Changeset 153985

Timestamp:

Feb 22, 2012, 11:29:04 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, 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:

a8ae6d

Parents:

826e8c

git-author:

Frederik Heber <heber@…> (01/04/12 09:34:58)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:29:04)

Message:

Rewrote CountHydrogenBridgeBonds() to use new LinkedCell construct.

• enhanced verbosity of CheckHydrogenBridgeBondAngle() and changed parameters to be refs not pointers.
• CountHydrogenBridgeBonds() uses LinkedCell to not go through O(N^{2) molecules but through all molecules and then through all molecules in the neighborhood that have oxygen atoms close enough.}

File:

• src/Analysis/analysis_bonds.cpp (modified) (4 diffs)

src/Analysis/analysis_bonds.cpp

@@ -123 +123 @@
  * \return true - angle criteria fulfilled, false - criteria not fulfilled, angle greater than 30 degrees.
  */
-bool CheckHydrogenBridgeBondAngle(atom *Oxygen, atom *Hydrogen, atom *OtherOxygen)
+bool CheckHydrogenBridgeBondAngle(const atom & Oxygen, const atom & Hydrogen, const atom & OtherOxygen)
 {
   Info FunctionInfo(__func__);
 
   // check angle
-  if (CalculateAngle(Hydrogen->getPosition(), Oxygen->getPosition(), OtherOxygen->getPosition()) < M_PI*(30./180.)) {
+  const double angle = CalculateAngle(
+      Hydrogen.getPosition(),
+      Oxygen.getPosition(),
+      OtherOxygen.getPosition());
+  LOG(3, "INFO: Hydrogen bridge bond angle is " << angle << ", < " << M_PI*(30./180.) << "?");
+  if (angle < M_PI*(30./180.)) {
     return true;
   } else {
@@ -144 +149 @@
 int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
 {
+  Info FunctionInfo(__func__);
+
   int count = 0;
   int OtherHydrogens = 0;
@@ -150 +157 @@
   bool Interface2Flag = false;
   bool OtherHydrogenFlag = true;
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
-    molecule::iterator Walker = (*MolWalker)->begin();
-    for(;Walker!=(*MolWalker)->end();++Walker){
-      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); ++MolRunner) {
-        molecule::iterator Runner = (*MolRunner)->begin();
-        for(;Runner!=(*MolRunner)->end();++Runner){
-          if (((*Walker)->getType()->getAtomicNumber()  == 8) && ((*Runner)->getType()->getAtomicNumber()  == 8)) {
-            // check distance
-            const double distance = (*Runner)->DistanceSquared(*(*Walker));
-            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);
-              Interface2Flag = (Interface2Element == NULL);
-              const BondList& ListOfBonds = (*Runner)->getListOfBonds();
-              for (BondList::const_iterator BondRunner = ListOfBonds.begin();
-                  BondRunner != ListOfBonds.end();
-                  BondRunner++) {
-                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
-                // if hydrogen, check angle to be greater(!) than 30 degrees
-                if (OtherAtom->getType()->getAtomicNumber() == 1) {
-                  const double angle = CalculateAngle(OtherAtom->getPosition(), (*Runner)->getPosition(), (*Walker)->getPosition());
-                  OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
-                  Otherangle += angle;
-                  OtherHydrogens++;
-                }
-                InterfaceFlag = InterfaceFlag || (OtherAtom->getType() == InterfaceElement);
-                Interface2Flag = Interface2Flag || (OtherAtom->getType() == Interface2Element);
-              }
-              LOG(1, "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens.");
-              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 && Interface2Flag && OtherHydrogenFlag) {
-                // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
-                const BondList& ListOfBonds = (*Walker)->getListOfBonds();
+  LinkedCell::LinkedCell_View LC = World::getInstance().getLinkedCell(HBRIDGEDISTANCE);
+
+  // go through every molecule
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();
+      MolWalker != molecules->ListOfMolecules.end();
+      ++MolWalker) {
+    LOG(2, "INFO: Current molecule is " << (*MolWalker)->getName() << ".");
+
+    // go through every atom
+    typedef std::set<const molecule *> Moleculeset;
+    for(molecule::const_iterator Walker = (*MolWalker)->begin();
+        Walker!=(*MolWalker)->end();
+        ++Walker) {
+      // go through every oxygen
+      if ((*Walker)->getType()->getAtomicNumber() == 8) {
+        LOG(2, "INFO: Current oxygen atom is " << *(*Walker) << ".");
+
+        // get all its neighbors
