Ignore:
Timestamp:
Jul 28, 2010, 9:21:14 AM (15 years ago)
Author:
Tillmann Crueger <crueger@…>
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:
400170, a7b777c
Parents:
7067bd6 (diff), 0430e3 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'stable' into StructureRefactoring

Conflicts:

src/Makefile.am

Location:
src/Actions/AnalysisAction
Files:
4 added
6 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    r7067bd6 r677e13  
    99
    1010#include "Actions/AnalysisAction/MolecularVolumeAction.hpp"
     11#include "Actions/ActionRegistry.hpp"
    1112#include "boundary.hpp"
    1213#include "config.hpp"
    … …  
    2425#include "UIElements/UIFactory.hpp"
    2526#include "UIElements/Dialog.hpp"
    26 #include "Actions/MapOfActions.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2728
    2829const char AnalysisMolecularVolumeAction::NAME[] = "molecular-volume";
    … …  
    3536{}
    3637
     38void AnalysisMolecularVolume() {
     39  ActionRegistry::getInstance().getActionByName(AnalysisMolecularVolumeAction::NAME)->call(Action::NonInteractive);
     40};
     41
     42Dialog * AnalysisMolecularVolumeAction::createDialog() {
     43  Dialog *dialog = UIFactory::getInstance().makeDialog();
     44
     45  dialog->queryEmpty(NAME, ValueStorage::getInstance().getDescription(NAME));
     46
     47  return dialog;
     48}
     49
    3750Action::state_ptr AnalysisMolecularVolumeAction::performCall() {
    38   Dialog *dialog = UIFactory::getInstance().makeDialog();
    39   molecule *mol = NULL;
     51  int molID = -1;
     52  // obtain information
     53  ValueStorage::getInstance().queryCurrentValue(NAME, molID);
    4054
    41   dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
    42 
    43   if(dialog->display()) {
     55  // execute action
     56  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     57    molecule *mol = iter->second;
    4458    class Tesselation *TesselStruct = NULL;
    4559    const LinkedCell *LCList = NULL;
    … …  
    5771    delete(TesselStruct);
    5872    delete(LCList);
    59     delete dialog;
    60     return Action::success;
    61   } else {
    62     delete dialog;
    63     return Action::failure;
    6473  }
     74  return Action::success;
    6575}
    6676
    6777Action::state_ptr AnalysisMolecularVolumeAction::performUndo(Action::state_ptr _state) {
    68 //  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
    69 
    70   return Action::failure;
    71 //  string newName = state->mol->getName();
    72 //  state->mol->setName(state->lastName);
    73 //
    74 //  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
     78  return Action::success;
    7579}
    7680
    7781Action::state_ptr AnalysisMolecularVolumeAction::performRedo(Action::state_ptr _state){
    78   return Action::failure;
     82  return Action::success;
    7983}
    8084
    8185bool AnalysisMolecularVolumeAction::canUndo() {
    82   return false;
     86  return true;
    8387}
    8488
    8589bool AnalysisMolecularVolumeAction::shouldUndo() {
    86   return false;
     90  return true;
    8791}
    8892

  • src/Actions/AnalysisAction/MolecularVolumeAction.hpp

    r7067bd6 r677e13  
    1111#include "Actions/Action.hpp"
    1212
     13void AnalysisMolecularVolume();
     14
    1315class AnalysisMolecularVolumeAction : public Action {
     16  friend void AnalysisMolecularVolume();
    1417public:
    1518  AnalysisMolecularVolumeAction();
    … …  
    2124  virtual const std::string getName();
    2225private:
     26  virtual Dialog * createDialog();
    2327  virtual Action::state_ptr performCall();
    2428  virtual Action::state_ptr performUndo(Action::state_ptr);

