Ignore:
Timestamp:
Jan 14, 2015, 9:03:24 PM (10 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:
cad383
Parents:
601ef8
git-author:
Frederik Heber <heber@…> (01/14/15 20:31:24)
git-committer:
Frederik Heber <heber@…> (01/14/15 21:03:24)
Message:

FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was given.

  • however, the action is still not tested to work.
  • TESTFIX: suspend-in-water gets parameter density via "density" not via "suspend-in-water", set desired density to faulting 1 for the moment.
  • TESTFIX: added water molecule to test.conf, to have at least two molecules.
Location:
tests/regression/Filling/SuspendInWater
Files:
1 added
2 edited

Legend:

Unmodified
Added
Removed

  • tests/regression/Filling/SuspendInWater/pre/test.conf

    r601ef8 r2440ce  
    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
    … …  
    3535RelEpsTotalE    1e-07   # relative change in total energy
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    37 MaxMinStopStep  0       # check every ..th steps
    38 MaxMinGapStopStep       0       # check every ..th steps
     37MaxMinStopStep  12      # check every ..th steps
     38MaxMinGapStopStep       1       # check every ..th steps
    3939
    4040# Values specifying when to stop for INIT, otherwise same as above
    … …  
    4242InitRelEpsTotalE        1e-05   # relative change in total energy
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    44 InitMaxMinStopStep      0       # check every ..th steps
    45 InitMaxMinGapStopStep   0       # check every ..th steps
     44InitMaxMinStopStep      12      # check every ..th steps
     45InitMaxMinGapStopStep   1       # check every ..th steps
    4646
    4747BoxLength                       # (Length of a unit cell)
    … …  
    5555RiemannTensor   0       # (Use metric)
    5656PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
    57 MaxPsiDouble    0       # here: specifying both maximum number of SpinUp- and -Down-states
    58 PsiMaxNoUp      0       # here: specifying maximum number of SpinUp-states
    59 PsiMaxNoDown    0       # here: specifying maximum number of SpinDown-states
     57MaxPsiDouble    12      # here: specifying both maximum number of SpinUp- and -Down-states
     58PsiMaxNoUp      12      # here: specifying maximum number of SpinUp-states
     59PsiMaxNoDown    12      # here: specifying maximum number of SpinDown-states
    6060AddPsis         0       # Additional unoccupied Psis for bandgap determination
    6161
    … …  
    6464IsAngstroem     1       # 0 - Bohr, 1 - Angstroem
    6565RelativeCoord   0       # whether ion coordinates are relative (1) or absolute (0)
    66 MaxTypes        2       # maximum number of different ion types
     66MaxTypes        3       # maximum number of different ion types
    6767
    6868# Ion type data (PP = PseudoPotential, Z = atomic number)
    6969#Ion_TypeNr.    Amount  Z       RGauss  L_Max(PP)L_Loc(PP)IonMass       # chemical name, symbol
    70 Ion_Type1       8       1       1.0     3       3       1.00800000000   Hydrogen        H
     70Ion_Type1       10      1       1.0     3       3       1.00800000000   Hydrogen        H
    7171Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
     72Ion_Type3       1       8       1.0     3       3       15.99900000000  Oxygen  O
    7273#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
     74Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 0
     75Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 1
     76Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 2
     77Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 3
     78Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 4
     79Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 5
     80Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 6
     81Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 7
     82Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 8
     83Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 9
     84Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 10
     85Ion_Type3_1     2.000000000     2.000000000     2.000000000     0 # molecule nr 11
     86Ion_Type1_9     2.758602000     2.000000000     2.504284000     0 # molecule nr 12
     87Ion_Type1_10    2.758602000     2.000000000     1.495716000     0 # molecule nr 13

  • tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at

    r601ef8 r2440ce  
    1818### suspend in water with certain density
    1919
     20AT_SETUP([Filling - suspend in water fails with rho=1])
     21AT_KEYWORDS([filling suspend-in-water])
     22
     23file=test.conf
     24AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
     25AT_CHECK([chmod u+w $file], 0)
     26AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 1.], 5, [stdout], [stderr])
     27
     28AT_CLEANUP
     29
     30AT_SETUP([Filling - suspend in water fails with just one molecule])
     31AT_KEYWORDS([filling suspend-in-water])
     32
     33file=single_molecule.conf
     34AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
     35AT_CHECK([chmod u+w $file], 0)
     36AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 1.], 5, [stdout], [stderr])
     37AT_CHECK([grep "at least two molecules" stdout], 0, [ignore], [ignore])
     38
     39AT_CLEANUP
     40
     41# rho must be on same side of 1 as the present density
     42AT_SETUP([Filling - suspend in water fails with wrong rho])
     43AT_KEYWORDS([filling suspend-in-water])
     44
     45file=test.conf
     46AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
     47AT_CHECK([chmod u+w $file], 0)
     48AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density .5], 5, [stdout], [stderr])
     49AT_CHECK([grep "Desired and present molecular densities must both be either" stdout], 0, [ignore], [ignore])
     50
     51AT_CLEANUP
     52
    2053AT_SETUP([Filling - suspend in water])
    2154AT_XFAIL_IF([/bin/true])
    … …  
    2356
    2457file=test.conf
    25 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
     58AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
    2659AT_CHECK([chmod u+w $file], 0)
    27 AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3], 0, [stdout], [stderr])
     60AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2.], 5, [stdout], [stderr])
    2861AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    2962
    3063AT_CLEANUP
    31 
    3264
    3365AT_SETUP([Filling - suspend in water with Undo])
    … …  
    3870AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
    3971AT_CHECK([chmod u+w $file], 0)
    40 AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3 --undo], 0, [stdout], [stderr])
     72AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2. --undo], 0, [stdout], [stderr])
    4173AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    4274
    … …  
    5183AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
    5284AT_CHECK([chmod u+w $file], 0)
    53 AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3 --undo --redo], 0, [stdout], [stderr])
     85AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2. --undo --redo], 0, [stdout], [stderr])
    5486AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    5587
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