Changeset 5f612ee for src/parser.cpp


Ignore:
Timestamp:
Apr 27, 2010, 2:25:42 PM (16 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
632bc3
Parents:
13d5a9 (diff), c695c9 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

  • new molecule() replaced by World::getInstance().createMolecule()
  • new atom() replaced by World::getInstance().createAtom() where appropriate.
  • Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
  • DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
  • ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/parser.cpp

    r13d5a9 r5f612ee  
    3232  if (input == NULL) {
    3333    if (!test)
    34       Log() << Verbose(0) << endl << "Unable to open " << filename << ", is the directory correct?" << endl;
     34      DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << filename << ", is the directory correct?" << endl);
    3535    return false;
    3636  }
    … …  
    109109bool MatrixContainer::InitialiseIndices(class MatrixContainer *Matrix)
    110110{
    111   Log() << Verbose(0) << "Initialising indices";
     111  DoLog(0) && (Log() << Verbose(0) << "Initialising indices");
    112112  if (Matrix == NULL) {
    113     Log() << Verbose(0) << " with trivial mapping." << endl;
     113    DoLog(0) && (Log() << Verbose(0) << " with trivial mapping." << endl);
    114114    Indices = Malloc<int*>(MatrixCounter + 1, "MatrixContainer::InitialiseIndices: **Indices");
    115115    for(int i=MatrixCounter+1;i--;) {
    … …  
    119119    }
    120120  } else {
    121     Log() << Verbose(0) << " from other MatrixContainer." << endl;
     121    DoLog(0) && (Log() << Verbose(0) << " from other MatrixContainer." << endl);
    122122    if (MatrixCounter != Matrix->MatrixCounter)
    123123      return false;
    … …  
    160160  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
    161161  if (input == NULL) {
    162     eLog() << Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
     162    DoeLog(1) && (eLog()<< Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl);
    163163    //performCriticalExit();
    164164    return false;
    … …  
    183183  //Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
    184184  if (ColumnCounter[MatrixNr] == 0) {
    185     eLog() << Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
     185    DoeLog(0) && (eLog()<< Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
    186186    performCriticalExit();
    187187  }
    … …  
    199199  //Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
    200200  if (RowCounter[MatrixNr] == 0) {
    201     eLog() << Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
     201    DoeLog(0) && (eLog()<< Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
    202202    performCriticalExit();
    203203  }
    … …  
    232232    }
    233233  } else {
    234     eLog() << Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl;
     234    DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl);
    235235  }
    236236  input.close();
    … …  
    269269  input.open(file.str().c_str(), ios::in);
    270270  if (input == NULL) {
    271     Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl;
     271    DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
    272272    return false;
    273273  }
    … …  
    278278  }
    279279  input.close();
    280   Log() << Verbose(0) << "Determined " << MatrixCounter << " fragments." << endl;
    281 
    282   Log() << Verbose(0) << "Parsing through each fragment and retrieving " << prefix << suffix << "." << endl;
     280  DoLog(0) && (Log() << Verbose(0) << "Determined " << MatrixCounter << " fragments." << endl);
     281
     282  DoLog(0) && (Log() << Verbose(0) << "Parsing through each fragment and retrieving " << prefix << suffix << "." << endl);
    283283  Header = ReAlloc<char*>(Header, MatrixCounter + 1, "MatrixContainer::ParseFragmentMatrix: **Header"); // one more each for the total molecule
    284284  Matrix = ReAlloc<double**>(Matrix, MatrixCounter + 1, "MatrixContainer::ParseFragmentMatrix: ***Matrix"); // one more each for the total molecule
    … …  
    433433              //Log() << Verbose(0) << "Corresponding index in CurrentFragment is " << m << "." << endl;
    434434              if (m > RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
    435                 eLog() << Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current force index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     435                DoeLog(0) && (eLog()<< Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current force index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl);
    436436                performCriticalExit();
    437437                return false;
    … …  
    469469  char *FragmentNumber = NULL;
    470470
    471   Log() << Verbose(0) << "Writing fragment files." << endl;
     471  DoLog(0) && (Log() << Verbose(0) << "Writing fragment files." << endl);
    472472  for(int i=0;i<MatrixCounter;i++) {
    473473    stringstream line;
    … …  
    477477    output.open(line.str().c_str(), ios::out);
    478478    if (output == NULL) {
