Changeset fe238c

Timestamp:

Apr 1, 2010, 6:52:09 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:

734816

Parents:

388049

Message:

Enhanced CountHydrogenBridgeBonds() a bit.

• new functions CheckHydrogenBridgeBondAngle() and CalculateAngle()
• CountHydrogenBridgeBonds() now discards when two oxygen show each both a hydrogen (two test cases in CountBondsUnitTest.cpp for this)
• this however also no effect over the criteria by Marry, Rotenberg and Turq.

Location:

src

Files:

• analysis_bonds.cpp (modified) (3 diffs)
• unittests/CountBondsUnitTest.cpp (modified) (7 diffs)

src/analysis_bonds.cpp

@@ -82 +82 @@
 };
 
+/** Calculate the angle between \a *first and \a *origin and \a *second and \a *origin.
+ * \param *first first Vector
+ * \param *origin origin of angle taking
+ * \param *second second Vector
+ * \return angle between \a *first and \a *second, both relative to origin at \a *origin.
+ */
+double CalculateAngle(Vector *first, Vector *central, Vector *second)
+{
+  Vector OHBond;
+  Vector OOBond;
+
+  OHBond.CopyVector(first);
+  OHBond.SubtractVector(central);
+  OOBond.CopyVector(second);
+  OOBond.SubtractVector(central);
+  const double angle = OHBond.Angle(&OOBond);
+  return angle;
+};
+
+/** Checks whether the angle between \a *Oxygen and \a *Hydrogen and \a *Oxygen and \a *OtherOxygen is less than 30 degrees.
+ * Note that distance criterion is not checked.
+ * \param *Oxygen first oxygen atom, bonded to \a *Hydrogen
+ * \param *Hydrogen hydrogen bonded to \a *Oxygen
+ * \param *OtherOxygen other oxygen atom
+ * \return true - angle criteria fulfilled, false - criteria not fulfilled, angle greater than 30 degrees.
+ */
+bool CheckHydrogenBridgeBondAngle(atom *Oxygen, atom *Hydrogen, atom *OtherOxygen)
+{
+  Info FunctionInfo(__func__);
+
+  // check angle
+  if (CalculateAngle(&Hydrogen->x, &Oxygen->x, &OtherOxygen->x) < M_PI*(30./180.)) {
+    return true;
+  } else {
+    return false;
+  }
+};
 
 /** Counts the number of hydrogen bridge bonds.
@@ -91 +128 @@
 int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
 {
-  Info FunctionInfo(__func__);
   atom *Walker = NULL;
   atom *Runner = NULL;
-  Vector OHBond;
-  Vector OOBond;
   int count = 0;
+  int OtherHydrogens = 0;
+  double Otherangle = 0.;
   bool InterfaceFlag = false;
+  bool OtherHydrogenFlag = true;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
     Walker = (*MolWalker)->start;
     while (Walker->next != (*MolWalker)->end) {
       Walker = Walker->next;
-      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != MolWalker; MolRunner++) {
+      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); MolRunner++) {
         Runner = (*MolRunner)->start;
         while (Runner->next != (*MolRunner)->end) {
           Runner = Runner->next;
-          if ((Runner != Walker) && (Walker->type->Z  == 8) && (Runner->type->Z  == 8)) {
+          if ((Walker->type->Z  == 8) && (Runner->type->Z  == 8)) {
             // check distance
             const double distance = Runner->x.DistanceSquared(&Walker->x);
             if ((distance > MYEPSILON) && (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE)) { // distance >0 means  different atoms
+              // on other atom(Runner) we check for bond to interface element and
+              // check that O-O line is not in between the shanks of the two connected hydrogens (Otherangle > 104.5)
+              OtherHydrogenFlag = true;
+              Otherangle = 0.;
+              OtherHydrogens = 0;
               InterfaceFlag = (InterfaceElement == NULL);
-              // on other atom(Runner) we check for bond to interface element
-              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); ((!InterfaceFlag) && (BondRunner != Runner->ListOfBonds.end())); BondRunner++) {
+              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
                 atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
+                // if hydrogen, check angle to be greater(!) than 30 degrees
+                if (OtherAtom->type->Z == 1) {
+                  const double angle = CalculateAngle(&OtherAtom->x, &Runner->x, &Walker->x);
+                  OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
+                  Otherangle += angle;
+                  OtherHydrogens++;
+                }
                 InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
               }
-              if (InterfaceFlag) {
+              DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
+              switch (OtherHydrogens) {
+                case 0:
+                case 1:
+                  break;
+                case 2:
+                  OtherHydrogenFlag = OtherHydrogenFlag && (Otherangle > M_PI*(104.5/180.) + MYEPSILON);
+                  break;
+                default: // 3 or more hydrogens ...
+                  OtherHydrogenFlag = false;
+                  break;
+              }
+              if (InterfaceFlag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
                 for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
@@ -122 +182 @@
                   if (OtherAtom->type->Z == 1) {
                     // check angle
-                    OHBond.CopyVector(&OtherAtom->x);
-                    OHBond.SubtractVector(&Walker->x);
-                    OOBond.CopyVector(&Runner->x);
-                    OOBond.SubtractVector(&Walker->x);
-                    const double angle = OHBond.Angle(&OOBond);
-                    if (angle < M_PI*(30./180.)) {
-                      DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << OtherAtom->Name << " and " << Runner->Name << " have a hydrogen bridge bond with " << sqrt(distance) << " and at angle " << (180./M_PI)*angle << " degrees." << endl);
+                    if (CheckHydrogenBridgeBondAngle(Walker, OtherAtom, Runner)) {
+                      DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << OtherAtom->Name << " and " << Runner->Name << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &Walker->x, &Runner->x)*(180./M_PI) << "." << endl);
                       count++;
                       break;

