Changeset cff66c

Timestamp:

Mar 1, 2011, 1:17:08 PM (14 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:

607eab

Parents:

111f4a

git-author:

Frederik Heber <heber@…> (02/28/11 15:16:58)

git-committer:

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

Message:

Removed bool is Angstroem from all BondGraph::...() member functions.

• we set IsAngstroem in constructor, and that's it.

Location:

src

Files:

• Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) (2 diffs)
• bondgraph.cpp (modified) (6 diffs)
• bondgraph.hpp (modified) (6 diffs)
• molecule.cpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (2 diffs)
• molecule_geometry.cpp (modified) (1 diff)

src/Actions/FragmentationAction/CreateAdjacencyAction.cpp

@@ -56 +56 @@
   DoLog(1) && (Log() << Verbose(1) << "Constructing bond graph for selected atoms ... " << endl);
 
-  config *configuration = World::getInstance().getConfig();
   BondGraph *BG = World::getInstance().getBondGraph();
   ASSERT(BG != NULL, "FragmentationCreateAdjacencyAction: BondGraph is NULL.");
   double BondDistance = BG->getMaxPossibleBondDistance(AtomSetMixin<std::vector<atom *> >(World::getInstance().getSelectedAtoms()));
-  bool IsAngstroem = configuration->GetIsAngstroem();
 
   atom *Walker = NULL;
@@ -136 +134 @@
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           range<double> MinMaxDistanceSquared(0.,0.);
-                          BG->getMinMaxDistanceSquared(Walker, OtherWalker, MinMaxDistanceSquared, IsAngstroem);
+                          BG->getMinMaxDistanceSquared(Walker, OtherWalker, MinMaxDistanceSquared);
                           const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
                           const bool status = MinMaxDistanceSquared.isInRange(distance);

src/bondgraph.cpp

@@ -100 +100 @@
     const element * const Walker,
     const element * const OtherWalker,
-    range<double> &MinMaxDistance,
-    bool IsAngstroem) const
+    range<double> &MinMaxDistance) const
 {
   MinMaxDistance.first = OtherWalker->getCovalentRadius() + Walker->getCovalentRadius();
@@ -112 +111 @@
     const element * const Walker,
     const element * const OtherWalker,
-    range<double> &MinMaxDistance,
-    bool IsAngstroem) const
+    range<double> &MinMaxDistance) const
 {
   ASSERT(BondLengthMatrix, "BondGraph::BondLengthMatrixMinMaxDistance() called without NULL BondLengthMatrix.");
@@ -127 +125 @@
     const element * const Walker,
     const element * const OtherWalker,
-    range<double> &MinMaxDistance,
-    bool IsAngstroem) const
+    range<double> &MinMaxDistance) 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, MinMaxDistance, IsAngstroem);
+    CovalentMinMaxDistance(Walker, OtherWalker, MinMaxDistance);
   } else {
     LOG(2, "INFO: Using Covalent radii criterion for [min,max) distances.");
-    BondLengthMatrixMinMaxDistance(Walker, OtherWalker, MinMaxDistance, IsAngstroem);
+    BondLengthMatrixMinMaxDistance(Walker, OtherWalker, MinMaxDistance);
   }
 }
@@ -142 +139 @@
     const BondedParticle * const Walker,
     const BondedParticle * const OtherWalker,
-    range<double> &MinMaxDistance,
-    bool IsAngstroem) const
-{
-  getMinMaxDistance(Walker->getType(), OtherWalker->getType(),MinMaxDistance, IsAngstroem);
+    range<double> &MinMaxDistance) const
+{
+  getMinMaxDistance(Walker->getType(), OtherWalker->getType(),MinMaxDistance);
 }
 
@@ -151 +147 @@
     const BondedParticle * const Walker,
     const BondedParticle * const OtherWalker,
-    range<double> &MinMaxDistance,
-    bool IsAngstroem) const
+    range<double> &MinMaxDistance) const
 {
   // use non-squared version
-  getMinMaxDistance(Walker, OtherWalker,MinMaxDistance, IsAngstroem);
+  getMinMaxDistance(Walker, OtherWalker,MinMaxDistance);
   // and square
   MinMaxDistance.first *= MinMaxDistance.first;
@@ -195 +190 @@
                             "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
                         range<double> MinMaxDistanceSquared(0.,0.);
-                        getMinMaxDistanceSquared(Walker, OtherWalker, MinMaxDistanceSquared, IsAngstroem);
+                        getMinMaxDistanceSquared(Walker, OtherWalker, MinMaxDistanceSquared);
                         const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
                         LOG(2, "INFO: Checking squared distance " << distance << " against typical bond length of " << MinMaxDistanceSquared << ".");

src/bondgraph.hpp

@@ -93 +93 @@
           ++otheriter) {
         range<double> MinMaxDistance(0.,0.);
-        getMinMaxDistance((*iter),(*otheriter), MinMaxDistance, IsAngstroem);
+        getMinMaxDistance((*iter),(*otheriter), MinMaxDistance);
         if (MinMaxDistance.last > max_distance)
           max_distance = MinMaxDistance.last;
@@ -106 +106 @@
    * \param *OtherWalker second BondedParticle
    * \param &MinMaxDistance Range for interval on return
-   * \param IsAngstroem whether units are in angstroem or bohr radii
    */
   void getMinMaxDistance(
       const BondedParticle * const Walker,
       const BondedParticle * const OtherWalker,
-      range<double> &MinMaxDistance,
-      bool IsAngstroem) const;
+      range<double> &MinMaxDistance) const;
 
   /** Returns SQUARED bond criterion for given pair based on a bond length matrix.
@@ -120 +118 @@
    * \param *OtherWalker second BondedParticle
    * \param &MinMaxDistance Range for interval on return
-   * \param IsAngstroem whether units are in angstroem or bohr radii
    */
   void getMinMaxDistanceSquared(
       const BondedParticle * const Walker,
       const BondedParticle * const OtherWalker,
-      range<double> &MinMaxDistance,
-      bool IsAngstroem) const;
+      range<double> &MinMaxDistance) const;
 
   /** Creates the adjacency list for a given \a Range of iterable atoms.
@@ -324 +320 @@
    * \param *OtherWalker second BondedParticle
    * \param &MinMaxDistance Range for interval on return
-   * \param IsAngstroem whether units are in angstroem or bohr radii
    */
   void getMinMaxDistance(
       const element * const Walker,
       const element * const OtherWalker,
-      range<double> &MinMaxDistance,
-      bool IsAngstroem) const;
+      range<double> &MinMaxDistance) const;
 
   /** Returns bond criterion for given pair of elements based on a bond length matrix.
@@ -338 +332 @@
    * \param *OtherWalker second element
    * @param MinMaxDistance reference to range type set on return
-   * \param IsAngstroem whether units are in angstroem or bohr radii
    */
   void BondLengthMatrixMinMaxDistance(
       const element * const Walker,
       const element * const OtherWalker,
-      range<double> &DistanceInterval,
-      bool IsAngstroem) const;
+      range<double> &MinMaxDistance) const;
 
   /** Returns bond criterion for given pair of elements based on covalent radius.
@@ -350 +342 @@
    * \param *OtherWalker second element
    * @param MinMaxDistance reference to range type set on return
-   * \param IsAngstroem whether units are in angstroem or bohr radii
    */
   void CovalentMinMaxDistance(
       const element * const Walker,
       const element * const OtherWalker,
-      range<double> &DistanceInterval,
-      bool IsAngstroem) const;
+      range<double> &MinMaxDistance) const;
 
 

src/molecule.cpp

@@ -346 +346 @@
   range<double> MinMaxBondDistance(0.,0.);
   const BondGraph * const BG = World::getInstance().getBondGraph();
-  BG->getMinMaxDistance(TopOrigin,TopReplacement,MinMaxBondDistance,IsAngstroem);
+  BG->getMinMaxDistance(TopOrigin,TopReplacement,MinMaxBondDistance);
   if (!MinMaxBondDistance.isInRange(bondlength)) {
 //    Log() << Verbose(4) << "InBondvector is: ";

src/molecule_fragmentation.cpp

@@ -1812 +1812 @@
           //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
           range<double> MinMaxDistance(0.,0.);
-          BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinMaxDistance, true);
+          BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinMaxDistance);
           if (!MinMaxDistance.isInRange(tmp)) {
             DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
@@ -1827 +1827 @@
         tmp = Binder->leftatom->at(i) - Binder->rightatom->at(i);
         range<double> MinMaxDistance(0.,0.);
-        BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinMaxDistance, true);
+        BG->getMinMaxDistance(Binder->leftatom, Binder->rightatom, MinMaxDistance);
         if (fabs(tmp) > MinMaxDistance.last)  // check against Min is not useful for components
           Translationvector[i] = (tmp < 0) ? +1. : -1.;

src/molecule_geometry.cpp

@@ -394 +394 @@
               tmp = (*iter)->at(j) - (*Runner)->GetOtherAtom(*iter)->at(j);
               range<double> MinMaxBondDistance(0.,0.);
-              BG->getMinMaxDistance((*iter), (*Runner)->GetOtherAtom(*iter), MinMaxBondDistance, true);
+              BG->getMinMaxDistance((*iter), (*Runner)->GetOtherAtom(*iter), MinMaxBondDistance);
               if (fabs(tmp) > MinMaxBondDistance.last) {  // check against Min is not useful for components
                 flag = false;