Changeset 2affd1 for src/Actions


Ignore:
Timestamp:
Feb 11, 2016, 8:07:11 AM (9 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:
eb6552
Parents:
df5b8c
git-author:
Frederik Heber <heber@…> (12/30/15 10:02:58)
git-committer:
Frederik Heber <heber@…> (02/11/16 08:07:11)
Message:

Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase.

  • this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore".
Location:
src/Actions
Files:
15 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillRegularGridAction.cpp

    rdf5b8c r2affd1  
    4646#include "Filling/Preparators/BoxFillerPreparator.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "Parser/FormatParserInterface.hpp"
    5049#include "Parser/FormatParserStorage.hpp"

  • src/Actions/FillAction/FillVolumeAction.cpp

    rdf5b8c r2affd1  
    4646#include "Filling/Preparators/ShapeVolumeFillerPreparator.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "Parser/FormatParserInterface.hpp"
    5049#include "Parser/FormatParserStorage.hpp"

  • src/Actions/FillAction/SuspendInMoleculeAction.cpp

    rdf5b8c r2affd1  
    4949#include "LinkedCell/PointCloudAdaptor.hpp"
    5050#include "molecule.hpp"
    51 #include "MoleculeListClass.hpp"
    5251#include "Parser/FormatParserInterface.hpp"
    5352#include "Parser/FormatParserStorage.hpp"

  • src/Actions/GraphAction/UpdateMoleculesAction.cpp

    rdf5b8c r2affd1  
    4646#include "Graph/DepthFirstSearchAnalysis.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "World.hpp"
    5049
    … …  
    8382  // 0a. remove all present molecules
    8483  LOG(0, "STATUS: Removing all present molecules.");
    85   MoleculeListClass *molecules = World::getInstance().getMolecules();
    8684  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    87   for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    88     molecules->erase(*MolRunner);
     85  for (vector<molecule *>::iterator MolRunner = allmolecules.begin();
     86      MolRunner != allmolecules.end();
     87      ++MolRunner)
    8988    World::getInstance().destroyMolecule(*MolRunner);
    90   }
    9189
    9290  // 2. scan for connected subgraphs
    … …  
    112110  {
    113111    // remove all present molecules
    114     MoleculeListClass *molecules = World::getInstance().getMolecules();
    115112    vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    116     for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    117       molecules->erase(*MolRunner);
     113    for (vector<molecule *>::iterator MolRunner = allmolecules.begin();
     114        MolRunner != allmolecules.end();
     115        ++MolRunner)
    118116      World::getInstance().destroyMolecule(*MolRunner);
    119     }
    120117  }
    121118
    122119  {
    123120    // construct the old state
    124     MoleculeListClass *molecules = World::getInstance().getMolecules();
    125121    molecule *mol = NULL;
    126122    for (MolAtomList::const_iterator iter = state->moleculelist.begin(); iter != state->moleculelist.end(); ++iter) {
    … …  
    132128        mol->AddAtom(Walker);
    133129      }
    134       molecules->insert(mol);
    135130    }
    136131  }

  • src/Actions/MoleculeAction/BondFileAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/ChangeNameAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210#include "Parameters/Validators/GenericValidators.hpp"

  • src/Actions/MoleculeAction/LoadAction.cpp

    rdf5b8c r2affd1  
    3838#include "CodePatterns/Verbose.hpp"
    3939#include "Descriptors/MoleculeIdDescriptor.hpp"
     40#include "Descriptors/MoleculeOrderDescriptor.hpp"
    4041#include "Parser/Exceptions.hpp"
    4142#include "Parser/FormatParserInterface.hpp"
    … …  
    4344#include "Parser/FormatParser_Parameters.hpp"
    4445#include "molecule.hpp"
    45 #include "MoleculeListClass.hpp"
    4646#include "World.hpp"
    4747
    … …  
    102102
    103103    // set file name of last molecule
    104     MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
    105     (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
    106     LOG(0, "Chemical formula is " << (*iter)->getFormula());
     104    molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     105    mol->SetNameFromFilename(FilenamePrefix.c_str());
     106    LOG(0, "Chemical formula is " << mol->getFormula());
    107107
    108108    return ActionState::ptr(
    109         new MoleculeLoadState((*iter)->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
     109        new MoleculeLoadState(mol->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
    110110    );
    111111  }
    … …  
    151151
    152152  // set file name of last molecule
    153   MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
    154   (*iter)->SetNameFromFilename(state->FilenamePrefix.c_str());
    155   (*iter)->setId(state->molId);
    156   LOG(0, "Chemical formula is " << (*iter)->getFormula());
     153  molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     154  mol->SetNameFromFilename(state->FilenamePrefix.c_str());
     155  mol->setId(state->molId);
     156  LOG(0, "Chemical formula is " << mol->getFormula());
    157157
    158158  return ActionState::ptr(
    159       new MoleculeLoadState((*iter)->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
     159      new MoleculeLoadState(mol->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
    160160  );
    161161}

  • src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    109class Vector;
    1110

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

    rdf5b8c r2affd1  
    99#include "Actions/Values.hpp"
    1010#include "LinearAlgebra/Vector.hpp"
    11 
    12 class MoleculeListClass;
    1311
    1412#include "Parameters/Validators/Specific/VectorNotZeroValidator.hpp"

  • src/Actions/MoleculeAction/SaveAdjacencyAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/SaveBondsAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/SaveTemperatureAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/WorldAction/InputAction.cpp

    rdf5b8c r2affd1  
    3636
    3737#include "CodePatterns/Log.hpp"
     38
     39#include "Descriptors/MoleculeOrderDescriptor.hpp"
    3840#include "molecule.hpp"
    39 #include "MoleculeListClass.hpp"
    4041#include "Parser/Exceptions.hpp"
    4142#include "Parser/FormatParserStorage.hpp"
    … …  
    5758/** =========== define the function ====================== */
    5859ActionState::ptr WorldInputAction::performCall() {
    59 //  MoleculeListClass *molecules = World::getInstance().getMolecules();
    60 //  molecule *mol = NULL;
    6160  boost::filesystem::ifstream test;
    6261  FormatParserStorage &parsers = FormatParserStorage::getInstance();
    … …  
    9998
    10099    // set file name of last molecule
    101     MoleculeList::const_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.end();
    102     iter--;
    103     (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
    104     LOG(0, "Chemical formula is " << (*iter)->getFormula());
     100    molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     101    mol->SetNameFromFilename(FilenamePrefix.c_str());
     102    LOG(0, "Chemical formula is " << mol->getFormula());
    105103  }
    106104  return Action::success;

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    rdf5b8c r2affd1  
    4040#include "CodePatterns/Log.hpp"
    4141#include "molecule.hpp"
    42 #include "MoleculeListClass.hpp"
    4342#include "LinearAlgebra/Vector.hpp"
    4443#include "LinearAlgebra/RealSpaceMatrix.hpp"
    … …  
    8685  // add molecules in each repeated domain part
    8786  std::vector<Vector> vectors;
    88   MoleculeListClass *molecules = World::getInstance().getMolecules();
    8987  for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
    9088    y[0] = n[0];
    … …  
    9997          LOG(2, "DEBUG: Current mol is " << mol->name << "." << endl);
    10098          molecule * const newmol = mol->CopyMolecule();
    101           // TODO: remove this when World does not have MoleculeListClass anymore.
    102           molecules->insert(newmol);
    10399          x = y;
    104100          x *= M;
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