Changeset 13a574 for src/vector.cpp

Timestamp:

Oct 5, 2009, 6:45:06 PM (16 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:

33f9f7

Parents:

aba92d (diff), fa861b (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 'ConvexHull' into ActOnAll

Conflicts:

molecuilder/src/Makefile.am

Boost implementation commit was overlapping with ActOnAllTest

File:

• src/vector.cpp (modified) (5 diffs)

src/vector.cpp

@@ -8 +8 @@
 #include "defs.hpp"
 #include "helpers.hpp"
+#include "memoryallocator.hpp"
 #include "leastsquaremin.hpp"
 #include "vector.hpp"
@@ -473 +474 @@
 };
 
-/** Rotates the vector around the axis given by \a *axis by an angle of \a alpha.
+/** 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
@@ -484 +485 @@
   a.ProjectOntoPlane(axis);
   // construct normal vector
-  y.MakeNormalVector(axis,this);
+  bool rotatable = y.MakeNormalVector(axis,&a);
+  // 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.
+  if (!rotatable) {
+    return;
+  }
   y.Scale(Norm());
   // scale normal vector by sine and this vector by cosine
   y.Scale(sin(alpha));
-  Scale(cos(alpha));
+  a.Scale(cos(alpha));
+  CopyVector(Projection(axis));
   // add scaled normal vector onto this vector
   AddVector(&y);
@@ -674 +681 @@
 double * Vector::InverseMatrix(double *A)
 {
-  double *B = (double *) Malloc(sizeof(double)*NDIM*NDIM, "Vector::InverseMatrix: *B");
+  double *B = Malloc<double>(NDIM * NDIM, "Vector::InverseMatrix: *B");
   double detA = RDET3(A);
   double detAReci;
@@ -1221 +1228 @@
   return true;
 };
+
+/**
+ * Checks whether this vector is within the parallelepiped defined by the given three vectors and
+ * their offset.
+ *
+ * @param offest for the origin of the parallelepiped
+ * @param three vectors forming the matrix that defines the shape of the parallelpiped
+ */
+bool Vector::IsInParallelepiped(Vector offset, double *parallelepiped)
+{
+  Vector a;
+  a.CopyVector(this);
+  a.SubtractVector(&offset);
+  a.InverseMatrixMultiplication(parallelepiped);
+  bool isInside = true;
+
+  for (int i=NDIM;i--;)
+    isInside = isInside && ((a.x[i] <= 1) && (a.x[i] >= 0));
+
+  return isInside;
+}