+        LinkedCell::LinkedList NeighborList = LC.getAllNeighbors(HBRIDGEDISTANCE, (*Walker)->getPosition());
+        // go through each candidate and gather the molecules of all other oxygens
+        Moleculeset MoleculeNeighbors;
+        for(LinkedCell::LinkedList::const_iterator Runner = NeighborList.begin();
+            Runner != NeighborList.end(); ++Runner) {
+          const atom * const OtherAtom = dynamic_cast<const atom *>(*Runner);
+          if ((OtherAtom->getType()->getAtomicNumber() == 8) &&
+              (OtherAtom->getMolecule() != (*MolWalker))) {
+            LOG(3, "INFO: Possible neighboring molecule is " << OtherAtom->getMolecule()->getName() << ".");
+            MoleculeNeighbors.insert(OtherAtom->getMolecule());
+          }
+        }
+
+        // now go through the molecules
+        for (Moleculeset::const_iterator moliter = MoleculeNeighbors.begin();
+            moliter != MoleculeNeighbors.end();
+            ++moliter) {
+          LOG(2, "INFO: Current other molecule is " << (*moliter)->getName() << ".");
+
+          // go through every other atom
+          for(molecule::const_iterator Runner = (*moliter)->begin();
+              Runner != (*moliter)->end();
+              ++Runner) {
+            // go through each oxygen
+            if ((*Runner)->getType()->getAtomicNumber() == 8) {
+
+              // check distance
+              const double distance = (*Runner)->DistanceSquared(*(*Walker));
+              if ((distance > MYEPSILON) && (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE)) {
+                LOG(2, "INFO: Distance between oxygen atom "
+                    << (*Walker)->getName() << " and  "
+                    << (*Runner)->getName() << " is "
+                    << sqrt(distance) << ".");
+                // 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);
+                Interface2Flag = (Interface2Element == NULL);
+                const BondList& ListOfBonds = (*Runner)->getListOfBonds();
                 for (BondList::const_iterator BondRunner = ListOfBonds.begin();
                     BondRunner != ListOfBonds.end();
                     BondRunner++) {
-                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
+                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
+                  // if hydrogen, check angle to be greater(!) than 30 degrees
                   if (OtherAtom->getType()->getAtomicNumber() == 1) {
-                    // check angle
-                    if (CheckHydrogenBridgeBondAngle(*Walker, OtherAtom, *Runner)) {
-                      LOG(1, (*Walker)->getName() << ", " << OtherAtom->getName() << " and " << (*Runner)->getName() << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(OtherAtom->getPosition(), (*Walker)->getPosition(), (*Runner)->getPosition())*(180./M_PI) << ".");
-                      count++;
-                      break;
+                    const double angle = CalculateAngle(OtherAtom->getPosition(), (*Runner)->getPosition(), (*Walker)->getPosition());
+                    OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
+                    Otherangle += angle;
+                    OtherHydrogens++;
+                  }
+                  InterfaceFlag = InterfaceFlag || (OtherAtom->getType() == InterfaceElement);
+                  Interface2Flag = Interface2Flag || (OtherAtom->getType() == Interface2Element);
+                }
+                LOG(1, "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens.");
+                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 && Interface2Flag && OtherHydrogenFlag) {
+                  // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
+                  const BondList& ListOfBonds = (*Walker)->getListOfBonds();
+                  for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+                      BondRunner != ListOfBonds.end();
+                      BondRunner++) {
+                    atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
+                    if (OtherAtom->getType()->getAtomicNumber() == 1) {
+                      // check angle
+                      if (CheckHydrogenBridgeBondAngle(*(*Walker), *OtherAtom, *(*Runner))) {
+                        count++;
+                        break;
+                      }
                     }
                   }
@@ -212 +261 @@
               }
             }
-          }
-        }
-      }
-    }
+          } // end go through molecules
+        } // end gather molecules
+      } // end go through every oxygen
+    } // end go through every atom
   }
   return count;