    479       eLog() << Verbose(0) << "Unable to open output energy file " << line.str() << "!" << endl;
     479      DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open output energy file " << line.str() << "!" << endl);
    480480      performCriticalExit();
    481481      return false;
    … …  
    503503  stringstream line;
    504504
    505   Log() << Verbose(0) << "Writing matrix values of " << suffix << "." << endl;
     505  DoLog(0) && (Log() << Verbose(0) << "Writing matrix values of " << suffix << "." << endl);
    506506  line << name << prefix << suffix;
    507507  output.open(line.str().c_str(), ios::out);
    508508  if (output == NULL) {
    509     eLog() << Verbose(0) << "Unable to open output matrix file " << line.str() << "!" << endl;
     509    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open output matrix file " << line.str() << "!" << endl);
    510510    performCriticalExit();
    511511    return false;
    … …  
    529529bool EnergyMatrix::ParseIndices()
    530530{
    531   Log() << Verbose(0) << "Parsing energy indices." << endl;
     531  DoLog(0) && (Log() << Verbose(0) << "Parsing energy indices." << endl);
    532532  Indices = Malloc<int*>(MatrixCounter + 1, "EnergyMatrix::ParseIndices: **Indices");
    533533  for(int i=MatrixCounter+1;i--;) {
    … …  
    588588    }
    589589    // allocate last plus one matrix
    590     Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl;
     590    DoLog(0) && (Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl);
    591591    Matrix[MatrixCounter] = Malloc<double*>(RowCounter[MatrixCounter] + 1, "MatrixContainer::ParseFragmentMatrix: **Matrix[]");
    592592    for(int j=0;j<=RowCounter[MatrixCounter];j++)
    … …  
    615615  stringstream line;
    616616
    617   Log() << Verbose(0) << "Parsing force indices for " << MatrixCounter << " matrices." << endl;
     617  DoLog(0) && (Log() << Verbose(0) << "Parsing force indices for " << MatrixCounter << " matrices." << endl);
    618618  Indices = Malloc<int*>(MatrixCounter + 1, "ForceMatrix::ParseIndices: **Indices");
    619619  line << name << FRAGMENTPREFIX << FORCESFILE;
    … …  
    621621  //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
    622622  if (input == NULL) {
    623     Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl;
     623    DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl);
    624624    return false;
    625625  }
    … …  
    664664      int j = Indices[ FragmentNr ][l];
    665665      if (j > RowCounter[MatrixCounter]) {
    666         eLog() << Verbose(0) << "Current force index " << j << " is greater than " << RowCounter[MatrixCounter] << "!" << endl;
     666        DoeLog(0) && (eLog()<< Verbose(0) << "Current force index " << j << " is greater than " << RowCounter[MatrixCounter] << "!" << endl);
    667667        performCriticalExit();
    668668        return false;
    … …  
    700700    input.open(file.str().c_str(), ios::in);
    701701    if (input == NULL) {
    702       Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl;
     702      DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
    703703      return false;
    704704    }
    … …  
    724724 
    725725    // allocate last plus one matrix
    726     Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl;
     726    DoLog(0) && (Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl);
    727727    Matrix[MatrixCounter] = Malloc<double*>(RowCounter[MatrixCounter] + 1, "MatrixContainer::ParseFragmentMatrix: **Matrix[]");
    728728    for(int j=0;j<=RowCounter[MatrixCounter];j++)
    … …  
    753753  stringstream line;
    754754 
    755   Log() << Verbose(0) << "Parsing hessian indices for " << MatrixCounter << " matrices." << endl;
     755  DoLog(0) && (Log() << Verbose(0) << "Parsing hessian indices for " << MatrixCounter << " matrices." << endl);
    756756  Indices = Malloc<int*>(MatrixCounter + 1, "HessianMatrix::ParseIndices: **Indices");
    757757  line << name << FRAGMENTPREFIX << FORCESFILE;
    … …  
    759759  //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
    760760  if (input == NULL) {
    761     Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl;
     761    DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl);
    762762    return false;
    763763  }
    … …  
    802802      int j = Indices[ FragmentNr ][l];
    803803      if (j > RowCounter[MatrixCounter]) {
    804         eLog() << Verbose(0) << "Current hessian index " << j << " is greater than " << RowCounter[MatrixCounter] << ", where i=" << i << ", Order=" << Order << ", l=" << l << " and FragmentNr=" << FragmentNr << "!" << endl;
     804        DoeLog(0) && (eLog()<< Verbose(0) << "Current hessian index " << j << " is greater than " << RowCounter[MatrixCounter] << ", where i=" << i << ", Order=" << Order << ", l=" << l << " and FragmentNr=" << FragmentNr << "!" << endl);
    805805        performCriticalExit();
    806806        return false;
    … …  
    810810          int k = Indices[ FragmentNr ][m];
    811811          if (k > ColumnCounter[MatrixCounter]) {
    812             eLog() << Verbose(0) << "Current hessian index " << k << " is greater than " << ColumnCounter[MatrixCounter] << ", where m=" << m << ", j=" << j << ", i=" << i << ", Order=" << Order << ", l=" << l << " and FragmentNr=" << FragmentNr << "!" << endl;
     812            DoeLog(0) && (eLog()<< Verbose(0) << "Current hessian index " << k << " is greater than " << ColumnCounter[MatrixCounter] << ", where m=" << m << ", j=" << j << ", i=" << i << ", Order=" << Order << ", l=" << l << " and FragmentNr=" << FragmentNr << "!" << endl);
    813813            performCriticalExit();
    814814            return false;
    … …  
    863863              //Log() << Verbose(0) << "Corresponding row index for " << k << " in CurrentFragment is " << m << "." << endl;
    864864              if (m > RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
    865                 eLog() << Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current row index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     865                DoeLog(0) && (eLog()<< Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current row index " << m << " is greater than " << RowCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl);
    866866                performCriticalExit();
    867867                return false;
    … …  
    881881                  //Log() << Verbose(0) << "Corresponding column index for " << l << " in CurrentFragment is " << n << "." << endl;
    882882                  if (n > ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ]) {
    883                     eLog() << Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current column index " << n << " is greater than " << ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl;
     883                    DoeLog(0) && (eLog()<< Verbose(0) << "In fragment No. " << KeySets.OrderSet[Order][CurrentFragment]   << " current column index " << n << " is greater than " << ColumnCounter[ KeySets.OrderSet[Order][CurrentFragment] ] << "!" << endl);
    884884                    performCriticalExit();
    885885                    return false;
    … …  
    930930    input.open(file.str().c_str(), ios::in);
    931931    if (input == NULL) {
    932       Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl;
     932      DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
    933933      return false;
    934934    }
    … …  
    952952 
    953953    // allocate last plus one matrix
    954     Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl;
     954    DoLog(0) && (Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl);
    955955    Matrix[MatrixCounter] = Malloc<double*>(RowCounter[MatrixCounter] + 1, "MatrixContainer::ParseFragmentMatrix: **Matrix[]");
    956956    for(int j=0;j<=RowCounter[MatrixCounter];j++)
    … …  
    10071007
    10081008  FragmentCounter = FCounter;
    1009   Log() << Verbose(0) << "Parsing key sets." << endl;
     1009  DoLog(0) && (Log() << Verbose(0) << "Parsing key sets." << endl);
    10101010  KeySets = Malloc<int*>(FragmentCounter, "KeySetsContainer::ParseKeySets: **KeySets");
    10111011  for(int i=FragmentCounter;i--;)
    … …  
    10141014  input.open(file.str().c_str(), ios::in);
    10151015  if (input == NULL) {
    1016     Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl;
     1016    DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
    10171017    return false;
    10181018  }
    … …  
    10481048  int Counter;
    10491049
    1050   Log() << Verbose(0) << "Creating Fragment terms." << endl;
     1050  DoLog(0) && (Log() << Verbose(0) << "Creating Fragment terms." << endl);
    10511051  // scan through all to determine maximum order
    10521052  Order=0;
    … …  
    10591059      Order = Counter;
    10601060  }
    1061   Log() << Verbose(0) << "Found Order is " << Order << "." << endl;
     1061  DoLog(0) && (Log() << Verbose(0) << "Found Order is " << Order << "." << endl);
    10621062
    10631063  // scan through all to determine fragments per order
    … …  
    10731073  }
    10741074  for(int i=0;i<Order;i++)
    1075     Log() << Verbose(0) << "Found No. of Fragments of Order " << i+1 << " is " << FragmentsPerOrder[i] << "." << endl;
     1075    DoLog(0) && (Log() << Verbose(0) << "Found No. of Fragments of Order " << i+1 << " is " << FragmentsPerOrder[i] << "." << endl);
    10761076
    10771077  // scan through all to gather indices to each order set
    … …  
    10891089    FragmentsPerOrder[Counter-1]++;
    10901090  }
    1091   Log() << Verbose(0) << "Printing OrderSet." << endl;
     1091  DoLog(0) && (Log() << Verbose(0) << "Printing OrderSet." << endl);
    10921092  for(int i=0;i<Order;i++) {
    10931093    for (int j=0;j<FragmentsPerOrder[i];j++) {
    1094       Log() << Verbose(0) << " " << OrderSet[i][j];
    1095     }
    1096     Log() << Verbose(0) << endl;
    1097   }
    1098   Log() << Verbose(0) << endl;
     1094      DoLog(0) && (Log() << Verbose(0) << " " << OrderSet[i][j]);
     1095    }
     1096    DoLog(0) && (Log() << Verbose(0) << endl);
     1097  }
     1098  DoLog(0) && (Log() << Verbose(0) << endl);
    10991099
    11001100
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