Changeset acf800


Ignore:
Timestamp:
Jun 1, 2010, 8:02:48 AM (15 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:
0de7e8
Parents:
bd6bfa
Message:

TESTFIX: Wrong (old) ordering of conf files (IonTyp2 before IonType1) causes wrong id's in dbond and adj.

  • replaced test.conf, replaced test.dbond and test.adj to correct.
  • bonds are ok and have been checked to be correct.

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

Files:
4 edited

Legend:

Unmodified
Added
Removed

  • src/molecule_graph.cpp

    rbd6bfa racf800  
    10371037    line << filename;
    10381038  AdjacencyFile.open(line.str().c_str(), ios::out);
    1039   DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... ");
     1039  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
    10401040  if (AdjacencyFile != NULL) {
    10411041    AdjacencyFile << "m\tn" << endl;
    10421042    ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
    10431043    AdjacencyFile.close();
    1044     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     1044    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
    10451045  } else {
    1046     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     1046    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
    10471047    status = false;
    10481048  }
    … …  
    10691069    line << filename;
    10701070  BondFile.open(line.str().c_str(), ios::out);
    1071   DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... ");
     1071  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
    10721072  if (BondFile != NULL) {
    10731073    BondFile << "m\tn" << endl;
    10741074    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
    10751075    BondFile.close();
    1076     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     1076    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
    10771077  } else {
    1078     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     1078    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
    10791079    status = false;
    10801080  }

  • tests/regression/Molecules/2/post/test.adj

    rbd6bfa racf800  
    11m       n
    2 0       1       3       4       5       
    3 1       2       6       7       0       
    4 2       8       9       10      1       
    5 3       0       
    6 4       0       
    7 5       0       
    8 6       1       
    9 7       1       
    10 8       2       
    11 9       2       
    12 10      2       
     20       8       
     31       8       
     42       8       
     53       9       
     64       9       
     75       10     
     86       10     
     97       10     
     108       0       9       1       2       
     119       3       10      4       8       
     1210      5       6       7       9       

  • tests/regression/Molecules/2/post/test.dbond

    rbd6bfa racf800  
    11m       n
    2 0       1
    3 0       3
    4 0       4
    5 0       5
    6 1       2
    7 1       6
    8 1       7
     20       8
     31       8
    942       8
    10 2       9
    11 2       10
     53       9
     64       9
     75       10
     86       10
     97       10
     108       9
     119       10

  • tests/regression/Molecules/2/pre/test.conf

    rbd6bfa racf800  
    2828OutSrcStep      5       # Output "restart" data every ..th step
    2929TargetTemp      0.000950045     # Target temperature
    30 MaxPsiStep      0       # number of Minimisation steps per state (0 - default)
     30MaxPsiStep      3       # number of Minimisation steps per state (0 - default)
    3131EpsWannier      1e-07   # tolerance value for spread minimisation of orbitals
    3232
    … …  
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    3737MaxMinStopStep  0       # check every ..th steps
    38 MaxMinGapStopStep       0       # check every ..th steps
     38MaxMinGapStopStep       1       # check every ..th steps
    3939
    4040# Values specifying when to stop for INIT, otherwise same as above
    … …  
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    4444InitMaxMinStopStep      0       # check every ..th steps
    45 InitMaxMinGapStopStep   0       # check every ..th steps
     45InitMaxMinGapStopStep   1       # check every ..th steps
    4646
    4747BoxLength                       # (Length of a unit cell)
    … …  
    7171Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
    7272#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
    73 Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 0
    74 Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 1
    75 Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 2
    76 Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 3
    77 Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 4
    78 Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 5
    79 Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 6
    80 Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 7
    81 Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 8
    82 Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 9
    83 Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 10
     73Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 0
     74Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 1
     75Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 2
     76Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 3
     77Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 4
     78Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 5
     79Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 6
     80Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 7
     81Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 8
     82Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 9
     83Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 10
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