Changeset 73faf4 for src

Timestamp:

May 8, 2017, 2:00:47 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_goodresults, ForceAnnealing_tocheck

Children:

c8165c

Parents:

ce254c (diff), cb6357 (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 'GeometryObjects' into Candidate_v1.6.1

Location:

src

Files:

• Actions/Action_impl_pre.hpp (modified) (1 diff)
• Actions/CommandAction/HelpAction.cpp (modified) (1 diff)
• Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added)
• Actions/GeometryAction/GeometryDistanceToVectorAction.def (added)
• Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added)
• Actions/GeometryAction/GeometryInputToVectorAction.cpp (added)
• Actions/GeometryAction/GeometryInputToVectorAction.def (added)
• Actions/GeometryAction/GeometryInputToVectorAction.hpp (added)
• Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added)
• Actions/GeometryAction/GeometryPlaneToVectorAction.def (added)
• Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added)
• Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added)
• Actions/GeometryAction/GeometryPositionToVectorAction.def (added)
• Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added)
• Actions/GeometryAction/GeometryRemoveAction.cpp (added)
• Actions/GeometryAction/GeometryRemoveAction.def (added)
• Actions/GeometryAction/GeometryRemoveAction.hpp (added)
• Actions/GlobalListOfActions.hpp (modified) (1 diff)
• Actions/Makefile.am (modified) (4 diffs)
• Actions/MakroAction_impl_pre.hpp (modified) (1 diff)
• Actions/Values.cpp (modified) (3 diffs)
• Actions/Values.hpp (modified) (1 diff)
• Geometry/GeometryObject.cpp (added)
• Geometry/GeometryObject.hpp (added)
• Geometry/GeometryRegistry.cpp (added)
• Geometry/GeometryRegistry.hpp (added)
• Geometry/Makefile.am (added)
• Makefile.am (modified) (1 diff)
• Parameters/Makefile.am (modified) (6 diffs)
• Parameters/Parameter.hpp (modified) (3 diffs)
• Parameters/Parameter_impl.hpp (modified) (4 diffs)
• Parameters/Specifics/Parameter_vector.cpp (added)
• Parameters/Specifics/Parameter_vector.hpp (added)
• Parameters/Specifics/Value_vector.cpp (added)
• Parameters/Specifics/Value_vector.hpp (added)
• Parameters/Validators/Specific/GeometryNameValidator.cpp (added)
• Parameters/Validators/Specific/GeometryNameValidator.hpp (added)
• Parameters/Validators/Specific/PresentGeometryNameValidator.cpp (added)
• Parameters/Validators/Specific/PresentGeometryNameValidator.hpp (added)
• Parameters/Value.hpp (modified) (3 diffs)
• Parameters/Value_impl.hpp (modified) (2 diffs)
• Parameters/unittests/Makefile.am (modified) (2 diffs)
• UIElements/CommandLineUI/CommandLineDialog.hpp (modified) (2 diffs)
• UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) (2 diffs)
• UIElements/Dialog.cpp (modified) (1 diff)
• UIElements/Dialog.hpp (modified) (3 diffs)
• UIElements/GlobalListOfParameterQueries.hpp (modified) (2 diffs)
• UIElements/Makefile.am (modified) (3 diffs)
• UIElements/Menu/MenuDescription.cpp (modified) (3 diffs)
• UIElements/Qt4/QtDialog.hpp (modified) (2 diffs)
• UIElements/Qt4/QtMainWindow.cpp (modified) (3 diffs)
• UIElements/Qt4/QtMainWindow.hpp (modified) (2 diffs)
• UIElements/Qt4/Query/QtQuery.hpp (modified) (2 diffs)
• UIElements/Qt4/Query/QtQueryList.hpp (modified) (1 diff)
• UIElements/Qt4/Query/VectorQtQuery.cpp (modified) (7 diffs)
• UIElements/TextUI/Query/TextQuery.hpp (modified) (1 diff)
• UIElements/TextUI/Query/VectorTextQuery.cpp (modified) (1 diff)
• UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) (2 diffs)
• UIElements/TextUI/TextDialog.hpp (modified) (2 diffs)
• UIElements/Views/Qt4/QtGeometryList.cpp (added)
• UIElements/Views/Qt4/QtGeometryList.hpp (added)
• cleanUp.cpp (modified) (2 diffs)

src/Actions/Action_impl_pre.hpp

@@ -173 +173 @@
     output << \
     BOOST_PP_IF(n, ", ", "") \
-    << "\"" << toPythonString(params. \
+    << "\"" << params. \
         BOOST_PP_SEQ_ELEM(n, paramreferences) \
-        .getUnvalidated()) \
+        .getAsStringUnvalidated() \
     << "\"";
 

src/Actions/CommandAction/HelpAction.cpp

@@ -73 +73 @@
   std::cout << "\t - List/vector of strings: gives as \"first\" \"second\" \"third\"." << std::endl;
   std::cout << "\t - Vector: give as \"x,y,z\", i.e. its 3 components." << std::endl;
+  std::cout << "\t -         or give as \"<name>\", where <name> is a stored geometry name." << std::endl;
   std::cout << "\t - Domain: give as \"xx,yx,yy,zx,zy,zz\", i.e. symmetric 3x3 matrix." << std::endl;
   std::cout << "\t - Path/filename: give as \"<path/filename>\"." << std::endl;

src/Actions/GlobalListOfActions.hpp

@@ -69 +69 @@
   (FragmentationStoreSaturatedFragment) \
   (FragmentationStructuralOptimization) \
+  (GeometryDistanceToVector) \
+  (GeometryInputToVector) \
+  (GeometryPlaneToVector) \
+  (GeometryPositionToVector) \
+  (GeometryRemove) \
   (GraphUpdateMolecules) \
   (GraphCorrectBondDegree) \

