Changeset 7d9416

Timestamp:

Jun 13, 2012, 5:39:06 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, 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:

d496fd

Parents:

a483e4

git-author:

Michael Ankele <ankele@…> (05/10/12 15:00:12)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:39:06)

Message:

Turned query<Box> into query<RealSpaceMatrix>

• CenterInBox and ChangeBox require RealSpaceMatrix instead of Box now for parameter cell_size.
• changed all query instances for Box, now query for RealSpaceMatrix.
• renamed BoxValue to RealSpaceMatrixValue (no other changes required). This is needed by the CommandLineUI only.

Location:

src

Files:

• Actions/Values.cpp (modified) (1 diff)
• Actions/Values.hpp (modified) (2 diffs)
• Actions/WorldAction/CenterInBoxAction.cpp (modified) (2 diffs)
• Actions/WorldAction/CenterInBoxAction.def (modified) (2 diffs)
• Actions/WorldAction/ChangeBoxAction.cpp (modified) (2 diffs)
• Actions/WorldAction/ChangeBoxAction.def (modified) (1 diff)
• Actions/unittests/stubs/DummyUI.hpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineDialog.cpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineDialog.hpp (modified) (3 diffs)
• UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/CommandLineParser_validate.hpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (moved) (moved from src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp ) (1 diff)
• UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/TypeEnumContainer.hpp (modified) (2 diffs)
• UIElements/Dialog.cpp (modified) (2 diffs)
• UIElements/Dialog.hpp (modified) (4 diffs)
• UIElements/Makefile.am (modified) (11 diffs)
• UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.cpp (moved) (moved from src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp ) (3 diffs)
• UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.hpp (moved) (moved from src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp ) (2 diffs)
• UIElements/Qt4/QtDialog.cpp (modified) (1 diff)
• UIElements/Qt4/QtDialog.hpp (modified) (2 diffs)
• UIElements/Qt4/Query/QtQuery.hpp (modified) (3 diffs)
• UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (moved) (moved from src/UIElements/Qt4/Query/BoxQtQuery.cpp ) (3 diffs)
• UIElements/Query/RealSpaceMatrixQuery.cpp (moved) (moved from src/UIElements/Query/BoxQuery.cpp ) (1 diff)
• UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (moved) (moved from src/UIElements/TextUI/Query/BoxTextQuery.cpp ) (2 diffs)
• UIElements/TextUI/Query/TextQuery.hpp (modified) (1 diff)
• UIElements/TextUI/TextDialog.cpp (modified) (1 diff)
• UIElements/TextUI/TextDialog.hpp (modified) (4 diffs)

src/Actions/Values.cpp

@@ -47 +47 @@
 }
 
-Box BoxValue::toBox() const
+RealSpaceMatrix RealSpaceMatrixValue::toRealSpaceMatrix() const
 {
-  Box returnBox(ReturnFullMatrixforSymmetric(matrix));
+  RealSpaceMatrix returnMatrix(ReturnFullMatrixforSymmetric(matrix));
 
-  return returnBox;
+  return returnMatrix;
 }

src/Actions/Values.hpp

@@ -18 +18 @@
 class Box;
 class BoxVector;
+class RealSpaceMatrix;
 class Vector;
 
@@ -37 +38 @@
  * as BoxValue and lateron inside the CommandLineQuery placed into the real Box.
  */
-struct BoxValue
+struct RealSpaceMatrixValue
 {
   double matrix[(NDIM*(NDIM+1))/2];
 
-  Box toBox() const;
+  RealSpaceMatrix toRealSpaceMatrix() const;
 };
 

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -69 +69 @@
 
   // set new domain
-  World::getInstance().setDomain(params.cell_size.get().getM());
+  World::getInstance().setDomain(params.cell_size.get());
 
   // center atoms
@@ -125 +125 @@
 
   // set new domain
-  World::getInstance().setDomain(state->params.cell_size.get().getM());
+  World::getInstance().setDomain(state->params.cell_size.get());
 
