Changeset 04488a for src/Actions

Timestamp:

Jun 25, 2010, 9:57:15 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:

b6dbff

Parents:

ce4487 (diff), 0d1ad0 (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 'StructureRefactoring' into QT4Refactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp

Location:

src/Actions

Files:

• ActionRegistry.cpp (modified) (6 diffs)
• ActionRegistry.hpp (modified) (3 diffs)
• CmdAction/BondLengthTableAction.cpp (modified) (1 diff)
• FragmentationAction/DepthFirstSearchAction.cpp (modified) (1 diff)
• FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)
• Makefile.am (modified) (2 diffs)
• MapOfActions.cpp (modified) (3 diffs)
• MoleculeAction/FillWithMoleculeAction.cpp (modified) (1 diff)
• MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) (1 diff)
• MoleculeAction/SaveAdjacencyAction.cpp (modified) (1 diff)
• MoleculeAction/SaveBondsAction.cpp (modified) (1 diff)
• ParserAction/LoadXyzAction.cpp (modified) (4 diffs)
• WorldAction/InputAction.cpp (added)
• WorldAction/InputAction.hpp (added)
• WorldAction/OutputAction.cpp (added)
• WorldAction/OutputAction.hpp (added)

src/Actions/ActionRegistry.cpp

@@ -19 +19 @@
 using namespace std;
 
+/** Constructor for class ActionRegistry.
+ */
 ActionRegistry::ActionRegistry()
 {
 }
 
+/** Destructor for class ActionRegistry.
+ */
 ActionRegistry::~ActionRegistry()
 {
@@ -32 +36 @@
 }
 
+/** Returns pointer to an action named by \a name.
+ * \param name name of action
+ * \return pointer to Action
+ */
 Action* ActionRegistry::getActionByName(const std::string name){
   map<const string,Action*>::iterator iter;
@@ -39 +47 @@
 }
 
+/** States whether action is present or not.
+ * \note This iss needed as ActionRegistry::getActionByName() ASSERT()s that action is in map.
+ * \param name name of action
+ * \return true - Action present, false - Action absent
+ */
 bool ActionRegistry::isActionByNamePresent(const std::string name){
   map<const string,Action*>::iterator iter;
@@ -45 +58 @@
 }
 
+/** Registers an Action with the ActionRegistry.
+ * \param *action pointer to Action.
+ */
 void ActionRegistry::registerAction(Action* action){
   pair<map<const string,Action*>::iterator,bool> ret;
+  //cout << "Trying to register action with name " << action->getName() << "." << endl;
   ret = actionMap.insert(pair<const string,Action*>(action->getName(),action));
   ASSERT(ret.second,"Two actions with the same name added to registry");
 }
 
+/** Unregisters an Action.
+ * \param *action pointer to Action.
+ */
 void ActionRegistry::unregisterAction(Action* action){
+  //cout << "Unregistering action with name " << action->getName() << "." << endl;
   actionMap.erase(action->getName());
 }
 
+/** Returns an iterator pointing to the start of the map of Action's.
+ * \return begin iterator
+ */
 std::map<const std::string,Action*>::iterator ActionRegistry::getBeginIter()
 {
@@ -60 +84 @@
 }
 
+/** Returns an iterator pointing to the end of the map of Action's.
+ * \return end iterator
+ */
 std::map<const std::string,Action*>::iterator ActionRegistry::getEndIter()
 {
@@ -65 +92 @@
 }
 
+/** Returns a const iterator pointing to the start of the map of Action's.
+ * \return constant begin iterator
+ */
+std::map<const std::string,Action*>::const_iterator ActionRegistry::getBeginIter() const
+{
+  return actionMap.begin();
+}
+
+/** Returns a const iterator pointing to the end of the map of Action's.
+ * \return constant end iterator
+ */
+std::map<const std::string,Action*>::const_iterator ActionRegistry::getEndIter() const
+{
+  return actionMap.end();
+}
+
+/** Prints the contents of the ActionRegistry \a &m to \a &ost.
+ * \param &ost output stream
+ * \param &m reference to ActionRegistry
+ * \return reference to the above out stream for concatenation
+ */
+ostream& operator<<(ostream& ost, const ActionRegistry& m)
+{
+  ost << "ActionRegistry contains:" << endl;
+  for (std::map<const std::string,Action*>::const_iterator iter = m.getBeginIter(); iter != m.getEndIter(); ++iter) {
+    ost << "\t" << iter->first << " with pointer " << iter->second << endl;
+  }
+  return ost;
+};
+
+
+
 CONSTRUCT_SINGLETON(ActionRegistry)

