Changeset d50b91 for tests/GuiChecks/Potential
- Timestamp:
- Mar 16, 2017, 6:48:58 AM (8 years ago)
- Branches:
- Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable
- Children:
- 917c46
- Parents:
- cb20c0
- Location:
- tests/GuiChecks/Potential
- Files:
-
- 2 added
- 3 edited
-
FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) (1 diff)
-
FitPotential/testsuite-potential-fit-potential.at (modified) (8 diffs)
-
SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (added)
-
SaveParsePotentials/testsuite-potential-save-parse-potentials.at (added)
-
testsuite-potential.at (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
tests/GuiChecks/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at
rcb20c0 rd50b91 18 18 ### fit partial particle charges 19 19 20 # the potential has been generated by: 21 # ./molecuilder -i pre/water.pdb --center-in-box "8,0,8,0,0,8" --select-all-atoms --fragment-molecule BondFragment --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 4 --DoPrintDebug 1 --DoValenceOnly 0 --analyse-fragment-results --store-grids 1 --save-homologies homology_grid_4_full.dat 20 AT_SETUP([Potential - Fit partial charges - atomfragment check]) 21 AT_KEYWORDS([potential parse-homologies fit-partial-charges save-particle-parameters]) 22 AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 23 24 input=water.pdb 25 homologyfile=homology_grid.dat 26 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$input $input], 0) 27 AT_CHECK([chmod u+w $input], 0, [ignore], [ignore]) 28 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$homologyfile $homologyfile], 0) 29 AT_CHECK([chmod u+w $homologyfile], 0, [ignore], [ignore]) 30 # fails because atomFragments has not been parsed 31 AT_CHECK([../../molecuilder --dry-run -l $input --select-all-atoms --parse-homologies $homologyfile --fit-partial-charges --radius 1.5 --save-particle-parameters water.particles --no-dry-run --store-session session-potential-fit-partial-charges.py --session-type python], 0, [stdout], [ignore]) 32 AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-partial-charges.py >session-potential-fit-partial-charges_new.py], 0, [ignore], [ignore]) 33 AT_CHECK([../../molecuilderguitest session-potential-fit-partial-charges_new.py], 5, [stdout], [ignore]) 34 35 AT_CLEANUP 22 36 23 37 AT_SETUP([Potential - Fit partial charges to water]) 24 AT_KEYWORDS([potential parse-homologies fit-partial-charges ])38 AT_KEYWORDS([potential parse-homologies fit-partial-charges save-particle-parameters]) 25 39 AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 26 40 27 41 # homology file created with water.pdb and as follows: 28 # molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat 29 file=homology_grid.dat 30 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$file $file], 0) 31 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore]) 32 AT_CHECK([../../molecuilder --dry-run --parse-homologies $file --fit-partial-charges --fragment-charges 8 1 1 --radius 1.5 --no-dry-run --store-session session-potential-fit-partial-charges.py --session-type python], 0, [stdout], [ignore]) 42 # molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat --save-atom-fragments atomfragments.dat 43 input=water.pdb 44 homologyfile=homology_grid.dat 45 atomfragmentsfile=atomfragments.dat 46 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$input $input], 0) 47 AT_CHECK([chmod u+w $input], 0, [ignore], [ignore]) 48 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$homologyfile $homologyfile], 0) 49 AT_CHECK([chmod u+w $homologyfile], 0, [ignore], [ignore]) 50 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$atomfragmentsfile $atomfragmentsfile], 0) 51 AT_CHECK([chmod u+w $atomfragmentsfile], 0, [ignore], [ignore]) 52 AT_CHECK([../../molecuilder --dry-run -l $input --select-all-atoms --parse-homologies $homologyfile --parse-atom-fragments $atomfragmentsfile --fit-partial-charges --radius 1.5 --save-particle-parameters water.particles --no-dry-run --store-session session-potential-fit-partial-charges.py --session-type python], 0, [stdout], [ignore]) 33 53 AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-partial-charges.py >session-potential-fit-partial-charges_new.py], 0, [ignore], [ignore]) 34 54 AT_CHECK([../../molecuilderguitest session-potential-fit-partial-charges_new.py], 0, [stdout], [ignore]) 35 55 # check that L_2 error is below 1e-6 56 AT_CHECK([diff water.particles ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/post/water.particles], 0) 36 57 37 58 AT_CLEANUP -
tests/GuiChecks/Potential/FitPotential/testsuite-potential-fit-potential.at
rcb20c0 rd50b91 22 22 AT_KEYWORDS([potential parse-homologies fit-potential morse]) 23 23 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 24 # homology files probably originate from Labspace/PotentialFitting/WaterAngle 25 # recreate homology file: PYTHONPATH=... /usr/bin/python .../tests/regression/Potential/FitPotential/pre/measurement_function.py length_common.pdb 2 0 0 5 4 127.0.0.1 2050 6-311G* 1 2. 10 .../share/molecuilder/data/bondtables/bondtable.dat 24 26 25 27 file=length_homology.dat … … 31 33 # check that L_2 error is below 1e-6 32 34 # check parameters to printed precision 33 AT_CHECK([grep "morse:.*particle_type1=8,.*particle_type2=1,.*spring_constant=1. 2.*,.*equilibrium_distance=1.7.*,.*dissociation_energy=0.19.*;" length.potentials], 0, [ignore], [ignore])35 AT_CHECK([grep "morse:.*particle_type1=8,.*particle_type2=1,.*spring_constant=1.3.*,.*equilibrium_distance=1.7.*,.*dissociation_energy=0.19.