   // center atoms

src/Actions/WorldAction/CenterInBoxAction.def

@@ -8 +8 @@
 // all includes and forward declarations necessary for non-integral types below
 #include "Actions/Values.hpp"
-#include "Box.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include <boost/shared_ptr.hpp>
@@ -15 +15 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (Box)
+#define paramtypes (RealSpaceMatrix)
 #define paramtokens ("center-in-box")
 #define paramdescriptions ("symmetric matrix of new domain")

src/Actions/WorldAction/ChangeBoxAction.cpp

@@ -50 +50 @@
   oa << matrix;
 
-  World::getInstance().setDomain(params.cell_size.get().getM()); // this is needed as only this function is OBSERVEd.
+  World::getInstance().setDomain(params.cell_size.get()); // this is needed as only this function is OBSERVEd.
 
   // give final box size
@@ -82 +82 @@
 
 Action::state_ptr WorldChangeBoxAction::performRedo(Action::state_ptr _state){
-  World::getInstance().setDomain(params.cell_size.get().getM()); // this is needed as only this function is OBSERVEd.
+  World::getInstance().setDomain(params.cell_size.get()); // this is needed as only this function is OBSERVEd.
 
   // give final box size

src/Actions/WorldAction/ChangeBoxAction.def

@@ -8 +8 @@
 // all includes and forward declarations necessary for non-integral types below
 #include "Actions/Values.hpp"
-#include "Box.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (Box)
+#define paramtypes (RealSpaceMatrix)
 #define paramtokens ("change-box")
 #define paramdescriptions ("symmetrc matrix of the new simulation domain")

src/Actions/unittests/stubs/DummyUI.hpp

@@ -40 +40 @@
   virtual void queryVector(Parameter<Vector> &, const char*,bool, std::string = ""){}
   virtual void queryVectors(Parameter<std::vector<Vector> > &, const char*,bool, std::string = ""){}
-  virtual void queryBox(Parameter<Box> &, const char*, std::string = ""){}
+  virtual void queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &, const char*, std::string = ""){}
   virtual void queryElement(Parameter<const element *> &, const char*, std::string = ""){}
   virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = ""){}

src/UIElements/CommandLineUI/CommandLineDialog.cpp

@@ -100 +100 @@
 }
 
-void CommandLineDialog::queryBox(Parameter<Box> &param, const char* title, std::string _description) {
-  registerQuery(new BoxCommandLineQuery(param, title,_description));
+void CommandLineDialog::queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &param, const char* title, std::string _description) {
+  registerQuery(new RealSpaceMatrixCommandLineQuery(param, title,_description));
 }
 

src/UIElements/CommandLineUI/CommandLineDialog.hpp

@@ -49 +49 @@
   virtual void queryVector(Parameter<Vector> &, const char*, bool, std::string = "");
   virtual void queryVectors(Parameter<std::vector<Vector> > &, const char*, bool, std::string = "");
-  virtual void queryBox(Parameter<Box> &, const char*, std::string = "");
+  virtual void queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &, const char*, std::string = "");
   virtual void queryElement(Parameter<const element *> &, const char*, std::string = "");
   virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "");
@@ -61 +61 @@
   class AtomsCommandLineQuery;
   class BooleanCommandLineQuery;
-  class BoxCommandLineQuery;
   class DoubleCommandLineQuery;
   class DoublesCommandLineQuery;
@@ -72 +71 @@
   class MoleculeCommandLineQuery;
   class MoleculesCommandLineQuery;
+  class RealSpaceMatrixCommandLineQuery;
   class StringCommandLineQuery;
   class StringsCommandLineQuery;

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -193 +193 @@
         ;
       break;
-    case TypeEnumContainer::BoxType:
-      OptionList->add_options()
-        (currentOption->getKeyAndShortForm().c_str(),
-//            currentOption->hasDefaultValue() ?
-//                  po::value < BoxValue >()->default_value(boost::lexical_cast<BoxValue>(currentOption->getDefaultValue().c_str())) :
-                  po::value < BoxValue >(),
-                  currentOption->getDescription().c_str())
-        ;
-      break;
     case TypeEnumContainer::FileType:
       OptionList->add_options()
@@ -370 +361 @@
                   po::value < std::string >()->default_value(boost::lexical_cast< std::string >(currentOption->getDefaultValue().c_str())) :
                   po::value < std::string >(),
+                  currentOption->getDescription().c_str())
+        ;
+      break;
+    case TypeEnumContainer::RealSpaceMatrixType:
+      OptionList->add_options()
+        (currentOption->getKeyAndShortForm().c_str(),
+//            currentOption->hasDefaultValue() ?
+//                  po::value < RealSpaceMatrixValue >()->default_value(boost::lexical_cast<BoxValue>(currentOption->getDefaultValue().c_str())) :
+                  po::value < RealSpaceMatrixValue >(),
                   currentOption->getDescription().c_str())
         ;

src/UIElements/CommandLineUI/CommandLineParser_validate.cpp

@@ -84 +84 @@
 }
 
-void validate(boost::any& v, const std::vector<std::string>& values, BoxValue *, int)
+void validate(boost::any& v, const std::vector<std::string>& values, RealSpaceMatrixValue *, int)
 {
-  BoxValue BV;
+  RealSpaceMatrixValue RSMV;
   std::vector<std::string> components;
 
@@ -129 +129 @@
   }
   for (size_t i=0;i<(NDIM*(NDIM+1))/2; ++i)
-    BV.matrix[i] = boost::lexical_cast<double>(components.at(i));
-  v = boost::any(BoxValue(BV));
+    RSMV.matrix[i] = boost::lexical_cast<double>(components.at(i));
+  v = boost::any(RealSpaceMatrixValue(RSMV));
 }
 

src/UIElements/CommandLineUI/CommandLineParser_validate.hpp

@@ -22 +22 @@
 #include <boost/lexical_cast.hpp>
 
-class BoxValue;
+class RealSpaceMatrixValue;
 class VectorValue;
 
 void validate(boost::any& v, const std::vector<std::string>& values, VectorValue *, int);
-void validate(boost::any& v, const std::vector<std::string>& values, BoxValue *, int);
+void validate(boost::any& v, const std::vector<std::string>& values, RealSpaceMatrixValue *, int);
 void validate(boost::any& v, const std::vector<std::string>& values, boost::filesystem::path *, int);
 

src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp

@@ -129 +129 @@
 };
 
-class CommandLineDialog::BoxCommandLineQuery : public Dialog::BoxQuery {
+class CommandLineDialog::RealSpaceMatrixCommandLineQuery : public Dialog::RealSpaceMatrixQuery {
 public:
-  BoxCommandLineQuery(Parameter<Box> &param, std::string title, std::string _description = "");
-  virtual ~BoxCommandLineQuery();
+  RealSpaceMatrixCommandLineQuery(Parameter<RealSpaceMatrix> &param, std::string title, std::string _description = "");
+  virtual ~RealSpaceMatrixCommandLineQuery();
   virtual bool handle();
 };

src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp

@@ -27 +27 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 
-CommandLineDialog::BoxCommandLineQuery::BoxCommandLineQuery(Parameter<Box> &param, std::string title, std::string _description) :
-    Dialog::BoxQuery(param, title, _description)
+CommandLineDialog::RealSpaceMatrixCommandLineQuery::RealSpaceMatrixCommandLineQuery(Parameter<RealSpaceMatrix> &param, std::string title, std::string _description) :
+    Dialog::RealSpaceMatrixQuery(param, title, _description)
 {}
 
-CommandLineDialog::BoxCommandLineQuery::~BoxCommandLineQuery()
+CommandLineDialog::RealSpaceMatrixCommandLineQuery::~RealSpaceMatrixCommandLineQuery()
 {}
 
-bool CommandLineDialog::BoxCommandLineQuery::handle() {
-  BoxValue temp;
+bool CommandLineDialog::RealSpaceMatrixCommandLineQuery::handle() {
+  RealSpaceMatrixValue temp;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as< BoxValue >();
-    tmp.set(temp.toBox());
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< RealSpaceMatrixValue >();
+    tmp.set(temp.toRealSpaceMatrix());
     return true;
   } else {

src/UIElements/CommandLineUI/TypeEnumContainer.cpp

@@ -31 +31 @@
 
 #include "Atom/atom.hpp"
-#include "Box.hpp"
 #include "LinearAlgebra/BoxVector.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "Element/element.hpp"
@@ -45 +45 @@
   TypeEnumMap[&typeid(void)] = NoneType;
   TypeEnumMap[&typeid(bool)] = BooleanType;
-  TypeEnumMap[&typeid(Box)] = BoxType;
+  TypeEnumMap[&typeid(RealSpaceMatrix)] = RealSpaceMatrixType;
   TypeEnumMap[&typeid(BoxVector)] = VectorType;
   TypeEnumMap[&typeid(Vector)] = VectorType;

src/UIElements/CommandLineUI/TypeEnumContainer.hpp

@@ -28 +28 @@
   enum EnumOfTypes { NoneType,
         BooleanType,
-        BoxType,
         FileType,
         ListOfFilesType,
@@ -47 +46 @@
         ElementType,
         ListOfElementsType,
-        RandomNumberDistribution_ParametersType
+        RandomNumberDistribution_ParametersType,
+        RealSpaceMatrixType
   };
 

src/UIElements/Dialog.cpp

@@ -29 +29 @@
 
 class Atom;
-class Box;
 class element;
 class RealSpaceMatrix;
@@ -193 +192 @@
 }
 
-template <> void Dialog::query<Box>(Parameter<Box> &param, const char *token, std::string description)
-{
-  queryBox(param, token, description);
+template <> void Dialog::query<RealSpaceMatrix>(Parameter<RealSpaceMatrix> &param, const char *token, std::string description)
+{
+  queryRealSpaceMatrix(param, token, description);
 }
 

src/UIElements/Dialog.hpp

@@ -20 +20 @@
 
 #include <boost/filesystem.hpp>
-#include "Box.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "RandomNumbers/RandomNumberDistribution_Parameters.hpp"
@@ -26 +26 @@
 
 class atom;
-class Box;
+class RealSpaceMatrix;
 class element;
 class molecule;
@@ -174 +174 @@
   virtual void queryVector(Parameter<Vector> &, const char*,bool, std::string = "")=0;
   virtual void queryVectors(Parameter<std::vector<Vector> > &, const char*,bool, std::string = "")=0;
-  virtual void queryBox(Parameter<Box> &, const char*, std::string = "")=0;
+  virtual void queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &, const char*, std::string = "")=0;
   virtual void queryElement(Parameter<const element *> &, const char*, std::string = "")=0;
   virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "")=0;
@@ -422 +422 @@
   };
 
-  class BoxQuery : public Query {
-  public:
-      BoxQuery(Parameter<Box> &param, std::string title, std::string _description = "");
-      virtual ~BoxQuery();
+  class RealSpaceMatrixQuery : public Query {
+  public:
+      RealSpaceMatrixQuery(Parameter<RealSpaceMatrix> &param, std::string title, std::string _description = "");
+      virtual ~RealSpaceMatrixQuery();
       virtual bool handle()=0;
       virtual void setResult();
     protected:
-      Parameter<Box> &tmp;
+      Parameter<RealSpaceMatrix> &tmp;
   };
 

src/UIElements/Makefile.am

@@ -5 +5 @@
   UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp \
-  UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp \
@@ -16 +15 @@
   UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp \
+  UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp \
   UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp \
@@ -74 +74 @@
   UIElements/TextUI/Query/AtomTextQuery.cpp \
   UIElements/TextUI/Query/BooleanTextQuery.cpp \
-  UIElements/TextUI/Query/BoxTextQuery.cpp \
   UIElements/TextUI/Query/DoubleTextQuery.cpp \
   UIElements/TextUI/Query/DoublesTextQuery.cpp \
@@ -85 +84 @@
   UIElements/TextUI/Query/MoleculesTextQuery.cpp \
   UIElements/TextUI/Query/MoleculeTextQuery.cpp \
+  UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp \
   UIElements/TextUI/Query/StringTextQuery.cpp \
   UIElements/TextUI/Query/StringsTextQuery.cpp \
@@ -123 +123 @@
   UIElements/Query/AtomsQuery.cpp \
   UIElements/Query/BooleanQuery.cpp \
-  UIElements/Query/BoxQuery.cpp \
   UIElements/Query/DoubleQuery.cpp \
   UIElements/Query/DoublesQuery.cpp \
@@ -136 +135 @@
   UIElements/Query/Query.cpp \
   UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp \
+  UIElements/Query/RealSpaceMatrixQuery.cpp \
   UIElements/Query/StringQuery.cpp \
   UIElements/Query/StringsQuery.cpp \
@@ -158 +158 @@
   UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp \
   UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp \
-  UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp \
   UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp \
   UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp \
@@ -172 +171 @@
   UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp \
   UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp \
+  UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.cpp \
   UIElements/Qt4/Query/AtomQtQuery.cpp \
   UIElements/Qt4/Query/AtomsQtQuery.cpp \
   UIElements/Qt4/Query/BooleanQtQuery.cpp \
-  UIElements/Qt4/Query/BoxQtQuery.cpp \
   UIElements/Qt4/Query/DoubleQtQuery.cpp \
   UIElements/Qt4/Query/DoublesQtQuery.cpp \
@@ -186 +185 @@
   UIElements/Qt4/Query/MoleculeQtQuery.cpp \
   UIElements/Qt4/Query/MoleculesQtQuery.cpp \
+  UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp \
   UIElements/Qt4/Query/StringQtQuery.cpp \
   UIElements/Qt4/Query/StringsQtQuery.cpp \
@@ -215 +215 @@
   UIElements/Qt4/Pipe/AtomsQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/BooleanQtQueryPipe.hpp \
-  UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/DoubleQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp \
@@ -225 +224 @@
   UIElements/Qt4/Pipe/MoleculesQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.hpp \
+  UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/StringQtQueryPipe.hpp \
   UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.hpp \

src/UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.cpp

@@ -18 +18 @@
 #endif
 
-#include "UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp"
+#include "UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.hpp"
 #include "UIElements/Qt4/QtDialog.hpp"
 
@@ -26 +26 @@
 #include "CodePatterns/MemDebug.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
 
-BoxQtQueryPipe::BoxQtQueryPipe(Parameter<Box> &_content, QtDialog *_dialog, QTableWidget *_inputTable) :
+RealSpaceMatrixQtQueryPipe::RealSpaceMatrixQtQueryPipe(Parameter<RealSpaceMatrix> &_content, QtDialog *_dialog, QTableWidget *_inputTable) :
   content(_content),
   dialog(_dialog),
@@ -37 +36 @@
 }
 
-BoxQtQueryPipe::~BoxQtQueryPipe()
+RealSpaceMatrixQtQueryPipe::~RealSpaceMatrixQtQueryPipe()
 {
   delete tmpM;
 }
 
-void BoxQtQueryPipe::update(int row, int column)
+void RealSpaceMatrixQtQueryPipe::update(int row, int column)
 {
   tmpM->at(row, column) = inputTable->item(row, column)->text().toDouble();
-  Box b;
-  b.setM(*tmpM);
-  content.set(b);
+  content.set(*tmpM);
   dialog->update();
 }

src/UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.hpp

@@ -20 +20 @@
 class QTableWidget;
 
-class Box;
 class QtDialog;
 class RealSpaceMatrix;
 
 
-class BoxQtQueryPipe : public QWidget {
+class RealSpaceMatrixQtQueryPipe : public QWidget {
   Q_OBJECT
 public:
-  BoxQtQueryPipe(Parameter<Box> &_content, QtDialog *_dialog, QTableWidget *_inputTable);
-  virtual ~BoxQtQueryPipe();
+  RealSpaceMatrixQtQueryPipe(Parameter<RealSpaceMatrix> &_content, QtDialog *_dialog, QTableWidget *_inputTable);
+  virtual ~RealSpaceMatrixQtQueryPipe();
 
 public slots:
@@ -35 +34 @@
 
 private:
-  Parameter<Box> &content;
+  Parameter<RealSpaceMatrix> &content;
   QtDialog *dialog;
   QTableWidget *inputTable;

