Changes in / [0174b62:bd81f9]


Ignore:
Files:
46 added
33 edited

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Unmodified
Added
Removed

  • configure.ac

    r0174b62 rbd81f9  
    163163# Boost headers with libraries
    164164BOOST_FILESYSTEM
     165BOOST_IOSTREAMS
    165166BOOST_PROGRAM_OPTIONS
    166167AS_IF([test x"$enable_python" != x"no"], [BOOST_PYTHON])
    … …  
    169170
    170171
    171 # CodePatterns library (needs Chronos clock time conversion bugfix)
    172 AM_PATH_CODEPATTERNS([1.2.1], $have_debug,,[AC_MSG_ERROR([Missing CodePatterns library, please specify PKG_CONFIG_PATH or use --with-codepatterns...])])
     172# CodePatterns library (needs boost/archive/iserializer.hpp before MemDebug.hpp)
     173AM_PATH_CODEPATTERNS([1.2.2], $have_debug,,[AC_MSG_ERROR([Missing CodePatterns library, please specify PKG_CONFIG_PATH or use --with-codepatterns...])])
     174
     175# JobMarket library (needs boost/archive/iserializer.hpp before MemDebug.hpp)
     176AC_ARG_ENABLE(
     177  [jobmarket],
     178  AS_HELP_STRING([--enable-jobmarket],[turn on JobMarket feature [default=yes]]),
     179  enable_jobmarket=$enableval,
     180  enable_jobmarket="yes")
     181AC_MSG_RESULT($enable_jobmarket)
     182AS_IF([test x"$enable_jobmarket" != x"no"],[
     183  AM_PATH_JOBMARKET([1.0.0], $have_debug,[
     184    # the following is only required if we have JobMarket
     185    BOOST_ASIO
     186    AC_DEFINE(HAVE_JOBMARKET,1, ["use JobMarket to calculate fragment jobs."])
     187    ],[
     188      enable_jobmarket="no"
     189    ])
     190]
     191#[
     192#  AC_DEFINE(HAVE_JOBMARKET,0, ["use JobMarket to calculate fragment jobs."])
     193#]
     194)
     195AC_SUBST(HAVE_JOBMARKET)
     196AM_CONDITIONAL([CONDJOBMARKET], [test x"$enable_jobmarket" = x"yes"])
    173197
    174198# Checks for header files.
    … …  
    271295AC_CONFIG_FILES([tests/Fragmentations/molecuilder], [chmod +x tests/Fragmentations/molecuilder])
    272296
     297AC_CONFIG_TESTDIR(tests/JobMarket)
     298AC_CONFIG_FILES([
     299  tests/JobMarket/atlocal
     300  tests/JobMarket/Makefile])
     301AC_CONFIG_FILES([tests/JobMarket/molecuilder], [chmod +x tests/JobMarket/molecuilder])
     302
    273303AC_CONFIG_TESTDIR(tests/regression)
    274304AC_CONFIG_FILES([
    … …  
    296326        src/unittests/Makefile
    297327])
     328
    298329# produce python scripts and tests only when python's present
    299330AM_COND_IF([CONDPYTHON],[
    … …  
    305336        AC_CONFIG_FILES([tests/Python/Makefile])
    306337])
     338
    307339AC_OUTPUT

