Changes in / [45f835:9c27b0]


Ignore:
Files:
492 added
167 deleted
86 edited

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Added
Removed

  • configure.ac

    r45f835 r9c27b0  
    137137
    138138
    139 # CodePatterns library (needs Observer::Channels )
    140 AM_PATH_CODEPATTERNS([1.1.5], $have_debug,,[AC_MSG_ERROR([Missing CodePatterns library, please specify PKG_CONFIG_PATH or use --with-codepatterns...])])
     139# CodePatterns library (needs valarray in MemDebug )
     140AM_PATH_CODEPATTERNS([1.1.6], $have_debug,,[AC_MSG_ERROR([Missing CodePatterns library, please specify PKG_CONFIG_PATH or use --with-codepatterns...])])
    141141
    142142# Checks for header files.
    … …  
    218218
    219219# test suite
     220
    220221AC_CONFIG_FILES([
    221222        tests/Makefile])
    … …  
    230231        tests/Fragmentations/atlocal
    231232        tests/Fragmentations/Makefile])
     233AC_CONFIG_FILES([tests/Fragmentations/analyzer], [chmod +x tests/Fragmentations/analyzer])
     234AC_CONFIG_FILES([tests/Fragmentations/joiner], [chmod +x tests/Fragmentations/joiner])
    232235AC_CONFIG_FILES([tests/Fragmentations/molecuilder], [chmod +x tests/Fragmentations/molecuilder])
    233236
    … …  
    247250        doc/molecuilder.xml])
    248251AC_CONFIG_FILES([
    249   MoleCuilder.pc:MoleCuilder.pc.in])
     252        MoleCuilder.pc:MoleCuilder.pc.in])
    250253AC_CONFIG_FILES([
    251254        Makefile
    … …  
    254257])
    255258AC_CONFIG_FILES([
    256   src/unittests/Makefile
     259        src/unittests/Makefile
    257260])
    258261AC_OUTPUT

  • src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "analysis_correlation.hpp"
    23 #include "boundary.hpp"
     22#include "Analysis/analysis_correlation.hpp"
     23#include "Tesselation/boundary.hpp"
    2424#include "linkedcell.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "CodePatterns/Log.hpp"
    27 #include "element.hpp"
     27#include "Element/element.hpp"
    2828#include "molecule.hpp"
    29 #include "periodentafel.hpp"
     29#include "Element/periodentafel.hpp"
    3030#include "LinearAlgebra/Vector.hpp"
    3131#include "World.hpp"

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "boundary.hpp"
     22#include "Tesselation/boundary.hpp"
    2323#include "config.hpp"
    2424#include "molecule.hpp"
    … …  
    2727#include "CodePatterns/Verbose.hpp"
    2828#include "PointCloudAdaptor.hpp"
    29 #include "tesselation.hpp"
     29#include "Tesselation/tesselation.hpp"
    3030#include "World.hpp"
    3131

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "analysis_correlation.hpp"
    23 #include "boundary.hpp"
     22#include "Analysis/analysis_correlation.hpp"
     23#include "Tesselation/boundary.hpp"
    2424#include "linkedcell.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "CodePatterns/Log.hpp"
    27 #include "element.hpp"
     27#include "Element/element.hpp"
    2828#include "molecule.hpp"
    29 #include "periodentafel.hpp"
     29#include "Element/periodentafel.hpp"
    3030#include "LinearAlgebra/Vector.hpp"
    3131#include "World.hpp"

  • src/Actions/AnalysisAction/PointCorrelationAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "analysis_correlation.hpp"
    23 #include "boundary.hpp"
     22#include "Analysis/analysis_correlation.hpp"
     23#include "Tesselation/boundary.hpp"
    2424#include "linkedcell.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "CodePatterns/Log.hpp"
    27 #include "element.hpp"
     27#include "Element/element.hpp"
    2828#include "molecule.hpp"
    29 #include "periodentafel.hpp"
     29#include "Element/periodentafel.hpp"
    3030#include "LinearAlgebra/Vector.hpp"
    3131#include "World.hpp"

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    r45f835 r9c27b0  
    2424#include "LinearAlgebra/RealSpaceMatrix.hpp"
    2525#include "LinearAlgebra/Vector.hpp"
    26 #include "element.hpp"
     26#include "Element/element.hpp"
    2727#include "molecule.hpp"
    2828

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "analysis_correlation.hpp"
    23 #include "boundary.hpp"
     22#include "Analysis/analysis_correlation.hpp"
     23#include "Tesselation/boundary.hpp"
    2424#include "linkedcell.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "CodePatterns/Log.hpp"
    2727#include "Descriptors/MoleculeIdDescriptor.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "LinearAlgebra/Vector.hpp"
    3030#include "molecule.hpp"
    31 #include "periodentafel.hpp"
     31#include "Element/periodentafel.hpp"
    3232#include "PointCloudAdaptor.hpp"
    33 #include "tesselation.hpp"
     33#include "Tesselation/tesselation.hpp"
    3434#include "World.hpp"
    3535

  • src/Actions/AtomAction/AddAction.cpp

    r45f835 r9c27b0  
    2222#include "Descriptors/AtomIdDescriptor.hpp"
    2323#include "atom.hpp"
    24 #include "element.hpp"
     24#include "Element/element.hpp"
    2525#include "CodePatterns/Log.hpp"
    2626#include "molecule.hpp"

  • src/Actions/AtomAction/ChangeElementAction.cpp

    r45f835 r9c27b0  
    2222#include "Descriptors/AtomIdDescriptor.hpp"
    2323#include "atom.hpp"
    24 #include "element.hpp"
     24#include "Element/element.hpp"
    2525#include "CodePatterns/Log.hpp"
    2626#include "LinearAlgebra/Vector.hpp"

  • src/Actions/CommandAction/BondLengthTableAction.cpp

    r45f835 r9c27b0  
    1717#include <config.h>
    1818#endif
     19
     20// include headers that implement a archive in simple text format
     21#include <boost/archive/text_oarchive.hpp>
     22#include <boost/archive/text_iarchive.hpp>
    1923
    2024#include "CodePatterns/MemDebug.hpp"
    … …  
    4448
    4549  DoLog(0) && (Log() << Verbose(0) << "Using " << params.BondGraphFileName << " as bond length table." << endl);
    46   config *configuration = World::getInstance().getConfig();
    47   BondGraph *OldBG = World::getInstance().getBondGraph();
     50  BondGraph *&BG = World::getInstance().getBondGraph();
    4851
    49   BondGraph *BG = new BondGraph(configuration->GetIsAngstroem());
     52  // create undo state
     53  std::stringstream undostream;
     54  boost::archive::text_oarchive oa(undostream);
     55  oa << BG;
     56  CommandBondLengthTableState *UndoState =
     57      new CommandBondLengthTableState(
     58          undostream.str(),
     59          params
     60      );
     61
     62  BG->CleanupBondLengthTable();
    5063  if ((!params.BondGraphFileName.empty())
    5164      && boost::filesystem::exists(params.BondGraphFileName)) {
    … …  
    5467      DoLog(0) && (Log() << Verbose(0) << "Bond length table parsed successfully." << endl);
    5568      input.close();
    56       CommandBondLengthTableState *state = new CommandBondLengthTableState(*OldBG, params);
    57       World::getInstance().setBondGraph(BG);  // Changes OldBG, hence have to copy beforehand
    58       return Action::state_ptr(state);
     69      return Action::state_ptr(UndoState);
    5970    } else {
    6071      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table parsing failed." << endl);
    6172      input.close();
    62       return Action::failure;
    6373    }
    6474  } else {
    6575    DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
    66     return Action::failure;
    6776  }
     77  // recover bond graph
     78  boost::archive::text_iarchive ia(undostream);
     79  delete BG;
     80  ia >> BG;
     81  delete UndoState;
     82  return Action::failure;
    6883}
    6984
    … …  
    7186  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
    7287
    73   BondGraph *OldBG = World::getInstance().getBondGraph();
    74   CommandBondLengthTableState *restate = new CommandBondLengthTableState(*OldBG, params);
    75   World::getInstance().setBondGraph(new BondGraph(state->OldBG));  // Changes OldBG, hence have to copy beforehand
     88  BondGraph *BG;
     89  std::stringstream undostream(state->undostring);
     90  boost::archive::text_iarchive ia(undostream);
     91  ia >> BG;
     92  World::getInstance().setBondGraph(BG);
    7693
    77   return Action::state_ptr(restate);
     94  return Action::state_ptr(_state);
    7895}
    7996
    … …  
    8198  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
    8299
    83   BondGraph *OldBG = World::getInstance().getBondGraph();
    84   CommandBondLengthTableState *restate = new CommandBondLengthTableState(*OldBG, params);
    85   World::getInstance().setBondGraph(new BondGraph(state->OldBG));  // Changes OldBG, hence have to copy beforehand
     100  BondGraph *&BG = World::getInstance().getBondGraph();
     101  BG->CleanupBondLengthTable();
     102  std::ifstream input(state->params.BondGraphFileName.string().c_str());
     103  if ((input.good()) && (BG->LoadBondLengthTable(input))) {
     104    DoLog(0) && (Log() << Verbose(0) << "Bond length table parsed successfully." << endl);
     105    input.close();
     106  }
    86107
    87   return Action::state_ptr(restate);
     108  return Action::state_ptr(_state);
    88109}
    89110
    90111bool CommandBondLengthTableAction::canUndo() {
    91   return false;
     112  return true;
    92113}
    93114
    94115bool CommandBondLengthTableAction::shouldUndo() {
    95   return false;
     116  return true;
    96117}
    97118/** =========== end of function ====================== */

