Changeset 76c0d6 for src/vector_ops.cpp

Timestamp:

Jun 4, 2010, 9:28:46 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

2c8934

Parents:

e05826 (diff), 27ac00 (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 'StructureRefactoring' into stable

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/periodentafel.cpp

File:

• src/vector_ops.cpp (modified) (2 diffs)

src/vector_ops.cpp ¶

@@ -15 +15 @@
 #include "Helpers/fast_functions.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
+#include "Exceptions/SkewException.hpp"
 
 #include <gsl/gsl_linalg.h>
@@ -110 +111 @@
   return true;
 };
-
-/** Rotates the vector relative to the origin around the axis given by \a *axis by an angle of \a alpha.
- * \param *axis rotation axis
- * \param alpha rotation angle in radian
- */
-Vector RotateVector(const Vector &vec,const Vector &axis, const double alpha)
-{
-  Vector a,y;
-  Vector res;
-  // normalise this vector with respect to axis
-  a = vec;
-  a.ProjectOntoPlane(axis);
-  // construct normal vector
-  try {
-    y = Plane(axis,a,0).getNormal();
-  }
-  catch (MathException &excp) {
-    // The normal vector cannot be created if there is linar dependency.
-    // Then the vector to rotate is on the axis and any rotation leads to the vector itself.
-    return vec;
-  }
-  y.Scale(vec.Norm());
-  // scale normal vector by sine and this vector by cosine
-  y.Scale(sin(alpha));
-  a.Scale(cos(alpha));
-  res = vec.Projection(axis);
-  // add scaled normal vector onto this vector
-  res += y;
-  // add part in axis direction
-  res += a;
-  return res;
-};
-
-/** Calculates the intersection of the two lines that are both on the same plane.
- * This is taken from Weisstein, Eric W. "Line-Line Intersection." From MathWorld--A Wolfram Web Resource. http://mathworld.wolfram.com/Line-LineIntersection.html
- * \param *out output stream for debugging
- * \param *Line1a first vector of first line
- * \param *Line1b second vector of first line
- * \param *Line2a first vector of second line
- * \param *Line2b second vector of second line
- * \return true - \a this will contain the intersection on return, false - lines are parallel
- */
-Vector GetIntersectionOfTwoLinesOnPlane(const Vector &Line1a, const Vector &Line1b, const Vector &Line2a, const Vector &Line2b)
-{
-  Info FunctionInfo(__func__);
-
-  Vector res;
-
-  auto_ptr<GSLMatrix> M = auto_ptr<GSLMatrix>(new GSLMatrix(4,4));
-
-  M->SetAll(1.);
-  for (int i=0;i<3;i++) {
-    M->Set(0, i, Line1a[i]);
-    M->Set(1, i, Line1b[i]);
-    M->Set(2, i, Line2a[i]);
-    M->Set(3, i, Line2b[i]);
-  }
-
-  //Log() << Verbose(1) << "Coefficent matrix is:" << endl;
-  //for (int i=0;i<4;i++) {
-  //  for (int j=0;j<4;j++)
-  //    cout << "\t" << M->Get(i,j);
-  //  cout << endl;
-  //}
-  if (fabs(M->Determinant()) > MYEPSILON) {
-    Log() << Verbose(1) << "Determinant of coefficient matrix is NOT zero." << endl;
-    throw LinearDependenceException(__FILE__,__LINE__);
-  }
-
-  Log() << Verbose(1) << "INFO: Line1a = " << Line1a << ", Line1b = " << Line1b << ", Line2a = " << Line2a << ", Line2b = " << Line2b << "." << endl;
-
-
-  // constuct a,b,c
-  Vector a = Line1b - Line1a;
-  Vector b = Line2b - Line2a;
-  Vector c = Line2a - Line1a;
-  Vector d = Line2b - Line1b;
-  Log() << Verbose(1) << "INFO: a = " << a << ", b = " << b << ", c = " << c << "." << endl;
-  if ((a.NormSquared() < MYEPSILON) || (b.NormSquared() < MYEPSILON)) {
-   res.Zero();
-   Log() << Verbose(1) << "At least one of the lines is ill-defined, i.e. offset equals second vector." << endl;
-   throw LinearDependenceException(__FILE__,__LINE__);
-  }
-
-  // check for parallelity
-  Vector parallel;
-  double factor = 0.;
-  if (fabs(a.ScalarProduct(b)*a.ScalarProduct(b)/a.NormSquared()/b.NormSquared() - 1.) < MYEPSILON) {
-    parallel = Line1a - Line2a;
-    factor = parallel.ScalarProduct(a)/a.Norm();
-    if ((factor >= -MYEPSILON) && (factor - 1. < MYEPSILON)) {
-      res = Line2a;
-      Log() << Verbose(1) << "Lines conincide." << endl;
-      return res;
-    } else {
-      parallel = Line1a - Line2b;
-      factor = parallel.ScalarProduct(a)/a.Norm();
-      if ((factor >= -MYEPSILON) && (factor - 1. < MYEPSILON)) {
-        res = Line2b;
-        Log() << Verbose(1) << "Lines conincide." << endl;
-        return res;
-      }
-    }
-    Log() << Verbose(1) << "Lines are parallel." << endl;
-    res.Zero();
-    throw LinearDependenceException(__FILE__,__LINE__);
-  }
-
-  // obtain s
-  double s;
-  Vector temp1, temp2;
-  temp1 = c;
-  temp1.VectorProduct(b);
-  temp2 = a;
-  temp2.VectorProduct(b);
-  Log() << Verbose(1) << "INFO: temp1 = " << temp1 << ", temp2 = " << temp2 << "." << endl;
-  if (fabs(temp2.NormSquared()) > MYEPSILON)
-    s = temp1.ScalarProduct(temp2)/temp2.NormSquared();
-  else
-    s = 0.;
-  Log() << Verbose(1) << "Factor s is " << temp1.ScalarProduct(temp2) << "/" << temp2.NormSquared() << " = " << s << "." << endl;
-
-  // construct intersection
-  res = a;
-  res.Scale(s);
-  res += Line1a;
-  Log() << Verbose(1) << "Intersection is at " << res << "." << endl;
-
-  return res;
-};