  • src/Actions/GlobalListOfActions.hpp

    r0174b62 rbd81f9  
    1414#endif
    1515
     16#include <boost/preprocessor/seq/push_back.hpp>
     17
     18// this is global list of actions valid for all cases
     19#define GLOBALLISTOFACTIONS_initial \
     20  (Redo) \
     21  (GraphSubgraphDissection) \
     22  (GraphCreateAdjacency) \
     23  (GraphDepthFirstSearch) \
     24  (MoleculeSaveTemperature) \
     25  (MoleculeCopy) \
     26  (MoleculeSuspendInWater) \
     27  (MoleculeFillWithMolecule) \
     28  (MoleculeRotateToPrincipalAxisSystem) \
     29  (MoleculeSaveAdjacency) \
     30  (MoleculeFillVoidWithMolecule) \
     31  (MoleculeVerletIntegration) \
     32  (MoleculeChangeName) \
     33  (MoleculeRotateAroundSelfByAngle) \
     34  (MoleculeSaveSelectedMolecules) \
     35  (MoleculeSaveBonds) \
     36  (MoleculeLinearInterpolationofTrajectories) \
     37  (MoleculeLoad) \
     38  (MoleculeBondFile) \
     39  (TesselationNonConvexEnvelope) \
     40  (TesselationConvexEnvelope) \
     41  (CommandElementDb) \
     42  (CommandVerbose) \
     43  (CommandWarranty) \
     44  (CommandVersion) \
     45  (CommandHelp) \
     46  (CommandBondLengthTable) \
     47  (CommandFastParsing) \
     48  (ParserSetTremoloAtomdata) \
     49  (ParserParseTremoloPotentials) \
     50  (ParserSaveSelectedAtomsAsExtTypes) \
     51  (ParserSetParserParameters) \
     52  (ParserSetOutputFormats) \
     53  (AnalysisCalculateBoundingBox) \
     54  (AnalysisCalculateCellVolume) \
     55  (AnalysisCalculateMolarMass) \
     56  (AnalysisDipoleAngularCorrelation) \
     57  (AnalysisDipoleCorrelation) \
     58  (AnalysisPairCorrelation) \
     59  (AnalysisPointCorrelation) \
     60  (AnalysisSurfaceCorrelation) \
     61  (AnalysisMolecularVolume) \
     62  (AnalysisPrincipalAxisSystem) \
     63  (CommandSetRandomNumbersEngine) \
     64  (CommandSetRandomNumbersDistribution) \
     65  (Undo) \
     66  (AtomSaveSelectedAtoms) \
     67  (AtomRotateAroundOriginByAngle) \
     68  (AtomChangeElement) \
     69  (AtomRemove) \
     70  (AtomTranslate) \
     71  (AtomAdd) \
     72  (WorldCenterInBox) \
     73  (WorldRepeatBox) \
     74  (WorldChangeBox) \
     75  (WorldCenterOnEdge) \
     76  (WorldSetWorldTime) \
     77  (WorldSetBoundaryConditions) \
     78  (WorldOutput) \
     79  (WorldSetDefaultName) \
     80  (WorldScaleBox) \
     81  (WorldAddEmptyBoundary) \
     82  (WorldBoundInBox) \
     83  (WorldInput) \
     84  (SelectionNotMoleculeOfAtom) \
     85  (SelectionNotAllMolecules) \
     86  (SelectionNotMoleculeById) \
     87  (SelectionMoleculeByOrder) \
     88  (SelectionMoleculeOfAtom) \
     89  (SelectionNotMoleculeByOrder) \
     90  (SelectionMoleculeByName) \
     91  (SelectionMoleculeById) \
     92  (SelectionAllMolecules) \
     93  (SelectionClearAllMolecules) \
     94  (SelectionInvertMolecules) \
     95  (SelectionMoleculeByFormula) \
     96  (SelectionNotMoleculeByFormula) \
     97  (SelectionNotMoleculeByName) \
     98  (SelectionNotAtomById) \
     99  (SelectionNotAtomByOrder) \
     100  (SelectionAllAtomsInsideCuboid) \
     101  (SelectionAllAtoms) \
     102  (SelectionClearAllAtoms) \
     103  (SelectionInvertAtoms) \
     104  (SelectionNotAllAtoms) \
     105  (SelectionNotAtomByElement) \
     106  (SelectionAllAtomsInsideSphere) \
     107  (SelectionAllAtomsOfMolecule) \
     108  (SelectionNotAllAtomsInsideSphere) \
     109  (SelectionAtomByElement) \
     110  (SelectionNotAllAtomsOfMolecule) \
     111  (SelectionNotAllAtomsInsideCuboid) \
     112  (SelectionAtomById) \
     113  (SelectionAtomByOrder) \
     114  (FragmentationFragmentation) \
     115  (FillRegularGrid) \
     116  (FillSphericalSurface)
     117
     118// we need to append the automation action in case we have the JobMarket
     119#ifdef HAVE_JOBMARKET
    16120#define GLOBALLISTOFACTIONS \
    17         (Redo) \
    18         (GraphSubgraphDissection) \
    19         (GraphCreateAdjacency) \
    20         (GraphDepthFirstSearch) \
    21         (MoleculeSaveTemperature) \
    22         (MoleculeCopy) \
    23         (MoleculeSuspendInWater) \
    24         (MoleculeFillWithMolecule) \
    25         (MoleculeRotateToPrincipalAxisSystem) \
    26         (MoleculeSaveAdjacency) \
    27         (MoleculeFillVoidWithMolecule) \
    28         (MoleculeVerletIntegration) \
    29         (MoleculeChangeName) \
    30         (MoleculeRotateAroundSelfByAngle) \
    31         (MoleculeSaveSelectedMolecules) \
    32         (MoleculeSaveBonds) \
    33         (MoleculeLinearInterpolationofTrajectories) \
    34         (MoleculeLoad) \
    35         (MoleculeBondFile) \
    36         (TesselationNonConvexEnvelope) \
    37         (TesselationConvexEnvelope) \
    38         (CommandElementDb) \
    39         (CommandVerbose) \
    40         (CommandWarranty) \
    41         (CommandVersion) \
    42         (CommandHelp) \
    43         (CommandBondLengthTable) \
    44         (CommandFastParsing) \
    45         (ParserSetTremoloAtomdata) \
    46         (ParserParseTremoloPotentials) \
    47         (ParserSaveSelectedAtomsAsExtTypes) \
    48         (ParserSetParserParameters) \
    49         (ParserSetOutputFormats) \
    50         (AnalysisCalculateBoundingBox) \
    51         (AnalysisCalculateCellVolume) \
    52         (AnalysisCalculateMolarMass) \
    53         (AnalysisDipoleAngularCorrelation) \
    54         (AnalysisDipoleCorrelation) \
    55         (AnalysisPairCorrelation) \
    56         (AnalysisPointCorrelation) \
    57         (AnalysisSurfaceCorrelation) \
    58         (AnalysisMolecularVolume) \
    59         (AnalysisPrincipalAxisSystem) \
    60         (CommandSetRandomNumbersEngine) \
    61         (CommandSetRandomNumbersDistribution) \
    62         (Undo) \
    63         (AtomSaveSelectedAtoms) \
    64         (AtomRotateAroundOriginByAngle) \
    65         (AtomChangeElement) \
    66         (AtomRemove) \
    67         (AtomTranslate) \
    68         (AtomAdd) \
    69         (WorldCenterInBox) \
    70         (WorldRepeatBox) \
    71         (WorldChangeBox) \
    72         (WorldCenterOnEdge) \
    73         (WorldSetWorldTime) \
    74         (WorldSetBoundaryConditions) \
    75         (WorldOutput) \
    76         (WorldSetDefaultName) \
    77         (WorldScaleBox) \
    78         (WorldAddEmptyBoundary) \
    79         (WorldBoundInBox) \
    80         (WorldInput) \
    81         (SelectionNotMoleculeOfAtom) \
    82         (SelectionNotAllMolecules) \
    83         (SelectionNotMoleculeById) \
    84         (SelectionMoleculeByOrder) \
    85         (SelectionMoleculeOfAtom) \
    86         (SelectionNotMoleculeByOrder) \
    87         (SelectionMoleculeByName) \
    88         (SelectionMoleculeById) \
    89         (SelectionAllMolecules) \
    90         (SelectionClearAllMolecules) \
    91   (SelectionInvertMolecules) \
    92         (SelectionMoleculeByFormula) \
    93         (SelectionNotMoleculeByFormula) \
    94         (SelectionNotMoleculeByName) \
    95         (SelectionNotAtomById) \
    96         (SelectionNotAtomByOrder) \
    97         (SelectionAllAtomsInsideCuboid) \
    98         (SelectionAllAtoms) \
    99         (SelectionClearAllAtoms) \
    100   (SelectionInvertAtoms) \
    101         (SelectionNotAllAtoms) \
    102         (SelectionNotAtomByElement) \
    103         (SelectionAllAtomsInsideSphere) \
    104         (SelectionAllAtomsOfMolecule) \
    105         (SelectionNotAllAtomsInsideSphere) \
    106         (SelectionAtomByElement) \
    107         (SelectionNotAllAtomsOfMolecule) \
    108         (SelectionNotAllAtomsInsideCuboid) \
    109         (SelectionAtomById) \
    110         (SelectionAtomByOrder) \
    111         (FragmentationFragmentation) \
    112         (FillRegularGrid) \
    113         (FillSphericalSurface)
     121    BOOST_PP_SEQ_PUSH_BACK( \
     122        GLOBALLISTOFACTIONS_initial, \
     123        FragmentationFragmentationAutomation \
     124      )
     125#else
     126#define GLOBALLISTOFACTIONS \
     127    GLOBALLISTOFACTIONS_initial
     128#endif /* HAVE_JOBMARKET */
    114129
    115130#endif /* GLOBALLISTOFACTIONS_HPP_ */

