Changeset 34c338

Timestamp:

Aug 9, 2010, 2:13:27 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:

22c44bf

Parents:

75a80f

Message:

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

• removed periodic from TranslateAction, this will be replaced by another action (enforce-boundary-conditions or something like that)

Files:

• src/Actions/AtomAction/TranslateAction.cpp (added)
• src/Actions/AtomAction/TranslateAction.hpp (moved) (moved from src/Actions/MoleculeAction/TranslateAction.hpp ) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• src/Actions/MapOfActions.cpp (modified) (10 diffs)
• src/Actions/MoleculeAction/TranslateAction.cpp (deleted)
• tests/regression/testsuite-molecules.at (modified) (1 diff)

src/Actions/AtomAction/TranslateAction.hpp

@@ -14 +14 @@
 class MoleculeListClass;
 
-void MoleculeTranslate(Vector &x, bool periodic);
+void AtomTranslate(Vector &x, bool periodic);
 
-class MoleculeTranslateAction : public Action {
-  friend void MoleculeTranslate(Vector &x, bool periodic);
+class AtomTranslateAction : public Action {
+  friend void AtomTranslate(Vector &x);
 
 public:
-  MoleculeTranslateAction();
-  virtual ~MoleculeTranslateAction();
+  AtomTranslateAction();
+  virtual ~AtomTranslateAction();
 
   bool canUndo();

src/Actions/Makefile.am

@@ -50 +50 @@
   AtomAction/AddAction.cpp \
   AtomAction/ChangeElementAction.cpp \
-  AtomAction/RemoveAction.cpp
+  AtomAction/RemoveAction.cpp \
+  AtomAction/TranslateAction.cpp
 ATOMACTIONHEADER = \
   AtomAction/AddAction.hpp \
   AtomAction/ChangeElementAction.hpp \
-  AtomAction/RemoveAction.cpp
+  AtomAction/RemoveAction.cpp \
+  AtomAction/TranslateAction.hpp
 
 CMDACTIONSOURCE = \
@@ -92 +94 @@
   MoleculeAction/SaveTemperatureAction.cpp \
   MoleculeAction/SuspendInWaterAction.cpp \
-  MoleculeAction/TranslateAction.cpp \
   MoleculeAction/VerletIntegrationAction.cpp
 MOLECULEACTIONHEADER = \
@@ -106 +107 @@
   MoleculeAction/SaveTemperatureAction.hpp \
   MoleculeAction/SuspendInWaterAction.hpp \
-  MoleculeAction/TranslateAction.hpp \
   MoleculeAction/VerletIntegrationAction.hpp
                  

src/Actions/MapOfActions.cpp

@@ -42 +42 @@
 #include "Actions/AtomAction/ChangeElementAction.hpp"
 #include "Actions/AtomAction/RemoveAction.hpp"
+#include "Actions/AtomAction/TranslateAction.hpp"
 #include "Actions/CmdAction/BondLengthTableAction.hpp"
 #include "Actions/CmdAction/ElementDbAction.hpp"
@@ -62 +63 @@
 #include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
 #include "Actions/MoleculeAction/SuspendInWaterAction.hpp"
-#include "Actions/MoleculeAction/TranslateAction.hpp"
 #include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
 #include "Actions/ParserAction/LoadXyzAction.hpp"
@@ -232 +232 @@
   DescriptionMap["surface-correlation"] = "pair correlation analysis between element and surface";
   DescriptionMap["suspend-in-water"] = "suspend the given molecule in water such that in the domain the mean density is as specified";
-  DescriptionMap["translate-mol"] = "translate molecule by given vector";
+  DescriptionMap["translate-atoms"] = "translate all selected atoms by given vector";
   DescriptionMap["unselect-all-atoms"] = "unselect all atoms";
   DescriptionMap["unselect-all-molecules"] = "unselect all molecules";
@@ -302 +302 @@
   ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
-  ShortFormMap["translate-mol"] = "t";
+  ShortFormMap["translate-atoms"] = "t";
   ShortFormMap["verbose"] = "v";
   ShortFormMap["verlet-integrate"] = "P";
@@ -355 +355 @@
   TypeMap["surface-correlation"] = &typeid(void);
   TypeMap["suspend-in-water"] = &typeid(double);
-  TypeMap["translate-mol"] = &typeid(VectorValue);
+  TypeMap["translate-atoms"] = &typeid(VectorValue);
   TypeMap["unselect-all-atoms"] = &typeid(void);
   TypeMap["unselect-all-molecules"] = &typeid(void);
@@ -432 +432 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("atom", "change-element") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("atom", "remove-atom") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("atom", "translate-atoms") );
 
   MenuContainsActionMap.insert( pair<std::string, std::string> ("command", "bond-table") );
@@ -454 +455 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("molecule", "save-temperature") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("molecule", "suspend-in-water") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("molecule", "translate-mol") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("molecule", "verlet-integrate") );
 
@@ -543 +543 @@
   generic.insert("surface-correlation");
   generic.insert("suspend-in-water");
-  generic.insert("translate-mol");
+  generic.insert("translate-atoms");
   generic.insert("unselect-all-atoms");
   generic.insert("unselect-all-molecules");
@@ -835 +835 @@
   new AtomChangeElementAction();
   new AtomRemoveAction();
+  new AtomTranslateAction();
 
   new CommandLineBondLengthTableAction();
@@ -858 +859 @@
   new MoleculeSaveTemperatureAction();
   new MoleculeSuspendInWaterAction();
-  new MoleculeTranslateAction();
   new MoleculeVerletIntegrationAction();
 

tests/regression/testsuite-molecules.at

@@ -45 +45 @@
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --select-molecules-atoms 0 -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/post/$file], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test2.* .], 0)
-AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ --select-molecules-atoms 0 -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
 AT_CHECK([file=test2.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/post/$file], 0, [ignore], [ignore])
-AT_CLEANUP
-
-# 7. Periodic translation
-AT_SETUP([Molecules - Periodic translation])
-AT_KEYWORDS([Molecules])
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ --select-molecule-by-id 0 -t "12., 12., 12." --periodic 1], 0, [stdout], [stderr])
-AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP