Changeset f47e00b for src/Actions


Ignore:
Timestamp:
Apr 29, 2014, 12:42:43 PM (11 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:
9bac15
Parents:
237f93
git-author:
Frederik Heber <heber@…> (01/11/14 20:57:55)
git-committer:
Frederik Heber <heber@…> (04/29/14 12:42:43)
Message:

FIX: SubgraphDissectionAction is now a MakroAction, fixed store-session.

  • store-session would skip the select-atoms part.
  • hence, now we just write SubgraphDissection() command to python script.
Location:
src/Actions
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FragmentationAction/MolecularDynamicsAction.hpp

    r237f93 rf47e00b  
    2121
    2222#endif /* MOLECULARDYNAMICSACTION_HPP_ */
    23 
    24 //// some derived names: if CATEGORY is not given, we don't prefix with it
    25 //#ifdef CATEGORY
    26 //#define ACTION BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Action))
    27 //#define COMMAND BOOST_PP_CAT(CATEGORY, ACTIONNAME)
    28 //#define PARAMS BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Parameters))
    29 //#else
    30 //#define ACTION BOOST_PP_CAT(ACTIONNAME, Action)
    31 //#define COMMAND ACTIONNAME
    32 //#define PARAMS BOOST_PP_CAT(ACTIONNAME, Parameters)
    33 //#endif
    34 //// check if no lists given
    35 //#ifndef paramtypes
    36 //#define MAXPARAMTYPES 0
    37 //#else
    38 //#define MAXPARAMTYPES BOOST_PP_SEQ_SIZE(paramtypes)
    39 //#endif
    40 //#ifndef paramdefaults
    41 //#define MAXPARAMDEFAULTS 0
    42 //#else
    43 //#define MAXPARAMDEFAULTS BOOST_PP_SEQ_SIZE(paramdefaults)
    44 //#endif
    45 //
    46 //namespace MoleCuilder {
    47 //
    48 //// print a list of type ref followed, i.e. "int i, double position"
    49 //#define type_list(z,n,TYPELIST, VARLIST) \
    50 //  BOOST_PP_COMMA_IF(n)\
    51 //  BOOST_PP_SEQ_ELEM(n, TYPELIST) \
    52 //  BOOST_PP_SEQ_ELEM(n, VARLIST)
    53 //
    54 //void COMMAND(
    55 //#if defined paramtypes && defined paramreferences
    56 //#define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, paramtypes, paramreferences)
    57 //#define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    58 //#include BOOST_PP_LOCAL_ITERATE()
    59 //#endif
    60 //    );
    61 //
    62 //class FragmentationMolecularDynamicsAction;
    63 //
    64 //template <>
    65 //class ActionTraits<ACTION> : public ActionTrait {
    66 //public:
    67 //  ActionTraits() :
    68 //#ifndef SHORTFORM
    69 //    ActionTrait(OptionTrait(TOKEN, &typeid(void), DESCRIPTION, std::string()))
    70 //#else
    71 //    ActionTrait(OptionTrait(TOKEN, &typeid(void), DESCRIPTION, std::string(), SHORTFORM))
    72 //#endif /* SHORTFORM */
    73 //  {
    74 //  // initialize remainder of action info
    75 //#ifdef MENUNAME
    76 //    MenuTitle = MENUNAME;
    77 //#endif
    78 //#ifdef MENUPOSITION
    79 //    MenuPosition = MENUPOSITION;
    80 //#endif
    81 //
    82 //    // we got no options to initialize
    83 //  }
    84 //
    85 //  virtual ~ActionTraits() {
    86 //    //std::cout << "ActionTraits<" << BOOST_PP_STRINGIZE(ACTION) << ">::~ActionTraits() on instance " << this << " with name " << getName() << " called." << std::endl;
    87 //  }
    88 //};
    89 //
    90 //class FragmentationMolecularDynamicsAction : public MakroAction
    91 //{
    92 //public:
    93 //  FragmentationMolecularDynamicsAction();
    94 //  virtual ~FragmentationMolecularDynamicsAction();
    95 //
    96 //  // must be called after all primitive actions are present
    97 //  void prepare(ActionRegistry &AR);
    98 //  // must be called before alle primitive actions are removed
    99 //  void unprepare(ActionRegistry &AR);
    100 //
    101 //  virtual ActionState::ptr performCall();
    102 //  virtual ActionState::ptr performUndo(ActionState::ptr);
    103 //  virtual ActionState::ptr performRedo(ActionState::ptr);
    104 //
    105 //private:
    106 //  //!> flag to check whether actions have been prepared
    107 //  static bool isPrepared;
    108 //  //!> sequence of actions for this macro action
    109 //  static ActionSequence actions;
    110 //};
    111 //
    112 //}
    113 //
    114 //#undef ACTION
    115 //#undef COMMAND
    116 //#undef COMMANDFULL
    117 //#undef PARAMS
    118 //
    119 //#undef ACTIONNAME
    120 //#undef CATEGORY
    121 //#undef MENUNAME
    122 //#undef MENUPOSITION
    123 //#undef TOKEN
    124 //
    125 //#undef DESCRIPTION
    126 //#undef SHORTFORM
    127 //
    128 //#endif /* MOLECULARDYNAMICSACTION_HPP_ */

  • src/Actions/GraphAction/SubgraphDissectionAction.cpp

    r237f93 rf47e00b  
    4747#include "Descriptors/AtomDescriptor.hpp"
    4848
     49using namespace MoleCuilder;
     50
     51// and construct the stuff
    4952#include "SubgraphDissectionAction.def"
    50 
    51 // some derived names: if CATEGORY is not given, we don't prefix with it
    52 #ifdef CATEGORY
    53 #define ACTION BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Action))
    54 #define COMMAND BOOST_PP_CAT(CATEGORY, ACTIONNAME)
    55 #define PARAMS BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Parameters))
    56 #else
    57 #define ACTION BOOST_PP_CAT(ACTIONNAME, Action)
    58 #define COMMAND ACTIONNAME
    59 #define PARAMS BOOST_PP_CAT(ACTIONNAME, Parameters)
    60 #endif
    61 // check if no lists given
    62 #ifndef paramtypes
    63 #define MAXPARAMTYPES 0
    64 #else
    65 #define MAXPARAMTYPES BOOST_PP_SEQ_SIZE(paramtypes)
    66 #endif
    67 #ifndef paramdefaults
    68 #define MAXPARAMDEFAULTS 0
    69 #else
    70 #define MAXPARAMDEFAULTS BOOST_PP_SEQ_SIZE(paramdefaults)
    71 #endif
    72 
    73 namespace MoleCuilder {
     53#include "MakroAction_impl_pre.hpp"
     54/** =========== define the function ====================== */
    7455
    7556// static instances
    … …  
    7758bool GraphSubgraphDissectionAction::isPrepared = false;
    7859
    79 GraphSubgraphDissectionAction::GraphSubgraphDissectionAction() :
    80   MakroAction(ActionTraits< GraphSubgraphDissectionAction >(), actions)
    81 {}
    82 
    83 GraphSubgraphDissectionAction::~GraphSubgraphDissectionAction()
    84 {}
    85 
    8660void GraphSubgraphDissectionAction::prepare(ActionRegistry &AR)
    8761{
     62  actions.addAction(AR.getActionByName(std::string("select-all-atoms")));
    8863  actions.addAction(AR.getActionByName(std::string("destroy-adjacency")));
    8964  actions.addAction(AR.getActionByName(std::string("create-adjacency")));
    … …  
    11186  // we need to "emulate" that all atoms have been selected without destroying
    11287  // current selection
    113   Chronos::getInstance().startTiming(TOKEN);
    11488  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    115   World::getInstance().selectAllAtoms(AllAtoms());
    11689  ActionState::ptr state(MakroAction::performCall());
    11790  reselectAtoms(selected_atoms);
    118   Chronos::getInstance().endTiming(TOKEN);
    11991
    12092  return state;
    … …  
    12597  // current selection
    12698  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    127   World::getInstance().selectAllAtoms(AllAtoms());
    12899  ActionState::ptr state(MakroAction::performUndo(_state));
    129100  reselectAtoms(selected_atoms);
    … …  
    136107  // current selection
    137108  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    138   World::getInstance().selectAllAtoms(AllAtoms());
    139109  ActionState::ptr state(MakroAction::performRedo(_state));
    140110  reselectAtoms(selected_atoms);
    … …  
    143113}
    144114
    145 // =========== command for calling action directly ===========
    146 void COMMAND(
    147 #if defined paramtypes && defined paramreferences && BOOST_PP_NOT_EQUAL(MAXPARAMTYPES,0)
    148 #define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, paramtypes, paramreferences)
    149 #define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    150 #include BOOST_PP_LOCAL_ITERATE()
    151 #endif
    152 )
    153 {
    154   ACTION *ToCall = dynamic_cast<ACTION*>(ActionQueue::getInstance().getActionByName( TOKEN )); //->clone(params);
    155   //ACTION::PARAMS params;
    156 #if defined paramreferences && BOOST_PP_NOT_EQUAL(MAXPARAMTYPES,0)
    157 #define BOOST_PP_LOCAL_MACRO(n) value_print(~, n, paramreferences, ToCall->params.)
    158 #define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    159 #include BOOST_PP_LOCAL_ITERATE()
    160 #endif
    161   ActionQueue::getInstance().queueAction( ToCall, Action::NonInteractive);
    162 };
     115bool GraphSubgraphDissectionAction::canUndo(){
     116  return true;
     117}
    163118
    164 void BOOST_PP_CAT( COMMAND, _stringargs)(
    165 #if defined paramtypes && defined paramreferences && BOOST_PP_NOT_EQUAL(MAXPARAMTYPES,0)
    166 #define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_TRANSFORM( type2string, , paramtypes), paramreferences)
    167 #define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    168 #include BOOST_PP_LOCAL_ITERATE()
    169 #endif
    170   ) {
    171   ACTION *ToCall = dynamic_cast<ACTION*>(ActionQueue::getInstance().getActionByName( TOKEN )); //->clone(params);
    172   //ACTION::PARAMS params;
    173 #if defined paramtypes && defined paramtypes && BOOST_PP_NOT_EQUAL(MAXPARAMTYPES,0)
    174 #define BOOST_PP_LOCAL_MACRO(n) valuetype_print(~, n, paramreferences, paramtypes, ToCall->params. )
    175 #define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    176 #include BOOST_PP_LOCAL_ITERATE()
    177 #endif
    178   ActionQueue::getInstance().queueAction( ToCall, Action::NonInteractive);
    179 };
    180 
     119bool GraphSubgraphDissectionAction::shouldUndo(){
     120  return true;
    181121}

