source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ 4ecb2d

Action_Thermostats Add_AtomRandomPerturbation Add_RotateAroundBondAction Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install 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 JobMarket_unresolvable_hostname_fix ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks RotateToPrincipalAxisSystem_UndoRedo StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg ThirdParty_MPQC_rebuilt_buildsystem TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps Ubuntu_1604_changes stable
Last change on this file since 4ecb2d was f45a91, checked in by Frederik Heber <heber@…>, 8 years ago

TESTFIX: Redid all homology containers for potential fitting regression tests.

  • TESTFIX: removed XFAILs from potential regression tests.
  • TESTFIX: Need to change improper particle types order in regression test as the order in the binding model has changed.
  • Property mode set to 100644
File size: 10.4 KB
RevLine 
[48d20d]1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2013 University of Bonn
[5aaa43]4# Copyright (C) 2013 Frederik Heber
[48d20d]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
[f5724f]21AT_SETUP([Potential - Fit morse potential to water])
22AT_KEYWORDS([potential parse-homologies fit-potential morse])
[55feff5]23AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]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
[48d20d]26
27file=length_homology.dat
[f5724f]28AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[48d20d]29AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]30AT_CHECK([../../molecuilder \
31 --parse-homologies $file \
32 --set-random-number-engine "lagged_fibonacci607" \
33 --random-number-engine-parameters "seed=1;" \
34 --set-random-number-distribution "uniform_real" \
35 --random-number-distribution-parameters "min=0;max=1;" \
36 --fit-potential \
37 --potential-type "morse" \
38 --potential-charges 8 1 \
39 --fragment-charges 1 8 1 \
[b8f2ea]40 --set-threshold 5e-6 \
[0ea063]41 --save-potentials length.potentials], 0, [stdout], [ignore])
[48d20d]42# check that L_2 error is below 1e-6
[b8f2ea]43AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
[48d20d]44# check parameters to printed precision
[16c6f7]45AT_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])
[48d20d]46
47AT_CLEANUP
48
[f5724f]49AT_SETUP([Potential - Fit harmonic potential to water])
50AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
[55feff5]51AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]52# homology files probably originate from Labspace/PotentialFitting/Water
53# see morse fitting
[6550cf]54
[16c6f7]55file=length_homology.dat
[f5724f]56AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[6550cf]57AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]58AT_CHECK([../../molecuilder \
59 --parse-homologies $file \
60 --set-random-number-engine "lagged_fibonacci607" \
61 --random-number-engine-parameters "seed=1;" \
62 --set-random-number-distribution "uniform_real" \
63 --random-number-distribution-parameters "min=0;max=1;" \
64 --fit-potential \
65 --potential-type "harmonic_bond" \
66 --potential-charges 8 1 \
67 --fragment-charges 1 8 1 \
[16c6f7]68 --set-threshold 6e-4 \
[0ea063]69 --save-potentials harmonic.potentials], 0, [stdout], [ignore])
[16c6f7]70# check that L_2 error is below 6e-4
71AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore])
[6550cf]72# check parameters to printed precision
[16c6f7]73AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
[6550cf]74
75AT_CLEANUP
76
[f5724f]77AT_SETUP([Potential - Fit harmonic_angle potential to water])
78AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
[55feff5]79AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]80# homology files probably originate from Labspace/PotentialFitting/WaterAngle
81# 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
[48d20d]82
83file=angle_homology.dat
[f5724f]84AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[48d20d]85AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]86AT_CHECK([../../molecuilder \
87 --parse-homologies $file \
88 --set-random-number-engine "lagged_fibonacci607" \
89 --random-number-engine-parameters "seed=1;" \
90 --set-random-number-distribution "uniform_real" \
91 --random-number-distribution-parameters "min=0;max=1;" \
92 --fit-potential \
93 --potential-type "harmonic_angle" \
94 --potential-charges 1 8 1 \
95 --fragment-charges 1 8 1 \
96 --set-threshold 1e-6 \
97 --save-potentials angle.potentials], 0, [stdout], [ignore])
[48d20d]98# check that L_2 error is below 1e-6
99AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
100# check parameters to printed precision
[16c6f7]101AT_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])
[48d20d]102
103AT_CLEANUP
[1413f4]104
[f5724f]105AT_SETUP([Potential - Fit torsion potential to butane])
106AT_KEYWORDS([potential parse-homologies fit-potential torsion])
[55feff5]107AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]108# homology files probably originate from Labspace/PotentialFitting/Butane
109# 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
[e2037e]110
111file=torsion_homology.dat
[f5724f]112AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[e2037e]113AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]114AT_CHECK([../../molecuilder \
115 --parse-homologies $file \
116 --set-random-number-engine "lagged_fibonacci607" \
117 --random-number-engine-parameters "seed=1;" \
118 --set-random-number-distribution "uniform_real" \
119 --random-number-distribution-parameters "min=0;max=1;" \
120 --fit-potential \
121 --potential-type "torsion" \
122 --potential-charges 6 6 6 6 \
123 --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
[b8f2ea]124 --set-threshold 1e-9 \
[0ea063]125 --save-potentials torsion.potentials], 0, [stdout], [ignore])
[1dbbeb]126# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
[b8f2ea]127AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
[0ea063]128AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
129#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])
[e2037e]130
131AT_CLEANUP
132
[f5724f]133AT_SETUP([Potential - Fit improper potential to ammonia])
134AT_KEYWORDS([potential parse-homologies fit-potential improper])
[55feff5]135AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]136# homology files probably originate from Labspace/PotentialFitting/Ammonia
137# 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
[791a12]138
139file=improper_homology.dat
[f5724f]140AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[791a12]141AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]142AT_CHECK([../../molecuilder \
143 --parse-homologies $file \
144 --set-random-number-engine "lagged_fibonacci607" \
145 --random-number-engine-parameters "seed=1;" \
146 --set-random-number-distribution "uniform_real" \
147 --random-number-distribution-parameters "min=0;max=1;" \
148 --fit-potential \
149 --potential-type "improper" \
[f45a91]150 --potential-charges 7 1 1 1 \
[0ea063]151 --fragment-charges 7 1 1 1 \
152 --set-threshold 3e-4 \
153 --save-potentials improper.potentials], 0, [stdout], [ignore])
[791a12]154# check that L_2 error is below 3e-4
155AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
156# check parameters to printed precision
[f45a91]157AT_CHECK([grep "improper:.*particle_type1=7,.*particle_type2=1,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
158#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])
[791a12]159
160AT_CLEANUP
161
[f5724f]162AT_SETUP([Potential - Fit LJ potential to argon])
163AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
[55feff5]164AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]165# homology files probably originate from Labspace/PotentialFitting/Argon
166# 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
[1413f4]167
168file=lj_homology.dat
[f5724f]169AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[1413f4]170AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]171AT_CHECK([../../molecuilder \
172 --parse-homologies $file \
173 --set-random-number-engine "lagged_fibonacci607" \
174 --random-number-engine-parameters "seed=5;" \
175 --set-random-number-distribution "uniform_real" \
176 --random-number-distribution-parameters "min=0;max=1;" \
177 --fit-potential \
178 --potential-type "lennardjones" \
179 --potential-charges 18 18 \
180 --fragment-charges 18 18 \
[b8f2ea]181 --set-threshold 7e-8 \
[0ea063]182 --save-potentials lj.potentials], 0, [stdout], [ignore])
[b8f2ea]183# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
184AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
[1413f4]185# check parameters to printed precision
[0ea063]186AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
187#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
[1413f4]188
189AT_CLEANUP
Note: See TracBrowser for help on using the repository browser.