Changes in / [1bab08:8d6d31]

Files:

• src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (modified) (2 diffs)
• src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.hpp (modified) (1 diff)
• src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) (7 diffs)
• src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (modified) (1 diff)
• src/LinearAlgebra/Line.cpp (modified) (1 diff)
• src/LinearAlgebra/Line.hpp (modified) (2 diffs)
• tests/regression/Molecules/10/post/test-rotated-xYz20.xyz (added)
• tests/regression/Molecules/10/post/test-rotated-z180.xyz (added)
• tests/regression/Molecules/10/post/test-rotated-z360.xyz (added)
• tests/regression/Molecules/10/post/test-rotated-z90.xyz (added)
• tests/regression/Molecules/10/pre/test.xyz (added)
• tests/regression/Molecules/8/post/test-rotated-xYz20.xyz (added)
• tests/regression/Molecules/8/post/test-rotated-z180.xyz (added)
• tests/regression/Molecules/8/post/test-rotated-z360.xyz (added)
• tests/regression/Molecules/8/post/test-rotated-z90.xyz (added)
• tests/regression/Molecules/8/pre/test-rotated-xYz20.xyz (added)
• tests/regression/Molecules/8/pre/test-rotated-z180.xyz (added)
• tests/regression/Molecules/8/pre/test-rotated-z360.xyz (added)
• tests/regression/Molecules/8/pre/test-rotated-z90.xyz (added)
• tests/regression/Molecules/8/pre/test.conf (deleted)
• tests/regression/Molecules/9/post/test-rotated-xYz20.xyz (added)
• tests/regression/Molecules/9/post/test-rotated-z180.xyz (added)
• tests/regression/Molecules/9/post/test-rotated-z360.xyz (added)
• tests/regression/Molecules/9/post/test-rotated-z90.xyz (added)
• tests/regression/Molecules/9/pre/test.xyz (added)
• tests/regression/testsuite-molecules.at (modified) (1 diff)

src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp

@@ -52 +52 @@
 {}
 
-void MoleculeRotateAroundOriginByAngle(double angle) {
+void MoleculeRotateAroundOriginByAngle(const Vector &Axis, double angle) {
   ValueStorage::getInstance().setCurrentValue(MoleculeRotateAroundOriginByAngleAction::NAME, angle);
+  ValueStorage::getInstance().setCurrentValue("position", Axis);
   ActionRegistry::getInstance().getActionByName(MoleculeRotateAroundOriginByAngleAction::NAME)->call(Action::NonInteractive);
 };
@@ -82 +83 @@
   alpha *= M_PI/180.;
 
+  // Creation Line that is the rotation axis
+  Line RotationAxis(Vector(0.,0.,0.), Axis);
+
   DoLog(0) && (Log() << Verbose(0) << "Rotate around origin by " << alpha << " radian, axis from origin to " << Axis << "." << endl);
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
 
-    // Creation Line that is the rotation axis
-    Line RotationAxis(Vector(0.,0.,0.), Axis);
-
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
       *((*iter)->node) = RotationAxis.rotateVector(*((*iter)->node), alpha);
     }
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
   }
+  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
   return Action::state_ptr(new MoleculeRotateAroundOriginByAngleState(World::getInstance().getSelectedMolecules(), Axis, alpha));
 }

src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.hpp

@@ -17 +17 @@
 
 class MoleculeRotateAroundOriginByAngleAction : public Action {
-  friend void MoleculeRotateAroundOriginByAngle(double angle);
+  friend void MoleculeRotateAroundOriginByAngle(const Vector &Axis, double angle);
 
 public:

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp

@@ -34 +34 @@
 class MoleculeRotateAroundSelfByAngleState : public ActionState {
 public:
-    MoleculeRotateAroundSelfByAngleState(molecule * const _mol, const double _alpha) :
+    MoleculeRotateAroundSelfByAngleState(molecule * const _mol, const Vector &_Axis, const double _alpha) :
       mol(_mol),
+      Axis(_Axis),
       alpha(_alpha)
     {}
     molecule* const mol;
+    Vector Axis;
     double alpha;
 };
@@ -51 +53 @@
 {}
 
-void MoleculeRotateAroundSelfByAngle(double angle) {
+void MoleculeRotateAroundSelfByAngle(const Vector &Axis, const double angle) {
   ValueStorage::getInstance().setCurrentValue(MoleculeRotateAroundSelfByAngleAction::NAME, angle);
+  ValueStorage::getInstance().setCurrentValue("position", Axis);
   ActionRegistry::getInstance().getActionByName(MoleculeRotateAroundSelfByAngleAction::NAME)->call(Action::NonInteractive);
 };
@@ -60 +63 @@
 
   dialog->queryDouble(NAME, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryVector("position", false, MapOfActions::getInstance().getDescription(NAME));
 
   return dialog;
@@ -67 +71 @@
   molecule *mol = NULL;
   double alpha = 0.;
+  Vector Axis;
 
-  // obtain angle around which rotate
+  // obtain angle and axis around which rotate
   ValueStorage::getInstance().queryCurrentValue(NAME, alpha);
+  ValueStorage::getInstance().queryCurrentValue("position", Axis);
 
   // check whether a single atom and molecule is selected
-  if ((World::getInstance().getSelectedAtoms().size() != 1) || (World::getInstance().getSelectedMolecules().size() != 1))
+  if (World::getInstance().getSelectedMolecules().size() != 1)
+    return Action::failure;
+  mol = World::getInstance().beginMoleculeSelection()->second;
+
+  // check whether Axis is valid
+  if (Axis.IsZero())
     return Action::failure;
 
-  DoLog(0) && (Log() << Verbose(0) << "Rotate around self by " << alpha << "." << endl);
-  mol = World::getInstance().beginMoleculeSelection()->second;
+  // convert from degrees to radian
+  alpha *= M_PI/180.;
 
   // Creation Line that is the rotation axis
   Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
-  Line RotationAxis(*CenterOfGravity, (World::getInstance().beginAtomSelection()->second)->x);
+  Line RotationAxis(*CenterOfGravity, Axis);
   delete(CenterOfGravity);
+  DoLog(0) && (Log() << Verbose(0) << "Rotate around self by " << alpha << " along " << RotationAxis << "." << endl);
 
   for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
@@ -88 +100 @@
   DoLog(0) && (Log() << Verbose(0) << "done." << endl);
 
-  return Action::state_ptr(new MoleculeRotateAroundSelfByAngleState(mol, alpha));
+  return Action::state_ptr(new MoleculeRotateAroundSelfByAngleState(mol, Axis, alpha));
 }
 
@@ -95 +107 @@
 
   Vector *CenterOfGravity = state->mol->DetermineCenterOfGravity();
-  Line RotationAxis(*CenterOfGravity, (World::getInstance().beginAtomSelection()->second)->x);
+  Line RotationAxis(*CenterOfGravity, state->Axis);
   delete(CenterOfGravity);
 
@@ -109 +121 @@
 
   Vector *CenterOfGravity = state->mol->DetermineCenterOfGravity();
-  Line RotationAxis(*CenterOfGravity, (World::getInstance().beginAtomSelection()->second)->x);
+  Line RotationAxis(*CenterOfGravity, state->Axis);
   delete(CenterOfGravity);
 

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp

@@ -17 +17 @@
 
 class MoleculeRotateAroundSelfByAngleAction : public Action {
-  friend void MoleculeRotateAroundSelfByAngle(double angle);
+  friend void MoleculeRotateAroundSelfByAngle(const Vector &Axis, const double angle);
 
 public:

src/LinearAlgebra/Line.cpp

@@ -241 +241 @@
   return Line(x1,x1-x2);
 }
+
+ostream& operator<<(ostream& ost, const Line& m)
+{
+  const Vector origin = m.getOrigin();
+  const Vector direction = m.getDirection();
+  ost << "(";
+  for (int i=0;i<NDIM;i++) {
+    ost << origin[i];
+    if (i != 2)
+      ost << ",";
+  }
+  ost << ") -> (";
+  for (int i=0;i<NDIM;i++) {
+    ost << direction[i];
+    if (i != 2)
+      ost << ",";
+  }
+  ost << ")";
+  return ost;
+};
+

src/LinearAlgebra/Line.hpp

@@ -11 +11 @@
 #include "LinearAlgebra/Space.hpp"
 
+#include <iosfwd>
 #include <memory>
 #include <vector>
@@ -45 +46 @@
 };
 
+std::ostream & operator << (std::ostream& ost, const Line &m);
+
 /**
  * Named constructor to make a line through two points

tests/regression/testsuite-molecules.at

@@ -61 +61 @@
 
 # 8. Rotate to PAS
-AT_SETUP([Molecules - BROKEN: Rotate to PAS])
+AT_SETUP([Molecules - Rotate to PAS])
 AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
-#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/pre/test-*.xyz .], 0)
+AT_CHECK([../../molecuilder -i test-rotated-z90.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([file="test-rotated-z90.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test-rotated-z180.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([file="test-rotated-z180.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test-rotated-z360.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([file="test-rotated-z360.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test-rotated-xYz20.xyz -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -m "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([file="test-rotated-xYz20.xyz"; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
 
+# 9. Rotate around origin
+AT_SETUP([Molecules - Rotate around origin])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-origin 90. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-origin 180. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-origin 360. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-origin 20. --position "1,2,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/9/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+AT_CLEANUP
+
+# 9. Rotate around self
+AT_SETUP([Molecules - Rotate around self])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 90. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z90.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 180. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z180.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 360. --position "0,0,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-z360.xyz], 0, [ignore], [ignore])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz], 0, [ignore], [ignore])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/pre/test.xyz .], 0)
+AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-molecules --rotate-self 20. --position "1,2,1"], 0, [stdout], [stderr])
+AT_CHECK([diff test.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/10/post/test-rotated-xYz20.xyz], 0, [ignore], [ignore])
+AT_CLEANUP
+