src/UIElements/Qt4/QtDialog.cpp

@@ -95 +95 @@
 }
 
-void QtDialog::queryBox(Parameter<Box> &param, const char* title, std::string)
+void QtDialog::queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &param, const char* title, std::string)
 {
-  registerQuery(new BoxQtQuery(param,title,inputLayout,this));
+  registerQuery(new RealSpaceMatrixQtQuery(param,title,inputLayout,this));
 }
 

src/UIElements/Qt4/QtDialog.hpp

@@ -49 +49 @@
   virtual void queryVector(Parameter<Vector> &, const char*,bool,std::string = "");
   virtual void queryVectors(Parameter<std::vector<Vector> > &, const char*,bool,std::string = "");
-  virtual void queryBox(Parameter<Box> &, const char*, std::string = "");
+  virtual void queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &, const char*, std::string = "");
   virtual void queryElement(Parameter<const element *> &, const char*,std::string = "");
   virtual void queryElements(Parameter<std::vector<const element *> > &, const char*,std::string = "");
@@ -63 +63 @@
   class AtomsQtQuery;
   class BooleanQtQuery;
-  class BoxQtQuery;
+  class RealSpaceMatrixQtQuery;
   class DoubleQtQuery;
   class DoublesQtQuery;

src/UIElements/Qt4/Query/QtQuery.hpp

@@ -37 +37 @@
 class AtomsQtQueryPipe;
 class BooleanQtQueryPipe;
-class BoxQtQueryPipe;
+class RealSpaceMatrixQtQueryPipe;
 class DoubleQtQueryPipe;
 class DoublesQtQueryPipe;
@@ -98 +98 @@
 };
 
-class QtDialog::BoxQtQuery : public Dialog::BoxQuery {
-public:
-  BoxQtQuery(Parameter<Box> &, std::string _title, QBoxLayout *_parent,QtDialog *_dialog);
-  virtual ~BoxQtQuery();
+class QtDialog::RealSpaceMatrixQtQuery : public Dialog::RealSpaceMatrixQuery {
+public:
+  RealSpaceMatrixQtQuery(Parameter<RealSpaceMatrix> &, std::string _title, QBoxLayout *_parent,QtDialog *_dialog);
+  virtual ~RealSpaceMatrixQtQuery();
   virtual bool handle();
 private:
@@ -109 +109 @@
   QTableWidget *inputTable;
 
-  BoxQtQueryPipe *pipe;
+  RealSpaceMatrixQtQueryPipe *pipe;
 };
 

src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp

@@ -25 +25 @@
 
 #include "UIElements/Qt4/Query/QtQuery.hpp"
-#include "UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp"
+#include "UIElements/Qt4/Pipe/RealSpaceMatrixQtQueryPipe.hpp"
 
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "World.hpp"
 
-QtDialog::BoxQtQuery::BoxQtQuery(Parameter<Box> &param, std::string _title,QBoxLayout *_parent,QtDialog *_dialog) :
-    Dialog::BoxQuery(param, _title),
+QtDialog::RealSpaceMatrixQtQuery::RealSpaceMatrixQtQuery(Parameter<RealSpaceMatrix> &param, std::string _title,QBoxLayout *_parent,QtDialog *_dialog) :
+    Dialog::RealSpaceMatrixQuery(param, _title),
     parent(_parent)
 {
@@ -44 +44 @@
   inputTable->setVerticalHeaderLabels(CoordinateList);
 
-  pipe = new BoxQtQueryPipe(tmp,_dialog, inputTable);
+  pipe = new RealSpaceMatrixQtQueryPipe(tmp,_dialog, inputTable);
 
   // fill the box with current matrix
@@ -62 +62 @@
 }
 
-QtDialog::BoxQtQuery::~BoxQtQuery()
+QtDialog::RealSpaceMatrixQtQuery::~RealSpaceMatrixQtQuery()
 {
   delete pipe;
 }
 