  • src/Actions/Makefile.am

    r0174b62 rbd81f9  
    196196FRAGMENTATIONACTIONDEFS = \
    197197  Actions/FragmentationAction/FragmentationAction.def
     198
     199if CONDJOBMARKET
     200FRAGMENTATIONACTIONSOURCE += \
     201  Actions/FragmentationAction/FragmentationAutomationAction.cpp
     202FRAGMENTATIONACTIONHEADER += \
     203  Actions/FragmentationAction/FragmentationAutomationAction.hpp
     204FRAGMENTATIONACTIONDEFS += \
     205  Actions/FragmentationAction/FragmentationAutomationAction.def
     206endif
    198207
    199208GRAPHACTIONSOURCE = \
    … …  
    454463        libMolecuilderActionPrototypes.la
    455464#       libMolecuilderActionPython.la
     465libMolecuilderActionPrototypes_la_CPPFLAGS = $(AM_CPPFLAGS)
     466if CONDJOBMARKET
     467libMolecuilderActionPrototypes_la_CPPFLAGS += $(JobMarket_CFLAGS)
     468endif
    456469libMolecuilderActions_la_includedir = $(includedir)/MoleCuilder/Actions/
    457470libMolecuilderActionPrototypes_la_includedir = $(includedir)/MoleCuilder/Actions/

  • src/Actions/unittests/stubs/DummyUI.hpp

    r0174b62 rbd81f9  
    4444  virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = ""){}
    4545  virtual void queryFile(Parameter<boost::filesystem::path> &, const char*, std::string = ""){}
     46  virtual void queryFiles(Parameter<std::vector< boost::filesystem::path> >&, const char*, std::string = ""){}
    4647  virtual void queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &, const char*, std::string = ""){}
    4748};

  • src/Atom/atom_observable.cpp

    r0174b62 rbd81f9  
    4040{
    4141  std::map<Observable *, Channels*>::iterator iter = NotificationChannels.find(this);
     42  ASSERT(iter != NotificationChannels.end(),
     43      "~AtomObservable() - cannot find myself in NotificationChannels.");
    4244  delete iter->second;
    4345  NotificationChannels.erase(iter);

  • src/Fragmentation/MatrixContainer.cpp

    r0174b62 rbd81f9  
    8888 *    -# scan header lines for number of columns
    8989 *    -# scan lines for number of rows
    90  *    -# allocate matrix
     90 *    -# allocate a temporary matrix
    9191 *    -# loop over found column and row counts and parse in each entry
     92 *    -# use MatrixContainer::AddMatrix() to add the parsed matrix to the internal
    9293 * \param &input input stream
    9394 * \param skiplines number of inital lines to skip
    … …  
    109110
    110111  // parse header
    111   if (Header.size() <= MatrixNr)
    112     Header.resize(MatrixNr);
    113   Header[MatrixNr] = std::string("");
     112  std::string header;
    114113  char dummy[1024];
    115114  for (int m=skiplines+1;m--;)
    … …  
    117116  line.str(dummy);
    118117  for(int k=skipcolumns;k--;)
    119     line >> Header[MatrixNr];
     118    line >> header;
    120119  LOG(3, "INFO: Header of Matrix " << MatrixNr << " :" << line.str());
    121120
    122121  // scan header for number of columns
    123   if (ColumnCounter.size() <= MatrixNr)
    124     ColumnCounter.resize(MatrixNr);
    125   ColumnCounter[MatrixNr]=0;
     122  size_t ColumnCounter = 0;
    126123  while ( getline(line,token, '\t') ) {
    127124    if (token.length() > 0)
    128       ColumnCounter[MatrixNr]++;
     125      ColumnCounter++;
    129126  }
    130127  LOG(3, "INFO: "+line.str());
    131   LOG(4, "INFO: ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << ".");
    132   if (ColumnCounter[MatrixNr] == 0) {
    133     ELOG(0, "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream.");
    134     performCriticalExit();
    135   }
    136128
    137129  // scan rest for number of rows/lines
    138   if (RowCounter.size() <= MatrixNr)
    139     RowCounter.resize(MatrixNr);
    140   RowCounter[MatrixNr]=-1;    // counts one line too much
     130  size_t RowCounter = -1;
    141131  while (!input.eof()) {
    142132    input.getline(filename, 1023);
    143133    LOG(3, "INFO: Comparing: " << strncmp(filename,"MeanForce",9));
    144     RowCounter[MatrixNr]++; // then line was not last MeanForce
     134    RowCounter++; // then line was not last MeanForce
    145135    if (strncmp(filename,"MeanForce", 9) == 0) {
    146136      break;
    147137    }
    148138  }
    149   LOG(4, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
    150   if (RowCounter[MatrixNr] == 0) {
    151     ELOG(0, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
    152     performCriticalExit();
    153   }
    154 
    155   // allocate matrix if it's not zero dimension in one direction
    156   if (Matrix.size() <= MatrixNr)
    157     Matrix.resize(MatrixNr+1);
    158   if ((Matrix[MatrixNr].size() <= (size_t)RowCounter[MatrixNr] + 1) && (RowCounter[MatrixNr] > -1)) {
    159     Matrix[MatrixNr].resize(RowCounter[MatrixNr] + 2);
    160     for(int j=0;j<=RowCounter[MatrixNr];j++) {
    161       if ((Matrix[MatrixNr][j].size() <= (size_t)ColumnCounter[MatrixNr]) && (ColumnCounter[MatrixNr] > -1))
    162         Matrix[MatrixNr][j].resize(ColumnCounter[MatrixNr]+1);
    163       // clear
    164       for(int k=0;k<=ColumnCounter[MatrixNr];k++)
    165         Matrix[MatrixNr][j][k] = 0;
    166     }
    167   } else {
    168     ELOG(1, "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!");
    169     return false;
    170   }
     139
     140  // allocate temporary matrix
     141  MatrixArray temp_matrix;
     142  temp_matrix.resize(RowCounter);
     143  for(MatrixArray::iterator iter = temp_matrix.begin(); iter != temp_matrix.end(); ++iter)
     144    (*iter).resize(ColumnCounter);
    171145
    172146  // parse in each entry for this matrix
    … …  
    179153  for(int k=skipcolumns;k--;)  // skip columns in header too
    180154    line >> filename;
    181   Header[MatrixNr] = line.str();
    182   for(int j=0;j<RowCounter[MatrixNr];j++) {
     155  header = line.str();
     156  for(size_t j=0;j<RowCounter;j++) {
    183157    input.getline(filename, 1023);
    184158    std::stringstream lines(filename);
    … …  
    187161    for(int k=skipcolumns;k--;)
    188162      lines >> filename;
    189     for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
    190       lines >> Matrix[MatrixNr][j][k];
    191       output << " " << std::setprecision(2) << Matrix[MatrixNr][j][k] << endl;
     163    for(size_t k=0;(k<ColumnCounter) && (!lines.eof());k++) {
     164      lines >> temp_matrix[j][k];
     165      output << " " << std::setprecision(2) << temp_matrix[j][k] << endl;
    192166    }
    193167    LOG(3, output.str());
    194168  }
    195169
    196   return true;
    197 };
     170  // finally add the matrix
     171  return AddMatrix(header, temp_matrix, MatrixNr);
     172}
     173
     174/** Adds a matrix at position \a MatrixNr to MatrixContainer::Matrix.
     175 *
     176 * @param header header to add for this matrix
     177 * @param matrix to add
     178 * @param MatrixNr position in MatrixContainer::Matrix.
     179 * @return true - insertion ok, false - invalid matrix
     180 */
     181bool MatrixContainer::AddMatrix(const std::string &header, const MatrixArray &matrix, size_t MatrixNr)
     182{
     183  // make some pre-checks
     184  if (header.size() == 0)
     185    ELOG(2, "The given header of the matrix to add is empty.");
     186  if (matrix.size() == 0) {
     187    ELOG(1, "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
     188    return false;
     189  }
     190  if (matrix[0].size() == 0) {
     191    ELOG(1, "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream.");
     192    return false;
     193  }
     194
     195  // add header
     196  if (Header.size() <= MatrixNr)
     197    Header.resize(MatrixNr+1);
     198  Header[MatrixNr] = header;
     199
     200  // row count
     201  if (RowCounter.size() <= MatrixNr)
     202    RowCounter.resize(MatrixNr+1);
     203  RowCounter[MatrixNr] = matrix.size();
     204  LOG(4, "INFO: RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream.");
     205
     206  // column count
     207  if (ColumnCounter.size() <= MatrixNr)
     208    ColumnCounter.resize(MatrixNr+1);
     209  ColumnCounter[MatrixNr] = matrix[0].size();
     210  LOG(4, "INFO: ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << ".");
     211
     212  // allocate matrix ...
     213  if (Matrix.size() <= MatrixNr)
     214    Matrix.resize(MatrixNr+1);
     215  MatrixCounter = Matrix.size()-1;
     216  Matrix[MatrixNr].resize(RowCounter[MatrixNr] + 1);
     217  for(int j=0;j<=RowCounter[MatrixNr];++j)
     218    Matrix[MatrixNr][j].resize(ColumnCounter[MatrixNr]+1);
     219
     220  // .. and copy values
     221  for(int j=0;j<RowCounter[MatrixNr];++j)
     222    for(int k=0;k<ColumnCounter[MatrixNr];++k)
     223      Matrix[MatrixNr][j][k] = matrix[j][k];
     224  // reset last column
     225  for(int j=0;j<RowCounter[MatrixNr];++j)
     226    Matrix[MatrixNr][j][ ColumnCounter[MatrixNr] ] = 0.;
     227  // reset last row
     228  for(int k=0;k<=ColumnCounter[MatrixNr];++k)
     229    Matrix[MatrixNr][ RowCounter[MatrixNr] ][ k ] = 0.;
     230
     231  return true;
     232}
    198233
    199234/** Parsing a number of matrices.

  • src/Fragmentation/MatrixContainer.hpp

    r0174b62 rbd81f9  
    4141  bool InitialiseIndices(class MatrixContainer *Matrix = NULL);
    4242  bool ParseMatrix(std::istream &input, int skiplines, int skipcolumns, size_t MatrixNr);
     43  bool AddMatrix(const std::string &header, const MatrixArray &matrix, size_t MatrixNr);
    4344  virtual bool ParseFragmentMatrix(const std::string name, const std::string prefix, std::string suffix, int skiplines, int skipcolumns);
    4445  bool AllocateMatrix(StringVector GivenHeader, int MCounter, IntVector RCounter, IntVector CCounter);

  • src/Makefile.am

    r0174b62 rbd81f9  
    88BUILT_SOURCES =
    99bin_PROGRAMS =
     10EXTRA_DIST =
    1011
    1112include Actions/Makefile.am
    … …  
    1718include Graph/Makefile.am
    1819include Helpers/Makefile.am
     20
     21if CONDJOBMARKET
     22include Jobs/Makefile.am
     23endif
     24
    1925include LinkedCell/Makefile.am
    2026include Parameters/Makefile.am
    … …  
    2430include UIElements/Makefile.am
    2531
    26 AM_LDFLAGS = -ldl ${BOOST_LDFLAGS}
     32AM_LDFLAGS = -ldl ${BOOST_LDFLAGS} ${CodePatterns_LDFLAGS}
    2733AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    2834
    … …  
    247253
    248254
    249 INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements -I$(top_srcdir)/LinearAlgebra/src
     255INCLUDES = \
     256        -I$(top_srcdir)/src/unittests \
     257        -I$(top_srcdir)/src/Actions \
     258        -I$(top_srcdir)/src/UIElements \
     259        -I$(top_srcdir)/LinearAlgebra/src
    250260
    251261libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    252262noinst_LIBRARIES = libmenu.a
    253 bin_PROGRAMS += molecuilder joiner analyzer
     263bin_PROGRAMS += molecuilder joiner analyzer 
    254264EXTRA_PROGRAMS = unity
    255265
    … …  
    287297
    288298
    289 molecuilder_CXXFLAGS = $(AM_CPPFLAGS)
     299molecuilder_CPPFLAGS = $(AM_CPPFLAGS)
    290300#molecuilder_CXXFLAGS += -DNO_CACHING
    291301molecuilder_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
    … …  
    352362        $(BOOST_THREAD_LIBS)
    353363
     364if CONDJOBMARKET
     365CONTROLLERSOURCE = \
     366        controller_MPQCCommandJob.cpp \
     367        ControllerOptions_MPQCCommandJob.cpp
     368
     369CONTROLLERHEADER = \
     370        controller_MPQCCommandJob.hpp \
     371        ControllerOptions_MPQCCommandJob.hpp
     372
     373
     374noinst_LTLIBRARIES += libFragmentationAutomationController.la
     375libFragmentationAutomationController_la_includedir = $(includedir)/MoleCuilder/JobMarket
     376nobase_libFragmentationAutomationController_la_include_HEADERS = $(CONTROLLERHEADER)
     377libFragmentationAutomationController_la_SOURCES = $(CONTROLLERSOURCE)
     378 libFragmentationAutomationController_la_CPPFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
     379libFragmentationAutomationController_la_LIBADD = \
     380        ${JobMarket_Controller_LIBS} \
     381        $(JobMarket_LIBS)
     382
     383bin_PROGRAMS += Controller PoolWorker Server
     384
     385Controller_SOURCES = controller.cpp controller_AddOn_MPQCCommandJob.cpp
     386Controller_LDFLAGS = $(AM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) ${CodePatterns_LDFLAGS}
     387Controller_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
     388Controller_LDADD = \
     389        libFragmentationAutomationController.la \
     390        libMolecuilderJobs.la \
     391        libMolecuilderFragmentation.la \
     392        libMolecuilderHelpers.la \
     393        $(JobMarket_Controller_LIBS) \
     394        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     395        $(BOOST_PROGRAM_OPTIONS_LIBS) \
     396        ${CodePatterns_LIBS}
     397
     398PoolWorker_SOURCES = poolworker.cpp
     399PoolWorker_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
     400PoolWorker_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
     401PoolWorker_LDADD = \
     402        libMolecuilderJobs.la \
     403        ${JobMarket_PoolWorker_LIBS} \
     404        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     405        ${CodePatterns_LIBS}
     406
     407Server_SOURCES = Server.cpp
     408Server_LDFLAGS = $(AM_LDFLAGS) ${CodePatterns_LDFLAGS}
     409Server_CXXFLAGS = $(AM_CPPFLAGS) $(JobMarket_CFLAGS)
     410Server_LDADD = \
     411        libMolecuilderJobs.la \
     412        ${JobMarket_Server_LIBS} \
     413        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     414        ${CodePatterns_LIBS}
     415endif
     416
    354417unity_SOURCES = unity.cpp
    355418unity_CXXFLAGS = $(AM_CPPFLAGS)
    … …  
    374437        fi
    375438
    376 EXTRA_DIST = \
     439EXTRA_DIST += \
    377440        $(srcdir)/.git-version \
    378441        $(bondtable_DATA) \

  • src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp

    r0174b62 rbd81f9  
    5454void TesselationBoundaryTriangleTest::createTriangle(const std::vector<Vector> &Vectors)
    5555{
    56   CPPUNIT_ASSERT_EQUAL( (size_t)3, Vectors.size() );
     56  CPPUNIT_ASSERT_EQUAL( (size_t)NDIM, Vectors.size() );
    5757
    5858  // create nodes
    … …  
    7676}
    7777
     78/** This cleanly removes a triangle created via createTriangle() from memory.
     79 *
     80 */
     81void TesselationBoundaryTriangleTest::removeTriangle()
     82{
     83  delete(triangle);
     84  for (int i=0;i<NDIM;++i) {
     85    // TesselPoint does not delete its vector as it only got a reference
     86    delete tesselpoints[i];
     87  }
     88}
     89
    7890void TesselationBoundaryTriangleTest::setUp()
    7991{
    … …  
    92104void TesselationBoundaryTriangleTest::tearDown()
    93105{
    94   delete(triangle);
    95   for (int i=0;i<3;++i) {
    96     // TesselPoint does not delete its vector as it only got a reference
    97     delete tesselpoints[i];
    98   }
     106  removeTriangle();
    99107  logger::purgeInstance();
    100108  errorLogger::purgeInstance();
    … …  
    187195{
    188196  {
    189     delete triangle;
     197    removeTriangle();
    190198    // test is from --create-micelle 200 --radius 30. --position "0,0,0" of sles.data
    191199    // failure is: Intersection (23.1644,24.1867,65.1272) is not inside triangle [659|Na2451,O3652,Na3762].
    … …  
    200208  }
    201209  {
    202     delete triangle;
     210    removeTriangle();
    203211    // test is from --create-micelle 200 --radius 30. --position "0,0,0" of sles.data
    204212    // failure is: Intersection (20.6787,70.655,71.5657) is not inside triangle [622|Na1197,Na2166,O3366].
    … …  
    214222  }
    215223  {
    216     delete triangle;
     224    removeTriangle();
    217225    // test is from --create-micelle 200 --radius 30. --position "0,0,0" of sles.data
    218226    // failure is:Intersection (27.56537519896,13.40256646925,6.672946688134) is not inside triangle [702|Na5016,O6388,Na6498].
    … …  
    254262  }
    255263
    256   delete triangle;
     264  removeTriangle();
    257265  // create better triangle;
    258266  VECTORSET(std::vector) Vectors;
    … …  
    289297{
    290298  {
    291     delete triangle;
     299    removeTriangle();
    292300    // test is from --create-micelle 200 --radius 30. --position "0,0,0" of sles.data
    293301    // failure is:Intersection (27.56537519896,13.40256646925,6.672946688134) is not inside triangle [702|Na5016,O6388,Na6498].

  • src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp

    r0174b62 rbd81f9  
    5252private:
    5353      void createTriangle(const std::vector<Vector> &Vectors);
     54      void removeTriangle();
    5455
    5556      static const double SPHERERADIUS;

  • src/UIElements/CommandLineUI/CommandLineDialog.cpp

    r0174b62 rbd81f9  
    116116}
    117117
     118void CommandLineDialog::queryFiles(Parameter<std::vector< boost::filesystem::path> > &param, const char* title, std::string _description){
     119  registerQuery(new FilesCommandLineQuery(param, title, _description));
     120}
     121
    118122void CommandLineDialog::queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &param, const char* title, std::string _description){
    119123  registerQuery(new RandomNumberDistribution_ParametersCommandLineQuery(param, title, _description));

  • src/UIElements/CommandLineUI/CommandLineDialog.hpp

    r0174b62 rbd81f9  
    5353  virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "");
    5454  virtual void queryFile(Parameter<boost::filesystem::path> &, const char*, std::string = "");
     55  virtual void queryFiles(Parameter<std::vector< boost::filesystem::path> > &, const char*, std::string = "");
    5556  virtual void queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &, const char*, std::string = "");
    56 protected:
    5757  // specialized stuff for command line queries
    5858  // all placed into Query/CommandLineQuery.hpp
    … …  
    6767  class EmptyCommandLineQuery;
    6868  class FileCommandLineQuery;
     69  class FilesCommandLineQuery;
    6970  class IntCommandLineQuery;
    7071  class IntsCommandLineQuery;

  • src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp

    r0174b62 rbd81f9  
    157157};
    158158
     159class CommandLineDialog::FilesCommandLineQuery : public Dialog::FilesQuery {
     160public:
     161  FilesCommandLineQuery(Parameter<std::vector< boost::filesystem::path> > &param, std::string title, std::string _description = "");
     162  virtual ~FilesCommandLineQuery();
     163  virtual bool handle();
     164};
     165
    159166class CommandLineDialog::RandomNumberDistribution_ParametersCommandLineQuery : public Dialog::RandomNumberDistribution_ParametersQuery {
    160167public:

  • src/UIElements/Dialog.cpp

    r0174b62 rbd81f9  
    212212}
    213213
     214template <> void Dialog::query< std::vector<boost::filesystem::path> >(Parameter<std::vector< boost::filesystem::path> > &param, const char *token, std::string description)
     215{
     216  queryFiles(param, token, description);
     217}
     218
    214219template <> void Dialog::query< RandomNumberDistribution_Parameters >(Parameter<RandomNumberDistribution_Parameters> &param, const char *token, std::string description)
    215220{

  • src/UIElements/Dialog.hpp

    r0174b62 rbd81f9  
    178178  virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "")=0;
    179179  virtual void queryFile(Parameter<boost::filesystem::path> &, const char*, std::string = "")=0;
     180  virtual void queryFiles(Parameter< std::vector<boost::filesystem::path> > &, const char*, std::string = "")=0;
    180181  virtual void queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &, const char*, std::string = "")=0;
    181182
    … …  
    463464  };
    464465
     466  class FilesQuery : public Query {
     467  public:
     468    FilesQuery(Parameter<std::vector<boost::filesystem::path> > &param, std::string title, std::string _description = "");
     469    virtual ~FilesQuery();
     470    virtual bool handle()=0;
     471    virtual void setResult();
     472  protected:
     473    Parameter<std::vector<boost::filesystem::path> > &tmp;
     474  };
     475
    465476  class RandomNumberDistribution_ParametersQuery : public Query {
    466477  public:

  • src/UIElements/Makefile.am

    r0174b62 rbd81f9  
    1111  UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp \
    1212  UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp \
     13  UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp \
    1314  UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp \
    1415  UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp \
    … …  
    8081  UIElements/TextUI/Query/EmptyTextQuery.cpp \
    8182  UIElements/TextUI/Query/FileTextQuery.cpp \
     83  UIElements/TextUI/Query/FilesTextQuery.cpp \
    8284  UIElements/TextUI/Query/IntTextQuery.cpp \
    8385  UIElements/TextUI/Query/IntsTextQuery.cpp \
    … …  
    129131  UIElements/Query/EmptyQuery.cpp \
    130132  UIElements/Query/FileQuery.cpp \
     133  UIElements/Query/FilesQuery.cpp \
    131134  UIElements/Query/IntQuery.cpp \
    132135  UIElements/Query/IntsQuery.cpp \
    … …  
    181184  UIElements/Qt4/Query/EmptyQtQuery.cpp \
    182185  UIElements/Qt4/Query/FileQtQuery.cpp \
     186  UIElements/Qt4/Query/FilesQtQuery.cpp \
    183187  UIElements/Qt4/Query/IntQtQuery.cpp \
    184188  UIElements/Qt4/Query/IntsQtQuery.cpp \
    … …  
    256260lib_LTLIBRARIES += libMolecuilderUI.la
    257261libMolecuilderUI_la_includedir = $(includedir)/MoleCuilder/UIElements/
    258 libMolecuilderUI_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    259 libMolecuilderUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
     262libMolecuilderUI_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     263if CONDJOBMARKET
     264libMolecuilderUI_la_CPPFLAGS += ${JobMarket_CFLAGS}
     265endif
     266libMolecuilderUI_la_LDFLAGS = \
     267        $(AM_LDFLAGS) \
     268        $(BOOST_FILESYSTEM_LDFLAGS) \
     269        $(BOOST_PROGRAM_OPTIONS_LDFLAGS) \
     270        $(BOOST_RANDOM_LDFLAGS) \
     271        $(BOOST_SERIALIZATION_LDFLAGS)
     272        $(BOOST_SYSTEM_LDFLAGS) \
     273        $(BOOST_THREAD_LDFLAGS)
    260274
    261275# NOTE: ActionPrototypes BEFORE Actions!
    … …  
    277291        libMolecuilderHelpers.la \
    278292        libMolecuilderElement.la \
     293        libMolecuilderJobs.la \
    279294        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    280         libMolecuilderRandomNumbers.la \
     295        libMolecuilderRandomNumbers.la
     296if CONDJOBMARKET
     297libMolecuilderUI_la_LIBADD += ${JobMarket_Controller_LIBS}
     298endif
     299libMolecuilderUI_la_LIBADD += \
    281300        ${CodePatterns_LIBS} \
    282301        $(BOOST_SERIALIZATION_LIBS) \
    … …  
    328347
    329348libMolecuilderQtUI_la_includedir = $(includedir)/MoleCuilder/UIElements/
    330 libMolecuilderQtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     349libMolecuilderQtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS}
    331350libMolecuilderQtUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
    332351

  • src/UIElements/Qt4/QtDialog.cpp

    r0174b62 rbd81f9  
    175175}
    176176
     177void QtDialog::queryFiles(Parameter<std::vector< boost::filesystem::path> >&param, const char* title, std::string)
     178{
     179  registerQuery(new FilesQtQuery(param, title,inputLayout,this));
     180}
     181
    177182void QtDialog::queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &param, const char* title, std::string)
    178183{

  • src/UIElements/Qt4/QtDialog.hpp

    r0174b62 rbd81f9  
    5353  virtual void queryElements(Parameter<std::vector<const element *> > &, const char*,std::string = "");
    5454  virtual void queryFile(Parameter<boost::filesystem::path> &, const char*,std::string = "");
     55  virtual void queryFiles(Parameter<std::vector< boost::filesystem::path> > &, const char*,std::string = "");
    5556  virtual void queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &, const char*,std::string = "");
    5657
    … …  
    7071  class EmptyQtQuery;
    7172  class FileQtQuery;
     73  class FilesQtQuery;
    7274  class IntQtQuery;
    7375  class IntsQtQuery;

  • src/UIElements/Qt4/Query/QtQuery.hpp

    r0174b62 rbd81f9  
    4444class EmptyQtQueryPipe;
    4545class FileQtQueryPipe;
     46class FilesQtQueryPipe;
    4647class IntQtQueryPipe;
    4748class MoleculeQtQueryPipe;
    … …  
    196197};
    197198
     199class QtDialog::FilesQtQuery : public Dialog::FilesQuery {
     200public:
     201  FilesQtQuery(Parameter<std::vector< boost::filesystem::path> > &param, std::string _title, QBoxLayout *_parent, QtDialog *_dialog);
     202  virtual ~FilesQtQuery();
     203  virtual bool handle();
     204  void IntegerEntered(const QString&);
     205  void IntegerSelected();
     206  void AddInteger();
     207  void RemoveInteger();
     208private:
     209  QBoxLayout *parent;
     210  QBoxLayout *thisLayout;
     211  QLabel *titleLabel;
     212
     213  QtQueryListPipe<boost::filesystem::path> *pipe;
     214};
     215
    198216class QtDialog::IntQtQuery : public Dialog::IntQuery {
    199217public:

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

    r0174b62 rbd81f9  
    4848      std::cin.clear();
    4949      std::cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
    50       std::cout << "Input was not a number!" << std::endl;
     50      std::cout << "Input was not a file!" << std::endl;
    5151      continue;
    5252    }

  • src/UIElements/TextUI/Query/TextQuery.hpp

    r0174b62 rbd81f9  
    8787};
    8888
     89class TextDialog::FilesTextQuery : public Dialog::FilesQuery {
     90public:
     91  FilesTextQuery(Parameter<std::vector< boost::filesystem::path> > &param, std::string title, std::string _description = NULL);
     92  virtual ~FilesTextQuery();
     93  virtual bool handle();
     94};
     95
    8996class TextDialog::IntTextQuery : public Dialog::IntQuery {
    9097public:

  • src/UIElements/TextUI/TextDialog.cpp

    r0174b62 rbd81f9  
    114114}
    115115
     116void TextDialog::queryFiles(Parameter<std::vector< boost::filesystem::path> > &param, const char* title, std::string description){
     117  registerQuery(new FilesTextQuery(param, title,description));
     118}
     119
    116120void TextDialog::queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &param, const char* title, std::string description){
    117121  registerQuery(new RandomNumberDistribution_ParametersTextQuery(param, title,description));

  • src/UIElements/TextUI/TextDialog.hpp

    r0174b62 rbd81f9  
    5151  virtual void queryElements(Parameter<std::vector<const element *> > &, const char*, std::string = "");
    5252  virtual void queryFile(Parameter<boost::filesystem::path> &, const char*, std::string = "");
     53  virtual void queryFiles(Parameter<std::vector<boost::filesystem::path> > &, const char*, std::string = "");
    5354  virtual void queryRandomNumberDistribution_Parameters(Parameter<RandomNumberDistribution_Parameters> &, const char*, std::string = "");
    5455
    … …  
    6667  class EmptyTextQuery;
    6768  class FileTextQuery;
     69  class FilesTextQuery;
    6870  class IntTextQuery;
    6971  class IntsTextQuery;

  • src/unittests/Makefile.am

    r0174b62 rbd81f9  
    1515include ../../src/Fragmentation/unittests/Makefile.am
    1616include ../../src/Graph/unittests/Makefile.am
     17
     18if CONDJOBMARKET
     19include ../../src/Jobs/unittests/Makefile.am
     20endif
     21
    1722include ../../src/LinkedCell/unittests/Makefile.am
    1823include ../../src/Parameters/unittests/Makefile.am
    … …  
    2429include ../../src/UIElements/Menu/unittests/Makefile.am
    2530
    26 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src
     31INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src 
    2732
    2833AM_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    … …  
    5358        $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIBS) \
    5459        $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_FILESYSTEM_LIBS) \
    55         $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
     60        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
     61        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
    5662
    5763GENERALLIBS = \
    … …  
    134140        ../libMolecuilderShapes.la \
    135141        ../libMolecuilderHelpers.la \
    136         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la
     142        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     143        ${CodePatterns_LIBS}
    137144
    138145AtomIdSetUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

  • tests/CodeChecks/Makefile.am

    r0174b62 rbd81f9  
    6060                echo 'm4_define([AT_PACKAGE_STRING],    [@PACKAGE_STRING@])' && \
    6161                echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
    62         } >'$(srcdir)/package.m4'
     62        } >'package.m4'

  • tests/CodeChecks/testsuite-globallistofactions_hpp.at

    r0174b62 rbd81f9  
    2323  if test $found -eq 0
    2424  then
    25     AT_CHECK([grep "(${actionname})" ${abs_top_srcdir}/src/Actions/GlobalListOfActions.hpp], 0, [stdout], [ignore])
     25    AT_CHECK([grep "${actionname}" ${abs_top_srcdir}/src/Actions/GlobalListOfActions.hpp], 0, [stdout], [ignore])
    2626  else
    2727    echo "excluded."

  • tests/Fragmentations/Makefile.am

    r0174b62 rbd81f9  
    88        joiner.in \
    99        molecuilder.in \
    10         $(srcdir)/package.m4 \
     10        package.m4 \
    1111        $(srcdir)/Analyzing/heptan \
    1212        $(srcdir)/Fragmenting/1_2-dimethoxyethane \
    … …  
    155155                echo 'm4_define([AT_PACKAGE_STRING],    [@PACKAGE_STRING@])' && \
    156156                echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
    157         } >'$(srcdir)/package.m4'
     157        } >'package.m4'

  • tests/Makefile.am

    r0174b62 rbd81f9  
    1111endif
    1212
     13if CONDJOBMARKET
     14SUBDIRS += JobMarket
     15endif

  • tests/Python/AllActions/options.dat

    r0174b62 rbd81f9  
    7070fill-void       "water.data"
    7171fill-void       "water.xyz"
     72fragment-executable     "mpqc"
     73fragment-jobs   "Job00.in"
    7274fragment-molecule       "./"
     75fragment-path   "test/"
    7376id-mapping      "1"
    7477input   "test.data"
    … …  
    161164select-molecules-by-formula     "H2O"
    162165select-molecules-by-name        "water"
     166server-address  "127.0.0.1"
     167server-port     "1026"
    163168set-boundary-conditions "Wrap, Wrap, Wrap"
    164169set-parser-parameters   "basis = 4-31G"

  • tests/Python/Makefile.am

    r0174b62 rbd81f9  
    55        $(TESTSUITE) \
    66        atlocal.in \
    7         $(srcdir)/package.m4 \
     7        package.m4 \
    88        AllActions \
    99        BoxMaker \
    … …  
    6868                echo 'm4_define([AT_PACKAGE_STRING],    [@PACKAGE_STRING@])' && \
    6969                echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
    70         } >'$(srcdir)/package.m4'
     70        } >'package.m4'

  • tests/Tesselations/Makefile.am

    r0174b62 rbd81f9  
    66        atlocal.in \
    77        molecuilder.in \
    8         $(srcdir)/package.m4 \
     8        package.m4 \
    99        $(srcdir)/1_2-dimethoxyethane \
    1010        $(srcdir)/1_2-dimethylbenzene \
    … …  
    8383                echo 'm4_define([AT_PACKAGE_STRING],    [@PACKAGE_STRING@])' && \
    8484                echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
    85         } >'$(srcdir)/package.m4'
     85        } >'package.m4'

  • tests/regression/Fragmentation/testsuite-fragmentation.at

    r0174b62 rbd81f9  
    1 AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
     1AT_BANNER([MoleCuilder - fragmentation tests])
    22
    3 # fragment the molecule and check the number of configs
     3# check fragmentation
    44m4_include([Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at])
    55

  • tests/regression/Makefile.am

    r0174b62 rbd81f9  
    66        atlocal.in \
    77        molecuilder.in \
    8         $(srcdir)/package.m4 \
     8        package.m4 \
    99        Analysis \
    1010        Atoms \
    … …  
    235235                echo 'm4_define([AT_PACKAGE_STRING],    [@PACKAGE_STRING@])' && \
    236236                echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
    237         } >'$(srcdir)/package.m4'
     237        } >'package.m4'
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