  • src/Actions/CommandAction/BondLengthTableAction.def

    r45f835 r9c27b0  
    1919#define paramreferences (BondGraphFileName)
    2020
    21 #define statetypes (BondGraph)
    22 #define statereferences (OldBG)
     21#define statetypes (std::string)
     22#define statereferences (undostring)
    2323
    2424// some defines for all the names, you may use ACTION, STATE and PARAMS

  • src/Actions/CommandAction/ElementDbAction.cpp

    r45f835 r9c27b0  
    2525
    2626#include "config.hpp"
    27 #include "element.hpp"    // we need element because of serialization!
    28 #include "periodentafel.hpp"
     27#include "Element/element.hpp"    // we need element because of serialization!
     28#include "Element/periodentafel.hpp"
    2929#include "CodePatterns/Log.hpp"
    3030#include "CodePatterns/Verbose.hpp"

  • src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

    r45f835 r9c27b0  
    2222#include "atom.hpp"
    2323#include "Graph/BondGraph.hpp"
    24 #include "boundary.hpp"
     24#include "Tesselation/boundary.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "config.hpp"

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    r45f835 r9c27b0  
    2222#include "atom.hpp"
    2323#include "Graph/BondGraph.hpp"
    24 #include "boundary.hpp"
     24#include "Tesselation/boundary.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    2626#include "config.hpp"

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    r45f835 r9c27b0  
    2525#include "LinearAlgebra/RealSpaceMatrix.hpp"
    2626#include "LinearAlgebra/Vector.hpp"
    27 #include "element.hpp"
     27#include "Element/element.hpp"
    2828#include "molecule.hpp"
    2929

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "boundary.hpp"
     22#include "Tesselation/boundary.hpp"
    2323#include "config.hpp"
    2424#include "CodePatterns/Log.hpp"

  • src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp

    r45f835 r9c27b0  
    2323#include "Descriptors/AtomSelectionDescriptor.hpp"
    2424#include "atom.hpp"
    25 #include "element.hpp"
     25#include "Element/element.hpp"
    2626#include "CodePatterns/Log.hpp"
    2727#include "CodePatterns/Verbose.hpp"

  • src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp

    r45f835 r9c27b0  
    2323#include "Descriptors/AtomTypeDescriptor.hpp"
    2424#include "atom.hpp"
    25 #include "element.hpp"
     25#include "Element/element.hpp"
    2626#include "CodePatterns/Log.hpp"
    2727#include "CodePatterns/Verbose.hpp"

  • src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "boundary.hpp"
     22#include "Tesselation/boundary.hpp"
    2323#include "CodePatterns/Log.hpp"
    2424#include "CodePatterns/Verbose.hpp"
    … …  
    2727#include "molecule.hpp"
    2828#include "PointCloudAdaptor.hpp"
    29 #include "tesselation.hpp"
     29#include "Tesselation/tesselation.hpp"
    3030#include "World.hpp"
    3131

  • src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

    r45f835 r9c27b0  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
    22 #include "boundary.hpp"
     22#include "Tesselation/boundary.hpp"
    2323#include "CodePatterns/Log.hpp"
    2424#include "CodePatterns/Verbose.hpp"
    … …  
    2626#include "molecule.hpp"
    2727#include "PointCloudAdaptor.hpp"
    28 #include "tesselation.hpp"
     28#include "Tesselation/tesselation.hpp"
    2929#include "World.hpp"
    3030

  • src/Actions/ValueStorage.cpp

    r45f835 r9c27b0  
    3737#include "atom.hpp"
    3838#include "Box.hpp"
    39 #include "element.hpp"
     39#include "Element/element.hpp"
    4040#include "molecule.hpp"
    41 #include "periodentafel.hpp"
     41#include "Element/periodentafel.hpp"
    4242#include "World.hpp"
    4343

  • src/AtomicInfo.cpp

    r45f835 r9c27b0  
    2222#include "atom.hpp"
    2323#include "AtomicInfo.hpp"
    24 #include "element.hpp"
     24#include "Element/element.hpp"
    2525#include "LinearAlgebra/Vector.hpp"
    2626

  • src/Bond/bond.cpp

    r45f835 r9c27b0  
    2323#include "atom.hpp"
    2424#include "Bond/bond.hpp"
    25 #include "element.hpp"
     25#include "Element/element.hpp"
    2626
    2727

  • src/Descriptors/AtomTypeDescriptor.cpp

    r45f835 r9c27b0  
    2525#include "atom.hpp"
    2626#include "World.hpp"
    27 #include "periodentafel.hpp"
     27#include "Element/periodentafel.hpp"
    2828
    2929AtomTypeDescriptor_impl::AtomTypeDescriptor_impl(const element* _type) :

  • src/Dynamics/LinearInterpolationBetweenSteps.hpp

    r45f835 r9c27b0  
    2525#include "Dynamics/MinimiseConstrainedPotential.hpp"
    2626#include "molecule.hpp"
    27 #include "parser.hpp"
    2827#include "World.hpp"
    2928

  • src/Dynamics/MinimiseConstrainedPotential.cpp

    r45f835 r9c27b0  
    2626#include "atom.hpp"
    2727#include "config.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "CodePatterns/enumeration.hpp"
    3030#include "CodePatterns/Info.hpp"
    3131#include "CodePatterns/Verbose.hpp"
    3232#include "CodePatterns/Log.hpp"
     33#include "Fragmentation/ForceMatrix.hpp"
    3334#include "Helpers/helpers.hpp"
    3435#include "molecule.hpp"
    35 #include "parser.hpp"
    3636#include "LinearAlgebra/Plane.hpp"
    3737#include "World.hpp"

  • src/Dynamics/VerletForceIntegration.hpp

    r45f835 r9c27b0  
    2121#include "CodePatterns/Verbose.hpp"
    2222#include "Dynamics/MinimiseConstrainedPotential.hpp"
     23#include "Fragmentation/ForceMatrix.hpp"
    2324#include "Helpers/helpers.hpp"
    2425#include "LinearAlgebra/Vector.hpp"
    25 #include "parser.hpp"
    2626#include "ThermoStatContainer.hpp"
    2727#include "Thermostats/Berendsen.hpp"

  • src/Formula.cpp

    r45f835 r9c27b0  
    2525
    2626#include "World.hpp"
    27 #include "periodentafel.hpp"
    28 #include "element.hpp"
     27#include "Element/periodentafel.hpp"
     28#include "Element/element.hpp"
    2929#include "CodePatterns/Assert.hpp"
    3030#include "CodePatterns/Range.hpp"

  • src/Graph/BondGraph.cpp

    r45f835 r9c27b0  
    2626#include "Graph/BondGraph.hpp"
    2727#include "Box.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "CodePatterns/Info.hpp"
    3030#include "CodePatterns/Log.hpp"
    … …  
    3232#include "CodePatterns/Verbose.hpp"
    3333#include "molecule.hpp"
    34 #include "parser.hpp"
    35 #include "periodentafel.hpp"
     34#include "Element/periodentafel.hpp"
     35#include "Fragmentation/MatrixContainer.hpp"
    3636#include "LinearAlgebra/Vector.hpp"
    3737#include "World.hpp"
    … …  
    3939
    4040const double BondGraph::BondThreshold = 0.4;   //!< CSD threshold in bond check which is the width of the interval whose center is the sum of the covalent radii
     41
     42BondGraph::BondGraph() :
     43    BondLengthMatrix(NULL),
     44    IsAngstroem(true)
     45{}
    4146
    4247BondGraph::BondGraph(bool IsA) :
    … …  
    4752BondGraph::~BondGraph()
    4853{
     54  CleanupBondLengthTable();
     55}
     56
     57void BondGraph::CleanupBondLengthTable()
     58{
    4959  if (BondLengthMatrix != NULL) {
    5060    delete(BondLengthMatrix);
    … …  
    6373    LOG(1, "MatrixContainer for Bond length already present, removing.");
    6474    delete(BondLengthMatrix);
     75    BondLengthMatrix = NULL;
    6576  }
    6677  TempContainer = new MatrixContainer;
    … …  
    222233}
    223234
     235bool BondGraph::operator==(const BondGraph &other) const
     236{
     237  if (IsAngstroem != other.IsAngstroem)
     238    return false;
     239  if (((BondLengthMatrix != NULL) && (other.BondLengthMatrix == NULL))
     240      || ((BondLengthMatrix == NULL) && (other.BondLengthMatrix != NULL)))
     241    return false;
     242  if ((BondLengthMatrix != NULL) && (other.BondLengthMatrix != NULL))
     243    if (*BondLengthMatrix != *other.BondLengthMatrix)
     244      return false;
     245  return true;
     246}

  • src/Graph/BondGraph.hpp

    r45f835 r9c27b0  
    2020#include <iosfwd>
    2121
     22#include <boost/serialization/array.hpp>
     23
    2224#include "AtomSet.hpp"
    2325#include "Bond/bond.hpp"
    … …  
    2628#include "CodePatterns/Range.hpp"
    2729#include "CodePatterns/Verbose.hpp"
    28 #include "element.hpp"
     30#include "Element/element.hpp"
     31#include "Fragmentation/MatrixContainer.hpp"
    2932#include "linkedcell.hpp"
    3033#include "IPointCloud.hpp"
    … …  
    6568   */
    6669  bool LoadBondLengthTable(std::istream &input);
     70
     71  /** Removes allocated bond length table.
     72   *
     73   */
     74  void CleanupBondLengthTable();
    6775
    6876  /** Determines the maximum of all element::CovalentRadius for elements present in \a &Set.
    … …  
    300308  }
    301309
     310  /** Equality comparator for class BondGraph.
     311   *
     312   * @param other other instance to compare to
     313   * @return true - if equal in every member variable, except static
     314   *         \a BondGraph::BondThreshold.
     315   */
     316  bool operator==(const BondGraph &other) const;
     317
     318  /** Unequality comparator for class BondGraph.
     319   *
     320   * @param other other instance to compare to
     321   * @return false - if equal in every member variable, except static
     322   *         \a BondGraph::BondThreshold.
     323   */
     324  bool operator!=(const BondGraph &other) const {
     325    return !(*this == other);
     326  }
     327
    302328private:
    303   static const double BondThreshold;
    304329
    305330  /** Returns the BondLengthMatrix entry for a given index pair.
    … …  
    383408  }
    384409
     410  bool operator==(const periodentafel &other) const;
     411
     412  bool operator!=(const periodentafel &other) const {
     413    return !(*this == other);
     414  }
     415
     416private:
     417  // default constructor for serialization
     418  BondGraph();
     419
     420  friend class boost::serialization::access;
     421  // serialization
     422  template<class Archive>
     423  void serialize(Archive & ar, const unsigned int version)
     424  {
     425    //ar & const_cast<double &>(BondThreshold);
     426    ar & BondLengthMatrix;
     427    ar & IsAngstroem;
     428  }
     429
     430  //!> half width of the interval for allowed bond distances
     431  static const double BondThreshold;
    385432  //!> Matrix with bond lenth per two elements
    386433  MatrixContainer *BondLengthMatrix;

  • src/Graph/CyclicStructureAnalysis.cpp

    r45f835 r9c27b0  
    2828#include "CodePatterns/Log.hpp"
    2929#include "CodePatterns/Verbose.hpp"
    30 #include "element.hpp"
     30#include "Element/element.hpp"
    3131#include "molecule.hpp"
    3232

  • src/Helpers/defs.hpp

    r45f835 r9c27b0  
    55 */
    66
    7 #ifndef DEFS_HPP_
    8 #define DEFS_HPP_
     7#ifndef HELPERS_DEFS_HPP_
     8#define HELPERS_DEFS_HPP_
    99
    1010// include config.h
    … …  
    8989const extern unsigned int MAX_FRAGMENTATION_SKIPS;
    9090
    91 #endif /*DEFS_HPP_*/
     91#endif /* HELPERS_DEFS_HPP_*/

  • src/Helpers/helpers.hpp

    r45f835 r9c27b0  
    44 */
    55
    6 #ifndef HELPERS_HPP_
    7 #define HELPERS_HPP_
     6#ifndef HELPERS_HELPERS_HPP_
     7#define HELPERS_HELPERS_HPP_
    88
    99using namespace std;
    … …  
    5151};
    5252
    53 #endif /*HELPERS_HPP_*/
     53#endif /* HELPERS_HELPERS_HPP_*/

  • src/Makefile.am

    r45f835 r9c27b0  
    88
    99include Actions/Makefile.am
     10include Analysis/Makefile.am
     11include Element/Makefile.am
    1012include Graph/Makefile.am
     13include Helpers/Makefile.am
     14include Fragmentation/Makefile.am
    1115include Parser/Makefile.am
    1216include RandomNumbers/Makefile.am
    … …  
    1620AM_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    1721AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    18 
    19 ANALYSISSOURCE = \
    20   analysis_bonds.cpp \
    21   analysis_correlation.cpp
    22 ANALYSISHEADER = \
    23   analysis_bonds.hpp \
    24   analysis_correlation.hpp
    2522
    2623ATOMSOURCE = \
    … …  
    116113        Dynamics/VerletForceIntegration.hpp
    117114
    118 HELPERSSOURCE = \
    119         Helpers/defs.cpp
    120 
    121 HELPERSHEADER = \
    122         Helpers/defs.hpp \
    123         Helpers/helpers.hpp
    124 
    125115THERMOSTATSOURCE = \
    126116  Thermostats/Berendsen.cpp \
    … …  
    142132
    143133TESSELATIONSOURCE = \
    144   BoundaryLineSet.cpp \
    145   BoundaryPointSet.cpp \
    146   BoundaryPolygonSet.cpp \
    147   BoundaryTriangleSet.cpp \
    148   CandidateForTesselation.cpp \
    149   tesselation.cpp \
    150   tesselationhelpers.cpp \
    151   TesselPoint.cpp
     134  Tesselation/boundary.cpp \
     135  Tesselation/BoundaryLineSet.cpp \
     136  Tesselation/BoundaryPointSet.cpp \
     137  Tesselation/BoundaryPolygonSet.cpp \
     138  Tesselation/BoundaryTriangleSet.cpp \
     139  Tesselation/CandidateForTesselation.cpp \
     140  Tesselation/ellipsoid.cpp \
     141  Tesselation/tesselation.cpp \
     142  Tesselation/tesselationhelpers.cpp \
     143  Tesselation/TesselPoint.cpp \
     144  Tesselation/triangleintersectionlist.cpp
    152145 
    153146TESSELATIONHEADER = \
    154   BoundaryLineSet.hpp \
    155   BoundaryMaps.hpp \
    156   BoundaryPointSet.hpp \
    157   BoundaryPolygonSet.hpp \
    158   BoundaryTriangleSet.hpp \
    159   CandidateForTesselation.hpp \
     147  Tesselation/boundary.hpp \
     148  Tesselation/BoundaryLineSet.hpp \
     149  Tesselation/BoundaryMaps.hpp \
     150  Tesselation/BoundaryPointSet.hpp \
     151  Tesselation/BoundaryPolygonSet.hpp \
     152  Tesselation/BoundaryTriangleSet.hpp \
     153  Tesselation/CandidateForTesselation.hpp \
     154  Tesselation/ellipsoid.hpp \
    160155  IPointCloud.hpp \
    161156  PointCloudAdaptor.hpp \
    162   tesselation.hpp \
    163   tesselationhelpers.hpp \
    164   TesselPoint.hpp
     157  Tesselation/tesselation.hpp \
     158  Tesselation/tesselationhelpers.hpp \
     159  Tesselation/TesselPoint.hpp \
     160  Tesselation/triangleintersectionlist.hpp
    165161
    166162MOLECUILDERSOURCE = \
    167   ${ANALYSISSOURCE} \
    168163  ${ATOMSOURCE} \
    169164  ${BONDSOURCE} \
    170165  ${DESCRIPTORSOURCE} \
    171166  ${DYNAMICSSOURCE} \
    172   ${HELPERSSOURCE} \
    173167  ${THERMOSTATSOURCE} \
    174168  ${TESSELATIONSOURCE} \
    175   boundary.cpp \
    176169  Box.cpp \
    177170  config.cpp \
    178171  ConfigFileBuffer.cpp \
    179   element.cpp \
    180   elements_db.cpp \
    181   ellipsoid.cpp \
    182172  Formula.cpp \
    183173  graph.cpp \
    … …  
    188178  molecule_geometry.cpp \
    189179  molecule_graph.cpp \
    190   parser.cpp \
    191   periodentafel.cpp \
    192180  ThermoStatContainer.cpp \
    193   triangleintersectionlist.cpp \
    194181  UIElements/UIFactory.cpp \
    195182  version.c \
    … …  
    198185
    199186MOLECUILDERHEADER = \
    200   ${ANALYSISHEADER} \
    201187  ${ATOMHEADER} \
    202188  ${BONDHEADER} \
    … …  
    204190  ${DESCRIPTORIMPLHEADER} \
    205191  ${DYNAMICSHEADER} \
    206   ${HELPERSHEADER} \
    207192  ${THERMOSTATHEADER} \
    208193  ${TESSELATIONHEADER} \
    209   boundary.hpp \
    210194  Box.hpp \
    211195  config.hpp \
    212196  ConfigFileBuffer.hpp \
    213   element.hpp \
    214   elements_db.hpp \
    215   ellipsoid.hpp \
    216197  Formula.hpp \
    217198  graph.hpp \
    218199  linkedcell.hpp \
    219200  molecule.hpp \
    220   parser.hpp \
    221   periodentafel.hpp \
    222201  ThermoStatContainer.hpp \
    223   triangleintersectionlist.hpp \
    224202  types.hpp \
    225203  UIElements/UIFactory.hpp \
    … …  
    281259libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    282260
    283 molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
     261molecuilder_DATA = Element/elements.db Element/valence.db Element/orbitals.db Element/Hbonddistance.db Element/Hbondangle.db
    284262
    285263molecuilder_CXXFLAGS = $(AM_CPPFLAGS)
    … …  
    313291        $(GUI_LIBS)
    314292
    315 joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
     293joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
    316294joiner_LDADD = \
    317         libMolecuilder.la \
    318         libMolecuilderParser.la \
    319         libMolecuilderShapes.la \
    320         libMolecuilderRandomNumbers.la \
     295        libMolecuilderFragmentation.la \
     296        libMolecuilderHelpers.la \
     297        libMolecuilderElement.la \
    321298        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    322299        ${CodePatterns_LIBS} \
    323300        $(BOOST_THREAD_LIBS)
    324301
    325 analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp
     302analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
    326303analyzer_LDADD = \
    327         libMolecuilder.la \
    328         libMolecuilderParser.la \
    329         libMolecuilderShapes.la \
    330         libMolecuilderRandomNumbers.la \
     304        libMolecuilderFragmentation.la \
     305        libMolecuilderHelpers.la \
     306        libMolecuilderElement.la \
    331307        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    332308        ${CodePatterns_LIBS} \

  • src/Parser/MpqcParser.cpp

    r45f835 r9c27b0  
    2929#include "atom.hpp"
    3030#include "config.hpp"
    31 #include "element.hpp"
     31#include "Element/element.hpp"
    3232#include "molecule.hpp"
    3333#include "CodePatterns/Log.hpp"
    … …  
    3535#include "CodePatterns/Verbose.hpp"
    3636#include "LinearAlgebra/Vector.hpp"
    37 #include "periodentafel.hpp"
     37#include "Element/periodentafel.hpp"
    3838#include "World.hpp"
    3939

  • src/Parser/PcpParser.cpp

    r45f835 r9c27b0  
    2727#include "config.hpp"
    2828#include "ConfigFileBuffer.hpp"
    29 #include "element.hpp"
     29#include "Element/element.hpp"
    3030#include "CodePatterns/Assert.hpp"
    3131#include "CodePatterns/Log.hpp"
    … …  
    3434#include "molecule.hpp"
    3535#include "PcpParser.hpp"
    36 #include "periodentafel.hpp"
     36#include "Element/periodentafel.hpp"
    3737#include "ThermoStatContainer.hpp"
    3838#include "World.hpp"

  • src/Parser/PdbParser.cpp

    r45f835 r9c27b0  
    2828#include "atom.hpp"
    2929#include "Bond/bond.hpp"
    30 #include "element.hpp"
     30#include "Element/element.hpp"
    3131#include "molecule.hpp"
    32 #include "periodentafel.hpp"
     32#include "Element/periodentafel.hpp"
    3333#include "Descriptors/AtomIdDescriptor.hpp"
    3434#include "Parser/PdbParser.hpp"

  • src/Parser/TremoloParser.cpp

    r45f835 r9c27b0  
    2929#include "atom.hpp"
    3030#include "Bond/bond.hpp"
    31 #include "element.hpp"
     31#include "Element/element.hpp"
    3232#include "molecule.hpp"
    33 #include "periodentafel.hpp"
     33#include "Element/periodentafel.hpp"
    3434#include "Descriptors/AtomIdDescriptor.hpp"
    3535#include <map>

  • src/Parser/XyzParser.cpp

    r45f835 r9c27b0  
    2828#include "atom.hpp"
    2929#include "molecule.hpp"
    30 #include "element.hpp"
    31 #include "periodentafel.hpp"
     30#include "Element/element.hpp"
     31#include "Element/periodentafel.hpp"
    3232
    3333using namespace std;

  • src/Parser/unittests/ParserMpqcUnitTest.cpp

    r45f835 r9c27b0  
    2828#include "World.hpp"
    2929#include "atom.hpp"
    30 #include "element.hpp"
    31 #include "periodentafel.hpp"
     30#include "Element/element.hpp"
     31#include "Element/periodentafel.hpp"
    3232#include "Descriptors/AtomTypeDescriptor.hpp"
    3333#include "CodePatterns/Assert.hpp"

  • src/Parser/unittests/ParserPcpUnitTest.cpp

    r45f835 r9c27b0  
    2727#include "World.hpp"
    2828#include "atom.hpp"
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "CodePatterns/Log.hpp"
    3232#include "Descriptors/AtomTypeDescriptor.hpp"

  • src/Parser/unittests/ParserPdbUnitTest.cpp

    r45f835 r9c27b0  
    2727#include "World.hpp"
    2828#include "atom.hpp"
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "CodePatterns/Log.hpp"
    3232#include "Descriptors/AtomTypeDescriptor.hpp"

  • src/Parser/unittests/ParserTremoloUnitTest.cpp

    r45f835 r9c27b0  
    2626#include "atom.hpp"
    2727#include "Descriptors/AtomTypeDescriptor.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "Parser/MpqcParser.hpp"
    3030#include "Parser/PdbParser.hpp"
    … …  
    3232#include "Parser/TremoloParser.hpp"
    3333#include "Parser/XyzParser.hpp"
    34 #include "periodentafel.hpp"
     34#include "Element/periodentafel.hpp"
    3535#include "World.hpp"
    3636#include "WorldTime.hpp"

  • src/Parser/unittests/ParserXyzUnitTest.cpp

    r45f835 r9c27b0  
    2727#include "World.hpp"
    2828#include "atom.hpp"
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "CodePatterns/Log.hpp"
    3232#include "Descriptors/AtomTypeDescriptor.hpp"

  • src/PointCloudAdaptor.hpp

    r45f835 r9c27b0  
    1616#include "CodePatterns/Assert.hpp"
    1717#include "IPointCloud.hpp"
    18 #include "TesselPoint.hpp"
     18#include "Tesselation/TesselPoint.hpp"
    1919#include "LinearAlgebra/Vector.hpp"
    2020

  • src/RandomNumbers/unittests/Makefile.am

    r45f835 r9c27b0  
    3030
    3131RANDOMNUMBERLIBS = \
    32         ${CodePatterns_LIBS}
    33 #       $(BOOST_LIB)
     32        ../libMolecuilderRandomNumbers.la \
     33        ${CodePatterns_LIBS} \
     34        $(BOOST_LIB)
    3435
    3536RandomNumberDistributionFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    3637        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp \
    3738        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.hpp
    38 RandomNumberDistributionFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS} \
    39         ../libMolecuilderRandomNumbers.la
     39RandomNumberDistributionFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4040
    4141RandomNumberEngineFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4242        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp \
    4343        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.hpp
    44 RandomNumberEngineFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS} \
    45         ../libMolecuilderRandomNumbers.la
     44RandomNumberEngineFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4645
    4746RandomNumberGeneratorFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    4847        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp \
    4948        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp
    50 RandomNumberGeneratorFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS} \
    51         ../libMolecuilderRandomNumbers.la
     49RandomNumberGeneratorFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    5250
    5351RandomNumberGeneratorUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    5452        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp \
    5553        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.hpp
    56 RandomNumberGeneratorUnitTest_LDADD = ${RANDOMNUMBERLIBS} \
    57         ../libMolecuilderRandomNumbers.la
     54RandomNumberGeneratorUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    5855
    5956

  • src/Thermostats/Berendsen.cpp

    r45f835 r9c27b0  
    1414
    1515#include "Berendsen.hpp"
    16 #include "element.hpp"
     16#include "Element/element.hpp"
    1717#include "config.hpp"
    1818#include "CodePatterns/Verbose.hpp"

  • src/Thermostats/GaussianThermostat.cpp

    r45f835 r9c27b0  
    1919#include "LinearAlgebra/Vector.hpp"
    2020#include "AtomSet.hpp"
    21 #include "element.hpp"
     21#include "Element/element.hpp"
    2222#include "config.hpp"
    2323#include "World.hpp"

  • src/Thermostats/Langevin.cpp

    r45f835 r9c27b0  
    1414
    1515#include "Langevin.hpp"
    16 #include "element.hpp"
     16#include "Element/element.hpp"
    1717#include "config.hpp"
    1818#include "CodePatterns/Verbose.hpp"

  • src/Thermostats/NoseHoover.cpp

    r45f835 r9c27b0  
    1515#include "NoseHoover.hpp"
    1616
    17 #include "element.hpp"
     17#include "Element/element.hpp"
    1818#include "config.hpp"
    1919#include "CodePatterns/Verbose.hpp"

  • src/Thermostats/Woodcock.cpp

    r45f835 r9c27b0  
    1515#include "Woodcock.hpp"
    1616
    17 #include "element.hpp"
     17#include "Element/element.hpp"
    1818#include "config.hpp"
    1919#include "CodePatterns/Verbose.hpp"

  • src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp

    r45f835 r9c27b0  
    2424#include "CodePatterns/Log.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    26 #include "element.hpp"
    27 #include "periodentafel.hpp"
     26#include "Element/element.hpp"
     27#include "Element/periodentafel.hpp"
    2828#include "World.hpp"
    2929

  • src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp

    r45f835 r9c27b0  
    2424#include "CodePatterns/Log.hpp"
    2525#include "CodePatterns/Verbose.hpp"
    26 #include "element.hpp"
    27 #include "periodentafel.hpp"
     26#include "Element/element.hpp"
     27#include "Element/periodentafel.hpp"
    2828#include "World.hpp"
    2929

  • src/UIElements/CommandLineUI/TypeEnumContainer.cpp

    r45f835 r9c27b0  
    3434#include "LinearAlgebra/BoxVector.hpp"
    3535#include "LinearAlgebra/Vector.hpp"
    36 #include "element.hpp"
     36#include "Element/element.hpp"
    3737#include "molecule.hpp"
    3838#include "RandomNumbers/RandomNumberDistribution_Parameters.hpp"

  • src/UIElements/Makefile.am

    r45f835 r9c27b0  
    264264        libMolecuilderActionPrototypes.la \
    265265        libMolecuilderActions.la \
     266        libMolecuilderAnalysis.la \
    266267        libMolecuilderGraph.la \
    267268        libMolecuilder.la \
     269        libMolecuilderFragmentation.la \
    268270        libMolecuilderParser.la \
    269271        libMolecuilderShapes.la \
     272        libMolecuilderHelpers.la \
     273        libMolecuilderElement.la \
    270274        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    271275        libMolecuilderRandomNumbers.la \

  • src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp

    r45f835 r9c27b0  
    2424
    2525#include "CodePatterns/MemDebug.hpp"
    26 #include "element.hpp"
    27 #include "periodentafel.hpp"
     26#include "Element/element.hpp"
     27#include "Element/periodentafel.hpp"
    2828#include "World.hpp"
    2929

  • src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp

    r45f835 r9c27b0  
    2626
    2727#include "CodePatterns/MemDebug.hpp"
    28 #include "element.hpp"
    29 #include "periodentafel.hpp"
     28#include "Element/element.hpp"
     29#include "Element/periodentafel.hpp"
    3030#include "World.hpp"
    3131

  • src/UIElements/Qt4/Query/ElementQtQuery.cpp

    r45f835 r9c27b0  
    2727#include "UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp"
    2828
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "World.hpp"
    3232

  • src/UIElements/Qt4/Query/ElementsQtQuery.cpp

    r45f835 r9c27b0  
    2727#include "UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp"
    2828
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "World.hpp"
    3232

  • src/UIElements/TextUI/Query/ElementTextQuery.cpp

    r45f835 r9c27b0  
    2626#include "CodePatterns/Log.hpp"
    2727#include "CodePatterns/Verbose.hpp"
    28 #include "element.hpp"
    29 #include "periodentafel.hpp"
     28#include "Element/element.hpp"
     29#include "Element/periodentafel.hpp"
    3030#include "World.hpp"
    3131

  • src/UIElements/TextUI/Query/ElementsTextQuery.cpp

    r45f835 r9c27b0  
    2727#include "CodePatterns/Log.hpp"
    2828#include "CodePatterns/Verbose.hpp"
    29 #include "element.hpp"
    30 #include "periodentafel.hpp"
     29#include "Element/element.hpp"
     30#include "Element/periodentafel.hpp"
    3131#include "World.hpp"
    3232

  • src/UIElements/TextUI/TextWindow.cpp

    r45f835 r9c27b0  
    4545// all needed due to config::SaveAll()
    4646#include "config.hpp"
    47 #include "periodentafel.hpp"
     47#include "Element/periodentafel.hpp"
    4848
    4949// config::SaveAll() and enumerate()

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp

    r45f835 r9c27b0  
    3333
    3434#include "Helpers/defs.hpp"
    35 #include "element.hpp"
    36 #include "periodentafel.hpp"
     35#include "Element/element.hpp"
     36#include "Element/periodentafel.hpp"
    3737#include "World.hpp"
    3838

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

    r45f835 r9c27b0  
    3030
    3131#include "Descriptors/AtomIdDescriptor.hpp"
    32 #include "element.hpp"
     32#include "Element/element.hpp"
    3333#include "LinearAlgebra/Vector.hpp"
    3434#include "World.hpp"

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp

    r45f835 r9c27b0  
    3232#include "atom.hpp"
    3333#include "Bond/bond.hpp"
    34 #include "element.hpp"
     34#include "Element/element.hpp"
    3535#include "Helpers/defs.hpp"
    3636#include "LinearAlgebra/Line.hpp"

  • src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp

    r45f835 r9c27b0  
    145145//#include "atom.hpp"
    146146//#include "Bond/bond.hpp"
    147 //#include "element.hpp"
     147//#include "Element/element.hpp"
    148148//#include "molecule.hpp"
    149 //#include "periodentafel.hpp"
     149//#include "Element/periodentafel.hpp"
    150150//#include "World.hpp"
    151151//

  • src/World.cpp

    r45f835 r9c27b0  
    4040#include "LinearAlgebra/RealSpaceMatrix.hpp"
    4141#include "molecule.hpp"
    42 #include "periodentafel.hpp"
     42#include "Element/periodentafel.hpp"
    4343#include "ThermoStatContainer.hpp"
    4444#include "WorldTime.hpp"
    … …  
    802802    Observable("World"),
    803803    BG(new BondGraph(true)),  // assume Angstroem for the moment
    804     periode(new periodentafel),
     804    periode(new periodentafel(true)),
    805805    configuration(new config),
    806806    Thermostats(new ThermoStatContainer),

  • src/atom.cpp

    r45f835 r9c27b0  
    2323#include "CodePatterns/Log.hpp"
    2424#include "config.hpp"
    25 #include "element.hpp"
    26 #include "parser.hpp"
     25#include "Element/element.hpp"
    2726#include "LinearAlgebra/Vector.hpp"
    2827#include "World.hpp"

  • src/atom.hpp

    r45f835 r9c27b0  
    2626#include "atom_graphnode.hpp"
    2727#include "atom_particleinfo.hpp"
    28 #include "TesselPoint.hpp"
     28#include "Tesselation/TesselPoint.hpp"
    2929#include "types.hpp"
    3030

  • src/atom_atominfo.cpp

    r45f835 r9c27b0  
    2323#include "CodePatterns/Verbose.hpp"
    2424#include "config.hpp"
    25 #include "element.hpp"
    26 #include "parser.hpp"
    27 #include "periodentafel.hpp"
     25#include "Element/element.hpp"
     26#include "Element/periodentafel.hpp"
     27#include "Fragmentation/ForceMatrix.hpp"
    2828#include "World.hpp"
    2929#include "WorldTime.hpp"

  • src/atom_bondedparticle.cpp

    r45f835 r9c27b0  
    2626#include "CodePatterns/Log.hpp"
    2727#include "CodePatterns/Verbose.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "WorldTime.hpp"
    3030

  • src/builder_init.cpp

    r45f835 r9c27b0  
    2626#include "CodePatterns/Log.hpp"
    2727#include "molecule.hpp"
    28 #include "periodentafel.hpp"
    29 #include "tesselationhelpers.hpp"
     28#include "Element/periodentafel.hpp"
     29#include "Tesselation/tesselationhelpers.hpp"
    3030#include "UIElements/UIFactory.hpp"
    3131#include "UIElements/Menu/MenuDescription.hpp"

  • src/config.cpp

    r45f835 r9c27b0  
    3434#include "config.hpp"
    3535#include "ConfigFileBuffer.hpp"
    36 #include "element.hpp"
     36#include "Element/element.hpp"
    3737#include "Graph/BondGraph.hpp"
    3838#include "Helpers/helpers.hpp"
    … …  
    4040#include "molecule.hpp"
    4141#include "molecule.hpp"
    42 #include "periodentafel.hpp"
     42#include "Element/periodentafel.hpp"
    4343#include "ThermoStatContainer.hpp"
    4444#include "World.hpp"

  • src/linkedcell.cpp

    r45f835 r9c27b0  
    2626#include "molecule.hpp"
    2727#include "IPointCloud.hpp"
    28 #include "tesselation.hpp"
     28#include "Tesselation/tesselation.hpp"
    2929#include "LinearAlgebra/Vector.hpp"
    3030

  • src/molecule.cpp

    r45f835 r9c27b0  
    3232#include "CodePatterns/Log.hpp"
    3333#include "config.hpp"
    34 #include "element.hpp"
     34#include "Element/element.hpp"
    3535#include "graph.hpp"
    3636#include "Graph/BondGraph.hpp"
    … …  
    4242#include "linkedcell.hpp"
    4343#include "molecule.hpp"
    44 #include "periodentafel.hpp"
    45 #include "tesselation.hpp"
     44#include "Element/periodentafel.hpp"
     45#include "Tesselation/tesselation.hpp"
    4646#include "World.hpp"
    4747#include "WorldTime.hpp"

  • src/molecule_fragmentation.cpp

    r45f835 r9c27b0  
    2828#include "CodePatterns/Log.hpp"
    2929#include "config.hpp"
    30 #include "element.hpp"
     30#include "Element/element.hpp"
    3131#include "Graph/BondGraph.hpp"
    3232#include "Graph/CheckAgainstAdjacencyFile.hpp"
    … …  
    3636#include "LinearAlgebra/RealSpaceMatrix.hpp"
    3737#include "molecule.hpp"
    38 #include "periodentafel.hpp"
     38#include "Element/periodentafel.hpp"
    3939#include "World.hpp"
    4040

  • src/molecule_geometry.cpp

    r45f835 r9c27b0  
    2626#include "CodePatterns/Verbose.hpp"
    2727#include "config.hpp"
    28 #include "element.hpp"
     28#include "Element/element.hpp"
    2929#include "Graph/BondGraph.hpp"
    3030#include "LinearAlgebra/leastsquaremin.hpp"

  • src/molecule_graph.cpp

    r45f835 r9c27b0  
    3131#include "config.hpp"
    3232#include "Graph/DepthFirstSearchAnalysis.hpp"
    33 #include "element.hpp"
     33#include "Element/element.hpp"
    3434#include "Graph/BondGraph.hpp"
    3535#include "Helpers/defs.hpp"

  • src/moleculelist.cpp

    r45f835 r9c27b0  
    2626#include "atom.hpp"
    2727#include "Bond/bond.hpp"
    28 #include "boundary.hpp"
     28#include "Tesselation/boundary.hpp"
    2929#include "Box.hpp"
    3030#include "CodePatterns/Assert.hpp"
    … …  
    3232#include "CodePatterns/Verbose.hpp"
    3333#include "config.hpp"
    34 #include "element.hpp"
     34#include "Element/element.hpp"
    3535#include "Graph/BondGraph.hpp"
    3636#include "Helpers/helpers.hpp"
    … …  
    4040#include "Parser/MpqcParser.hpp"
    4141#include "Parser/FormatParserStorage.hpp"
    42 #include "periodentafel.hpp"
    43 #include "tesselation.hpp"
     42#include "Element/periodentafel.hpp"
     43#include "Tesselation/tesselation.hpp"
    4444#include "World.hpp"
    4545#include "WorldTime.hpp"

  • src/unittests/LinkedCellUnitTest.cpp

    r45f835 r9c27b0  
    3030#include "atom.hpp"
    3131#include "Descriptors/MoleculeDescriptor.hpp"
    32 #include "element.hpp"
     32#include "Element/element.hpp"
    3333#include "linkedcell.hpp"
    3434#include "molecule.hpp"
    35 #include "periodentafel.hpp"
     35#include "Element/periodentafel.hpp"
    3636#include "PointCloudAdaptor.hpp"
    3737#include "World.hpp"

  • src/unittests/ListOfBondsUnitTest.cpp

    r45f835 r9c27b0  
    3030#include "atom.hpp"
    3131#include "Bond/bond.hpp"
    32 #include "element.hpp"
     32#include "Element/element.hpp"
    3333#include "molecule.hpp"
    34 #include "periodentafel.hpp"
     34#include "Element/periodentafel.hpp"
    3535#include "World.hpp"
    3636#include "WorldTime.hpp"

  • src/unittests/Makefile.am

    r45f835 r9c27b0  
    77
    88include ../../src/Actions/unittests/Makefile.am
     9include ../../src/Analysis/unittests/Makefile.am
    910include ../../src/Descriptors/unittests/Makefile.am
     11include ../../src/Element/unittests/Makefile.am
     12include ../../src/Fragmentation/unittests/Makefile.am
     13include ../../src/Graph/unittests/Makefile.am
    1014include ../../src/Parser/unittests/Makefile.am
    1115include ../../src/RandomNumbers/unittests/Makefile.am
    1216include ../../src/Shapes/unittests/Makefile.am
     17include ../../src/Tesselation/unittests/Makefile.am
    1318include ../../src/UIElements/CommandLineUI/unittests/Makefile.am
    1419include ../../src/UIElements/Menu/unittests/Makefile.am
    … …  
    2025
    2126GENERALTESTS = \
    22   AnalysisBondsUnitTest \
    23   AnalysisCorrelationToPointUnitTest \
    24   AnalysisCorrelationToSurfaceUnitTest \
    25   AnalysisPairCorrelationUnitTest \
    26   BondGraphUnitTest \
    2727  BoxUnitTest \
    28   CountBondsUnitTest \
    29   ElementUnitTest \
    3028  FormulaUnittest \
    3129  LinkedCellUnitTest \
    3230  ListOfBondsUnitTest \
    33   PeriodentafelUnitTest \
    34   TesselationUnitTest \
    35   Tesselation_BoundaryTriangleUnitTest \
    36   Tesselation_InOutsideUnitTest \
    3731  WorldTimeUnitTest
    3832
    … …  
    4943        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
    5044
     45GENERALLIBS = \
     46        ../libMolecuilder.la \
     47        ../libMolecuilderHelpers.la \
     48        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     49        ${CodePatterns_LIBS} \
     50        $(BOOST_LIB)
     51
    5152ALLLIBS = \
    5253        ../libMolecuilderUI.la \
    … …  
    5859TESTSOURCES = \
    5960        ${ACTIONTESTSSOURCES} \
     61        ${ANALYSISTESTSSOURCES} \
    6062        ${DESCRIPTORTESTSSOURCES} \
     63        ${ELEMENTTESTSSOURCES} \
     64        ${FRAGMENTATIONTESTSSOURCES} \
     65        ${GRAPHTESTSSOURCES} \
    6166        ${LINEARALGEBRATESTSSOURCES} \
    6267        ${PARSERTESTSSOURCES} \
    6368        ${RANDOMNUMBERTESTSSOURCES} \
    6469        ${SHAPETESTSSOURCES} \
     70        ${TESSELATIONTESTSSOURCES} \
    6571        $(UIELEMENTSCOMMANDLINEPARSERTESTSSOURCES) \
    6672        ${UIELEMENTSMENUTESTSSOURCES} \
    67   AnalysisBondsUnitTest.cpp \
    68   AnalysisCorrelationToPointUnitTest.cpp \
    69   AnalysisCorrelationToSurfaceUnitTest.cpp  \
    70   AnalysisPairCorrelationUnitTest.cpp \
    71   BondGraphUnitTest.cpp \
    7273  BoxUnitTest.cpp \
    73   CountBondsUnitTest.cpp \
    74   ElementUnitTest.cpp \
    7574  FormulaUnitTest.cpp \
    7675  LinkedCellUnitTest.cpp \
    7776  ListOfBondsUnitTest.cpp \
    78   PeriodentafelUnitTest.cpp \
    79   TesselationUnitTest.cpp \
    80   Tesselation_BoundaryTriangleUnitTest.cpp \
    81   Tesselation_InsideOutsideUnitTest.cpp \
    8277  WorldTimeUnitTest.cpp
    8378
    8479TESTHEADERS = \
    8580        ${ACTIONTESTSHEADERS} \
     81        ${ANALYSISTESTSHEADERS} \
    8682        ${DESCRIPTORTESTSHEADERS} \
     83        ${ELEMENTTESTSHEADERS} \
     84        ${FRAGMENTATIONTESTSHEADERS} \
     85        ${GRAPHTESTSHEADERS} \
    8786        ${LINEARALGEBRATESTSHEADERS} \
    8887        ${PARSERTESTSHEADERS} \
    8988        ${RANDOMNUMBERTESTSHEADERS} \
    9089        ${SHAPETESTSHEADERS} \
     90        ${TESSELATIONTESTSHEADERS} \
    9191        $(UIELEMENTSCOMMANDLINEPARSERTESTSHEADERS) \
    9292        ${UIELEMENTSMENUTESTSHEADERS} \
    93   AnalysisBondsUnitTest.hpp \
    94   AnalysisCorrelationToPointUnitTest.hpp \
    95   AnalysisCorrelationToSurfaceUnitTest.hpp  \
    96   AnalysisPairCorrelationUnitTest.hpp \
    97   BondGraphUnitTest.hpp \
    9893  BoxUnitTest.hpp \
    99   CountBondsUnitTest.hpp \
    100   ElementUnitTest.hpp \
    10194  FormulaUnitTest.hpp \
    10295  LinkedCellUnitTest.hpp \
    10396  ListOfBondsUnitTest.hpp \
    104   PeriodentafelUnitTest.hpp \
    105   TesselationUnitTest.hpp \
    106   Tesselation_BoundaryTriangleUnitTest.hpp \
    107   Tesselation_InsideOutsideUnitTest.hpp \
    10897  WorldTimeUnitTest.hpp
    10998 
    110 
    111 AnalysisBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    112         AnalysisBondsUnitTest.cpp \
    113         AnalysisBondsUnitTest.hpp
    114 AnalysisBondsUnitTest_LDADD = ${ALLLIBS}
    115 
    116 AnalysisCorrelationToPointUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    117         AnalysisCorrelationToPointUnitTest.cpp \
    118         AnalysisCorrelationToPointUnitTest.hpp
    119 AnalysisCorrelationToPointUnitTest_LDADD = ${ALLLIBS}
    120 
    121 AnalysisCorrelationToSurfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    122         AnalysisCorrelationToSurfaceUnitTest.cpp \
    123         AnalysisCorrelationToSurfaceUnitTest.hpp
    124 AnalysisCorrelationToSurfaceUnitTest_LDADD = ${ALLLIBS}
    125 
    126 AnalysisPairCorrelationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    127         AnalysisPairCorrelationUnitTest.cpp \
    128         AnalysisPairCorrelationUnitTest.hpp
    129 AnalysisPairCorrelationUnitTest_LDADD = ${ALLLIBS}
    130 
    131 BondGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    132         BondGraphUnitTest.cpp \
    133         BondGraphUnitTest.hpp
    134 BondGraphUnitTest_LDADD = ${ALLLIBS}
    13599
    136100BoxUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    137101        BoxUnitTest.cpp \
    138102        BoxUnitTest.hpp
    139 BoxUnitTest_LDADD = ${ALLLIBS}
    140 
    141 CountBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    142         CountBondsUnitTest.cpp \
    143         CountBondsUnitTest.hpp
    144 CountBondsUnitTest_LDADD = ${ALLLIBS}
    145 
    146 ElementUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    147         ElementUnitTest.cpp \
    148         ../element.cpp \
    149         ElementUnitTest.hpp \
    150         ../element.hpp
    151 ElementUnitTest_LDADD = \
    152         $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
     103BoxUnitTest_LDADD = \
     104        ../libMolecuilder.la \
     105        ../libMolecuilderShapes.la \
     106        ../libMolecuilderHelpers.la \
     107        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la
    153108
    154109FormulaUnittest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    155110        FormulaUnitTest.cpp \
    156111        FormulaUnitTest.hpp
    157 FormulaUnittest_LDADD = ${ALLLIBS}
     112FormulaUnittest_LDADD = $(ALLLIBS)
    158113
    159114LinkedCellUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    160115        LinkedCellUnitTest.cpp \
    161116        LinkedCellUnitTest.hpp
    162 LinkedCellUnitTest_LDADD = ${ALLLIBS}
     117LinkedCellUnitTest_LDADD = $(ALLLIBS)
    163118
    164119ListOfBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    165120        ListOfBondsUnitTest.cpp \
    166121        ListOfBondsUnitTest.hpp
    167 ListOfBondsUnitTest_LDADD = ${ALLLIBS}
    168 
    169 PeriodentafelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    170         PeriodentafelUnitTest.cpp \
    171         PeriodentafelUnitTest.hpp
    172 PeriodentafelUnitTest_LDADD = ${ALLLIBS}
    173 
    174 TesselationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    175         TesselationUnitTest.cpp \
    176         TesselationUnitTest.hpp
    177 TesselationUnitTest_LDADD = ${ALLLIBS}
    178 
    179 Tesselation_BoundaryTriangleUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    180         Tesselation_BoundaryTriangleUnitTest.cpp \
    181         Tesselation_BoundaryTriangleUnitTest.hpp
    182 Tesselation_BoundaryTriangleUnitTest_LDADD = ${ALLLIBS}
    183 
    184 Tesselation_InOutsideUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    185         Tesselation_InsideOutsideUnitTest.cpp \
    186         Tesselation_InsideOutsideUnitTest.hpp
    187 Tesselation_InOutsideUnitTest_LDADD = ${ALLLIBS}
     122ListOfBondsUnitTest_LDADD = $(ALLLIBS)
    188123
    189124WorldTimeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

  • tests/Fragmentations/Makefile.am

    r45f835 r9c27b0  
    44        testsuite.at \
    55        $(TESTSUITE) \
     6        analyzer.in \
    67        atlocal.in \
     8        joiner.in \
    79        molecuilder.in \
    810        $(srcdir)/package.m4 \
    9         $(srcdir)/1_2-dimethoxyethane \
    10         $(srcdir)/1_2-dimethylbenzene \
    11         $(srcdir)/2-methylcyclohexanone \
    12         $(srcdir)/benzene \
    13         $(srcdir)/cholesterol \
    14         $(srcdir)/cycloheptane \
    15         $(srcdir)/dimethyl_bromomalonate \
    16         $(srcdir)/glucose \
    17         $(srcdir)/heptan \
    18         $(srcdir)/isoleucine \
    19         $(srcdir)/neohexane \
    20         $(srcdir)/N_N-dimethylacetamide \
    21         $(srcdir)/proline \
    22         $(srcdir)/putrescine \
    23         $(srcdir)/tartaric_acid
     11        $(srcdir)/Analyzing/heptan \
     12        $(srcdir)/Fragmenting/1_2-dimethoxyethane \
     13        $(srcdir)/Fragmenting/1_2-dimethylbenzene \
     14        $(srcdir)/Fragmenting/2-methylcyclohexanone \
     15        $(srcdir)/Fragmenting/benzene \
     16        $(srcdir)/Fragmenting/cholesterol \
     17        $(srcdir)/Fragmenting/cycloheptane \
     18        $(srcdir)/Fragmenting/dimethyl_bromomalonate \
     19        $(srcdir)/Fragmenting/glucose \
     20        $(srcdir)/Fragmenting/heptan \
     21        $(srcdir)/Fragmenting/isoleucine \
     22        $(srcdir)/Fragmenting/neohexane \
     23        $(srcdir)/Fragmenting/N_N-dimethylacetamide \
     24        $(srcdir)/Fragmenting/proline \
     25        $(srcdir)/Fragmenting/putrescine \
     26        $(srcdir)/Fragmenting/tartaric_acid \
     27        $(srcdir)/Joining/heptan
    2428
    2529TESTSUITE = $(srcdir)/testsuite
    … …  
    2832
    2933TESTSCRIPTS = \
    30         1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order1.at \
    31         1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order2.at \
    32         1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order3.at \
    33         1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order4.at \
    34         1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order1.at \
    35         1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order2.at \
    36         1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order3.at \
    37         1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order4.at \
    38         2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order1.at \
    39         2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order2.at \
    40         2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order3.at \
    41         2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order4.at \
    42         benzene/testsuite-benzene-order1.at \
    43         benzene/testsuite-benzene-order2.at \
    44         benzene/testsuite-benzene-order3.at \
    45         benzene/testsuite-benzene-order4.at \
    46         benzene/testsuite-benzene-order5.at \
    47         benzene/testsuite-benzene-order6.at \
    48         cholesterol/testsuite-cholesterol-order1.at \
    49         cholesterol/testsuite-cholesterol-order2.at \
    50         cholesterol/testsuite-cholesterol-order3.at \
    51         cholesterol/testsuite-cholesterol-order4.at \
    52         cycloheptane/testsuite-cycloheptane-order1.at \
    53         cycloheptane/testsuite-cycloheptane-order2.at \
    54         cycloheptane/testsuite-cycloheptane-order3.at \
    55         cycloheptane/testsuite-cycloheptane-order4.at \
    56         cycloheptane/testsuite-cycloheptane-order5.at \
    57         cycloheptane/testsuite-cycloheptane-order6.at \
    58         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order1.at \
    59         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order2.at \
    60         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order3.at \
    61         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order4.at \
    62         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order5.at \
    63         dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order6.at \
    64         glucose/testsuite-glucose-order1.at \
    65         glucose/testsuite-glucose-order2.at \
    66         glucose/testsuite-glucose-order3.at \
    67         glucose/testsuite-glucose-order4.at \
    68         glucose/testsuite-glucose-order5.at \
    69         glucose/testsuite-glucose-order6.at \
    70         heptan/testsuite-heptan-order1.at \
    71         heptan/testsuite-heptan-order2.at \
    72         heptan/testsuite-heptan-order3.at \
    73         heptan/testsuite-heptan-order4.at \
    74         isoleucine/testsuite-isoleucine-order1.at \
    75         isoleucine/testsuite-isoleucine-order2.at \
    76         isoleucine/testsuite-isoleucine-order3.at \
    77         isoleucine/testsuite-isoleucine-order4.at \
    78         isoleucine/testsuite-isoleucine-order5.at \
    79         isoleucine/testsuite-isoleucine-order6.at \
    80         neohexane/testsuite-neohexane-order1.at \
    81         neohexane/testsuite-neohexane-order2.at \
    82         neohexane/testsuite-neohexane-order3.at \
    83         neohexane/testsuite-neohexane-order4.at \
    84         neohexane/testsuite-neohexane-order5.at \
    85         neohexane/testsuite-neohexane-order6.at \
    86         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order1.at \
    87         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order2.at \
    88         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order3.at \
    89         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order4.at \
    90         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order5.at \
    91         N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order6.at \
    92         proline/testsuite-proline-order1.at \
    93         proline/testsuite-proline-order2.at \
    94         proline/testsuite-proline-order3.at \
    95         proline/testsuite-proline-order4.at \
    96         proline/testsuite-proline-order5.at \
    97         proline/testsuite-proline-order6.at \
    98         putrescine/testsuite-putrescine-order1.at \
    99         putrescine/testsuite-putrescine-order2.at \
    100         putrescine/testsuite-putrescine-order3.at \
    101         putrescine/testsuite-putrescine-order4.at \
    102         putrescine/testsuite-putrescine-order5.at \
    103         putrescine/testsuite-putrescine-order6.at \
    104         tartaric_acid/testsuite-tartaric_acid-order1.at \
    105         tartaric_acid/testsuite-tartaric_acid-order2.at \
    106         tartaric_acid/testsuite-tartaric_acid-order3.at \
    107         tartaric_acid/testsuite-tartaric_acid-order4.at \
    108         tartaric_acid/testsuite-tartaric_acid-order5.at \
    109         tartaric_acid/testsuite-tartaric_acid-order6.at
     34        Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at \
     35        Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at \
     36        Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at \
     37        Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at \
     38        Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at \
     39        Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at \
     40        Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at \
     41        Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at \
     42        Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at \
     43        Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at \
     44        Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at \
     45        Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at \
     46        Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at \
     47        Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at \
     48        Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at \
     49        Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at \
     50        Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at \
     51        Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at \
     52        Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at \
     53        Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at \
     54        Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at \
     55        Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at \
     56        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at \
     57        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at \
     58        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at \
     59        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at \
     60        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at \
     61        Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at \
     62        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at \
     63        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at \
     64        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at \
     65        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at \
     66        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at \
     67        Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at \
     68        Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at \
     69        Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at \
     70        Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at \
     71        Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at \
     72        Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at \
     73        Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at \
     74        Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at \
     75        Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at \
     76        Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at \
     77        Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at \
     78        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at \
     79        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at \
     80        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at \
     81        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at \
     82        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at \
     83        Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at \
     84        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at \
     85        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at \
     86        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at \
     87        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at \
     88        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at \
     89        Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at \
     90        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at \
     91        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at \
     92        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at \
     93        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at \
     94        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at \
     95        Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at \
     96        Fragmenting/proline/testsuite-fragmenting-proline-order1.at \
     97        Fragmenting/proline/testsuite-fragmenting-proline-order2.at \
     98        Fragmenting/proline/testsuite-fragmenting-proline-order3.at \
     99        Fragmenting/proline/testsuite-fragmenting-proline-order4.at \
     100        Fragmenting/proline/testsuite-fragmenting-proline-order5.at \
     101        Fragmenting/proline/testsuite-fragmenting-proline-order6.at \
     102        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at \
     103        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at \
     104        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at \
     105        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at \
     106        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at \
     107        Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at \
     108        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at \
     109        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at \
     110        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at \
     111        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at \
     112        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at \
     113        Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at \
     114        Joining/heptan/testsuite-joining-heptan.at \
     115        Analyzing/heptan/testsuite-analyzing-heptan.at
    110116
    111117max_jobs = 4

  • tests/Fragmentations/testsuite.at

    r45f835 r9c27b0  
    1111
    1212# fragmentation of 1_2-dimethoxyethane
    13 m4_include(1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order1.at)
    14 m4_include(1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order2.at)
    15 m4_include(1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order3.at)
    16 m4_include(1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane-order4.at)
     13m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at)
     14m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at)
     15m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at)
     16m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at)
    1717
    1818# fragmentation of 1_2-dimethylbenzene
    19 m4_include(1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order1.at)
    20 m4_include(1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order2.at)
    21 m4_include(1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order3.at)
    22 m4_include(1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene-order4.at)
     19m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at)
     20m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at)
     21m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at)
     22m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at)
    2323
    2424# fragmentation of 2-methylcyclohexanone
    25 m4_include(2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order1.at)
    26 m4_include(2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order2.at)
    27 m4_include(2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order3.at)
    28 m4_include(2-methylcyclohexanone/testsuite-2-methylcyclohexanone-order4.at)
     25m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at)
     26m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at)
     27m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at)
     28m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at)
    2929
    3030# fragmentation of benzene
    31 m4_include(benzene/testsuite-benzene-order1.at)
    32 m4_include(benzene/testsuite-benzene-order2.at)
    33 m4_include(benzene/testsuite-benzene-order3.at)
    34 m4_include(benzene/testsuite-benzene-order4.at)
    35 m4_include(benzene/testsuite-benzene-order5.at)
    36 m4_include(benzene/testsuite-benzene-order6.at)
     31m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at)
     32m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at)
     33m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at)
     34m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at)
     35m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at)
     36m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at)
    3737
    3838# fragmentation of cholesterol
    39 m4_include(cholesterol/testsuite-cholesterol-order1.at)
    40 m4_include(cholesterol/testsuite-cholesterol-order2.at)
    41 m4_include(cholesterol/testsuite-cholesterol-order3.at)
    42 m4_include(cholesterol/testsuite-cholesterol-order4.at)
     39m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at)
     40m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at)
     41m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at)
     42m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at)
    4343
    4444# fragmentation of cycloheptane
    45 m4_include(cycloheptane/testsuite-cycloheptane-order1.at)
    46 m4_include(cycloheptane/testsuite-cycloheptane-order2.at)
    47 m4_include(cycloheptane/testsuite-cycloheptane-order3.at)
    48 m4_include(cycloheptane/testsuite-cycloheptane-order4.at)
    49 m4_include(cycloheptane/testsuite-cycloheptane-order5.at)
    50 m4_include(cycloheptane/testsuite-cycloheptane-order6.at)
     45m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at)
     46m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at)
     47m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at)
     48m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at)
     49m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at)
     50m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at)
    5151
    5252# fragmentation of dimethyl_bromomalonate
    53 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order1.at)
    54 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order2.at)
    55 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order3.at)
    56 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order4.at)
    57 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order5.at)
    58 m4_include(dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate-order6.at)
     53m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at)
     54m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at)
     55m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at)
     56m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at)
     57m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at)
     58m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at)
    5959
    6060# fragmentation of glucose
    61 m4_include(glucose/testsuite-glucose-order1.at)
    62 m4_include(glucose/testsuite-glucose-order2.at)
    63 m4_include(glucose/testsuite-glucose-order3.at)
    64 m4_include(glucose/testsuite-glucose-order4.at)
    65 m4_include(glucose/testsuite-glucose-order5.at)
    66 m4_include(glucose/testsuite-glucose-order6.at)
     61m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at)
     62m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at)
     63m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at)
     64m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at)
     65m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at)
     66m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at)
    6767
    6868# fragmentation of heptan
    69 m4_include(heptan/testsuite-heptan-order1.at)
    70 m4_include(heptan/testsuite-heptan-order2.at)
    71 m4_include(heptan/testsuite-heptan-order3.at)
    72 m4_include(heptan/testsuite-heptan-order4.at)
     69m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at)
     70m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at)
     71m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at)
     72m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at)
    7373
    7474# fragmentation of isoleucine
    75 m4_include(isoleucine/testsuite-isoleucine-order1.at)
    76 m4_include(isoleucine/testsuite-isoleucine-order2.at)
    77 m4_include(isoleucine/testsuite-isoleucine-order3.at)
    78 m4_include(isoleucine/testsuite-isoleucine-order4.at)
    79 m4_include(isoleucine/testsuite-isoleucine-order5.at)
    80 m4_include(isoleucine/testsuite-isoleucine-order6.at)
     75m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at)
     76m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at)
     77m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at)
     78m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at)
     79m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at)
     80m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at)
    8181
    8282# fragmentation of neohexane
    83 m4_include(neohexane/testsuite-neohexane-order1.at)
    84 m4_include(neohexane/testsuite-neohexane-order2.at)
    85 m4_include(neohexane/testsuite-neohexane-order3.at)
    86 m4_include(neohexane/testsuite-neohexane-order4.at)
    87 m4_include(neohexane/testsuite-neohexane-order5.at)
    88 m4_include(neohexane/testsuite-neohexane-order6.at)
     83m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at)
     84m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at)
     85m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at)
     86m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at)
     87m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at)
     88m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at)
    8989
    9090# fragmentation of N_N-dimethylacetamide
    91 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order1.at)
    92 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order2.at)
    93 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order3.at)
    94 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order4.at)
    95 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order5.at)
    96 m4_include(N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide-order6.at)
     91m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at)
     92m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at)
     93m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at)
     94m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at)
     95m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at)
     96m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at)
    9797
    9898# fragmentation of proline
    99 m4_include(proline/testsuite-proline-order1.at)
    100 m4_include(proline/testsuite-proline-order2.at)
    101 m4_include(proline/testsuite-proline-order3.at)
    102 m4_include(proline/testsuite-proline-order4.at)
    103 m4_include(proline/testsuite-proline-order5.at)
    104 m4_include(proline/testsuite-proline-order6.at)
     99m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order1.at)
     100m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order2.at)
     101m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order3.at)
     102m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order4.at)
     103m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order5.at)
     104m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order6.at)
    105105
    106106# fragmentation of putrescine
    107 m4_include(putrescine/testsuite-putrescine-order1.at)
    108 m4_include(putrescine/testsuite-putrescine-order2.at)
    109 m4_include(putrescine/testsuite-putrescine-order3.at)
    110 m4_include(putrescine/testsuite-putrescine-order4.at)
    111 m4_include(putrescine/testsuite-putrescine-order5.at)
    112 m4_include(putrescine/testsuite-putrescine-order6.at)
     107m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at)
     108m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at)
     109m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at)
     110m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at)
     111m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at)
     112m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at)
    113113
    114114# fragmentation of tartaric_acid
    115 m4_include(tartaric_acid/testsuite-tartaric_acid-order1.at)
    116 m4_include(tartaric_acid/testsuite-tartaric_acid-order2.at)
    117 m4_include(tartaric_acid/testsuite-tartaric_acid-order3.at)
    118 m4_include(tartaric_acid/testsuite-tartaric_acid-order4.at)
    119 m4_include(tartaric_acid/testsuite-tartaric_acid-order5.at)
    120 m4_include(tartaric_acid/testsuite-tartaric_acid-order6.at)
     115m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at)
     116m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at)
     117m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at)
     118m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at)
     119m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at)
     120m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at)
     121
     122# Joining of heptan
     123m4_include(Joining/heptan/testsuite-joining-heptan.at)
     124
     125# Analyzing of heptan
     126m4_include(Analyzing/heptan/testsuite-analyzing-heptan.at)

  • tests/Makefile.am

    r45f835 r9c27b0  
    1 SUBDIRS = CodeChecks regression Fragmentations Tesselations
     1SUBDIRS = \
     2        CodeChecks \
     3        regression \
     4        Fragmentations \
     5        Tesselations
    26

  • tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at

    r45f835 r9c27b0  
    1616
    1717AT_SETUP([Standard Options - bond length table with Undo])
    18 AT_XFAIL_IF([/bin/true])
    1918AT_KEYWORDS([options bond-table undo])
    2019
    … …  
    3130
    3231AT_SETUP([Standard Options - bond length table with Redo])
    33 AT_XFAIL_IF([/bin/true])
    3432AT_KEYWORDS([options bond-table redo])
    3533
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