source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ 0932c2

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
Last change on this file since 0932c2 was 0932c2, checked in by Frederik Heber <heber@…>, 11 years ago

FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype.

  • this caused all engines to always start with default seed of 1, irrespective of the set parameter. The engine is always cloned from prototypes in the factory that can be manipulated to change their parameters. Hence, clone needs to set the seed (the engine's only parameter).
  • EmpiricalPotentials now use RandomNumberGenerator to obtain random starting values.
  • TESTFIX: fit-potential regression tests now use fixed seed in order to always take the same amount of time (some test runs in debug mode take very long because of ill-chosen random values).
  • Property mode set to 100644
File size: 7.7 KB
Line 
1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2013 University of Bonn
4# Copyright (C) 2013 Frederik Heber
5#
6# This program is free software: you can redistribute it and/or modify
7# it under the terms of the GNU General Public License as published by
8# the Free Software Foundation, either version 3 of the License, or
9# (at your option) any later version.
10#
11# This program is distributed in the hope that it will be useful,
12# but WITHOUT ANY WARRANTY; without even the implied warranty of
13# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14# GNU General Public License for more details.
15#
16# You should have received a copy of the GNU General Public License
17# along with this program. If not, see <http://www.gnu.org/licenses/>.
18#
19### fit some potentials
20
21AT_SETUP([Potential - Fit morse potential to water])
22AT_KEYWORDS([potential parse-homologies fit-potential morse])
23AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
24
25file=length_homology.dat
26AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
27AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
28AT_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])
29# check that L_2 error is below 1e-6
30AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
31# check parameters to printed precision
32AT_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])
33
34AT_CLEANUP
35
36AT_SETUP([Potential - Fit harmonic potential to water])
37AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
38AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
39
40file=harmonic_homology.dat
41AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
42AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
43AT_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])
44# check that L_2 error is below 1e-6
45AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
46# check parameters to printed precision
47AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.29.*,.*equilibrium_distance=1.8.*;" stdout], 0, [ignore], [ignore])
48
49AT_CLEANUP
50
51AT_SETUP([Potential - Fit harmonic_angle potential to water])
52AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
53AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
54
55file=angle_homology.dat
56AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
57AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
58AT_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])
59# check that L_2 error is below 1e-6
60AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
61# check parameters to printed precision
62AT_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])
63
64AT_CLEANUP
65
66AT_SETUP([Potential - Fit torsion potential to butane])
67AT_KEYWORDS([potential parse-homologies fit-potential torsion])
68AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
69
70file=torsion_homology.dat
71AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
72AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
73AT_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 9e-12], 0, [stdout], [ignore])
74# check that L_2 error is below 9e-12
75AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 9e-12) exit 1}'], 0, [ignore], [ignore])
76AT_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])
77
78AT_CLEANUP
79
80AT_SETUP([Potential - Fit improper potential to ammonia])
81AT_KEYWORDS([potential parse-homologies fit-potential improper])
82AT_XFAIL_IF([/bin/true])
83AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
84
85file=improper_homology.dat
86AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
87AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
88AT_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])
89# check that L_2 error is below 3e-4
90AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
91# check parameters to printed precision
92AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=1,.*particle_type3=7,.*particle_type4=1,.*spring_constant=1.02.*,.*equilibrium_distance=0.85.*;" stdout], 0, [ignore], [ignore])
93
94AT_CLEANUP
95
96AT_SETUP([Potential - Fit LJ potential to argon])
97AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
98AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
99
100file=lj_homology.dat
101AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
102AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
103AT_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-11], 0, [stdout], [ignore])
104# check that L_2 error is below 7e-11
105AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-11) exit 1}'], 0, [ignore], [ignore])
106# check parameters to printed precision
107AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" stdout], 0, [ignore], [ignore])
108
109AT_CLEANUP
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