src/unittests/CountBondsUnitTest.cpp

@@ -159 +159 @@
   //OutputTestMolecule(TestMolecule1, "testmolecule1.xyz");
 
-  // offset of (3,0,0), hence angles are (104.5, 0, 75.5, 180) < 30
+  cout << "Case 1: offset of (3,0,0), hence angles are (104.5, 0, 75.5, 180) < 30." << endl;
   Translator.Init(3,0,0);
   TestMolecule2->Translate(&Translator);
@@ -168 +168 @@
   TestMolecule2->Translate(&Translator);
 
-  // offset of (0,3,0), hence angle are (14.5, 165.5, 90) < 30 (only three, because other 90 is missing due to first H01 only fulfilling H-bond criteria)
+  cout << "Case 2: offset of (0,3,0), hence angle are (14.5, 165.5, 90) < 30 (only three, because other 90 is missing due to first H01 only fulfilling H-bond criteria)." << endl;
   Translator.Init(0,3,0);
   TestMolecule2->Translate(&Translator);
@@ -176 +176 @@
   TestMolecule2->Translate(&Translator);
 
-  // offset of (0,-3,0) and mirror, hence angle are (165.5, 90, 165.5, 90) > 30
+  cout << "Case 3: offset of (0,-3,0) and mirror, hence angle are (165.5, 90, 165.5, 90) > 30." << endl;
   Translator.Init(0,-3,0);
   TestMolecule2->Scale((const double ** const)&mirror);
@@ -186 +186 @@
   TestMolecule2->Scale((const double ** const)&mirror);
 
-  // offset of (2,1,0), hence angle are (78, 26.6, 102, 153.4) < 30
+  cout << "Case 4: offset of (2,1,0), hence angle are (78, 26.6, 102, 153.4) < 30." << endl;
   Translator.Init(2,1,0);
   TestMolecule2->Translate(&Translator);
@@ -194 +194 @@
   TestMolecule2->Translate(&Translator);
 
-  // offset of (0,0,3), hence angle are (90, 90, 90, 90) > 30
+  cout << "Case 5: offset of (0,0,3), hence angle are (90, 90, 90, 90) > 30." << endl;
   Translator.Init(0,0,3);
   TestMolecule2->Translate(&Translator);
@@ -202 +202 @@
   TestMolecule2->Translate(&Translator);
 
-  // offset of (-3,0,0) and mirror, hence angle are (75.5, 180, 104.5, 180) > 30
+  cout << "Case 6: offset of (-3,0,0) and mirror, hence angle are (75.5, 180, 104.5, 180) > 30." << endl;
   Translator.Init(-3,0,0);
   TestMolecule2->Scale((const double ** const)&mirror);
@@ -211 +211 @@
   TestMolecule2->Translate(&Translator);
   TestMolecule2->Scale((const double ** const)&mirror);
+
+  cout << "Case 7: offset of (3,0,0) and mirror, hence angles are (104.5, 0, 104.5, 0) < 30, but interfering hydrogens." << endl;
+  Translator.Init(3,0,0);
+  TestMolecule2->Scale((const double ** const)&mirror);
+  TestMolecule2->Translate(&Translator);
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  //OutputTestMolecule(TestMolecule2, "testmolecule2-7.xyz");
+  Translator.Init(-3,0,0);
+  TestMolecule2->Translate(&Translator);
+  TestMolecule2->Scale((const double ** const)&mirror);
+
+  cout << "Case 8: offset of (0,3,0), hence angle are (14.5, 90, 14.5, 90) < 30, but interfering hydrogens." << endl;
+  Translator.Init(0,3,0);
+  TestMolecule2->Scale((const double ** const)&mirror);
+  TestMolecule2->Translate(&Translator);
+  //OutputTestMolecule(TestMolecule2, "testmolecule2-8.xyz");
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  Translator.Init(0,-3,0);
+  TestMolecule2->Translate(&Translator);
+  TestMolecule2->Scale((const double ** const)&mirror);
+
   delete(mirror);
 };