Changeset 97f9b9


Ignore:
Timestamp:
Jun 13, 2012, 5:39:04 PM (13 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
a483e4
Parents:
8ea3e7
git-author:
Frederik Heber <heber@…> (05/10/12 10:31:17)
git-committer:
Frederik Heber <heber@…> (06/13/12 17:39:04)
Message:

SetBoundaryConditionsAction requires vector<string> instead of string for parameter newconditions.

  • we also added new setters to Box and Box_BoundaryConditions to enable it.
  • TESTFIX: Boundary conditions now have to be supplied as e.g. Wrap Wrap Wrap and not "Wrap,Wrap,Wrap" on the command line.
  • stream operator for Box_BoundaryConditions now also splits by "," and by " ", enhanced unit test function inputTest() on this.
Files:
10 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/WorldAction/SetBoundaryConditionsAction.def

    r8ea3e7 r97f9b9  
    1313// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    1414// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    15 #define paramtypes (std::string)
     15#define paramtypes (std::vector< std::string >)
    1616#define paramtokens ("set-boundary-conditions")
    1717#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'wrap wrap ignore'")

  • src/Box.cpp

    r8ea3e7 r97f9b9  
    365365}
    366366
     367void Box::setConditions(const std::vector< std::string >& _conditions)
     368{
     369  OBSERVE;
     370  NOTIFY(BoundaryConditionsChanged);
     371  conditions.set(_conditions);
     372}
     373
    367374const std::vector<std::pair<Plane,Plane> >  Box::getBoundingPlanes() const
    368375{

  • src/Box.hpp

    r8ea3e7 r97f9b9  
    134134  void setConditions(const BoundaryConditions::Conditions_t & _conditions);
    135135  void setConditions(const std::string & _conditions);
     136  void setConditions(const std::vector< std::string >& _conditions);
    136137
    137138  const std::vector<std::pair<Plane,Plane> > getBoundingPlanes() const;

  • src/Box_BoundaryConditions.cpp

    r8ea3e7 r97f9b9  
    107107}
    108108
     109void BoundaryConditions::BCContainer::set(const std::vector< std::string > &_conditions)
     110{
     111  BoundaryConditions::Conditions_t newconditions;
     112  for (std::vector< std::string >::const_iterator iter = _conditions.begin();
     113      iter != _conditions.end(); ++iter)
     114    newconditions.push_back(getEnum(*iter));
     115  set(newconditions);
     116}
     117
    109118void BoundaryConditions::BCContainer::set(size_t index, const BoundaryConditions::BoundaryCondition_t _condition)
    110119{
    … …  
    118127}
    119128
     129void BoundaryConditions::BCContainer::set(size_t index, const std::string &_condition)
     130{
     131  set(index, getEnum(_condition));
     132}
     133
    120134/** Converter from enum to string.
    121135 *
    … …  
    156170  for (BoundaryConditions::BCContainer::const_iterator iter = t.begin(); iter != t.end(); ++iter) {
    157171    if (iter != t.begin())
    158       out << ", ";
     172      out << " ";
    159173    out << t.getName(*iter);
    160174  }
    … …  
    179193  typedef boost::tokenizer< boost::char_separator<char> > tokens;
    180194  BoundaryConditions::Conditions_t conditions;
    181   boost::char_separator<char> commasep(",");
     195  boost::char_separator<char> commasep(", ");
    182196  // it is imperative to copy the content of the stringbuffer, otherwise we'll
    183197  // get strange bug where 'Wrap' != 'Wrap' and so on.

  • src/Box_BoundaryConditions.hpp

    r8ea3e7 r97f9b9  
    5555    const BoundaryCondition_t get(size_t index) const;
    5656    void set(const Conditions_t &_conditions);
     57    void set(const std::vector< std::string > &_conditions);
    5758    void set(size_t index, const BoundaryCondition_t _condition);
     59    void set(size_t index, const std::string &_conditions);
    5860
    5961    // converter

  • src/unittests/Box_BoundaryConditionsUnitTest.cpp

    r8ea3e7 r97f9b9  
    102102  std::stringstream outstream;
    103103  outstream << *bc;
    104   CPPUNIT_ASSERT( outstream.str() == std::string("Wrap, Wrap, Wrap"));
     104  CPPUNIT_ASSERT( outstream.str() == std::string("Wrap Wrap Wrap"));
    105105}
    106106
    … …  
    132132{
    133133  // set by string
    134   std::stringstream inputstream(" Bounce, Wrap, Ignore");
    135   CPPUNIT_ASSERT_NO_THROW( inputstream >> *bc );
     134  std::stringstream inputstream(" Bounce,Wrap,Ignore");
     135  std::stringstream otherinputstream(" Bounce Wrap Ignore");
     136  std::stringstream anotherinputstream(" Bounce, Wrap, Ignore");
    136137
    137138  // check
     139  CPPUNIT_ASSERT_NO_THROW( inputstream >> *bc );
     140  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Bounce, bc->get(0) );
     141  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Wrap, bc->get(1) );
     142  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Ignore, bc->get(2) );
     143
     144  // check
     145  CPPUNIT_ASSERT_NO_THROW( otherinputstream >> *bc );
     146  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Bounce, bc->get(0) );
     147  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Wrap, bc->get(1) );
     148  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Ignore, bc->get(2) );
     149
     150  // check
     151  CPPUNIT_ASSERT_NO_THROW( anotherinputstream >> *bc );
    138152  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Bounce, bc->get(0) );
    139153  CPPUNIT_ASSERT_EQUAL( BoundaryConditions::Wrap, bc->get(1) );

  • tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at

    r8ea3e7 r97f9b9  
    55
    66AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
    7 AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions "Wrap,Wrap,Wrap" --pair-correlation --elements 1 8 --output-file output-5.csv --bin-output-file bin_output-5.csv --bin-start 0 --bin-end 5], 0, [stdout], [stderr])
     7AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions Wrap Wrap Wrap --pair-correlation --elements 1 8 --output-file output-5.csv --bin-output-file bin_output-5.csv --bin-start 0 --bin-end 5], 0, [stdout], [stderr])
    88#AT_CHECK([file=output-5.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/output-5.csv], 0, [ignore], [ignore])
    99AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-5.csv], 0, [ignore], [ignore])
    1010
    1111AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
    12 AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions "Wrap,Wrap,Wrap" --pair-correlation --elements 1 8 --output-file output-10.csv --bin-output-file bin_output-10.csv --bin-start 5 --bin-end 10], 0, [stdout], [stderr])
     12AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions Wrap Wrap Wrap --pair-correlation --elements 1 8 --output-file output-10.csv --bin-output-file bin_output-10.csv --bin-start 5 --bin-end 10], 0, [stdout], [stderr])
    1313#AT_CHECK([file=output-10.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/output-10.csv], 0, [ignore], [ignore])
    1414AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-10.csv], 0, [ignore], [ignore])
    1515
    1616AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/pre/test.conf .], 0)
    17 AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions "Wrap,Wrap,Wrap" --pair-correlation --elements 1 8 --output-file output-20.csv --bin-output-file bin_output-20.csv --bin-start 10 --bin-end 20], 0, [stdout], [stderr])
     17AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions Wrap Wrap Wrap --pair-correlation --elements 1 8 --output-file output-20.csv --bin-output-file bin_output-20.csv --bin-start 10 --bin-end 20], 0, [stdout], [stderr])
    1818#AT_CHECK([file=output-20.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/output-20.csv], 0, [ignore], [ignore])
    1919AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-20.csv], 0, [ignore], [ignore])

  • tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at

    r8ea3e7 r97f9b9  
    55
    66AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation/pre/test.conf .], 0)
    7 AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions "Wrap,Wrap,Wrap" --pair-correlation --elements 1 8 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
     7AT_CHECK([../../molecuilder -i test.conf  -v 3 --set-boundary-conditions Wrap Wrap Wrap --pair-correlation --elements 1 8 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-end 20], 0, [stdout], [stderr])
    88AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
    99#AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/tests/regression/Analysis/PairCorrelation/post/output.csv], 0, [ignore], [ignore])

  • tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at

    r8ea3e7 r97f9b9  
    44AT_KEYWORDS([domain set-boundary-conditions])
    55
    6 BC="Wrap, Wrap, Wrap"
    7 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC"], 0, [stdout], [stderr])
     6BC="Wrap Wrap Wrap"
     7AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC], 0, [stdout], [stderr])
    88AT_CHECK([fgrep "Boundary conditions are now ${BC}" stdout], 0, [ignore], [ignore])
    9 BC="Bounce, Bounce, Bounce"
    10 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC"], 0, [stdout], [stderr])
     9BC="Bounce Bounce Bounce"
     10AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC], 0, [stdout], [stderr])
    1111AT_CHECK([fgrep "Boundary conditions are now ${BC}" stdout], 0, [ignore], [ignore])
    12 BC="Ignore, Ignore, Ignore"
    13 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC"], 0, [stdout], [stderr])
     12BC="Ignore Ignore Ignore"
     13AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC], 0, [stdout], [stderr])
    1414AT_CHECK([fgrep "Boundary conditions are now ${BC}" stdout], 0, [ignore], [ignore])
    15 BC="Wrap, Bounce, Ignore"
    16 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC"], 0, [stdout], [stderr])
     15BC="Wrap Bounce Ignore"
     16AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC], 0, [stdout], [stderr])
    1717AT_CHECK([fgrep "Boundary conditions are now ${BC}" stdout], 0, [ignore], [ignore])
    1818
    … …  
    2323AT_KEYWORDS([domain set-boundary-conditions undo])
    2424
    25 Check_BC="Wrap, Wrap, Wrap"
    26 BC="Wrap, Wrap, Wrap"
    27 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo], 0, [stdout], [stderr])
     25Check_BC="Wrap Wrap Wrap"
     26BC="Wrap Wrap Wrap"
     27AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo], 0, [stdout], [stderr])
    2828AT_CHECK([fgrep "Boundary conditions are set back to ${Check_BC}" stdout], 0, [ignore], [ignore])
    29 BC="Bounce, Bounce, Bounce"
    30 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo], 0, [stdout], [stderr])
     29BC="Bounce Bounce Bounce"
     30AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo], 0, [stdout], [stderr])
    3131AT_CHECK([fgrep "Boundary conditions are set back to ${Check_BC}" stdout], 0, [ignore], [ignore])
    32 BC="Ignore, Ignore, Ignore"
    33 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo], 0, [stdout], [stderr])
     32BC="Ignore Ignore Ignore"
     33AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo], 0, [stdout], [stderr])
    3434AT_CHECK([fgrep "Boundary conditions are set back to ${Check_BC}" stdout], 0, [ignore], [ignore])
    35 BC="Wrap, Bounce, Ignore"
    36 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo], 0, [stdout], [stderr])
     35BC="Wrap Bounce Ignore"
     36AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo], 0, [stdout], [stderr])
    3737AT_CHECK([fgrep "Boundary conditions are set back to ${Check_BC}" stdout], 0, [ignore], [ignore])
    3838
    … …  
    4343AT_KEYWORDS([domain set-boundary-conditions redo])
    4444
    45 BC="Wrap, Wrap, Wrap"
    46 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo --redo], 0, [stdout], [stderr])
     45BC="Wrap Wrap Wrap"
     46AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo --redo], 0, [stdout], [stderr])
    4747AT_CHECK([fgrep "Boundary conditions are again ${BC}" stdout], 0, [ignore], [ignore])
    48 BC="Bounce, Bounce, Bounce"
    49 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo --redo], 0, [stdout], [stderr])
     48BC="Bounce Bounce Bounce"
     49AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo --redo], 0, [stdout], [stderr])
    5050AT_CHECK([fgrep "Boundary conditions are again ${BC}" stdout], 0, [ignore], [ignore])
    51 BC="Ignore, Ignore, Ignore"
    52 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo --redo], 0, [stdout], [stderr])
     51BC="Ignore Ignore Ignore"
     52AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo --redo], 0, [stdout], [stderr])
    5353AT_CHECK([fgrep "Boundary conditions are again ${BC}" stdout], 0, [ignore], [ignore])
    54 BC="Wrap, Bounce, Ignore"
    55 AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions "$BC" --undo --redo], 0, [stdout], [stderr])
     54BC="Wrap Bounce Ignore"
     55AT_CHECK([../../molecuilder -B "5,0,5,0,0,5" --set-boundary-conditions $BC --undo --redo], 0, [stdout], [stderr])
    5656AT_CHECK([fgrep "Boundary conditions are again ${BC}" stdout], 0, [ignore], [ignore])
    5757

  • tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at

    r8ea3e7 r97f9b9  
    77AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    88AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    9 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Wrap, Wrap, Wrap" -v 3 -I], 0, [stdout], [stderr])
     9AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
    1010AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    1111file=water-bounced.xyz
    1212AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    1313AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    14 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Wrap, Wrap, Wrap" -v 3 -I], 0, [stdout], [stderr])
     14AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
    1515AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    1616file=water-wrapped.xyz
    1717AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    1818AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    19 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Wrap, Wrap, Wrap" -v 3 -I], 0, [stdout], [stderr])
     19AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Wrap Wrap Wrap -v 3 -I], 0, [stdout], [stderr])
    2020AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    2121
    … …  
    2828AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    2929AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    30 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Bounce, Bounce, Bounce" -v 3 -I], 0, [stdout], [stderr])
     30AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
    3131AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    3232file=water-bounced.xyz
    3333AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    3434AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    35 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Bounce, Bounce, Bounce" -v 3 -I], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
    3636AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    3737file=water-wrapped.xyz
    3838AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    3939AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    40 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Bounce, Bounce, Bounce" -v 3 -I], 0, [stdout], [stderr])
     40AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Bounce Bounce Bounce -v 3 -I], 0, [stdout], [stderr])
    4141AT_CHECK([fgrep "I scanned 2 molecules." stdout], 0, [ignore], [ignore])
    4242
    … …  
    4949AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    5050AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    51 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Ignore, Ignore, Ignore" -v 3 -I], 0, [stdout], [stderr])
     51AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
    5252AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    5353file=water-bounced.xyz
    5454AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    5555AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    56 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Ignore, Ignore, Ignore" -v 3 -I], 0, [stdout], [stderr])
     56AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
    5757AT_CHECK([fgrep "I scanned 1 molecules." stdout], 0, [ignore], [ignore])
    5858file=water-wrapped.xyz
    5959AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/$file $file], 0)
    6060AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    61 AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions "Ignore, Ignore, Ignore" -v 3 -I], 0, [stdout], [stderr])
     61AT_CHECK([../../molecuilder -i $file -B "5,0,5,0,0,5" --set-boundary-conditions Ignore Ignore Ignore -v 3 -I], 0, [stdout], [stderr])
    6262AT_CHECK([fgrep "I scanned 2 molecules." stdout], 0, [ignore], [ignore])
    6363
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