Ignore:
Timestamp:
Oct 19, 2014, 5:08:51 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:
9e1bfb
Parents:
f1eabd
git-author:
Frederik Heber <heber@…> (09/12/14 07:54:12)
git-committer:
Frederik Heber <heber@…> (10/19/14 17:08:51)
Message:

Extracted SavePotentialsAction.

  • PotentialTrainer::StorePotentials removed.
  • Fit...Actions do not store anymore.
  • TESTFIX: potential regression tests now use save-potentials and compare against stored file.
File:
1 edited

Legend:

Unmodified
Added
Removed

  • tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at

    rf1eabd r0ea063  
    2626AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    2727AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    28 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=1;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "morse" --potential-charges 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
     28AT_CHECK([../../molecuilder \
     29        --parse-homologies $file \
     30        --set-random-number-engine "lagged_fibonacci607" \
     31                --random-number-engine-parameters "seed=1;" \
     32        --set-random-number-distribution "uniform_real" \
     33                --random-number-distribution-parameters "min=0;max=1;" \
     34        --fit-potential \
     35                --potential-type "morse" \
     36                --potential-charges 8 1 \
     37                --fragment-charges 1 8 1 \
     38                --set-threshold 1e-6 \
     39        --save-potentials length.potentials], 0, [stdout], [ignore])
    2940# check that L_2 error is below 1e-6
    3041AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
    3142# check parameters to printed precision
    32 AT_CHECK([grep "morse:.*particle_type1=8,.*particle_type2=1,.*spring_constant=1.27.*,.*equilibrium_distance=1.78.*,.*dissociation_energy=0.19.*;" stdout], 0, [ignore], [ignore])
     43AT_CHECK([grep "morse:.*particle_type1=8,.*particle_type2=1,.*spring_constant=1.27.*,.*equilibrium_distance=1.78.*,.*dissociation_energy=0.19.*;" length.potentials], 0, [ignore], [ignore])
    3344
    3445AT_CLEANUP
    … …  
    4152AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    4253AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    43 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=1;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "harmonic_bond" --potential-charges 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
     54AT_CHECK([../../molecuilder \
     55        --parse-homologies $file \
     56        --set-random-number-engine "lagged_fibonacci607" \
     57                --random-number-engine-parameters "seed=1;" \
     58        --set-random-number-distribution "uniform_real" \
     59                --random-number-distribution-parameters "min=0;max=1;" \
     60        --fit-potential \
     61                --potential-type "harmonic_bond" \
     62                --potential-charges 8 1 \
     63                --fragment-charges 1 8 1 \
     64                --set-threshold 1e-6 \
     65        --save-potentials harmonic.potentials], 0, [stdout], [ignore])
    4466# check that L_2 error is below 1e-6
    4567AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
    4668# check parameters to printed precision
    47 AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.29.*,.*equilibrium_distance=1.8.*;" stdout], 0, [ignore], [ignore])
     69AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.29.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
    4870
    4971AT_CLEANUP
    … …  
    5678AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    5779AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    58 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=1;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "harmonic_angle" --potential-charges 1 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
     80AT_CHECK([../../molecuilder \
     81        --parse-homologies $file \
     82        --set-random-number-engine "lagged_fibonacci607" \
     83                --random-number-engine-parameters "seed=1;" \
     84        --set-random-number-distribution "uniform_real" \
     85                --random-number-distribution-parameters "min=0;max=1;" \
     86        --fit-potential \
     87                --potential-type "harmonic_angle" \
     88                --potential-charges 1 8 1 \
     89                --fragment-charges 1 8 1 \
     90                --set-threshold 1e-6 \
     91        --save-potentials angle.potentials], 0, [stdout], [ignore])
    5992# check that L_2 error is below 1e-6
    6093AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
    6194# check parameters to printed precision
    62 AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.10.*,.*equilibrium_distance=-0.27.*;" stdout], 0, [ignore], [ignore])
     95AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.10.*,.*equilibrium_distance=-0.27.*;" angle.potentials], 0, [ignore], [ignore])
    6396
    6497AT_CLEANUP
    … …  