src/Actions/ActionRegistry.hpp

@@ -9 +9 @@
 #define ACTIONREGISTRY_HPP_
 
+#include <iostream>
 #include <string>
 #include <map>
@@ -26 +27 @@
 
   std::map<const std::string,Action*>::iterator getBeginIter();
+  std::map<const std::string,Action*>::const_iterator getBeginIter() const;
   std::map<const std::string,Action*>::iterator getEndIter();
+  std::map<const std::string,Action*>::const_iterator getEndIter() const;
 
 private:
@@ -36 +39 @@
 };
 
+std::ostream& operator<<(std::ostream& ost, const ActionRegistry& m);
+
 #endif /* ACTIONREGISTRY_HPP_ */

src/Actions/CmdAction/BondLengthTableAction.cpp

@@ -9 +9 @@
 
 #include "Actions/CmdAction/BondLengthTableAction.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "log.hpp"

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -10 +10 @@
 #include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
 #include "atom.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "log.hpp"

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -10 +10 @@
 #include "Actions/FragmentationAction/FragmentationAction.hpp"
 #include "atom.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "log.hpp"
@@ -41 +42 @@
   double distance = -1.;
   int order = 0;
+  std::string path;
   config *configuration = World::getInstance().getConfig();
   int ExitFlag = 0;
 
   cout << "pre-dialog"<< endl;
-  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryString(NAME, &path, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   dialog->queryDouble("distance", &distance, MapOfActions::getInstance().getDescription("distance"));
   dialog->queryInt("order", &order, MapOfActions::getInstance().getDescription("order"));
@@ -58 +61 @@
     DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
     if (mol->hasBondStructure()) {
-      ExitFlag = mol->FragmentMolecule(order, configuration);
+      ExitFlag = mol->FragmentMolecule(order, path);
     }
     World::getInstance().setExitFlag(ExitFlag);

src/Actions/Makefile.am

@@ -120 +120 @@
   WorldAction/CenterOnEdgeAction.cpp \
   WorldAction/ChangeBoxAction.cpp \
+  WorldAction/InputAction.cpp \
+  WorldAction/OutputAction.cpp \
   WorldAction/RemoveSphereOfAtomsAction.cpp \
   WorldAction/RepeatBoxAction.cpp \
@@ -131 +133 @@
   WorldAction/CenterOnEdgeAction.hpp \
   WorldAction/ChangeBoxAction.hpp \
+  WorldAction/InputAction.hpp \
+  WorldAction/OutputAction.hpp \
   WorldAction/RemoveSphereOfAtomsAction.hpp \
   WorldAction/RepeatBoxAction.hpp \

src/Actions/MapOfActions.cpp

@@ -83 +83 @@
   DescriptionMap["fragment-mol"] = "create for a given molecule into fragments up to given order";
   DescriptionMap["help"] = "Give this help screen";
+  DescriptionMap["input"] = "specify input files";
   DescriptionMap["linear-interpolate"] = "linear interpolation in discrete steps between start and end position of a molecule";
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
   DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
+  DescriptionMap["output"] = "specify output formats";
   DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
@@ -185 +187 @@
   TypeMap["fastparsing"] = Boolean;
   TypeMap["fill-molecule"] = String;
-  TypeMap["fragment-mol"] = Molecule;
+  TypeMap["fragment-mol"] = String;
   TypeMap["input"] = String;
   TypeMap["linear-interpolate"] = String;
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
+  TypeMap["output"] = String;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -262 +265 @@
   generic.insert("fragment-mol");
   generic.insert("help");
-        generic.insert("linear-interpolate");
+  generic.insert("input");
+  generic.insert("linear-interpolate");
 //  generic.insert("molecular-volume");
   generic.insert("nonconvex-envelope");
+  generic.insert("output");
         generic.insert("pair-correlation");
-//      generic.insert("parse-xyz");
+        generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
   generic.insert("remove-atom");

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -102 +102 @@
       World::getInstance().getMolecules()->insert(Filling);
     }
+    for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
+      atom *Walker = *iter;
+      filler->erase(iter);
+      World::getInstance().destroyAtom(Walker);
+    }
     World::getInstance().destroyMolecule(filler);
 