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    r7067bd6 r677e13  
    99
    1010#include "Actions/AnalysisAction/PairCorrelationAction.hpp"
     11#include "Actions/ActionRegistry.hpp"
    1112#include "analysis_correlation.hpp"
    1213#include "boundary.hpp"
    … …  
    2728#include "UIElements/UIFactory.hpp"
    2829#include "UIElements/Dialog.hpp"
    29 #include "Actions/MapOfActions.hpp"
     30#include "UIElements/ValueStorage.hpp"
    3031
    3132const char AnalysisPairCorrelationAction::NAME[] = "pair-correlation";
    … …  
    3839{}
    3940
     41void AnalysisPairCorrelation(std::vector< element *> &elements, double BinStart, double BinWidth, double BinEnd, string &outputname, string &binoutputname, bool periodic) {
     42  ValueStorage::getInstance().setCurrentValue("elements", elements);
     43  ValueStorage::getInstance().setCurrentValue("bin-start", BinStart);
     44  ValueStorage::getInstance().setCurrentValue("bin-width", BinWidth);
     45  ValueStorage::getInstance().setCurrentValue("bin-end", BinEnd);
     46  ValueStorage::getInstance().setCurrentValue("output-file", outputname);
     47  ValueStorage::getInstance().setCurrentValue("bin-output-file", binoutputname);
     48  ValueStorage::getInstance().setCurrentValue("periodic", periodic);
     49  ActionRegistry::getInstance().getActionByName(AnalysisPairCorrelationAction::NAME)->call(Action::NonInteractive);
     50};
     51
     52
     53Dialog* AnalysisPairCorrelationAction::createDialog() {
     54  Dialog *dialog = UIFactory::getInstance().makeDialog();
     55
     56  dialog->queryElements("elements", ValueStorage::getInstance().getDescription("elements"));
     57  dialog->queryDouble("bin-start", ValueStorage::getInstance().getDescription("bin-start"));
     58  dialog->queryDouble("bin-width", ValueStorage::getInstance().getDescription("bin-width"));
     59  dialog->queryDouble("bin-end", ValueStorage::getInstance().getDescription("bin-end"));
     60  dialog->queryString("output-file", ValueStorage::getInstance().getDescription("output-file"));
     61  dialog->queryString("bin-output-file", ValueStorage::getInstance().getDescription("bin-output-file"));
     62  dialog->queryBoolean("periodic", ValueStorage::getInstance().getDescription("periodic"));
     63
     64  return dialog;
     65}
     66
    4067Action::state_ptr AnalysisPairCorrelationAction::performCall() {
    41   Dialog *dialog = UIFactory::getInstance().makeDialog();
    4268  int ranges[3] = {1, 1, 1};
    4369  double BinEnd = 0.;
    … …  
    5480  Vector Point;
    5581  BinPairMap *binmap = NULL;
    56   MoleculeListClass *molecules = World::getInstance().getMolecules();
    5782
    58   // first dialog: Obtain which type of correlation
    59   dialog->queryString(NAME, &type, MapOfActions::getInstance().getDescription(NAME));
    60   if(dialog->display()) {
    61     delete dialog;
    62   } else {
    63     delete dialog;
    64     return Action::failure;
    65   }
     83  // obtain information
     84  ValueStorage::getInstance().queryCurrentValue("elements", elements);
     85  ValueStorage::getInstance().queryCurrentValue("bin-start", BinStart);
     86  ValueStorage::getInstance().queryCurrentValue("bin-width", BinWidth);
     87  ValueStorage::getInstance().queryCurrentValue("bin-end", BinEnd);
     88  ValueStorage::getInstance().queryCurrentValue("output-file", outputname);
     89  ValueStorage::getInstance().queryCurrentValue("bin-output-file", binoutputname);
     90  ValueStorage::getInstance().queryCurrentValue("periodic", periodic);
    6691
    67   // second dialog: Obtain parameters specific to this type
    68   dialog = UIFactory::getInstance().makeDialog();
    69   if (type == "P")
    70     dialog->queryVector("position", &Point, false, MapOfActions::getInstance().getDescription("position"));
    71   if (type == "S")
    72     dialog->queryMolecule("molecule-by-id", &Boundary, MapOfActions::getInstance().getDescription("molecule-by-id"));
    73   dialog->queryElement("elements", &elements, MapOfActions::getInstance().getDescription("elements"));
    74   dialog->queryDouble("bin-start", &BinStart, MapOfActions::getInstance().getDescription("bin-start"));
    75   dialog->queryDouble("bin-width", &BinWidth, MapOfActions::getInstance().getDescription("bin-width"));
    76   dialog->queryDouble("bin-end", &BinEnd, MapOfActions::getInstance().getDescription("bin-end"));
    77   dialog->queryString("output-file", &outputname, MapOfActions::getInstance().getDescription("output-file"));
    78   dialog->queryString("bin-output-file", &binoutputname, MapOfActions::getInstance().getDescription("bin-output-file"));
    79   dialog->queryBoolean("periodic", &periodic, MapOfActions::getInstance().getDescription("periodic"));
    80 
    81   if(dialog->display()) {
    82     output.open(outputname.c_str());
    83     binoutput.open(binoutputname.c_str());
    84     if (type == "E") {
    85       PairCorrelationMap *correlationmap = NULL;
    86       if (periodic)
    87         correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
