Changeset f63e41

Timestamp:

Dec 14, 2012, 2:30:23 PM (13 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

8b886f

Parents:

cb2465

git-author:

Frederik Heber <heber@…> (11/14/12 10:37:48)

git-committer:

Frederik Heber <heber@…> (12/14/12 14:30:23)

Message:

Added Actions to add and remove a bond in between two atoms.

• added new menu "bond".
• added new CommandLineParser options "bond".
• added new regression test folder "bond".
• also added regression tests with undo/redo for the new actions.

Files:

• src/Actions/BondAction/BondAddAction.cpp (added)
• src/Actions/BondAction/BondAddAction.def (added)
• src/Actions/BondAction/BondAddAction.hpp (added)
• src/Actions/BondAction/BondRemoveAction.cpp (added)
• src/Actions/BondAction/BondRemoveAction.def (added)
• src/Actions/BondAction/BondRemoveAction.hpp (added)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (4 diffs)
• src/Atom/atom_bondedparticle.cpp (modified) (2 diffs)
• src/Atom/atom_bondedparticle.hpp (modified) (1 diff)
• src/Atom/atom_bondedparticleinfo.hpp (modified) (1 diff)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) (1 diff)
• src/UIElements/Menu/MenuDescription.cpp (modified) (4 diffs)
• tests/regression/Bond/Add/post/test.pdb (added)
• tests/regression/Bond/Add/pre/test.pdb (added)
• tests/regression/Bond/Add/testsuite-bond-add.at (added)
• tests/regression/Bond/Remove/post/test.pdb (added)
• tests/regression/Bond/Remove/pre/test.pdb (added)
• tests/regression/Bond/Remove/testsuite-bond-remove.at (added)
• tests/regression/Bond/testsuite-bond.at (added)
• tests/regression/Makefile.am (modified) (2 diffs)
• tests/regression/testsuite.at (modified) (1 diff)

src/Actions/GlobalListOfActions.hpp

@@ -72 +72 @@
   (AtomTranslate) \
   (AtomAdd) \
+  (BondAdd) \
+  (BondRemove) \
   (WorldCenterInBox) \
   (WorldRepeatBox) \

src/Actions/Makefile.am

@@ -51 +51 @@
   ${ANALYSISACTIONSOURCE} \
   ${ATOMACTIONSOURCE} \
+  ${BONDACTIONSOURCE} \
   ${CMDACTIONSOURCE} \
   ${FILLACTIONSOURCE} \
@@ -69 +70 @@
   ${ANALYSISACTIONHEADER} \
   ${ATOMACTIONHEADER} \
+  ${BONDACTIONHEADER} \
   ${CMDACTIONHEADER} \
   ${FILLACTIONHEADER} \
@@ -87 +89 @@
   ${ANALYSISACTIONDEFS} \
   ${ATOMACTIONDEFS} \
+  ${BONDACTIONDEFS} \
   ${CMDACTIONDEFS} \
   ${FILLACTIONDEFS} \
@@ -157 +160 @@
   Actions/AtomAction/SaveSelectedAtomsAction.def \
   Actions/AtomAction/TranslateAction.def
+
+BONDACTIONSOURCE = \
+  Actions/BondAction/BondAddAction.cpp \
+  Actions/BondAction/BondRemoveAction.cpp
+BONDACTIONHEADER = \
+  Actions/BondAction/BondAddAction.hpp \
+  Actions/BondAction/BondRemoveAction.hpp
+BONDACTIONDEFS = \
+  Actions/BondAction/BondAddAction.def \
+  Actions/BondAction/BondRemoveAction.def
 
 CMDACTIONSOURCE = \

src/Atom/atom_bondedparticle.cpp

@@ -34 +34 @@
 
 #include "CodePatterns/MemDebug.hpp"
+
+#include <algorithm>
+#include <boost/bind.hpp>
 
