Changeset d74077 for src/analysis_bonds.cpp

Timestamp:

Jul 31, 2010, 3:23:10 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, Candidate_v1.7.0, 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:

8f4df1

Parents:

5fbaeb

Message:

Member variable Vector and element of class atom are now private.

• renamed to AtomicPosition
• created interface class VectorInterface with alle functions from class Vector as virtual ones
• implemented in AtomInfo
• everywhere direct access to AtomicPosition has been replaced by get/setPosition() and others
• for element get/setType() have been present already, direct access has been replaced by calling of these.
• class TesselPoint now derives from AtomInfo and ParticleInfo
• tesselation.cpp split up
  • new files for the classes: BoundaryLineSet, BoundaryPointSet, BoundaryPolygonSet, BoundaryTriangleSet, CandidateForTesselation, PointCloud, TesselPoint
  • all defines are in BoundaryMaps.hpp

File:

• src/analysis_bonds.cpp (modified) (9 diffs)

src/analysis_bonds.cpp

@@ -60 +60 @@
   int AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    if ((*iter)->type == type1)
+    if ((*iter)->getType() == type1)
       for (BondList::const_iterator BondRunner = (*iter)->ListOfBonds.begin(); BondRunner != (*iter)->ListOfBonds.end(); BondRunner++)
-        if ((*BondRunner)->GetOtherAtom((*iter))->type == type2) {
+        if ((*BondRunner)->GetOtherAtom((*iter))->getType() == type2) {
           const double distance = (*BondRunner)->GetDistanceSquared();
           if (Min > distance)
@@ -87 +87 @@
  * \return angle between \a *first and \a *second, both relative to origin at \a *origin.
  */
-double CalculateAngle(Vector *first, Vector *central, Vector *second)
+double CalculateAngle(const Vector &first, const Vector &central, const Vector &second)
 {
   Vector OHBond;
   Vector OOBond;
 
-  OHBond = (*first) - (*central);
-  OOBond = (*second) - (*central);
+  OHBond = first - central;
+  OOBond = second - central;
   const double angle = OHBond.Angle(OOBond);
   return angle;
@@ -110 +110 @@
 
   // check angle
-  if (CalculateAngle(&Hydrogen->x, &Oxygen->x, &OtherOxygen->x) < M_PI*(30./180.)) {
+  if (CalculateAngle(Hydrogen->getPosition(), Oxygen->getPosition(), OtherOxygen->getPosition()) < M_PI*(30./180.)) {
     return true;
   } else {
@@ -138 +138 @@
         molecule::iterator Runner = (*MolRunner)->begin();
         for(;Runner!=(*MolRunner)->end();++Runner){
-          if (((*Walker)->type->Z  == 8) && ((*Runner)->type->Z  == 8)) {
+          if (((*Walker)->getType()->Z  == 8) && ((*Runner)->getType()->Z  == 8)) {
             // check distance
-            const double distance = (*Runner)->x.DistanceSquared((*Walker)->x);
+            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
@@ -152 +152 @@
                 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);
+                if (OtherAtom->getType()->Z == 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->type == InterfaceElement);
-                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
+                InterfaceFlag = InterfaceFlag || (OtherAtom->getType() == InterfaceElement);
+                Interface2Flag = Interface2Flag || (OtherAtom->getType() == Interface2Element);
               }
               DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
@@ -177 +177 @@
                 for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {
                   atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
-                  if (OtherAtom->type->Z == 1) {
+                  if (OtherAtom->getType()->Z == 1) {
                     // check angle
                     if (CheckHydrogenBridgeBondAngle(*Walker, OtherAtom, *Runner)) {
-                      DoLog(1) && (Log() << Verbose(1) << (*Walker)->getName() << ", " << OtherAtom->getName() << " and " << (*Runner)->getName() << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &(*Walker)->x, &(*Runner)->x)*(180./M_PI) << "." << endl);
+                      DoLog(1) && (Log() << Verbose(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) << "." << endl);
                       count++;
                       break;
@@ -210 +210 @@
     for(;Walker!=(*MolWalker)->end();++Walker){
       atom * theAtom = *Walker;
-      if ((theAtom->type == first) || (theAtom->type == second)) {  // first element matches
+      if ((theAtom->getType() == first) || (theAtom->getType() == second)) {  // first element matches
         for (BondList::const_iterator BondRunner = theAtom->ListOfBonds.begin(); BondRunner != theAtom->ListOfBonds.end(); BondRunner++) {
           atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
-          if (((OtherAtom->type == first) || (OtherAtom->type == second)) && (theAtom->nr < OtherAtom->nr)) {
+          if (((OtherAtom->getType() == first) || (OtherAtom->getType() == second)) && (theAtom->nr < OtherAtom->nr)) {
             count++;
             DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << " bond found between " << *Walker << " and " << *OtherAtom << "." << endl);
@@ -246 +246 @@
     for(;Walker!=(*MolWalker)->end();++Walker){
       atom *theAtom = *Walker;
-      if (theAtom->type == second) {  // first element matches
+      if (theAtom->getType() == second) {  // first element matches
         for (int i=0;i<2;i++)
           MatchFlag[i] = false;
@@ -252 +252 @@
           atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
           for (int i=0;i<2;i++)
-            if ((!MatchFlag[i]) && (OtherAtom->type == ElementArray[i])) {
+            if ((!MatchFlag[i]) && (OtherAtom->getType() == ElementArray[i])) {
               MatchFlag[i] = true;
               break;  // each bonding atom can match at most one element we are looking for