  • src/Actions/GraphAction/SubgraphDissectionAction.def

    r237f93 rf47e00b  
    2121#undef paramvalids
    2222
    23 #define statetypes (MolAtomList)
    24 #define statereferences (moleculelist)
     23#undef statetypes
     24#undef statereferences
    2525
    2626// some defines for all the names, you may use ACTION, STATE and PARAMS

  • src/Actions/GraphAction/SubgraphDissectionAction.hpp

    r237f93 rf47e00b  
    1414#endif
    1515
    16 #include "Actions/ActionSequence.hpp"
    17 #include "Actions/ActionTraits.hpp"
     16
    1817#include "Actions/MakroAction.hpp"
    1918
    2019#include "SubgraphDissectionAction.def"
    21 
    22 // some derived names: if CATEGORY is not given, we don't prefix with it
    23 #ifdef CATEGORY
    24 #define ACTION BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Action))
    25 #define COMMAND BOOST_PP_CAT(CATEGORY, ACTIONNAME)
    26 #define PARAMS BOOST_PP_CAT(CATEGORY, BOOST_PP_CAT(ACTIONNAME, Parameters))
    27 #else
    28 #define ACTION BOOST_PP_CAT(ACTIONNAME, Action)
    29 #define COMMAND ACTIONNAME
    30 #define PARAMS BOOST_PP_CAT(ACTIONNAME, Parameters)
    31 #endif
    32 // check if no lists given
    33 #ifndef paramtypes
    34 #define MAXPARAMTYPES 0
    35 #else
    36 #define MAXPARAMTYPES BOOST_PP_SEQ_SIZE(paramtypes)
    37 #endif
    38 #ifndef paramdefaults
    39 #define MAXPARAMDEFAULTS 0
    40 #else
    41 #define MAXPARAMDEFAULTS BOOST_PP_SEQ_SIZE(paramdefaults)
    42 #endif
    43 
    44 namespace MoleCuilder {
    45 
    46 // print a list of type ref followed, i.e. "int i, double position"
    47 #define type_list(z,n,TYPELIST, VARLIST) \
    48   BOOST_PP_COMMA_IF(n)\
    49   BOOST_PP_SEQ_ELEM(n, TYPELIST) \
    50   BOOST_PP_SEQ_ELEM(n, VARLIST)
    51 
    52 void COMMAND(
    53 #if defined paramtypes && defined paramreferences
    54 #define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, paramtypes, paramreferences)
    55 #define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    56 #include BOOST_PP_LOCAL_ITERATE()
    57 #endif
    58     );
    59 
    60 class GraphSubgraphDissectionAction;
    61 
    62 template <>
    63 class ActionTraits<ACTION> : public ActionTrait {
    64 public:
    65   ActionTraits() :
    66 #ifndef SHORTFORM
    67     ActionTrait(OptionTrait(TOKEN, &typeid(void), DESCRIPTION, std::string()))
    68 #else
    69     ActionTrait(OptionTrait(TOKEN, &typeid(void), DESCRIPTION, std::string(), SHORTFORM))
    70 #endif /* SHORTFORM */
    71   {
    72   // initialize remainder of action info
    73 #ifdef MENUNAME
    74     MenuTitle = MENUNAME;
    75 #endif
    76 #ifdef MENUPOSITION