*;" length.potentials], 0, [ignore], [ignore]) 34 36 35 37 AT_CLEANUP … … 38 40 AT_KEYWORDS([potential parse-homologies fit-potential harmonic]) 39 41 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 42 # homology files probably originate from Labspace/PotentialFitting/Water 43 # see morse fitting 40 44 41 file= harmonic_homology.dat45 file=length_homology.dat 42 46 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0) 43 47 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore]) 44 AT_CHECK([../../molecuilder --dry-run --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 5e-6--save-potentials harmonic.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])48 AT_CHECK([../../molecuilder --dry-run --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 6e-4 --save-potentials harmonic.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore]) 45 49 AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore]) 46 50 AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore]) 47 # check that L_2 error is below 5e-651 # check that L_2 error is below 6e-4 48 52 # check parameters to printed precision 49 AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0. 29.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])53 AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore]) 50 54 51 55 AT_CLEANUP … … 54 58 AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle]) 55 59 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 60 # homology files probably originate from Labspace/PotentialFitting/WaterAngle 61 # recreate homology file: PYTHONPATH=... /usr/bin/python .../tests/regression/Potential/FitPotential/pre/measurement_function.py angle_common.pdb 2 0 0 5 4 127.0.0.1 2050 6-311G* 1 2. 10 .../share/molecuilder/data/bondtables/bondtable.dat 56 62 57 63 file=angle_homology.dat … … 63 69 # check that L_2 error is below 1e-6 64 70 # check parameters to printed precision 65 AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.10.*,.*equilibrium_distance=-0.2 7.*;" angle.potentials], 0, [ignore], [ignore])71 AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.10.*,.*equilibrium_distance=-0.29.*;" angle.potentials], 0, [ignore], [ignore]) 66 72 67 73 AT_CLEANUP … … 70 76 AT_KEYWORDS([potential parse-homologies fit-potential torsion]) 71 77 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 78 # homology files probably originate from Labspace/PotentialFitting/Butane 79 # recreate homology file: PYTHONPATH=... /usr/bin/python .../tests/regression/Potential/FitPotential/pre/measurement_function.py torsion_common.pdb 4 0 0 5 4 127.0.0.1 2050 6-311G* 1 2. 10 .../share/molecuilder/data/bondtables/bondtable.dat 72 80 73 81 file=torsion_homology.dat … … 86 94 AT_KEYWORDS([potential parse-homologies fit-potential improper]) 87 95 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 96 # homology files probably originate from Labspace/PotentialFitting/Ammonia 97 # recreate homology file: PYTHONPATH=... /usr/bin/python .../tests/regression/Potential/FitPotential/pre/measurement_function.py improper_common.pdb 2 0 0 5 4 127.0.0.1 2050 6-311G* 1 2. 10 .../share/molecuilder/data/bondtables/bondtable.dat 88 98 89 99 file=improper_homology.dat 90 100 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0) 91 101 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore]) 92 AT_CHECK([../../molecuilder --dry-run --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 71 1 --fragment-charges 7 1 1 1 --set-threshold 3e-4 --save-potentials improper.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])102 AT_CHECK([../../molecuilder --dry-run --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 7 1 1 1 --fragment-charges 7 1 1 1 --set-threshold 3e-4 --save-potentials improper.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore]) 93 103 AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore]) 94 104 AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore]) 95 105 # check that L_2 error is below 3e-4 96 106 # check parameters to printed precision 97 AT_CHECK([grep "improper:.*particle_type1= 1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])98 #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])107 AT_CHECK([grep "improper:.*particle_type1=7,.*particle_type2=1,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore]) 108 #AT_CHECK([grep "improper:.*particle_type1=7,.*particle_type2=1,.*particle_type3=1,.*particle_type4=1,.*spring_constant=1.02.*,.*equilibrium_distance=0.85.*;" improper.potentials], 0, [ignore], [ignore]) 99 109 100 110 AT_CLEANUP … … 103 113 AT_KEYWORDS([potential parse-homologies fit-potential lennardjones]) 104 114 AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi]) 115 # homology files probably originate from Labspace/PotentialFitting/Argon 116 # recreate homology file: PYTHONPATH=... /usr/bin/python .../tests/regression/Potential/FitPotential/pre/measurement_function.py lj_common.pdb 2 0 0 5 4 127.0.0.1 2050 6-311G* 2 11. 10 .../share/molecuilder/data/bondtables/bondtable.dat 105 117 106 118 file=lj_homology.dat -
tests/GuiChecks/Potential/testsuite-potential.at
rcb20c0 rd50b91 19 19 AT_BANNER([MoleCuilder - potential tests]) 20 20 21 # parsing and saving potential file 22 m4_include([Potential/SaveParsePotentials/testsuite-potential-save-parse-potentials.at]) 23 21 24 # fitting potential to fragment results 22 25 m4_include([Potential/FitPotential/testsuite-potential-fit-potential.at]) 23 26 27 # parsing and saving particles file 28 m4_include([Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at]) 29 24 30 # fitting particle charges to fragment results 25 31 m4_include([Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at])
Note:
See TracChangeset
for help on using the changeset viewer.