src/Actions/Makefile.am

@@ -64 +64 @@
   ${FILLACTIONSOURCE} \
   ${FRAGMENTATIONACTIONSOURCE} \
+  ${GEOMETRYACTIONSOURCE} \
   ${GRAPHACTIONSOURCE} \
   ${MOLECULEACTIONSOURCE} \
@@ -84 +85 @@
   ${FILLACTIONHEADER} \
   ${FRAGMENTATIONACTIONHEADER} \
+  ${GEOMETRYACTIONHEADER} \
   ${GRAPHACTIONHEADER} \
   ${MOLECULEACTIONHEADER} \
@@ -104 +106 @@
   ${FILLACTIONDEFS} \
   ${FRAGMENTATIONACTIONDEFS} \
+  ${GEOMETRYACTIONDEFS} \
   ${GRAPHACTIONDEFS} \
   ${MOLECULEACTIONDEFS} \
@@ -285 +288 @@
   Actions/FragmentationAction/StoreSaturatedFragmentAction.def \
   Actions/FragmentationAction/StructuralOptimizationAction.def
+
+GEOMETRYACTIONSOURCE = \
+        Actions/GeometryAction/GeometryDistanceToVectorAction.cpp \
+        Actions/GeometryAction/GeometryInputToVectorAction.cpp \
+        Actions/GeometryAction/GeometryPlaneToVectorAction.cpp \
+        Actions/GeometryAction/GeometryPositionToVectorAction.cpp \
+        Actions/GeometryAction/GeometryRemoveAction.cpp
+GEOMETRYACTIONHEADER = \
+        Actions/GeometryAction/GeometryDistanceToVectorAction.hpp \
+        Actions/GeometryAction/GeometryInputToVectorAction.hpp \
+        Actions/GeometryAction/GeometryPlaneToVectorAction.hpp \
+        Actions/GeometryAction/GeometryPositionToVectorAction.hpp \
+        Actions/GeometryAction/GeometryRemoveAction.hpp
+GEOMETRYACTIONDEFS = \
+        Actions/GeometryAction/GeometryDistanceToVectorAction.def \
+        Actions/GeometryAction/GeometryInputToVectorAction.def \
+        Actions/GeometryAction/GeometryPlaneToVectorAction.def \
+        Actions/GeometryAction/GeometryPositionToVectorAction.def \
+        Actions/GeometryAction/GeometryRemoveAction.def
 
 GRAPHACTIONSOURCE = \

src/Actions/MakroAction_impl_pre.hpp

@@ -165 +165 @@
     output << \
     BOOST_PP_IF(n, ", ", "") \
-    << "\"" << toPythonString(params. \
+    << "\"" << params. \
         BOOST_PP_SEQ_ELEM(n, paramreferences) \
-        .get()) \
+        .getAsStringUnvalidated() \
     << "\"";
 

src/Actions/Values.cpp

@@ -37 +37 @@
 #include "CodePatterns/Assert.hpp"
 
+#include <boost/lexical_cast.hpp>
+#include <boost/tokenizer.hpp>
+
 #include "Box.hpp"
 #include "LinearAlgebra/BoxVector.hpp"
@@ -44 +47 @@
 #include "Values.hpp"
 
+static const Vector parseAsVector(const std::string &_string)
+{
+  Vector temp;
+  // dissect by ","
+  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
+  boost::char_separator<char> value_separator(",)(");
+
+  bool status = true;
+  tokenizer tokens(_string, value_separator);
+  if (!_string.empty()) {
+    tokenizer::iterator tok_iter = tokens.begin();
+    for (size_t i=0;i<NDIM;++i) {
+      if (tok_iter == tokens.end()) {
+        status = false;
+        break;
+      }
+      temp[i] = boost::lexical_cast<double>(*(tok_iter++));
+    }
+  }
+  if (!status)
+    temp.Zero();
+
+  return temp;
+}
+
 Vector VectorValue::toVector() const
 {
-  Vector returnVector(vector);
+  Vector returnVector = parseAsVector(vectorstring);
 
   return returnVector;
@@ -54 +82 @@
 {
   BoxVector returnVector;
-  static_cast<Vector>(returnVector) = Vector(vector); // under its hood it's still a Vector
+  static_cast<Vector>(returnVector) = parseAsVector(vectorstring); // under its hood it's still a Vector
 
   ASSERT(_box.isValid(returnVector),

src/Actions/Values.hpp

@@ -27 +27 @@
  * are registered as VectorValue and lateron inside the CommandLineQuery placed
  * into the real vector.
+ *
+ * We use this abstraction also for Geometry Objects, i.e. string names
+ * referencing vectors in the GeomtryRegistry.
  */
 struct VectorValue
 {
-  double vector[NDIM];
+  std::string vectorstring;
 
   Vector toVector() const;

src/Makefile.am

@@ -11 +11 @@
 # libMolecuilder.la requires the libraries listed below
 
+include Geometry/Makefile.am
 include Helpers/Makefile.am
 include Shapes/Makefile.am

src/Parameters/Makefile.am

@@ -4 +4 @@
 
 PARAMETERSOURCE = \
+        Parameters/Specifics/Parameter_vector.cpp \
         Parameters/Specifics/Value_atom.cpp \
         Parameters/Specifics/Value_element.cpp \
@@ -9 +10 @@
         Parameters/Specifics/Value_molecule.cpp \
         Parameters/Specifics/Value_string.cpp \
+        Parameters/Specifics/Value_vector.cpp \
         Parameters/Validators/Specific/ActionNameValidator.cpp \
         Parameters/Validators/Specific/AtomDataValidator.cpp \
@@ -17 +19 @@
         Parameters/Validators/Specific/FileSuffixValidator.cpp \
         Parameters/Validators/Specific/FormulaValidator.cpp \
+        Parameters/Validators/Specific/GeometryNameValidator.cpp \
         Parameters/Validators/Specific/KeyValueValidator.cpp \
         Parameters/Validators/Specific/MoleculeIdValidator.cpp \
         Parameters/Validators/Specific/ParserFileValidator.cpp \
         Parameters/Validators/Specific/ParserTypeValidator.cpp \
+        Parameters/Validators/Specific/PresentGeometryNameValidator.cpp \
         Parameters/Validators/Specific/RandomNumberValidators.cpp \
         Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp \
@@ -45 +49 @@
         Parameters/ValueInterface.hpp \
         Parameters/Specifics/KeyValuePair.hpp \
+        Parameters/Specifics/Parameter_vector.hpp \
         Parameters/Specifics/Value_atom.hpp \
         Parameters/Specifics/Value_element.hpp \
@@ -50 +55 @@
         Parameters/Specifics/Value_molecule.hpp \
         Parameters/Specifics/Value_string.hpp \
+        Parameters/Specifics/Value_vector.hpp \
         Parameters/Validators/DiscreteValidator.hpp \
         Parameters/Validators/DiscreteValidator_impl.hpp \
@@ -74 +80 @@
         Parameters/Validators/Specific/FileSuffixValidator.hpp \
         Parameters/Validators/Specific/FormulaValidator.hpp \
+        Parameters/Validators/Specific/GeometryNameValidator.hpp \
         Parameters/Validators/Specific/KeyValueValidator.hpp \
         Parameters/Validators/Specific/MoleculeIdValidator.hpp \
         Parameters/Validators/Specific/ParserFileValidator.hpp \
         Parameters/Validators/Specific/ParserTypeValidator.hpp \
+        Parameters/Validators/Specific/PresentGeometryNameValidator.hpp \
         Parameters/Validators/Specific/RandomNumberValidators.hpp \
         Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.hpp \

src/Parameters/Parameter.hpp

@@ -25 +25 @@
 class ParameterValueException;
 
-/** This class encapsulates a clonable, continuous value.
+/** This class encapsulates a cloneable, continuous value.
  *
  */
@@ -48 +48 @@
   bool isValidAsString(const std::string &_value) const throw(ParameterValidatorException);
   const std::string getAsString() const throw(ParameterValueException);
+  const std::string getAsStringUnvalidated() const throw(ParameterValueException);
   void setAsString(const std::string &_value) throw(ParameterValueException);
 
@@ -78 +79 @@
 };
 
+#include "Parameters/Specifics/Parameter_vector.hpp"
+
 #include "Parameter_impl.hpp"
 

src/Parameters/Parameter_impl.hpp

@@ -23 +23 @@
   value(instance.value.getValidator())
 {
-  value.set(instance.value.value);
+  value.set(instance.value.getUnvalidated());
 }
 
@@ -171 +171 @@
 }
 
+/** Catch call to value.getAsStringUnvalidated() to add exception information.
+ *
+ * @return parameter value as string
+ */
+template<typename T>
+inline const std::string Parameter<T>::getAsStringUnvalidated() const throw(ParameterValueException)
+{
+  try {
+    return value.getAsStringUnvalidated();
+  } catch(ParameterException &e) {
+    e << ParameterName(ParameterInterface::getName());
+    throw;
+  }
+}
+
 /** Catch call to value.isValid() to add exception information.
  *
@@ -258 +273 @@
   try {
     status = status &&
-        (value == _instance.value);
+        (getUnvalidated() == _instance.getUnvalidated());
     status = status && (ParameterInterface::getName() == _instance.ParameterInterface::getName());
   } catch(ParameterException &e) {
@@ -276 +291 @@
   Parameter<T> *instance = new Parameter<T>(ParameterInterface::getName(), value.getValidator());
   // do not use get, we do not check for validity here
-  if (value.ValueSet)
-    instance->set(value.value);
+  if (value.isSet())
+    instance->set(value.getUnvalidated());
   return instance;
 }

src/Parameters/Value.hpp

@@ -67 +67 @@
   friend class ValueTest;
   friend class ContinuousValueTest;
-  friend class Parameter<T>;
+//  friend class Parameter<T>;
 public:
   Value();
@@ -85 +85 @@
   bool isValidAsString(const std::string &_value) const throw(ParameterValidatorException);
   const std::string getAsString() const throw(ParameterValueException);
+  const std::string getAsStringUnvalidated() const throw(ParameterValueException);
   void setAsString(const std::string &_value) throw(ParameterException);
 
@@ -123 +124 @@
 #include "Specifics/Value_molecule.hpp"
 #include "Specifics/Value_string.hpp"
+#include "Specifics/Value_vector.hpp"
 
 #include "Value_impl.hpp"

src/Parameters/Value_impl.hpp

@@ -22 +22 @@
 #include "CodePatterns/Log.hpp"
 
+#include "Actions/toPythonString.hpp"
 #include "Validators/DummyValidator.hpp"
 #include "Validators/DiscreteValidator.hpp"
@@ -184 +185 @@
 {
   return toString(get());
+}
+
+/** Getter of unvalidated value, returning string.
+ *
+ * @return string value
+ */
+template <class T>
+inline const std::string Value<T>::getAsStringUnvalidated() const throw(ParameterValueException)
+{
+  return toPythonString(getUnvalidated());
 }
 

src/Parameters/unittests/Makefile.am

@@ -31 +31 @@
         libUnitTest.la \
         ../libMolecuilder.la \
+        ../libMolecuilderParameters.la \
+        ../libMolecuilderGeometry.la \
         $(top_builddir)/ThirdParty/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \
@@ -47 +49 @@
         ../Parameters/ValueInterface.hpp
 ContinuousValueTest_LDADD = \
+        ../libMolecuilderParameters.la \
+        ../libMolecuilderGeometry.la \
         $(PARAMETERSLIBS)
  

src/UIElements/CommandLineUI/CommandLineDialog.hpp

@@ -48 +48 @@
   #include <boost/preprocessor/facilities/empty.hpp>
 
+  virtual void queryVector(Parameter<Vector> &, const std::string ="", const std::string = "");
+  virtual void queryVectors(Parameter< std::vector<Vector> > &, const std::string ="", const std::string = "");
+
   // iterate over all parameter query types for query declarations
   #if defined GLOBALLISTOFPARAMETERQUERIES_Token && defined GLOBALLISTOFPARAMETERQUERIES_Type
@@ -57 +60 @@
   #undef SUFFIX
   #endif
+
+  class VectorCommandLineQuery;
+  class VectorsCommandLineQuery;
 
   // iterate over all parameter query types for forward declarations

src/UIElements/CommandLineUI/CommandLineParser_validate.cpp

@@ -66 +66 @@
         std::string("value"),
         std::string("VectorValue")
+    );
+#endif
+  }
+  VV.vectorstring = values.at(0);
+  v = boost::any(VectorValue(VV));
+}
+
+void validate(boost::any& v, const std::vector<std::string>& values, RealSpaceMatrixValue *, int)
+{
+  RealSpaceMatrixValue RSMV;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    std::cerr <<  "Not one vector but " << values.size() << " given " << std::endl;
+#if BOOST_VERSION < 104200
+    throw boost::program_options::validation_error("Unequal to one vector given");
+#else
+    throw boost::program_options::validation_error(
+        boost::program_options::validation_error::invalid_option_value,
+        std::string("value"),
+        std::string("BoxValue")
     );
 #endif
@@ -83 +105 @@
   components.push_back(std::string(Biter,argument.end()));
 
-  if (components.size() != 3) {
-    std::cerr <<  "Specified vector does not have three components but " << components.size() << std::endl;
-#if BOOST_VERSION < 104200
-    throw boost::program_options::validation_error("Specified vector does not have three components");
-#else
-    throw boost::program_options::validation_error(
-        boost::program_options::validation_error::invalid_option_value,
-        std::string("value"),
-        std::string("VectorValue")
-    );
-#endif
-  }
-  for (size_t i=0;i<NDIM;++i)
-    VV.vector[i] = boost::lexical_cast<double>(components.at(i));
-  v = boost::any(VectorValue(VV));
-}
-
-void validate(boost::any& v, const std::vector<std::string>& values, RealSpaceMatrixValue *, int)
-{
-  RealSpaceMatrixValue RSMV;
-  std::vector<std::string> components;
-
-  // split comma-separated values
-  if (values.size() != 1) {
-    std::cerr <<  "Not one vector but " << values.size() << " given " << std::endl;
-#if BOOST_VERSION < 104200
-    throw boost::program_options::validation_error("Unequal to one vector given");
-#else
-    throw boost::program_options::validation_error(
-        boost::program_options::validation_error::invalid_option_value,
-        std::string("value"),
-        std::string("BoxValue")
-    );
-#endif
-  }
-  std::string argument(values.at(0));
-  std::string::iterator Aiter = argument.begin();
-  std::string::iterator Biter = argument.begin();
-  for (; Aiter != argument.end(); ++Aiter) {
-    if (*Aiter == ',') {
-      components.push_back(std::string(Biter,Aiter));
-      do {
-        Aiter++;
-      } while (*Aiter == ' ' || *Aiter == '\t');
-      Biter = Aiter;
-    }
-  }
-  components.push_back(std::string(Biter,argument.end()));
-
   if (components.size() != 6) {
     std::cerr <<  "Specified vector does not have three components but " << components.size() << std::endl;

src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp

@@ -24 +24 @@
 };
 
+class CommandLineDialog::VectorCommandLineQuery : public Dialog::TQuery<Vector> {
+public:
+  VectorCommandLineQuery(Parameter<Vector> &_param, const std::string &_title, const std::string &_description = "");
+  virtual ~VectorCommandLineQuery();
+  virtual bool handle();
+};
+
+class CommandLineDialog::VectorsCommandLineQuery : public Dialog::TQuery< std::vector<Vector> > {
+public:
+  VectorsCommandLineQuery(Parameter< std::vector<Vector> > &_param, const std::string &_title, const std::string &_description = "");
+  virtual ~VectorsCommandLineQuery();
+  virtual bool handle();
+};
+
   /** With the following boost::preprocessor code we generate forward declarations
    * of query class for all desired query types in the Qt specialization class of

src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp

@@ -53 +53 @@
 
 bool CommandLineDialog::VectorCommandLineQuery::handle() {
-  VectorValue _temp;
+  VectorValue temporary;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    try {
-      _temp = CommandLineParser::getInstance().vm[getTitle()].as< VectorValue >();
-    } catch(boost::bad_any_cast &e) {
-      for (size_t i=0;i<NDIM;++i)
-        _temp.vector[i] = 0.;
-      return false;
-    }
-    temp = _temp.toVector();
+    temporary = CommandLineParser::getInstance().vm[getTitle()].as< VectorValue >();
+    temp = temporary.vectorstring;
     return true;
   }

src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp

@@ -46 +46 @@
 
 CommandLineDialog::VectorsCommandLineQuery::VectorsCommandLineQuery(Parameter<std::vector<Vector> > &_param, const std::string &_title, const std::string &_description) :
-    Dialog::TQuery<std::vector<Vector> >(_param, _title, _description)
+    Dialog::TQuery< std::vector<Vector> >(_param, _title, _description)
 {}
 
@@ -53 +53 @@
 
 bool CommandLineDialog::VectorsCommandLineQuery::handle() {
-  std::vector<VectorValue> temporary;
+  std::vector<std::string> temporary;
+  std::stringstream output;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    try {
-      temporary = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<VectorValue> >();
-    } catch(boost::bad_any_cast &e) {
-      temporary.clear();
-      return false;
-    }
-    for(std::vector<VectorValue>::iterator iter = temporary.begin(); iter != temporary.end(); ++iter) {
-      Vector temp_element = (*iter).toVector();
-      temp.push_back(temp_element);
-    }
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<std::string> >();
     return true;
   }

src/UIElements/Dialog.cpp

@@ -134 +134 @@
   queryEmpty(param, title, description);
 }*/
+template <>
+void Dialog::query<Vector>(Parameter<Vector> &param, const std::string title, const std::string description)
+{
+  queryVector(param, title, description);
+}
+template <>
+void Dialog::query< std::vector<Vector> >(Parameter< std::vector<Vector> > &param, const std::string title, const std::string description)
+{
+  queryVectors(param, title, description);
+}
+
+static const std::string concatenateStrings(const std::vector<std::string> &_strings)
+{
+  std::stringstream output;
+  for (std::vector<std::string>::const_iterator iter = _strings.begin();
+      iter != _strings.end(); ++iter)
+    output << *iter << " ";
+  return output.str();
+}
+
+bool Dialog::TQuery< std::vector<Vector> >::isValid()
+{
+  return param.isValidAsString(concatenateStrings(temp));
+}
+void Dialog::TQuery< std::vector<Vector> >::setResult()
+{
+  param.setAsString(concatenateStrings(temp));
+}
 