    77     MenuPosition = MENUPOSITION;
    78 #endif
    79 
    80     // we got no options to initialize
    81   }
    82 
    83   virtual ~ActionTraits() {
    84     //std::cout << "ActionTraits<" << BOOST_PP_STRINGIZE(ACTION) << ">::~ActionTraits() on instance " << this << " with name " << getName() << " called." << std::endl;
    85   }
    86 };
    87 
    88 class GraphSubgraphDissectionAction : public MakroAction
    89 {
    90 public:
    91   GraphSubgraphDissectionAction();
    92   virtual ~GraphSubgraphDissectionAction();
    93 
    94   // must be called after all primitive actions are present
    95   void prepare(ActionRegistry &AR);
    96   // must be called before alle primitive actions are removed
    97   void unprepare(ActionRegistry &AR);
    98 
    99   virtual ActionState::ptr performCall();
    100   virtual ActionState::ptr performUndo(ActionState::ptr);
    101   virtual ActionState::ptr performRedo(ActionState::ptr);
    102 
    103 private:
    104   //!> flag to check whether actions have been prepared
    105   static bool isPrepared;
    106   //!> sequence of actions for this macro action
    107   static ActionSequence actions;
    108 };
    109 
    110 }
    111 
    112 #undef ACTION
    113 #undef COMMAND
    114 #undef COMMANDFULL
    115 #undef PARAMS
    116 
    117 #undef ACTIONNAME
    118 #undef CATEGORY
    119 #undef MENUNAME
    120 #undef MENUPOSITION
    121 #undef TOKEN
    122 
    123 #undef DESCRIPTION
    124 #undef SHORTFORM
     20#include "MakroAction_impl_header.hpp"
    12521
    12622#endif /* SUBGRAPHDISSECTIONACTION_HPP_ */

  • src/Actions/MakroAction_impl_pre.hpp

    r237f93 rf47e00b  
    233233public:
    234234  STATE(
    235 #if defined statetypes && defined statereferences // if we have parameters, we have to add "_" before each reference and add the params as the last one
     235#if defined statetypes && defined statereferences // if we have states, we have to add "_" before each reference and add the params as the last one
    236236#define OP(s,data,elem) BOOST_PP_CAT(data, elem)  // OP to add "_"
    237237#define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_PUSH_BACK(statetypes, const ACTION::PARAMS &), BOOST_PP_SEQ_TRANSFORM(OP, _, BOOST_PP_SEQ_PUSH_BACK(statereferences, params)))
    … …  
    242242#include BOOST_PP_LOCAL_ITERATE()
    243243) :
    244 #if defined statetypes && defined statereferences // do we have parameters at all?
     244#if defined statetypes && defined statereferences // do we have states at all?
    245245BOOST_PP_REPEAT(MAXSTATETYPES, initialiser_print, statereferences)
    246246#endif
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