Changeset 31fb1d

Timestamp:

Aug 11, 2010, 2:58:43 PM (15 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:

2b7d1b

Parents:

03c902

Message:

(un)select-atoms-inside-cuboid: cuboid may be rotated.

• Matrix::rotate() sets contents to arbitrary rotation matrix.
• BUGFIX: Matrix::transpose() was working only for symmetric matrices.
• TEST: unit test cases for rotation() and transpose().
• new options "angle-x", "angle-y", "angle-z"
• (un)select-atoms-inside-cuboid: have these as optional arguments.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (3 diffs)
• Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) (5 diffs)
• Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (modified) (1 diff)
• Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) (5 diffs)
• Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (modified) (1 diff)
• LinearAlgebra/Matrix.cpp (modified) (3 diffs)
• LinearAlgebra/Matrix.hpp (modified) (2 diffs)
• unittests/MatrixUnittest.cpp (modified) (3 diffs)
• unittests/MatrixUnittest.hpp (modified) (2 diffs)

src/Actions/MapOfActions.cpp

@@ -256 +256 @@
   DescriptionMap["version"] = "show version";
   // keys for values
+  DescriptionMap["angle-x"] = "angle of a rotation around x axis";
+  DescriptionMap["angle-y"] = "angle of a rotation around y axis";
+  DescriptionMap["angle-z"] = "angle of a rotation around z axis";
   DescriptionMap["bin-output-file"] = "name of the bin output file";
   DescriptionMap["bin-end"] = "start of the last bin";
@@ -383 +386 @@
 
   // value types for the values
+  TypeMap["angle-x"] = &typeid(double);
+  TypeMap["angle-y"] = &typeid(double);
+  TypeMap["angle-z"] = &typeid(double);
   TypeMap["bin-output-file"] = &typeid(std::string);
   TypeMap["bin-end"] = &typeid(double);
@@ -583 +589 @@
 
     // hidden arguments
+  hidden.insert("angle-x");
+  hidden.insert("angle-y");
+  hidden.insert("angle-z");
   hidden.insert("bin-end");
   hidden.insert("bin-output-file");

src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp

@@ -20 +20 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/Matrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "Shapes/BaseShapes.hpp"
@@ -40 +41 @@
 class SelectionAllAtomsInsideCuboidState : public ActionState {
 public:
-  SelectionAllAtomsInsideCuboidState(std::vector<atom*> _selectedAtoms, const Vector &_position, const Vector &_extension) :
+  SelectionAllAtomsInsideCuboidState(std::vector<atom*> _selectedAtoms, const Vector &_position, const Vector &_extension, const double _Xangle, const double _Yangle, const double _Zangle) :
     selectedAtoms(_selectedAtoms),
     position(_position),
-    extension(_extension)
+    extension(_extension),
+    Xangle(_Xangle),
+    Yangle(_Yangle),
+    Zangle(_Zangle)
   {}
   std::vector<atom*> selectedAtoms;
   Vector position;
   Vector extension;
+  double Xangle;
+  double Yangle;
+  double Zangle;
 };
 
@@ -65 +72 @@
 };
 
+void SelectionAllAtomsInsideCuboid(const Vector &position, const Vector &extension, const double Xangle, const double Yangle, const double Zangle) {
+  ValueStorage::getInstance().setCurrentValue(SelectionAllAtomsInsideCuboidAction::NAME, extension);
+  ValueStorage::getInstance().setCurrentValue("position", position);
+  ValueStorage::getInstance().setCurrentValue("angle-x", Xangle);
+  ValueStorage::getInstance().setCurrentValue("angle-y", Yangle);
+  ValueStorage::getInstance().setCurrentValue("angle-z", Zangle);
+  ActionRegistry::getInstance().getActionByName(SelectionAllAtomsInsideCuboidAction::NAME)->call(Action::NonInteractive);
+};
+
 Dialog* SelectionAllAtomsInsideCuboidAction::fillDialog(Dialog *dialog) {
   ASSERT(dialog,"No Dialog given when filling action dialog");
@@ -78 +94 @@
   Vector position;
   Vector extension;
+  double Xangle = 0.;
+  double Yangle = 0.;
+  double Zangle = 0.;
+  Matrix RotationMatrix;
 