 /** With the following boost::preprocessor code we generate template

src/UIElements/Dialog.hpp

@@ -158 +158 @@
   virtual void queryEmpty(const std::string ="", const std::string = "")=0;
 
+  virtual void queryVector(Parameter<Vector> &, const std::string ="", const std::string = "")=0;
+  virtual void queryVectors(Parameter< std::vector<Vector> > &, const std::string ="", const std::string = "")=0;
+
   /** With the following boost::preprocessor code we generate virtual function
    * definitions for all desired query types in the abstract class Dialog.
@@ -250 +253 @@
   };
 
-
   template<class T>
   class TQuery : public Query {
@@ -282 +284 @@
 };
 
+// we have specialization of Vector to allow internal storing as string
+template <>
+void Dialog::query<Vector>(Parameter<Vector> &, const std::string, const std::string);
+template <>
+void Dialog::query< std::vector<Vector> >(Parameter< std::vector<Vector> > &, const std::string, const std::string);
+
+/** Template specialization for Query<Vector> to allow internal storing of a
+ * string instead of a Vector.
+ *
+ * Because we need to evaluate the string as a possible GeometryRegistry key
+ * and we may do this only when the Action (whose options we are querying)
+ * is executed, not before.
+ */
+template <>
+class Dialog::TQuery<Vector> : public Query {
+public:
+  TQuery(Parameter<Vector> &_param, const std::string title, const std::string _description = "") :
+    Query(title, _description), param(_param) {}
+  virtual ~TQuery(){}
+  virtual bool handle()=0;
+  virtual bool isValid(){ return param.isValidAsString(temp);  }
+  virtual void setResult(){ param.setAsString(temp);  }
+protected:
+  std::string temp;
+  Parameter<Vector> &param;
+};
+
+template <>
+class Dialog::TQuery< std::vector<Vector> > : public Query {
+public:
+  TQuery(Parameter< std::vector<Vector> > &_param, const std::string title, const std::string _description = "") :
+    Query(title, _description), param(_param) {}
+  virtual ~TQuery(){}
+  virtual bool handle()=0;
+  virtual bool isValid();
+  virtual void setResult();
+protected:
+  std::vector<std::string> temp;
+  Parameter< std::vector<Vector> > &param;
+};
+
+
 #endif /* DIALOG_HPP_ */

src/UIElements/GlobalListOfParameterQueries.hpp

@@ -28 +28 @@
         (Molecule) \
         (Molecules) \
-        (Vector) \
-        (Vectors) \
         (RealSpaceMatrix) \
         (Element) \
@@ -52 +50 @@
         (const molecule *) \
         (std::vector<const molecule *> ) \
-        (Vector) \
-        (std::vector<Vector> ) \
         (RealSpaceMatrix) \
         (const element *) \

src/UIElements/Makefile.am

@@ -190 +190 @@
   UIElements/Menu/Qt4/QtMenuPipe.cpp \
   UIElements/Views/Qt4/QtFragmentList.cpp \
+  UIElements/Views/Qt4/QtGeometryList.cpp \
   UIElements/Views/Qt4/QtHomologyList.cpp \
   UIElements/Views/Qt4/QtInfoBox.cpp \
@@ -225 +226 @@
   UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp \
   UIElements/Views/Qt4/QtFragmentList.hpp \
+  UIElements/Views/Qt4/QtGeometryList.hpp \
   UIElements/Views/Qt4/QtHomologyList.hpp \
   UIElements/Views/Qt4/QtInfoBox.hpp \
@@ -308 +310 @@
         libMolecuilderParser.la \
         libMolecuilderParameters.la \
+        libMolecuilderGeometry.la \
         libMolecuilderShapes.la \
         libMolecuilderLinkedCell.la \

src/UIElements/Menu/MenuDescription.cpp

@@ -61 +61 @@
   // put each menu into its place, "" means top level
   MenuPositionMap->insert(std::make_pair("analysis",TopPosition("tools",1)));
-  MenuPositionMap->insert(std::make_pair("atom",TopPosition("edit",1)));
-  MenuPositionMap->insert(std::make_pair("bond",TopPosition("edit",2)));
+  MenuPositionMap->insert(std::make_pair("atom",TopPosition("edit",2)));
+  MenuPositionMap->insert(std::make_pair("bond",TopPosition("edit",3)));
   MenuPositionMap->insert(std::make_pair("command",TopPosition("",3)));
   MenuPositionMap->insert(std::make_pair("edit",TopPosition("",2)));
   MenuPositionMap->insert(std::make_pair("fill",TopPosition("tools",5)));
   MenuPositionMap->insert(std::make_pair("fragmentation",TopPosition("tools",3)));
+  MenuPositionMap->insert(std::make_pair("geometry",TopPosition("edit",5)));
   MenuPositionMap->insert(std::make_pair("graph",TopPosition("tools",4)));
-  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",3)));
+  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",4)));
   MenuPositionMap->insert(std::make_pair("potential",TopPosition("tools",7)));
-  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",4)));
-  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",5)));
+  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",6)));
+  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",1)));
   MenuPositionMap->insert(std::make_pair("tesselation",TopPosition("tools",2)));
   MenuPositionMap->insert(std::make_pair("shape",TopPosition("tools",6)));
@@ -85 +86 @@
   MenuDescriptionsMap->insert(std::make_pair("fill","Fill"));
   MenuDescriptionsMap->insert(std::make_pair("fragmentation","Fragmentation"));
+  MenuDescriptionsMap->insert(std::make_pair("geometry","Geometry"));
   MenuDescriptionsMap->insert(std::make_pair("graph","Graph"));
   MenuDescriptionsMap->insert(std::make_pair("molecule","Parse files into system"));
@@ -103 +105 @@
   MenuNameMap->insert(std::make_pair("fill","Fill"));
   MenuNameMap->insert(std::make_pair("fragmentation","Fragmentation"));
+  MenuNameMap->insert(std::make_pair("geometry","Geometry"));
   MenuNameMap->insert(std::make_pair("graph","Graph"));
   MenuNameMap->insert(std::make_pair("molecule","Molecules"));

src/UIElements/Qt4/QtDialog.hpp

@@ -36 +36 @@
   virtual void queryEmpty(const std::string ="", const std::string = "");
 