    88       else
    89         correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
    90       OutputPairCorrelation(&output, correlationmap);
    91       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
    92       OutputCorrelation ( &binoutput, binmap );
    93       delete(binmap);
    94       delete(correlationmap);
    95     } else if (type == "P")  {
    96       cout << "Point to correlate to is  " << Point << endl;
    97       CorrelationToPointMap *correlationmap = NULL;
    98       if (periodic)
    99         correlationmap  = PeriodicCorrelationToPoint(molecules, elements, &Point, ranges);
    100       else
    101         correlationmap = CorrelationToPoint(molecules, elements, &Point);
    102       OutputCorrelationToPoint(&output, correlationmap);
    103       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
    104       OutputCorrelation ( &binoutput, binmap );
    105       delete(binmap);
    106       delete(correlationmap);
    107     } else if (type == "S") {
    108       ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
    109       const double radius = 4.;
    110       double LCWidth = 20.;
    111       if (BinEnd > 0) {
    112         if (BinEnd > 2.*radius)
    113           LCWidth = BinEnd;
    114         else
    115           LCWidth = 2.*radius;
    116       }
    117 
    118       // get the boundary
    119       class Tesselation *TesselStruct = NULL;
    120       const LinkedCell *LCList = NULL;
    121       // find biggest molecule
    122       int counter  = molecules->ListOfMolecules.size();
    123       bool *Actives = new bool[counter];
    124       counter = 0;
    125       for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
    126         Actives[counter++] = (*BigFinder)->ActiveFlag;
    127         (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
    128       }
    129       LCList = new LinkedCell(Boundary, LCWidth);
    130       FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
    131       CorrelationToSurfaceMap *surfacemap = NULL;
    132       if (periodic)
    133         surfacemap = PeriodicCorrelationToSurface( molecules, elements, TesselStruct, LCList, ranges);
    134       else
    135         surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
    136       delete LCList;
    137       OutputCorrelationToSurface(&output, surfacemap);
    138       // re-set ActiveFlag
    139       counter = 0;
    140       for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
    141         (*BigFinder)->ActiveFlag = Actives[counter++];
    142       }
    143       delete[] Actives;
    144       // check whether radius was appropriate
    145       {
    146         double start; double end;
    147         GetMinMax( surfacemap, start, end);
    148         if (LCWidth < end)
    149           DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
    150       }
    151       binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
    152       OutputCorrelation ( &binoutput, binmap );
    153       delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
    154       delete(binmap);
    155       delete(surfacemap);
    156     } else {
    157       return Action::failure;
    158     }
    159     output.close();
    160     binoutput.close();
    161     delete dialog;
    162     return Action::success;
    163   } else {
    164     delete dialog;
    165     return Action::failure;
    166   }
     92  // execute action
     93  output.open(outputname.c_str());
     94  binoutput.open(binoutputname.c_str());
     95  PairCorrelationMap *correlationmap = NULL;
     96  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
     97  if (periodic)
     98    correlationmap = PeriodicPairCorrelation(molecules, elements, ranges);
     99  else
     100    correlationmap = PairCorrelation(molecules, elements);
     101  OutputPairCorrelation(&output, correlationmap);
     102  binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
     103  OutputCorrelation ( &binoutput, binmap );
     104  delete(binmap);
     105  delete(correlationmap);
     106  output.close();
     107  binoutput.close();
     108  return Action::success;
    167109}
    168110
    169111Action::state_ptr AnalysisPairCorrelationAction::performUndo(Action::state_ptr _state) {
    170 //  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
    171 
    172   return Action::failure;
    173 //  string newName = state->mol->getName();
    174 //  state->mol->setName(state->lastName);
    175 //
    176 //  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
     112  return Action::success;
    177113}
    178114
    179115Action::state_ptr AnalysisPairCorrelationAction::performRedo(Action::state_ptr _state){
    180   return Action::failure;
     116  return Action::success;
    181117}
    182118
    183119bool AnalysisPairCorrelationAction::canUndo() {
    184   return false;
     120  return true;
    185121}
    186122
    187123bool AnalysisPairCorrelationAction::shouldUndo() {
    188   return false;
     124  return true;
    189125}
    190126

  • src/Actions/AnalysisAction/PairCorrelationAction.hpp

    r7067bd6 r677e13  
    1111#include "Actions/Action.hpp"
    1212
     13class element;
     14
     15void AnalysisPairCorrelation(std::vector< element *> &elements, double BinStart, double BinWidth, double BinEnd, std::string &outputname, std::string &binoutputname, bool periodic);
     16
    1317class AnalysisPairCorrelationAction : public Action {
     18  friend void AnalysisPairCorrelation(std::vector< element *> &elements, double BinStart, double BinWidth, double BinEnd, std::string &outputname, std::string &binoutputname, bool periodic);
    1419public:
    1520  AnalysisPairCorrelationAction();
    … …  
    2025
    2126  virtual const std::string getName();
     27
    2228private:
     29  virtual Dialog * createDialog();
    2330  virtual Action::state_ptr performCall();
    2431  virtual Action::state_ptr performUndo(Action::state_ptr);

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    r7067bd6 r677e13  
    99
    1010#include "Actions/AnalysisAction/PrincipalAxisSystemAction.hpp"
     11#include "Actions/ActionRegistry.hpp"
    1112#include "molecule.hpp"
    1213#include "log.hpp"
    … …  
    2021#include "UIElements/UIFactory.hpp"
    2122#include "UIElements/Dialog.hpp"
    22 #include "Actions/MapOfActions.hpp"
     23#include "UIElements/ValueStorage.hpp"
    2324
    2425const char AnalysisPrincipalAxisSystemAction::NAME[] = "principal-axis-system";
    … …  
    3132{}
    3233
     34void AnalysisPrincipalAxisSystem() {
     35  ActionRegistry::getInstance().getActionByName(AnalysisPrincipalAxisSystemAction::NAME)->call(Action::NonInteractive);
     36};
     37
     38Dialog* AnalysisPrincipalAxisSystemAction::createDialog() {
     39  Dialog *dialog = UIFactory::getInstance().makeDialog();
     40
     41  dialog->queryEmpty(NAME, ValueStorage::getInstance().getDescription(NAME));
     42
     43  return dialog;
     44}
     45
    3346Action::state_ptr AnalysisPrincipalAxisSystemAction::performCall() {
    34   Dialog *dialog = UIFactory::getInstance().makeDialog();
    3547  molecule *mol = NULL;
    3648
    37   dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
    38 
    39   if(dialog->display()) {
    40     DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);
     49  ValueStorage::getInstance().queryCurrentValue(NAME, mol);
     50  DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);
     51  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     52    molecule *mol = iter->second;
    4153    mol->PrincipalAxisSystem(false);
    42     delete dialog;
    43     return Action::success;
    44   } else {
    45     delete dialog;
    46     return Action::failure;
    4754  }
     55  return Action::success;
    4856}
    4957
    5058Action::state_ptr AnalysisPrincipalAxisSystemAction::performUndo(Action::state_ptr _state) {
    51 //  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
    52 
    53   return Action::failure;
    54 //  string newName = state->mol->getName();
    55 //  state->mol->setName(state->lastName);
    56 //
    57 //  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
     59  return Action::success;
    5860}
    5961
    6062Action::state_ptr AnalysisPrincipalAxisSystemAction::performRedo(Action::state_ptr _state){
    61   return Action::failure;
     63  return Action::success;
    6264}
    6365
    6466bool AnalysisPrincipalAxisSystemAction::canUndo() {
    65   return false;
     67  return true;
    6668}
    6769
    6870bool AnalysisPrincipalAxisSystemAction::shouldUndo() {
    69   return false;
     71  return true;
    7072}
    7173

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp

    r7067bd6 r677e13  
    1111#include "Actions/Action.hpp"
    1212
     13void AnalysisPrincipalAxisSystem();
     14
    1315class AnalysisPrincipalAxisSystemAction : public Action {
     16  friend void AnalysisPrincipalAxisSystem();
     17
    1418public:
    1519  AnalysisPrincipalAxisSystemAction();
    … …  
    2125  virtual const std::string getName();
    2226private:
     27  virtual Dialog * createDialog();
    2328  virtual Action::state_ptr performCall();
    2429  virtual Action::state_ptr performUndo(Action::state_ptr);
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