    71104AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    72105AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    73 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=1;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "torsion" --potential-charges 6 6 6 6 --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 --set-threshold 2e-10], 0, [stdout], [ignore])
     106AT_CHECK([../../molecuilder \
     107        --parse-homologies $file \
     108        --set-random-number-engine "lagged_fibonacci607" \
     109                --random-number-engine-parameters "seed=1;" \
     110        --set-random-number-distribution "uniform_real" \
     111                --random-number-distribution-parameters "min=0;max=1;" \
     112        --fit-potential \
     113                --potential-type "torsion" \
     114                --potential-charges 6 6 6 6 \
     115                --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
     116                --set-threshold 2e-10 \
     117        --save-potentials torsion.potentials], 0, [stdout], [ignore])
    74118# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
    75119AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 2e-10) exit 1}'], 0, [ignore], [ignore])
    76 AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" stdout], 0, [ignore], [ignore])
    77 #AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=0.001.*,.*equilibrium_distance=0.99.*;" stdout], 0, [ignore], [ignore])
     120AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
     121#AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=0.001.*,.*equilibrium_distance=0.99.*;" torsion.potentials], 0, [ignore], [ignore])
    78122
    79123AT_CLEANUP
    … …  
    86130AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    87131AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    88 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=1;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "improper" --potential-charges 1 7 1 1 --fragment-charges 7 1 1 1 --set-threshold 3e-4], 0, [stdout], [ignore])
     132AT_CHECK([../../molecuilder \
     133        --parse-homologies $file \
     134        --set-random-number-engine "lagged_fibonacci607" \
     135                --random-number-engine-parameters "seed=1;" \
     136        --set-random-number-distribution "uniform_real" \
     137                --random-number-distribution-parameters "min=0;max=1;" \
     138        --fit-potential \
     139                --potential-type "improper" \
     140                --potential-charges 1 7 1 1 \
     141                --fragment-charges 7 1 1 1 \
     142                --set-threshold 3e-4 \
     143        --save-potentials improper.potentials], 0, [stdout], [ignore])
    89144# check that L_2 error is below 3e-4
    90145AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
    91146# check parameters to printed precision
    92 AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" stdout], 0, [ignore], [ignore])
    93 #AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=1.02.*,.*equilibrium_distance=0.85.*;" stdout], 0, [ignore], [ignore])
     147AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
     148#AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=1.02.*,.*equilibrium_distance=0.85.*;" improper.potentials], 0, [ignore], [ignore])
    94149
    95150AT_CLEANUP
    … …  
    102157AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
    103158AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    104 AT_CHECK([../../molecuilder --parse-homologies $file --set-random-number-engine "lagged_fibonacci607" --random-number-engine-parameters "seed=5;" --set-random-number-distribution "uniform_real" --random-number-distribution-parameters "min=0;max=1;" --fit-potential --potential-type "lennardjones" --potential-charges 18 18 --fragment-charges 18 18 --set-threshold 7e-9], 0, [stdout], [ignore])
     159AT_CHECK([../../molecuilder \
     160        --parse-homologies $file \
     161        --set-random-number-engine "lagged_fibonacci607" \
     162                --random-number-engine-parameters "seed=5;" \
     163        --set-random-number-distribution "uniform_real" \
     164                --random-number-distribution-parameters "min=0;max=1;" \
     165        --fit-potential \
     166                --potential-type "lennardjones" \
     167                --potential-charges 18 18 \
     168                --fragment-charges 18 18 \
     169                --set-threshold 7e-9 \
     170        --save-potentials lj.potentials], 0, [stdout], [ignore])
    105171# check that L_2 error is below 7e-11 ... just 7e-9 otherwise test takes too long
    106172AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-9) exit 1}'], 0, [ignore], [ignore])
    107173# check parameters to printed precision
    108 AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" stdout], 0, [ignore], [ignore])
    109 #AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" stdout], 0, [ignore], [ignore])
     174AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
     175#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
    110176
    111177AT_CLEANUP
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