Changeset 300220 for src/bondgraph.cpp

Timestamp:

Mar 1, 2011, 1:17:08 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:

0ec7fe

Parents:

0cbad2

git-author:

Frederik Heber <heber@…> (02/28/11 15:00:34)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:08)

Message:

BondGraph::..MinMaxDistance() changed to use range<double>.

• requires CodePatterns 1.0.13 due to operator<< (range<T>)
• all ...BondGraph::..MinMaxDistance() work on range, not two doubles.
• only getMinMaxDistance(BondedParticle, BondedParticle, ...) available from outside.
• new function getMinMaxDistanceSquared( <see above> ) for squared interval boundaries.
• internal use element pointer:
  • getMinMaxDistance()
  • BondLengthMatrixMinMaxDistance()
  • CovalentMinMaxDistance()
• getBondLength is now private and only unit tests are friends.

File:

• src/bondgraph.cpp (modified) (5 diffs)

src/bondgraph.cpp

@@ -93 +93 @@
 }
 
-double BondGraph::GetBondLength(int firstZ, int secondZ)
+double BondGraph::GetBondLength(
+    int firstZ,
+    int secondZ) const
 {
   std::cout << "Request for length between " << firstZ << " and " << secondZ << ": ";
@@ -110 +112 @@
 }
 
-
-void BondGraph::CovalentMinMaxDistance(const BondedParticle * const Walker, const BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
-{
-  MinDistance = OtherWalker->getType()->getCovalentRadius() + Walker->getType()->getCovalentRadius();
-  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-  MaxDistance = MinDistance + BondThreshold;
-  MinDistance -= BondThreshold;
-}
-
-void BondGraph::BondLengthMatrixMinMaxDistance(const BondedParticle * const Walker, const BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
-{
-  ASSERT(BondLengthMatrix != NULL,
-      "BondGraph::BondLengthMatrixMinMaxDistance() called without NULL BondLengthMatrix.");
-  MinDistance = GetBondLength(Walker->getType()->getAtomicNumber()-1, OtherWalker->getType()->getAtomicNumber()-1);
-  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-  MaxDistance = MinDistance + BondThreshold;
-  MinDistance -= BondThreshold;
-}
-
-void BondGraph::getMinMaxDistance(const BondedParticle * const Walker, const BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
+void BondGraph::CovalentMinMaxDistance(
+    const element * const Walker,
+    const element * const OtherWalker,
+    range<double> &MinMaxDistance,
+    bool IsAngstroem) const
+{
+  MinMaxDistance.first = OtherWalker->getCovalentRadius() + Walker->getCovalentRadius();
+  MinMaxDistance.first *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
+  MinMaxDistance.last = MinMaxDistance.first + BondThreshold;
+  MinMaxDistance.first -= BondThreshold;
+}
+
+void BondGraph::BondLengthMatrixMinMaxDistance(
+    const element * const Walker,
+    const element * const OtherWalker,
+    range<double> &MinMaxDistance,
+    bool IsAngstroem) const
+{
+  ASSERT(BondLengthMatrix, "BondGraph::BondLengthMatrixMinMaxDistance() called without NULL BondLengthMatrix.");
+  ASSERT(Walker, "BondGraph::BondLengthMatrixMinMaxDistance() - illegal element given.");
+  ASSERT(OtherWalker, "BondGraph::BondLengthMatrixMinMaxDistance() - illegal other element given.");
+  MinMaxDistance.first = GetBondLength(Walker->getAtomicNumber()-1, OtherWalker->getAtomicNumber()-1);
+  MinMaxDistance.first *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
+  MinMaxDistance.last = MinMaxDistance.first + BondThreshold;
+  MinMaxDistance.first -= BondThreshold;
+}
+
+void BondGraph::getMinMaxDistance(
+    const element * const Walker,
+    const element * const OtherWalker,
+    range<double> &MinMaxDistance,
+    bool IsAngstroem) const
 {
   if (BondLengthMatrix == NULL) {// safety measure if no matrix has been parsed yet
-    LOG(2, "INFO: Using Covalent radii criterion for [min,max] distances.");
-    CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+    LOG(2, "INFO: Using Covalent radii criterion for [min,max) distances.");
+    CovalentMinMaxDistance(Walker, OtherWalker, MinMaxDistance, IsAngstroem);
   } else {
-    LOG(2, "INFO: Using Covalent radii criterion for [min,max] distances.");
-    BondLengthMatrixMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
-  }
+    LOG(2, "INFO: Using Covalent radii criterion for [min,max) distances.");
+    BondLengthMatrixMinMaxDistance(Walker, OtherWalker, MinMaxDistance, IsAngstroem);
+  }
+}
+
+void BondGraph::getMinMaxDistance(
+    const BondedParticle * const Walker,
+    const BondedParticle * const OtherWalker,
+    range<double> &MinMaxDistance,
+    bool IsAngstroem) const
+{
+  getMinMaxDistance(Walker->getType(), OtherWalker->getType(),MinMaxDistance, IsAngstroem);
+}
+
+void BondGraph::getMinMaxDistanceSquared(
+    const BondedParticle * const Walker,
+    const BondedParticle * const OtherWalker,
+    range<double> &MinMaxDistance,
+    bool IsAngstroem) const
+{
+  // use non-squared version
+  getMinMaxDistance(Walker, OtherWalker,MinMaxDistance, IsAngstroem);
+  // and square
+  MinMaxDistance.first *= MinMaxDistance.first;
+  MinMaxDistance.last *= MinMaxDistance.last;
 }
 
@@ -145 +181 @@
   atom *OtherWalker = NULL;
   int n[NDIM];
-  double MinDistance, MaxDistance;
   Box &domain = World::getInstance().getDomain();
 
@@ -174 +209 @@
                         ASSERT(OtherWalker != NULL,
                             "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
-                        getMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+                        range<double> MinMaxDistanceSquared(0.,0.);
+                        getMinMaxDistanceSquared(Walker, OtherWalker, MinMaxDistanceSquared, IsAngstroem);
                         const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
-                        LOG(2, "INFO: Checking distance " << distance << " against typical bond length of [" << MinDistance * MinDistance << "," << MaxDistance * MaxDistance << "].");
-                        const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
-                        LOG(3, "INFO: MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << ".");
+                        LOG(2, "INFO: Checking squared distance " << distance << " against typical bond length of " << MinMaxDistanceSquared << ".");
+                        const bool status = MinMaxDistanceSquared.isInRange(distance);
                         if (OtherWalker->father > Walker->father ) { // just to not add bonds from both sides
                           if (status) { // create bond if distance is smaller
@@ -188 +223 @@
                           } else {
                             LOG(1, "REJECT: Squared distance "
-                                << distance << " is out of covalent bounds ["
-                                << MinDistance*MinDistance << ","
-                                << MaxDistance * MaxDistance << "].");
+                                << distance << " is out of squared covalent bounds "
+                                << MinMaxDistanceSquared << ".");
                           }
                         } else {