-bool QtDialog::BoxQtQuery::handle() {
+bool QtDialog::RealSpaceMatrixQtQuery::handle() {
   return true;
 }

src/UIElements/Query/RealSpaceMatrixQuery.cpp

@@ -24 +24 @@
 
 // Box Queries
-Dialog::BoxQuery::BoxQuery(Parameter<Box> &param, std::string title, std::string _description) :
+Dialog::RealSpaceMatrixQuery::RealSpaceMatrixQuery(Parameter<RealSpaceMatrix> &param, std::string title, std::string _description) :
   Query(title, _description),
   tmp(param)
 {}
 
-Dialog::BoxQuery::~BoxQuery()
+Dialog::RealSpaceMatrixQuery::~RealSpaceMatrixQuery()
 {}
 
-void Dialog::BoxQuery::setResult() {
+void Dialog::RealSpaceMatrixQuery::setResult() {
   //ValueStorage::getInstance().setCurrentValue(title.c_str(), tmp);
 }

src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp

@@ -29 +29 @@
 
 
-TextDialog::BoxTextQuery::BoxTextQuery(Parameter<Box> &param, std::string title, std::string _description) :
-    Dialog::BoxQuery(param, title,_description)
+TextDialog::RealSpaceMatrixTextQuery::RealSpaceMatrixTextQuery(Parameter<RealSpaceMatrix> &param, std::string title, std::string _description) :
+    Dialog::RealSpaceMatrixQuery(param, title,_description)
 {}
 
-TextDialog::BoxTextQuery::~BoxTextQuery()
+TextDialog::RealSpaceMatrixTextQuery::~RealSpaceMatrixTextQuery()
 {}
 
-bool TextDialog::BoxTextQuery::handle() {
+bool TextDialog::RealSpaceMatrixTextQuery::handle() {
   std::cout << getTitle();
 
@@ -56 +56 @@
   M.set(2,1, temp[4]);
   M.set(2,2, temp[5]);
-  Box temp_box;
-  temp_box.setM(M);
-  tmp.set(temp_box);
+  tmp.set(M);
   return true;
 }

src/UIElements/TextUI/Query/TextQuery.hpp

@@ -38 +38 @@
 };
 
-class TextDialog::BoxTextQuery : public Dialog::BoxQuery {
+class TextDialog::RealSpaceMatrixTextQuery : public Dialog::RealSpaceMatrixQuery {
 public:
-  BoxTextQuery(Parameter<Box> &, std::string title, std::string _description = NULL);
-  virtual ~BoxTextQuery();
+  RealSpaceMatrixTextQuery(Parameter<RealSpaceMatrix> &, std::string title, std::string _description = NULL);
+  virtual ~RealSpaceMatrixTextQuery();
   virtual bool handle();
 };

src/UIElements/TextUI/TextDialog.cpp

@@ -98 +98 @@
 }
 
-void TextDialog::queryBox(Parameter<Box> &param, const char* title, std::string description) {
-  registerQuery(new BoxTextQuery(param, title,description));
+void TextDialog::queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &param, const char* title, std::string description) {
+  registerQuery(new RealSpaceMatrixTextQuery(param, title,description));
 }
 

src/UIElements/TextUI/TextDialog.hpp

@@ -22 +22 @@
 class element;
 class molecule;
+class RealSpaceMatrix;
 class Vector;
 
@@ -46 +47 @@
   virtual void queryVector(Parameter<Vector> &, const char*,bool, std::string = "");
   virtual void queryVectors(Parameter<std::vector<Vector> > &, const char*,bool, std::string = "");
-  virtual void queryBox(Parameter<Box> &, const char*, std::string = "");
+  virtual void queryRealSpaceMatrix(Parameter<RealSpaceMatrix> &, const char*, std::string = "");
   virtual void queryElement(Parameter<const element *> &, const char*, std::string = "");
   virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "");
@@ -59 +60 @@
   class AtomsTextQuery;
   class BooleanTextQuery;
-  class BoxTextQuery;
   class DoubleTextQuery;
   class DoublesTextQuery;
@@ -70 +70 @@
   class MoleculeTextQuery;
   class MoleculesTextQuery;
+  class RealSpaceMatrixTextQuery;
   class StringTextQuery;
   class StringsTextQuery;