   ValueStorage::getInstance().queryCurrentValue("position", position);
   ValueStorage::getInstance().queryCurrentValue(NAME, extension);
+  // check whether a rotation is given.
+  if (ValueStorage::getInstance().queryCurrentValue("angle-x", Xangle, true))
+    Xangle = 0.;
+  if (ValueStorage::getInstance().queryCurrentValue("angle-y", Yangle, true))
+    Yangle = 0.;
+  if (ValueStorage::getInstance().queryCurrentValue("angle-z", Zangle, true))
+    Zangle = 0.;
+  RotationMatrix.rotation(Xangle, Yangle, Zangle);
 
-  DoLog(1) && (Log() << Verbose(1) << "Selecting all atoms inside a cuboid at " << position << " and extension of " << extension << "." << endl);
-  Shape s = translate(stretch(Cuboid(),extension),position);
+  DoLog(1) && (Log() << Verbose(1) << "Selecting all atoms inside a rotated " << RotationMatrix << " cuboid at " << position << " and extension of " << extension << "." << endl);
+  Shape s = translate(transform(stretch(Cuboid(),extension),RotationMatrix),position);
   World::getInstance().selectAllAtoms(AtomByShape(s));
-  return Action::state_ptr(new SelectionAllAtomsInsideCuboidState(selectedAtoms, position, extension));
+  return Action::state_ptr(new SelectionAllAtomsInsideCuboidState(selectedAtoms, position, extension, Xangle, Yangle, Zangle));
 }
 
@@ -95 +123 @@
     World::getInstance().selectAtom(*iter);
 
-  return Action::state_ptr(new SelectionAllAtomsInsideCuboidState(state->selectedAtoms, state->position, state->extension));
+  return Action::state_ptr(_state);
 }
 
 Action::state_ptr SelectionAllAtomsInsideCuboidAction::performRedo(Action::state_ptr _state){
   SelectionAllAtomsInsideCuboidState *state = assert_cast<SelectionAllAtomsInsideCuboidState*>(_state.get());
+  Matrix RotationMatrix;
 
-  Shape s = translate(stretch(Cuboid(),state->extension),state->position);
+  RotationMatrix.rotation(state->Xangle, state->Yangle, state->Zangle);
+  Shape s = translate(transform(stretch(Cuboid(),state->extension),RotationMatrix),state->position);
   World::getInstance().selectAllAtoms(AtomByShape(s));
 
-  return Action::state_ptr(new SelectionAllAtomsInsideCuboidState(state->selectedAtoms, state->position, state->extension));
+  return Action::state_ptr(_state);
 }
 

src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp

@@ -17 +17 @@
 class SelectionAllAtomsInsideCuboidAction : public Action {
   friend void SelectionAllAtomsInsideCuboid(const Vector &position, const Vector &extension);
+  friend void SelectionAllAtomsInsideCuboid(const Vector &position, const Vector &extension, const double Xangle, const double Yangle, const double Zangle);
 
 public:

src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp

@@ -20 +20 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/Matrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "Shapes/BaseShapes.hpp"
@@ -40 +41 @@
 class SelectionNotAllAtomsInsideCuboidState : public ActionState {
 public:
-  SelectionNotAllAtomsInsideCuboidState(std::vector<atom*> _selectedAtoms, const Vector &_position, const Vector &_extension) :
+  SelectionNotAllAtomsInsideCuboidState(std::vector<atom*> _selectedAtoms, const Vector &_position, const Vector &_extension, const double _Xangle, const double _Yangle, const double _Zangle) :
     selectedAtoms(_selectedAtoms),
     position(_position),
-    extension(_extension)
+    extension(_extension),
+    Xangle(_Xangle),
+    Yangle(_Yangle),
+    Zangle(_Zangle)
   {}
   std::vector<atom*> selectedAtoms;
   Vector position;
   Vector extension;
+  double Xangle;
+  double Yangle;
+  double Zangle;
 };
 
@@ -65 +72 @@
 };
 
+void SelectionNotAllAtomsInsideCuboid(const Vector &position, const Vector &extension, const double Xangle, const double Yangle, const double Zangle) {
+  ValueStorage::getInstance().setCurrentValue(SelectionNotAllAtomsInsideCuboidAction::NAME, extension);
+  ValueStorage::getInstance().setCurrentValue("position", position);
+  ValueStorage::getInstance().setCurrentValue("angle-x", Xangle);
+  ValueStorage::getInstance().setCurrentValue("angle-y", Yangle);
+  ValueStorage::getInstance().setCurrentValue("angle-z", Zangle);
+  ActionRegistry::getInstance().getActionByName(SelectionNotAllAtomsInsideCuboidAction::NAME)->call(Action::NonInteractive);
+};
+
 Dialog* SelectionNotAllAtomsInsideCuboidAction::fillDialog(Dialog *dialog) {
   ASSERT(dialog,"No Dialog given when filling action dialog");
@@ -78 +94 @@
   Vector position;
   Vector extension;
+  double Xangle = 0.;
+  double Yangle = 0.;
+  double Zangle = 0.;
+  Matrix RotationMatrix;
 
   ValueStorage::getInstance().queryCurrentValue("position", position);
   ValueStorage::getInstance().queryCurrentValue(NAME, extension);
+  // check whether a rotation is given.
+  if (ValueStorage::getInstance().queryCurrentValue("angle-x", Xangle, true))
+    Xangle = 0.;
+  if (ValueStorage::getInstance().queryCurrentValue("angle-y", Yangle, true))
+    Yangle = 0.;
+  if (ValueStorage::getInstance().queryCurrentValue("angle-z", Zangle, true))
+    Zangle = 0.;
+  RotationMatrix.rotation(Xangle, Yangle, Zangle);
 
-  DoLog(1) && (Log() << Verbose(1) << "Unselecting all atoms inside a cuboid at " << position << " and extension of " << extension << "." << endl);
-  Shape s = translate(stretch(Cuboid(),extension),position);
+  DoLog(1) && (Log() << Verbose(1) << "Unselecting all atoms inside a rotated " << RotationMatrix << " cuboid at " << position << " and extension of " << extension << "." << endl);
+  Shape s = translate(transform(stretch(Cuboid(),extension),RotationMatrix),position);
+
   World::getInstance().unselectAllAtoms(AtomByShape(s));
-  return Action::state_ptr(new SelectionNotAllAtomsInsideCuboidState(selectedAtoms, position, extension));
+  return Action::state_ptr(new SelectionNotAllAtomsInsideCuboidState(selectedAtoms, position, extension, Xangle, Yangle, Zangle));
 }
 
@@ -95 +124 @@
     World::getInstance().selectAtom(*iter);
 
-  return Action::state_ptr(new SelectionNotAllAtomsInsideCuboidState(state->selectedAtoms, state->position, state->extension));
+  return Action::state_ptr(_state);
 }
 
 Action::state_ptr SelectionNotAllAtomsInsideCuboidAction::performRedo(Action::state_ptr _state){
   SelectionNotAllAtomsInsideCuboidState *state = assert_cast<SelectionNotAllAtomsInsideCuboidState*>(_state.get());
+  Matrix RotationMatrix;
 
-  Shape s = translate(stretch(Cuboid(),state->extension),state->position);
+  RotationMatrix.rotation(state->Xangle, state->Yangle, state->Zangle);
+  Shape s = translate(transform(stretch(Cuboid(),state->extension),RotationMatrix),state->position);
   World::getInstance().unselectAllAtoms(AtomByShape(s));
 
-  return Action::state_ptr(new SelectionNotAllAtomsInsideCuboidState(state->selectedAtoms, state->position, state->extension));
+  return Action::state_ptr(_state);
 }
 

src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp

@@ -17 +17 @@
 class SelectionNotAllAtomsInsideCuboidAction : public Action {
   friend void SelectionNotAllAtomsInsideCuboid(const Vector &position, const Vector &extension);
+  friend void SelectionNotAllAtomsInsideCuboid(const Vector &position, const Vector &extension, const double Xangle, const double Yangle, const double Zangle);
 
 public:

src/LinearAlgebra/Matrix.cpp

@@ -115 +115 @@
 }
 
+void Matrix::rotation(const double x, const double y, const double z)
+{
+  set(0,0, cos(y)*cos(z));
+  set(0,1, cos(z)*sin(x)*sin(y) - cos(x)*sin(z));
+  set(0,2, cos(x)*cos(z)*sin(y) + sin(x) * sin(z));
+  set(1,0, cos(y)*sin(z));
+  set(1,1, cos(x)*cos(z) + sin(x)*sin(y)*sin(z));
+  set(1,2, -cos(z)*sin(x) + cos(x)*sin(y)*sin(z));
+  set(2,0, -sin(y));
+  set(2,1, cos(y)*sin(x));
+  set(2,2, cos(x)*cos(y));
+}
+
 Matrix &Matrix::operator=(const Matrix &src){
   if(&src!=this){
@@ -220 +233 @@
 
 
-void Matrix::transpose()
+Matrix &Matrix::transpose()
 {
   double tmp;
@@ -226 +239 @@
     for (int j=i+1;j<NDIM;j++) {
       tmp = at(j,i);
+      at(j,i) = at(i,j);
       at(i,j) = tmp;
-      at(j,i) = tmp;
-    }
+    }
+  return *this;
 }
 

src/LinearAlgebra/Matrix.hpp

@@ -54 +54 @@
    */
   void zero();
+
+  /**
+   * Sets all matrix corresponding to a rotation matrix,
+   * first around the x-, then the y-, finally the z-axis
+   * with given angles.
+   */
+  void rotation(const double x, const double y, const double z);
 
   /**
@@ -113 +120 @@
    */
   Matrix transpose() const;
-  void transpose();
+  Matrix &transpose();
 
   // operators

src/unittests/MatrixUnittest.cpp

@@ -14 +14 @@
 #include <cppunit/extensions/TestFactoryRegistry.h>
 #include <cppunit/ui/text/TestRunner.h>
+
+#include <cmath>
 
 #include "MatrixUnittest.hpp"
@@ -156 +158 @@
     }
   }
+}
+
+void MatrixUnittest::TransposeTest(){
+  Matrix res;
+
+  // transpose of unit is unit
+  res.one();
+  (const Matrix)res.transpose();
+  CPPUNIT_ASSERT_EQUAL(res,*one);
+
+  // transpose of transpose is same matrix
+  res.zero();
+  res.set(2,2, 1.);
+  CPPUNIT_ASSERT_EQUAL(res.transpose().transpose(),res);
 }
 
@@ -230 +246 @@
 }
 
+void MatrixUnittest::RotationTest(){
+  Matrix res;
+  Matrix inverse;
+
+  // zero rotation angles yields unity matrix
+  res.rotation(0,0,0);
+  CPPUNIT_ASSERT_EQUAL(*one, res);
+
+  // arbitrary rotation matrix has det = 1
+  res.rotation(M_PI/3.,1.,M_PI/7.);
+  CPPUNIT_ASSERT(fabs(fabs(res.determinant()) -1.) < MYEPSILON);
+
+  // inverse is rotation matrix with negative angles
+  res.rotation(M_PI/3.,0.,0.);
+  inverse.rotation(-M_PI/3.,0.,0.);
+  CPPUNIT_ASSERT_EQUAL(*one, res * inverse);
+
+  // ... or transposed
+  res.rotation(M_PI/3.,0.,0.);
+  CPPUNIT_ASSERT_EQUAL(inverse, ((const Matrix) res).transpose());
+}
 
 void MatrixUnittest::InvertTest(){

src/unittests/MatrixUnittest.hpp

@@ -19 +19 @@
   CPPUNIT_TEST ( VectorTest );
   CPPUNIT_TEST ( OperationTest );
+  CPPUNIT_TEST ( TransposeTest );
+  CPPUNIT_TEST ( RotationTest );
   CPPUNIT_TEST ( InvertTest );
   CPPUNIT_TEST ( DeterminantTest );
@@ -31 +33 @@
   void VectorTest();
   void OperationTest();
+  void TransposeTest();
+  void RotationTest();
   void InvertTest();
   void DeterminantTest();