Changeset f63e41 for src


Ignore:
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.
Location:
src
Files:
6 added
8 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/GlobalListOfActions.hpp

    rcb2465 rf63e41  
    7272  (AtomTranslate) \
    7373  (AtomAdd) \
     74  (BondAdd) \
     75  (BondRemove) \
    7476  (WorldCenterInBox) \
    7577  (WorldRepeatBox) \

  • src/Actions/Makefile.am

    rcb2465 rf63e41  
    5151  ${ANALYSISACTIONSOURCE} \
    5252  ${ATOMACTIONSOURCE} \
     53  ${BONDACTIONSOURCE} \
    5354  ${CMDACTIONSOURCE} \
    5455  ${FILLACTIONSOURCE} \
    … …  
    6970  ${ANALYSISACTIONHEADER} \
    7071  ${ATOMACTIONHEADER} \
     72  ${BONDACTIONHEADER} \
    7173  ${CMDACTIONHEADER} \
    7274  ${FILLACTIONHEADER} \
    … …  
    8789  ${ANALYSISACTIONDEFS} \
    8890  ${ATOMACTIONDEFS} \
     91  ${BONDACTIONDEFS} \
    8992  ${CMDACTIONDEFS} \
    9093  ${FILLACTIONDEFS} \
    … …  
    157160  Actions/AtomAction/SaveSelectedAtomsAction.def \
    158161  Actions/AtomAction/TranslateAction.def
     162
     163BONDACTIONSOURCE = \
     164  Actions/BondAction/BondAddAction.cpp \
     165  Actions/BondAction/BondRemoveAction.cpp
     166BONDACTIONHEADER = \
     167  Actions/BondAction/BondAddAction.hpp \
     168  Actions/BondAction/BondRemoveAction.hpp
     169BONDACTIONDEFS = \
     170  Actions/BondAction/BondAddAction.def \
     171  Actions/BondAction/BondRemoveAction.def
    159172
    160173CMDACTIONSOURCE = \

  • src/Atom/atom_bondedparticle.cpp

    rcb2465 rf63e41  
    3434
    3535#include "CodePatterns/MemDebug.hpp"
     36
     37#include <algorithm>
     38#include <boost/bind.hpp>
    3639
    3740#include "atom.hpp"
    … …  
    116119
    117120  return newBond;
     121}
     122
     123/** Removes a bond of this atom to a given \a Partner.
     124 *
     125 * @param _step time step
     126 * @param Partner bond partner
     127 */
     128void BondedParticle::removeBond(const unsigned int _step, BondedParticle * const Partner)
     129{
     130  const BondList& ListOfBonds = getListOfBondsAtStep(_step);
     131  BondList::const_iterator iter = std::find_if(ListOfBonds.begin(), ListOfBonds.end(),
     132      boost::bind(
     133          static_cast<bool (bond::*)(const ParticleInfo * const) const>(&bond::Contains),
     134          _1,
     135          boost::cref(Partner)));
     136  if (iter != ListOfBonds.end()) {
     137    delete *iter; //dstor takes care of unregistering and all
     138  } else
     139    ELOG(1, "BondedParticle::removeBond() - I cannot find the bond in between "
     140        +toString(getName())+" and "+toString(Partner->getName())+".");
    118141}
    119142

  • src/Atom/atom_bondedparticle.hpp

    rcb2465 rf63e41  
    3838
    3939  bond * const addBond(const unsigned int _step, BondedParticle* Partner);
     40  void removeBond(const unsigned int _step, BondedParticle* Partner);
    4041  void removeBond(bond *binder);
    4142  void removeAllBonds();

  • src/Atom/atom_bondedparticleinfo.hpp

    rcb2465 rf63e41  
    2828class BondedParticle;
    2929
    30 #define BondList list<bond *>
     30#define BondList std::list<bond *>
    3131
    3232/********************************************** declarations *******************************/

  • src/UIElements/CommandLineUI/CommandLineParser.cpp

    rcb2465 rf63e41  
    6565  analysis("Analysis options"),
    6666  atom("Atom options"),
     67  bond("Bond options"),
    6768  command("Command options"),
    6869  fill("fill options"),
    … …  
    8081  CmdParserLookup["analysis"] = &analysis;
    8182  CmdParserLookup["atom"] = &atom;
     83  CmdParserLookup["bond"] = &bond;
    8284  CmdParserLookup["command"] = &command;
    8385  CmdParserLookup["edit"] = &edit;

  • src/UIElements/CommandLineUI/CommandLineParser.hpp

    rcb2465 rf63e41  
    5656  po::options_description analysis;
    5757  po::options_description atom;
     58  po::options_description bond;
    5859  po::options_description command;
    5960  po::options_description edit;

  • src/UIElements/Menu/MenuDescription.cpp

    rcb2465 rf63e41  
    6262  MenuPositionMap->insert(std::make_pair("analysis",TopPosition("tools",1)));
    6363  MenuPositionMap->insert(std::make_pair("atom",TopPosition("edit",1)));
     64  MenuPositionMap->insert(std::make_pair("bond",TopPosition("edit",2)));
    6465  MenuPositionMap->insert(std::make_pair("command",TopPosition("",3)));
    6566  MenuPositionMap->insert(std::make_pair("edit",TopPosition("",2)));
    … …  
    6768  MenuPositionMap->insert(std::make_pair("fragmentation",TopPosition("tools",3)));
    6869  MenuPositionMap->insert(std::make_pair("graph",TopPosition("tools",4)));
    69   MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",2)));
    70   MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",3)));
    71   MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",4)));
     70  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",3)));
     71  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",4)));
     72  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",5)));
    7273  MenuPositionMap->insert(std::make_pair("tesselation",TopPosition("tools",2)));
    7374  MenuPositionMap->insert(std::make_pair("shape",TopPosition("tools",6)));
    … …  
    7879  MenuDescriptionsMap->insert(std::make_pair("analysis","Analysis (pair correlation, volume)"));
    7980  MenuDescriptionsMap->insert(std::make_pair("atom","Edit atoms"));
     81  MenuDescriptionsMap->insert(std::make_pair("bond","Edit bonds"));
    8082  MenuDescriptionsMap->insert(std::make_pair("command","Configuration"));
    8183  MenuDescriptionsMap->insert(std::make_pair("edit","Edit"));
    … …  
    9496  MenuNameMap->insert(std::make_pair("analysis","Analysis"));
    9597  MenuNameMap->insert(std::make_pair("atom","Atoms"));
     98  MenuNameMap->insert(std::make_pair("bond","Bonds"));
    9699  MenuNameMap->insert(std::make_pair("command","Configuration"));
    97100  MenuNameMap->insert(std::make_pair("edit","Edit"));
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