+  virtual void queryVector(Parameter<Vector> &, const std::string ="", const std::string = "");
+  virtual void queryVectors(Parameter< std::vector<Vector> > &, const std::string ="", const std::string = "");
+
   /** With the following boost::preprocessor code we generate virtual function
    * definitions for all desired query types in the abstract class Dialog.
@@ -64 +67 @@
 
   class EmptyQtQuery;
+
+  class VectorQtQuery;
+  class VectorsQtQuery;
 
   /** With the following boost::preprocessor code we generate forward declarations

src/UIElements/Qt4/QtMainWindow.cpp

@@ -59 +59 @@
 #include "Views/Qt4/QtHomologyList.hpp"
 #include "UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp"
+#include "Views/Qt4/QtGeometryList.hpp"
 #include "Views/Qt4/QtLogBox.hpp"
 #include "Views/Qt4/QtShapeController.hpp"
@@ -112 +113 @@
   homologyList = new QtHomologyList(worldTab);
   fragmentList = new QtFragmentList(worldTab);
+  geometryList = new QtGeometryList(worldTab);
   logBox = new QtLogBox(std::cout, worldTab);
   errorlogBox = new QtLogBox(std::cerr, worldTab);
@@ -147 +149 @@
   worldTab->addTab(fragmentList, "All Fragments");
   worldTab->addTab(homologyList, "All Homologies");
+  worldTab->addTab(geometryList, "All Geometries");
   worldTab->addTab(logBox, "Log");
   worldTab->addTab(errorlogBox, "Errors");

src/UIElements/Qt4/QtMainWindow.hpp

@@ -27 +27 @@
 class QtElementList;
 class QtFragmentList;
+class QtGeometryList;
 class QtHomologyList;
 class QtLogBox;
@@ -60 +61 @@
   QtMoleculeList *moleculeList;
   QtElementList *elementList;
+  QtGeometryList *geometryList;
   QtHomologyList *homologyList;
   QtFragmentList *fragmentList;

src/UIElements/Qt4/Query/QtQuery.hpp

@@ -414 +414 @@
 
 public slots:
+  void pageChanged(int);
+  void onUpdateName(int);
   void onUpdateX(double);
   void onUpdateY(double);
@@ -424 +426 @@
   QBoxLayout *subLayout;
   QBoxLayout *coordLayout;
-  QLabel *coordLabel;
   QDoubleSpinBox *coordInputX;
   QDoubleSpinBox *coordInputY;
   QDoubleSpinBox *coordInputZ;
   Dialog *dialog;
-};
-
-class QtDialog::VectorsQtQuery : public QWidget, public QtQuery<std::vector<Vector> >, public QtQueryList<Vector> {
+  QBoxLayout *nameLayout;
+  QComboBox *nameComboBox;
+};
+
+class QtDialog::VectorsQtQuery :
+    public QWidget,
+    public QtQuery<std::vector<Vector> >,
+    public QtQueryList<Vector> {
   Q_OBJECT
 public:

src/UIElements/Qt4/Query/QtQueryList.hpp

@@ -100 +100 @@
   std::vector<T> &tempRef;
   Parameter<T> *subParam;
+};
+
+template<>
+class QtQueryList<Vector> : public QtQueryListUntyped {
+public:
+  QtQueryList(Parameter<std::vector<Vector> > &parentParam, QBoxLayout *parent, Dialog *_dialog, std::vector<std::string> &_temp) : QtQueryListUntyped(parent, _dialog), tempRef(_temp)
+  {
+    // do we have an STLVectorValidator?
+    Validator<std::vector<Vector> > *val = &parentParam.getValidator();
+    STLVectorValidator<std::vector<Vector> > *vector_val = NULL;
+
+    // might be hidden inside an And_Validator
+    And_Validator<std::vector<Vector> > * and_val = dynamic_cast<And_Validator<std::vector<Vector> > *>(val);
+    if (and_val){
+      if (dynamic_cast<STLVectorValidator<std::vector<Vector> > *>(and_val->getA()))
+        vector_val = dynamic_cast<STLVectorValidator<std::vector<Vector> > *>(and_val->getA());
+      else if (dynamic_cast<STLVectorValidator<std::vector<Vector> > *>(and_val->getB()))
+        vector_val = dynamic_cast<STLVectorValidator<std::vector<Vector> > *>(and_val->getB());
+    }else{
+      vector_val = dynamic_cast<STLVectorValidator<std::vector<Vector> > *>(val);
+    }
+
+    if (vector_val){
+      // if so, try to use its ElementwiseValidator
+      subParam = new Parameter<Vector>("sub-param", *(vector_val->getElementwiseValidator()));
+    }else{
+      subParam = new Parameter<Vector>("sub-param");
+    }
+  }
+  virtual ~QtQueryList()
+  {
+    delete(subParam);
+  }
+
+  void addElement() {
+    // add item to both
+    addElementToListWidget(subParam->getAsString());
+    tempRef.push_back(subParam->getAsString());
+    onUpdate();
+  }
+  void removeElements()
+  {
+    std::vector<int> rows = getSelectedRows();
+    removeSelectedRows(rows);
+    for (int i = rows.size() - 1; i >= 0; i --){
+      ASSERT((size_t)(rows[i]) < tempRef.size(), "QtQueryList<Vector>::removeElements() trying to remove invalid element.");
+      tempRef.erase(tempRef.begin() + rows[i]);
+    }
+    onUpdate();
+  }
+protected:
+  std::vector<std::string> &tempRef;
+  Parameter<Vector> *subParam;
 };
 

src/UIElements/Qt4/Query/VectorQtQuery.cpp

@@ -37 +37 @@
 #include <Qt/qcombobox.h>
 #include <Qt/qlabel.h>
+#include <Qt/qstackedwidget.h>
 