 #include "atom.hpp"
@@ -116 +119 @@
 
   return newBond;
+}
+
+/** Removes a bond of this atom to a given \a Partner.
+ *
+ * @param _step time step
+ * @param Partner bond partner
+ */
+void BondedParticle::removeBond(const unsigned int _step, BondedParticle * const Partner)
+{
+  const BondList& ListOfBonds = getListOfBondsAtStep(_step);
+  BondList::const_iterator iter = std::find_if(ListOfBonds.begin(), ListOfBonds.end(),
+      boost::bind(
+          static_cast<bool (bond::*)(const ParticleInfo * const) const>(&bond::Contains),
+          _1,
+          boost::cref(Partner)));
+  if (iter != ListOfBonds.end()) {
+    delete *iter; //dstor takes care of unregistering and all
+  } else
+    ELOG(1, "BondedParticle::removeBond() - I cannot find the bond in between "
+        +toString(getName())+" and "+toString(Partner->getName())+".");
 }
 

src/Atom/atom_bondedparticle.hpp

@@ -38 +38 @@
 
   bond * const addBond(const unsigned int _step, BondedParticle* Partner);
+  void removeBond(const unsigned int _step, BondedParticle* Partner);
   void removeBond(bond *binder);
   void removeAllBonds();

src/Atom/atom_bondedparticleinfo.hpp

@@ -28 +28 @@
 class BondedParticle;
 
-#define BondList list<bond *>
+#define BondList std::list<bond *>
 
 /********************************************** declarations *******************************/

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -65 +65 @@
   analysis("Analysis options"),
   atom("Atom options"),
+  bond("Bond options"),
   command("Command options"),
   fill("fill options"),
@@ -80 +81 @@
   CmdParserLookup["analysis"] = &analysis;
   CmdParserLookup["atom"] = &atom;
+  CmdParserLookup["bond"] = &bond;
   CmdParserLookup["command"] = &command;
   CmdParserLookup["edit"] = &edit;

src/UIElements/CommandLineUI/CommandLineParser.hpp

@@ -56 +56 @@
   po::options_description analysis;
   po::options_description atom;
+  po::options_description bond;
   po::options_description command;
   po::options_description edit;

src/UIElements/Menu/MenuDescription.cpp

@@ -62 +62 @@
   MenuPositionMap->insert(std::make_pair("analysis",TopPosition("tools",1)));
   MenuPositionMap->insert(std::make_pair("atom",TopPosition("edit",1)));
+  MenuPositionMap->insert(std::make_pair("bond",TopPosition("edit",2)));
   MenuPositionMap->insert(std::make_pair("command",TopPosition("",3)));
   MenuPositionMap->insert(std::make_pair("edit",TopPosition("",2)));
@@ -67 +68 @@
   MenuPositionMap->insert(std::make_pair("fragmentation",TopPosition("tools",3)));
   MenuPositionMap->insert(std::make_pair("graph",TopPosition("tools",4)));
-  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",2)));
-  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",3)));
-  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",4)));
+  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",3)));
+  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",4)));
+  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",5)));
   MenuPositionMap->insert(std::make_pair("tesselation",TopPosition("tools",2)));
   MenuPositionMap->insert(std::make_pair("shape",TopPosition("tools",6)));
@@ -78 +79 @@
   MenuDescriptionsMap->insert(std::make_pair("analysis","Analysis (pair correlation, volume)"));
   MenuDescriptionsMap->insert(std::make_pair("atom","Edit atoms"));
+  MenuDescriptionsMap->insert(std::make_pair("bond","Edit bonds"));
   MenuDescriptionsMap->insert(std::make_pair("command","Configuration"));
   MenuDescriptionsMap->insert(std::make_pair("edit","Edit"));
@@ -94 +96 @@
   MenuNameMap->insert(std::make_pair("analysis","Analysis"));
   MenuNameMap->insert(std::make_pair("atom","Atoms"));
+  MenuNameMap->insert(std::make_pair("bond","Bonds"));
   MenuNameMap->insert(std::make_pair("command","Configuration"));
   MenuNameMap->insert(std::make_pair("edit","Edit"));

tests/regression/Makefile.am

@@ -9 +9 @@
         Analysis \
         Atoms \
+        Bond \
         Domain \
         Filling \
@@ -35 +36 @@
         $(srcdir)/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at \
         $(srcdir)/Atoms/Translation/testsuite-atoms-translation.at \
+        $(srcdir)/Bond/testsuite-bond.at \
+        $(srcdir)/Bond/Add/testsuite-bond-add.at \
+        $(srcdir)/Bond/Remove/testsuite-bond-remove.at \
         $(srcdir)/Analysis/testsuite-analysis.at \
         $(srcdir)/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at \

tests/regression/testsuite.at

@@ -39 +39 @@
 m4_include(Atoms/testsuite-atoms.at)
 
+m4_include(Bond/testsuite-bond.at)
+
 m4_include(Selection/testsuite-selection.at)