Changeset 0c42f2 for src/Fragmentation/Exporters/SphericalPointDistribution.cpp

Timestamp:

Sep 12, 2016, 2:03:11 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

6cb1cd

Parents:

64cafb2

git-author:

Frederik Heber <heber@…> (05/10/16 20:04:47)

git-committer:

Frederik Heber <heber@…> (09/12/16 14:03:11)

Message:

Extended SaturateAction to be able to deal with bonded atoms.

• TESTFIX: Removed XFAIL from SaturateAction regression tests again.

File:

• src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) (13 diffs)

src/Fragmentation/Exporters/SphericalPointDistribution.cpp

@@ -39 +39 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/IteratorAdaptors.hpp"
+#include "CodePatterns/Log.hpp"
 #include "CodePatterns/toString.hpp"
 
@@ -57 +58 @@
 typedef std::vector<double> DistanceArray_t;
 
+// static instances
+const double SphericalPointDistribution::SQRT_3(sqrt(3.0));
+
 DistanceArray_t calculatePairwiseDistances(
-    const std::vector<Vector> &_points,
+    const std::vector<Vector> &_returnpolygon,
     const IndexList_t &_indices
     )
@@ -69 +73 @@
       if (firstiter == seconditer)
         continue;
-      const double distance = (_points[*firstiter] - _points[*seconditer]).NormSquared();
+      const double distance = (_returnpolygon[*firstiter] - _returnpolygon[*seconditer]).NormSquared();
       result.push_back(distance);
     }
@@ -89 +93 @@
  * \a _new.
  *
- * \param _old first set of points (fewer or equal to \a _new)
- * \param _new second set of points
+ * \param _old first set of returnpolygon (fewer or equal to \a _new)
+ * \param _new second set of returnpolygon
  * \param _Matching matching between the two sets
  * \return pair with L1 and squared L2 error
@@ -129 +133 @@
 
 SphericalPointDistribution::Polygon_t removeMatchingPoints(
-    const SphericalPointDistribution::Polygon_t &_points,
+    const SphericalPointDistribution::Polygon_t &_returnpolygon,
     const IndexList_t &_matchingindices
     )
 {
-  SphericalPointDistribution::Polygon_t remainingpoints;
+  SphericalPointDistribution::Polygon_t remainingreturnpolygon;
   IndexArray_t indices(_matchingindices.begin(), _matchingindices.end());
   std::sort(indices.begin(), indices.end());
   IndexArray_t::const_iterator valueiter = indices.begin();
   SphericalPointDistribution::Polygon_t::const_iterator pointiter =
-      _points.begin();
-  for (unsigned int i=0; i< _points.size(); ++i, ++pointiter) {
+      _returnpolygon.begin();
+  for (unsigned int i=0; i< _returnpolygon.size(); ++i, ++pointiter) {
     // skip all those in values
     if (*valueiter == i)
       ++valueiter;
     else
-      remainingpoints.push_back(*pointiter);
-  }
-
-  return remainingpoints;
+      remainingreturnpolygon.push_back(*pointiter);
+  }
+
+  return remainingreturnpolygon;
 }
 
 /** Rotates a given polygon around x, y, and z axis by the given angles.
  *
- * Essentially, we concentrate on the three points of the polygon to rotate
+ * Essentially, we concentrate on the three returnpolygon of the polygon to rotate
  * to the correct position. First, we rotate its center via \a angles,
  * then we rotate the "triangle" around itself/\a _RotationAxis by
  * \a _RotationAngle.
  *
- * \param _polygon polygon whose points to rotate
+ * \param _polygon polygon whose returnpolygon to rotate
  * \param _angles vector with rotation angles for x,y,z axis
  * \param _RotationAxis
@@ -188 +192 @@
   double bestL2;
   IndexList_t bestmatching;
-  VectorArray_t oldpoints;
-  VectorArray_t newpoints;
+  VectorArray_t oldreturnpolygon;
+  VectorArray_t newreturnpolygon;
 };
 
@@ -229 +233 @@
       // calculate errors
       std::pair<double, double> errors = calculateErrorOfMatching(
-          _MCS.oldpoints, _MCS.newpoints, _matching);
+          _MCS.oldreturnpolygon, _MCS.newreturnpolygon, _matching);
       if (errors.first < L1THRESHOLD) {
         _MCS.bestmatching = _matching;
@@ -248 +252 @@
     )
 {
-  SphericalPointDistribution::Polygon_t remainingpoints;
+  SphericalPointDistribution::Polygon_t remainingreturnpolygon;
   VectorArray_t remainingold(_polygon.begin(), _polygon.end());
   VectorArray_t remainingnew(_newpolygon.begin(), _newpolygon.end());
@@ -256 +260 @@
     MCS.foundflag = false;
     MCS.bestL2 = std::numeric_limits<double>::max();
-    MCS.oldpoints.insert(MCS.oldpoints.begin(), _polygon.begin(),_polygon.end() );
-    MCS.newpoints.insert(MCS.newpoints.begin(), _newpolygon.begin(),_newpolygon.end() );
+    MCS.oldreturnpolygon.insert(MCS.oldreturnpolygon.begin(), _polygon.begin(),_polygon.end() );
+    MCS.newreturnpolygon.insert(MCS.newreturnpolygon.begin(), _newpolygon.begin(),_newpolygon.end() );
 
     // search for bestmatching combinatorially
@@ -269 +273 @@
       const unsigned int matchingsize = _polygon.size();
       ASSERT( matchingsize <= indices.size(),
-          "SphericalPointDistribution::matchSphericalPointDistributions() - not enough new points to choose for matching to old ones.");
+          "SphericalPointDistribution::matchSphericalPointDistributions() - not enough new returnpolygon to choose for matching to old ones.");
       recurseMatchings(MCS, matching, indices, matchingsize);
     }
@@ -278 +282 @@
     Vector newCenter;
     {
-      // calculate center of triangle/line/point consisting of first points of matching
+      // calculate center of triangle/line/point consisting of first returnpolygon of matching
       Vector oldCenter;
       IndexList_t::const_iterator iter = MCS.bestmatching.begin();
@@ -313 +317 @@
         rotatePolygon(_newpolygon, angles, RotationAxis, RotationAngle);
 
-    // remove all points in matching and return remaining ones
+    // remove all returnpolygon in matching and return remaining ones
     return removeMatchingPoints(rotated_newpolygon, MCS.bestmatching);
   } else
@@ -319 +323 @@
 }
 
-
-
+SphericalPointDistribution::Polygon_t
+SphericalPointDistribution::getSimplePolygon(const int _NumberOfPoints) const
+{
+  Polygon_t returnpolygon;
+
+        switch (_NumberOfPoints)
+        {
+          case 0:
+            returnpolygon = get<0>();
+            break;
+          case 1:
+            returnpolygon = get<1>();
+            break;
+          case 2:
+            returnpolygon = get<2>();
+            break;
+          case 3:
+            returnpolygon = get<3>();
+            break;
+          case 4:
+            returnpolygon = get<4>();
+            break;
+          case 5:
+            returnpolygon = get<5>();
+            break;
+          case 6:
+            returnpolygon = get<6>();
+            break;
+          case 7:
+            returnpolygon = get<7>();
+            break;
+          case 8:
+            returnpolygon = get<8>();
+            break;
+          case 9:
+            returnpolygon = get<9>();
+            break;
+          case 10:
+            returnpolygon = get<10>();
+            break;
+          case 11:
+            returnpolygon = get<11>();
+            break;
+          case 12:
+            returnpolygon = get<12>();
+            break;
+          case 14:
+            returnpolygon = get<14>();
+            break;
+          default:
+            ASSERT(0, "SphericalPointDistribution::initSelf() - cannot deal with the case "
+                +toString(_NumberOfPoints)+".");
+        }
+
+        return returnpolygon;
+}
+