 //#include "CodePatterns/MemDebug.hpp"
@@ -42 +43 @@
 #include "UIElements/Qt4/Query/QtQuery.hpp"
 
+#include "CodePatterns/toString.hpp"
+
+#include "Geometry/GeometryRegistry.hpp"
+#include "Parameters/Specifics/Value_vector.hpp"
 
 QtDialog::VectorQtQuery::VectorQtQuery(Parameter<Vector> &_param, const std::string &_title, const std::string &_description, QBoxLayout *_parent,Dialog *_dialog) :
@@ -48 +53 @@
     dialog(_dialog)
 {
-  temp = Vector(0, 0, 0);
-  if (param.isSet())
-    temp = param.get();
+  Vector temporary(0, 0, 0);
+  temp = "0, 0, 0";
+  if (param.isSet()) {
+    temporary = param.get();
+    temp = param.getAsString();
+  }
   mainLayout= new QHBoxLayout();
   titleLabel = new QLabel(QString(getTitle().c_str()));
   titleLabel->setToolTip(QString(getDescription().c_str()));
   mainLayout->addWidget(titleLabel);
-  subLayout = new QVBoxLayout();
+  subLayout = new QHBoxLayout();
   mainLayout->addLayout(subLayout);
 //  QComboBox* inputBox = new QComboBox();
+
+  QWidget *firstPageWidget = new QWidget;
+  QWidget *secondPageWidget = new QWidget;
+
+  QStackedWidget *stackedWidget = new QStackedWidget;
+  stackedWidget->addWidget(firstPageWidget);
+  stackedWidget->addWidget(secondPageWidget);
+
+  QComboBox *pageComboBox = new QComboBox;
+  pageComboBox->addItem(tr("x,y,z"));
+  pageComboBox->addItem(tr("vector name"));
+  connect(pageComboBox, SIGNAL(activated(int)),
+      stackedWidget, SLOT(setCurrentIndex(int)));
+  connect(pageComboBox, SIGNAL(activated(int)),
+      this, SLOT(pageChanged(int)));
+  subLayout->addWidget(pageComboBox);
+  subLayout->addWidget(stackedWidget);
+
+   // first widget with coordinates
   coordLayout = new QHBoxLayout();
-  subLayout->addLayout(coordLayout);
-  coordLabel = new QLabel(QString("x,y,z"));
-  coordLayout->addWidget(coordLabel);
   coordInputX = new QDoubleSpinBox();
   coordInputX->setRange(-std::numeric_limits<double>::max(),std::numeric_limits<double>::max());
-  coordInputX->setValue(temp[0]);
+  coordInputX->setValue(temporary[0]);
 //  coordInputX->setRange(0,M.at(i,i));
   coordInputX->setDecimals(3);
@@ -70 +94 @@
   coordInputY = new QDoubleSpinBox();
   coordInputY->setRange(-std::numeric_limits<double>::max(),std::numeric_limits<double>::max());
-  coordInputY->setValue(temp[1]);
+  coordInputY->setValue(temporary[1]);
 //  coordInputY->setRange(0,M.at(i,i));
   coordInputY->setDecimals(3);
@@ -76 +100 @@
   coordInputZ = new QDoubleSpinBox();
   coordInputZ->setRange(-std::numeric_limits<double>::max(),std::numeric_limits<double>::max());
-  coordInputZ->setValue(temp[2]);
+  coordInputZ->setValue(temporary[2]);
 //  coordInputZ->setRange(0,M.at(i,i));
   coordInputZ->setDecimals(3);
@@ -83 +107 @@
   connect(coordInputY,SIGNAL(valueChanged(double)),this,SLOT(onUpdateY(double)));
   connect(coordInputZ,SIGNAL(valueChanged(double)),this,SLOT(onUpdateZ(double)));
+  firstPageWidget->setLayout(coordLayout);
+
+  // second widget with string field
+  nameLayout = new QHBoxLayout();
+  nameComboBox = new QComboBox;
+  GeometryRegistry &reg = GeometryRegistry::getInstance();
+//  nameComboBox->setEditable(true);
+  GeometryRegistry::const_iterator iter;
+  for (iter = reg.getBeginIter(); iter != reg.getEndIter(); iter ++){
+    GeometryObject *v = iter->second;
+    nameComboBox->addItem(tr(v->getName().c_str()));
+    nameComboBox->setItemData(nameComboBox->count()-1, tr(toString<Vector>(v->getVector()).c_str()), Qt::ToolTipRole);
+  }
+  connect(nameComboBox, SIGNAL(activated(int)),
+      this, SLOT(onUpdateName(int)));
+  nameLayout->addWidget(nameComboBox);
+  secondPageWidget->setLayout(nameLayout);
+
   parent->addLayout(mainLayout);
 }
@@ -89 +131 @@
 {}
 
