Changeset ee4f2d for LinearAlgebra/src

Timestamp:

Aug 20, 2014, 1:09:40 PM (11 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:

fc3aff

Parents:

2a03b0 (diff), 343c5a (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'EnhancingHydrogenSaturation' into stable

Location:

LinearAlgebra/src/LinearAlgebra

Files:

• Makefile.am (modified) (2 diffs)
• Plane.cpp (modified) (1 diff)
• Vector.cpp (modified) (2 diffs)
• Vector.hpp (modified) (1 diff)
• VectorContent.cpp (modified) (1 diff)

LinearAlgebra/src/LinearAlgebra/Makefile.am

@@ -4 +4 @@
 INCLUDES = -I$(top_srcdir)/src
 
-AM_LDFLAGS = ${CodePatterns_LIBS} -ldl
+AM_LDFLAGS = -ldl
 AM_CPPFLAGS = $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
 
@@ -52 +52 @@
 libLinearAlgebra_la_LIBADD = \
         $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
+        ${CodePatterns_LIBS} \
         $(GSL_LIBS)
 nobase_libLinearAlgebra_la_include_HEADERS = ${LINALGHEADER}

LinearAlgebra/src/LinearAlgebra/Plane.cpp

@@ -57 +57 @@
   Vector x1 = y1 - y2;
   Vector x2 = y3 - y2;
-  if ((x1.Norm() <= LINALG_MYEPSILON())) {
+  if ((x1.NormSquared() <= LINALG_MYEPSILON())) {
     throw LinearDependenceException() << LinearAlgebraVectorPair( make_pair(&y1, &y2) );
   }
-  if ((x2.Norm() <= LINALG_MYEPSILON())) {
+  if ((x2.NormSquared() <= LINALG_MYEPSILON())) {
     throw LinearDependenceException() << LinearAlgebraVectorPair( make_pair(&y2, &y3) );
   }
-  if((fabs(x1.Angle(x2)) <= LINALG_MYEPSILON())) {
+  const Vector lineardependent = x1.Projection(x2) - x1;
+  if((lineardependent.NormSquared() <= LINALG_MYEPSILON())) {
     throw LinearDependenceException() << LinearAlgebraVectorPair( make_pair(&x1, &x2) );
   }

LinearAlgebra/src/LinearAlgebra/Vector.cpp

@@ -290 +290 @@
 
 /** Checks whether vector has all components zero.
+ * @param epsilon numerical tolerance for equality
  * @return true - vector is zero, false - vector is not
  */
-bool Vector::IsZero() const
-{
-  return (fabs(at(0))+fabs(at(1))+fabs(at(2)) < LINALG_MYEPSILON());
+bool Vector::IsZero(const double _epsilon) const
+{
+  return (fabs(at(0))+fabs(at(1))+fabs(at(2)) < _epsilon);
 };
 
 /** Checks whether vector has length of 1.
+ * @param epsilon numerical tolerance for equality
  * @return true - vector is normalized, false - vector is not
  */
-bool Vector::IsOne() const
-{
-  return (fabs(Norm() - 1.) < LINALG_MYEPSILON());
+bool Vector::IsOne(const double _epsilon) const
+{
+  return (fabs(Norm() - 1.) < _epsilon);
 };
 
 /** Checks whether vector is normal to \a *normal.
+ * @param normal other supposedly normal vector
+ * @param epsilon numerical tolerance for equality
  * @return true - vector is normalized, false - vector is not
  */
-bool Vector::IsNormalTo(const Vector &normal) const
-{
-  if (ScalarProduct(normal) < LINALG_MYEPSILON())
+bool Vector::IsNormalTo(const Vector &normal, const double _epsilon) const
+{
+  if (ScalarProduct(normal) < _epsilon)
     return true;
   else
@@ -316 +320 @@
 };
 
+/** Checks whether vector is parallel to \a *parallel.
+ * @param parallel other supposedly parallel vector
+ * @param epsilon numerical tolerance for equality
+ * @return true - vector is parallel/linear dependent, false - vector is not
+ */
+bool Vector::IsParallelTo(const Vector &parallel, const double _epsilon) const
+{
+  if (1.-fabs(ScalarProduct(parallel)/parallel.Norm()/this->Norm()) < _epsilon)
+    return true;
+  else
+    return false;
+};
+
 /** Checks whether vector is normal to \a *normal.
+ * @param a other vector
+ * @param epsilon numerical tolerance for equality
  * @return true - vector is normalized, false - vector is not
  */
-bool Vector::IsEqualTo(const Vector &a) const
+bool Vector::IsEqualTo(const Vector &a, const double _epsilon) const
 {
   bool status = true;
   for (int i=0;i<NDIM;i++) {
-    if (fabs(at(i) - a[i]) > LINALG_MYEPSILON())
+    if (fabs(at(i) - a[i]) > _epsilon)
       status = false;
   }

LinearAlgebra/src/LinearAlgebra/Vector.hpp

@@ -46 +46 @@
   double ScalarProduct(const Vector &y) const;
   double Angle(const Vector &y) const;
-  bool IsZero() const;
-  bool IsOne() const;
-  bool IsNormalTo(const Vector &normal) const;
-  bool IsEqualTo(const Vector &a) const;
+  bool IsZero(const double epsilon = LINALG_MYEPSILON()) const;
+  bool IsOne(const double epsilon = LINALG_MYEPSILON()) const;
+  bool IsNormalTo(const Vector &normal, const double epsilon = LINALG_MYEPSILON()) const;
+  bool IsParallelTo(const Vector &normal, const double epsilon = LINALG_MYEPSILON()) const;
+  bool IsEqualTo(const Vector &a, const double epsilon = LINALG_MYEPSILON()) const;
 
   void AddVector(const Vector &y);

LinearAlgebra/src/LinearAlgebra/VectorContent.cpp

@@ -504 +504 @@
 {
   double factor = Norm();
-  (*this) *= 1/factor;
+  if (fabs(factor) > LINALG_MYEPSILON())
+    (*this) *= 1./factor;
 };