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

@@ -69 +69 @@
     if (IdMapping)
       DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    // TODO: LinearInterpolationBetweenConfiguration should use stream, not the filename directly! (better for unit test)
-    if (!mol->LinearInterpolationBetweenConfiguration(start, end, outputname, *(World::getInstance().getConfig()), IdMapping))
-      DoLog(2) && (Log() << Verbose(2) << "Could not store " << outputname << " files." << endl);
+    if (!mol->LinearInterpolationBetweenConfiguration(start, end, filename, *(World::getInstance().getConfig()), IdMapping))
+      DoLog(2) && (Log() << Verbose(2) << "Could not store " << filename << " files." << endl);
     else
       DoLog(2) && (Log() << Verbose(2) << "Steps created and " << filename << " files stored." << endl);

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -65 +65 @@
     World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
     // TODO: sollte stream nicht filename benutzen, besser fuer unit test
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    mol->StoreAdjacencyToFile(NULL, outputname);
+    mol->StoreAdjacencyToFile(filename);
     delete dialog;
     return Action::success;

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -64 +64 @@
     DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << filename << "." << endl);
     World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
-    // TODO: sollte stream, nicht filenamen direkt nutzen, beser fuer unit tests
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    mol->StoreBondsToFile(NULL, outputname);
+    // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
+    mol->StoreBondsToFile(filename);
     delete dialog;
     return Action::success;

src/Actions/ParserAction/LoadXyzAction.cpp

@@ -8 +8 @@
 #include "Helpers/MemDebug.hpp"
 
+using namespace std;
+
 #include "Actions/ParserAction/LoadXyzAction.hpp"
 #include "Parser/XyzParser.hpp"
 
 #include <iostream>
+#include <set>
 #include <string>
+#include <vector>
 
-using namespace std;
 
 #include "UIElements/UIFactory.hpp"
@@ -21 +24 @@
 
 #include "atom.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
+#include "verbose.hpp"
+#include "World.hpp"
 
 /****** ParserLoadXyzAction *****/
@@ -37 +43 @@
 //};
 
-const char ParserLoadXyzAction::NAME[] = "LoadXyz";
+const char ParserLoadXyzAction::NAME[] = "parse-xyz";
 
 ParserLoadXyzAction::ParserLoadXyzAction() :
@@ -48 +54 @@
 Action::state_ptr ParserLoadXyzAction::performCall() {
   string filename;
-  XyzParser parser;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  dialog->queryString("filename",&filename, "Filename of the xyz file");
+  dialog->queryString(NAME,&filename, NAME);
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Parsing xyz file for new atoms." << endl);
     // parse xyz file
     ifstream input;
     input.open(filename.c_str());
-    if (!input.fail())
+    if (!input.fail()) {
+      // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
+      set <atom*> UniqueList;
+      {
+        vector<atom *> ListBefore = World::getInstance().getAllAtoms();
+        for (vector<atom *>::iterator runner = ListBefore.begin();runner != ListBefore.end(); ++runner)
+          UniqueList.insert(*runner);
+      }
+      XyzParser parser; // briefly instantiate a parser which is removed at end of focus
       parser.load(&input);
+      {
+        vector<atom *> ListAfter = World::getInstance().getAllAtoms();
+        pair< set<atom *>::iterator, bool > Inserter;
+        if (UniqueList.size() != ListAfter.size()) { // only create if new atoms have been parsed
+          MoleculeListClass *molecules = World::getInstance().getMolecules();
+          molecule *mol= NULL;
+          if (molecules->ListOfMolecules.empty()) {
+            mol = World::getInstance().createMolecule();
+            molecules->insert(mol);
+          } else {
+            mol = *(molecules->ListOfMolecules.begin());
+          }
+          for (vector<atom *>::iterator runner = ListAfter.begin(); runner != ListAfter.end(); ++runner) {
+            Inserter = UniqueList.insert(*runner);
+            if (Inserter.second) { // if not present, then new (just parsed) atom, add ...
+              cout << "Adding new atom " << **runner << " to new mol." << endl;
+              mol->AddAtom(*runner);
+            }
+          }
+          mol->doCountAtoms();
+        } else {
+          cout << "No atoms parsed?" << endl;
+        }
+      }
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << filename << "." << endl);
+    }
     input.close();
   }