+static void updateVectorString(std::string &_temp, const double newDouble, int component)
+{
+  //!> Internal converter from string to internal type
+  Vector vec = Value<Vector>::parseAsVector(_temp);
+  vec[component] = newDouble;
+  _temp = Value<Vector>::setFromVector(vec);
+}
+
+void QtDialog::VectorQtQuery::pageChanged(int pagenr) {
+  if (pagenr == 1) {
+    // change from x,y,z input
+    onUpdateName(nameComboBox->currentIndex());
+    dialog->update();
+  } else if (pagenr == 0) {
+    // change from name input
+    if (GeometryRegistry::getInstance().isPresentByName(temp)) {
+      const GeometryObject * const v = GeometryRegistry::getInstance().getByName(temp);
+      coordInputX->setValue(v->getVector()[0]);
+      coordInputY->setValue(v->getVector()[1]);
+      coordInputZ->setValue(v->getVector()[2]);
+    } else {
+      coordInputX->setValue(0.);
+      coordInputY->setValue(0.);
+      coordInputZ->setValue(0.);
+    }
+    dialog->update();
+  } else {
+    ASSERT(0, "VectorQtQuery::pageChanged() - unknown page for pageComboBox.");
+  }
+}
+
+void QtDialog::VectorQtQuery::onUpdateName(int index) {
+  const QString itemtext = nameComboBox->itemText(index);
+  temp = itemtext.toStdString();
+  dialog->update();
+}
+
 void QtDialog::VectorQtQuery::onUpdateX(double newDouble) {
-  temp[0] = newDouble;
+  updateVectorString(temp, newDouble, 0);
   dialog->update();
 }
 
 void QtDialog::VectorQtQuery::onUpdateY(double newDouble) {
-  temp[1] = newDouble;
+  updateVectorString(temp, newDouble, 1);
   dialog->update();
 }
 
 void QtDialog::VectorQtQuery::onUpdateZ(double newDouble) {
-  temp[2] = newDouble;
+  updateVectorString(temp, newDouble, 2);
   dialog->update();
 }

src/UIElements/TextUI/Query/TextQuery.hpp

@@ -24 +24 @@
 };
 
+class TextDialog::VectorTextQuery : public Dialog::TQuery<Vector> {
+public:
+  VectorTextQuery(Parameter<Vector> &_param, const std::string &_title, const std::string &_description = "");
+  virtual ~VectorTextQuery();
+  virtual bool handle();
+};
+
+class TextDialog::VectorsTextQuery : public Dialog::TQuery< std::vector<Vector> > {
+public:
+  VectorsTextQuery(Parameter< std::vector<Vector> > &_param, const std::string &_title, const std::string &_description = "");
+  virtual ~VectorsTextQuery();
+  virtual bool handle();
+};
 
   /** With the following boost::preprocessor code we generate forward declarations

src/UIElements/TextUI/Query/VectorTextQuery.cpp

@@ -83 +83 @@
 
   // check vector
-  return World::getInstance().getDomain().isValid(temp);
+  return true;
 }
 

src/UIElements/TextUI/Query/VectorsTextQuery.cpp

@@ -41 +41 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Geometry/GeometryRegistry.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
@@ -54 +55 @@
 
 bool TextDialog::VectorsTextQuery::handle() {
+  std::stringstream output;
   std::cout << getDescription() << std::endl;
   char coords[3] = {'x', 'y', 'z'};
   const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
-  for (int i=0;i<3;i++)
-    std::cout << coords[i] << "[0.." << M.at(i,i) << ( (i!=2) ? "], " : "]: ");
+  std::cout << "Enter three comma-separated coordinates, vector name, ? for list or empty for end." << std::endl;
+  while (true) {
+    for (int i=0;i<3;i++)
+      std::cout << coords[i] << "[0.." << M.at(i,i) << ( (i!=2) ? "], " : "]: ");
 
-  std::string line;
-  getline(std::cin,line);
+    std::string line;
+    getline(std::cin,line);
 
-  // dissect by ","
-  double coord = 0.;
-  std::string::iterator olditerspace = line.begin();
-  std::string::iterator olditercomma = line.begin();
-  int counter = 0;
-  Vector temp_element;
-  for(std::string::iterator vectoriter = line.begin(); vectoriter != line.end(); ++vectoriter) {
-    if (*vectoriter == ',')
-      counter++;
-    if ((*vectoriter == ' ') && (counter == 2)) {
-      counter = 0;
-      for(std::string::iterator componentiter = olditerspace; (componentiter != vectoriter) && (counter !=3); ++componentiter) {
-        if (*componentiter == ',') {
-          std::istringstream stream(std::string(componentiter, olditercomma));
-          stream >> coord;
-          temp_element[counter++] = coord;
-          olditercomma = componentiter;
-        }
+    if (line == "?") {
+      GeometryRegistry &reg = GeometryRegistry::getInstance();
+
+      GeometryRegistry::const_iterator iter;
+      for (iter = reg.getBeginIter(); iter != reg.getEndIter(); iter ++){
+        GeometryObject *v = iter->second;
+        std::cout << "\t" << *v << std::endl;
       }
-      if ((olditercomma != line.begin()) && (counter != 3)) { // insert last part also
-        std::istringstream stream(std::string(olditercomma, vectoriter));
-        stream >> coord;
-        temp_element[counter++] = coord;
-      }
-      if (World::getInstance().getDomain().isValid(temp_element))
-        temp.push_back(temp_element);
-      olditerspace = vectoriter;
+    } else if (line.empty()) {
+      break;
+    } else {
+      // simply append with white-space delimiter
+      temp.push_back(line);
     }
   }

src/UIElements/TextUI/TextDialog.hpp

@@ -34 +34 @@
   virtual void queryEmpty(const std::string ="", const std::string = "");
 
+  virtual void queryVector(Parameter<Vector> &, const std::string ="", const std::string = "");
+  virtual void queryVectors(Parameter< std::vector<Vector> > &, const std::string ="", const std::string = "");
+
   /** With the following boost::preprocessor code we generate virtual function
    * definitions for all desired query types in the abstract class Dialog.
@@ -59 +62 @@
   class EmptyTextQuery;
 
+  class VectorTextQuery;
+  class VectorsTextQuery;
+
   /** With the following boost::preprocessor code we generate forward declarations
    * of query class for all desired query types in the Qt specialization class of

src/cleanUp.cpp

@@ -54 +54 @@
 #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
 
+#include "Geometry/GeometryRegistry.hpp"
+
 #include "MoleculeObserver.hpp"
 
@@ -95 +97 @@
   // make sure that ActionQueue is already purged!
   FragmentationResultContainer::purgeInstance();
+  GeometryRegistry::purgeInstance();
   Chronos::purgeInstance();
   PotentialFactory::purgeInstance();