 
-/** UnitTest for AnalysisBondsTest::LoadBondLengthTable().
+/** UnitTest for GetMaxMinMeanBondCount().
  */
-void AnalysisBondsTest::BondsTest()
+void AnalysisBondsTest::GetMaxMinMeanBondCountTest()
 {
-  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
-  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
-  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
-  CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
-
-  CPPUNIT_ASSERT_EQUAL( true , true );
+  double Min = 20.; // check that initialization resets these arbitrary values
+  double Mean = 200.;
+  double Max = 1e-6;
+  GetMaxMinMeanBondCount(TestMolecule, Min, Mean, Max);
+  CPPUNIT_ASSERT_EQUAL( 1., Min );
+  CPPUNIT_ASSERT_EQUAL( 1.6, Mean );
+  CPPUNIT_ASSERT_EQUAL( 4., Max );
 
 };
+
+/** UnitTest for MinMaxBondDistanceBetweenElements().
+ */
+void AnalysisBondsTest::MinMeanMaxBondDistanceBetweenElementsTest()
+{
+  double Min = 20.; // check that initialization resets these arbitrary values
+  double Mean = 2e+6;
+  double Max = 1e-6;
+  double Min2 = 20.;
+  double Mean2 = 2e+6;
+  double Max2 = 1e-6;
+  const double maxbondlength = sqrt(1.*1. + 1.*1. + .5*.5);
+  const double minbondlength = sqrt(.5*.5 + .5*.5 + .5*.5);
+  const double meanbondlength = (minbondlength+3.*maxbondlength)/4.;
+  // check bond lengths C-H
+  MinMeanMaxBondDistanceBetweenElements(TestMolecule, hydrogen, carbon, Min, Mean, Max);
+  CPPUNIT_ASSERT_EQUAL( minbondlength , Min );
+  CPPUNIT_ASSERT_EQUAL( meanbondlength , Mean );
+  CPPUNIT_ASSERT_EQUAL( maxbondlength , Max );
+
+  // check that elements are symmetric, i.e. C-H == H-C
+  MinMeanMaxBondDistanceBetweenElements(TestMolecule, carbon, hydrogen, Min2, Mean2, Max2);
+  CPPUNIT_ASSERT_EQUAL( Min , Min2 );
+  CPPUNIT_ASSERT_EQUAL( Mean , Mean2 );
+  CPPUNIT_ASSERT_EQUAL( Max , Max2 );
+
+  // check no bond case (no bonds H-H in system!)
+  MinMeanMaxBondDistanceBetweenElements(TestMolecule, hydrogen, hydrogen, Min, Mean, Max);
+  CPPUNIT_ASSERT_EQUAL( 0. , Min );
+  CPPUNIT_ASSERT_EQUAL( 0. , Mean );
+  CPPUNIT_ASSERT_EQUAL( 0. , Max );
+};
+
 
 /********************************************** Main routine **************************************/

src/unittests/analysisbondsunittest.hpp

@@ -11 +11 @@
 #include <cppunit/extensions/HelperMacros.h>
 
-#include "bondgraph.hpp"
-
+class BondGraph;
 class element;
 class molecule;
@@ -22 +21 @@
 {
     CPPUNIT_TEST_SUITE( AnalysisBondsTest) ;
-    CPPUNIT_TEST ( BondsTest );
+    CPPUNIT_TEST ( GetMaxMinMeanBondCountTest );
+    CPPUNIT_TEST ( MinMeanMaxBondDistanceBetweenElementsTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -28 +28 @@
       void setUp();
       void tearDown();
-      void BondsTest();
+      void GetMaxMinMeanBondCountTest();
+      void MinMeanMaxBondDistanceBetweenElementsTest();
 
 private: