Changeset 22c44bf

Timestamp:

Aug 9, 2010, 3:03:05 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:

c7f5c2

Parents:

34c338

Message:

Changed RotateAroundOriginByAngleAction from acting on molecules to acting on selected atoms.

Files:

• src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (added)
• src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (moved) (moved from src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.hpp ) (1 diff)
• src/Actions/AtomAction/TranslateAction.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (4 diffs)
• src/Actions/MapOfActions.cpp (modified) (5 diffs)
• src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (deleted)
• tests/regression/testsuite-molecules.at (modified) (1 diff)

src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-class MoleculeListClass;
 class Vector;
 
-void MoleculeRotateOrigin(Vector &Axis);
+void AtomRotateOrigin(Vector &Axis);
 
-class MoleculeRotateAroundOriginByAngleAction : public Action {
-  friend void MoleculeRotateAroundOriginByAngle(const Vector &Axis, double angle);
+class AtomRotateAroundOriginByAngleAction : public Action {
+  friend void AtomRotateAroundOriginByAngle(const Vector &Axis, double angle);
 
 public:
-  MoleculeRotateAroundOriginByAngleAction();
-  virtual ~MoleculeRotateAroundOriginByAngleAction();
+  AtomRotateAroundOriginByAngleAction();
+  virtual ~AtomRotateAroundOriginByAngleAction();
 
   bool canUndo();

src/Actions/AtomAction/TranslateAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 #include "LinearAlgebra/Vector.hpp"
-
-class MoleculeListClass;
 
 void AtomTranslate(Vector &x, bool periodic);

src/Actions/Makefile.am

@@ -51 +51 @@
   AtomAction/ChangeElementAction.cpp \
   AtomAction/RemoveAction.cpp \
+  AtomAction/RotateAroundOriginByAngleAction.cpp \
   AtomAction/TranslateAction.cpp
 ATOMACTIONHEADER = \
@@ -56 +57 @@
   AtomAction/ChangeElementAction.hpp \
   AtomAction/RemoveAction.cpp \
+  AtomAction/RotateAroundOriginByAngleAction.hpp \
   AtomAction/TranslateAction.hpp
 
@@ -87 +89 @@
   MoleculeAction/FillWithMoleculeAction.cpp \
   MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
-  MoleculeAction/RotateAroundOriginByAngleAction.cpp \
   MoleculeAction/RotateAroundSelfByAngleAction.cpp \
   MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
@@ -100 +101 @@
   MoleculeAction/FillWithMoleculeAction.hpp \
   MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
-  MoleculeAction/RotateAroundOriginByAngleAction.hpp \
   MoleculeAction/RotateAroundSelfByAngleAction.hpp \
   MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \

src/Actions/MapOfActions.cpp

@@ -42 +42 @@
 #include "Actions/AtomAction/ChangeElementAction.hpp"
 #include "Actions/AtomAction/RemoveAction.hpp"
+#include "Actions/AtomAction/RotateAroundOriginByAngleAction.hpp"
 #include "Actions/AtomAction/TranslateAction.hpp"
 #include "Actions/CmdAction/BondLengthTableAction.hpp"
@@ -56 +57 @@
 #include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"
 #include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
-#include "Actions/MoleculeAction/RotateAroundOriginByAngleAction.hpp"
 #include "Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp"
 #include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
@@ -213 +213 @@
   DescriptionMap["remove-sphere"] = "remove sphere of atoms of around a specified atom";
   DescriptionMap["repeat-box"] = "create periodic copies of the simulation box per axis";
-  DescriptionMap["rotate-origin"] = "rotates molecules by a specific angle around origin";
+  DescriptionMap["rotate-origin"] = "rotate selected atoms by a specific angle around origin";
   DescriptionMap["rotate-self"] = "rotates molecules by a specific angle around own center of gravity";
   DescriptionMap["rotate-to-pas"] = "calculate the principal axis system of the specified molecule and rotate specified axis to align with main axis";
@@ -835 +835 @@
   new AtomChangeElementAction();
   new AtomRemoveAction();
+  new AtomRotateAroundOriginByAngleAction();
   new AtomTranslateAction();
 
@@ -852 +853 @@
   new MoleculeFillWithMoleculeAction();
   new MoleculeLinearInterpolationofTrajectoriesAction();
-  new MoleculeRotateAroundOriginByAngleAction();
   new MoleculeRotateAroundSelfByAngleAction();
   new MoleculeRotateToPrincipalAxisSystemAction();

tests/regression/testsuite-molecules.at

@@ -70 +70 @@
 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([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --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([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --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([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --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([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-all-atoms --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
+# 10. Rotate around self
 AT_SETUP([Molecules - Rotate around self])
 AT_KEYWORDS([Molecules])