source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ bc069f

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 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 bc069f was 2124aa, checked in by Frederik Heber <heber@…>, 8 years ago

Extractors::reorderArgumentsByParticleTypes() rewritten to scan for all induced, connected subgraphs.

  • after filtering the arguments down to the required particle types, we use the adjacency graph that is passed down from creating the SaturatedFragments, stored in various FragmentationResultContainers and finally used to state whether in Extractors::gatherAllSymmetricDistances() a distance represents a bond or not. In this graph we look for all subgraphs that are homologous to the graph specified by the derived EmpiricalPotential. For each accepted subgraph we then gather again all symmetric distances and concatenate them all.
  • TESTFIX: Marked all potential fitting regression tests as XFAIL for the moment. On the one hand the homology container format changed (edges), and on the other hand we are in the middle of refactoring above function.
  • added test using edges for ExtractorsUnitTest.
  • lib dependency fixed for ..PotentialUnitTest.
  • NOTE: boost::graph is incompatible with CodePattern's MEMDEBUG. Hence, includes are placed prior to memdebug's.
  • Property mode set to 100644
File size: 10.5 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 fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
24AT_XFAIL_IF([/bin/true])
25# homology files probably originate from Labspace/PotentialFitting/WaterAngle
26# 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
27
28file=length_homology.dat
29AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
30AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
31AT_CHECK([../../molecuilder \
32 --parse-homologies $file \
33 --set-random-number-engine "lagged_fibonacci607" \
34 --random-number-engine-parameters "seed=1;" \
35 --set-random-number-distribution "uniform_real" \
36 --random-number-distribution-parameters "min=0;max=1;" \
37 --fit-potential \
38 --potential-type "morse" \
39 --potential-charges 8 1 \
40 --fragment-charges 1 8 1 \
41 --set-threshold 5e-6 \
42 --save-potentials length.potentials], 0, [stdout], [ignore])
43# check that L_2 error is below 1e-6
44AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
45# check parameters to printed precision
46AT_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])
47
48AT_CLEANUP
49
50AT_SETUP([Potential - Fit harmonic potential to water])
51AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
52AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
53AT_XFAIL_IF([/bin/true])
54# homology files probably originate from Labspace/PotentialFitting/Water
55# see morse fitting
56
57file=length_homology.dat
58AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
59AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
60AT_CHECK([../../molecuilder \
61 --parse-homologies $file \
62 --set-random-number-engine "lagged_fibonacci607" \
63 --random-number-engine-parameters "seed=1;" \
64 --set-random-number-distribution "uniform_real" \
65 --random-number-distribution-parameters "min=0;max=1;" \
66 --fit-potential \
67 --potential-type "harmonic_bond" \
68 --potential-charges 8 1 \
69 --fragment-charges 1 8 1 \
70 --set-threshold 6e-4 \
71 --save-potentials harmonic.potentials], 0, [stdout], [ignore])
72# check that L_2 error is below 6e-4
73AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore])
74# check parameters to printed precision
75AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
76
77AT_CLEANUP
78
79AT_SETUP([Potential - Fit harmonic_angle potential to water])
80AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
81AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
82AT_XFAIL_IF([/bin/true])
83# homology files probably originate from Labspace/PotentialFitting/WaterAngle
84# 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
85
86file=angle_homology.dat
87AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
88AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
89AT_CHECK([../../molecuilder \
90 --parse-homologies $file \
91 --set-random-number-engine "lagged_fibonacci607" \
92 --random-number-engine-parameters "seed=1;" \
93 --set-random-number-distribution "uniform_real" \
94 --random-number-distribution-parameters "min=0;max=1;" \
95 --fit-potential \
96 --potential-type "harmonic_angle" \
97 --potential-charges 1 8 1 \
98 --fragment-charges 1 8 1 \
99 --set-threshold 1e-6 \
100 --save-potentials angle.potentials], 0, [stdout], [ignore])
101# check that L_2 error is below 1e-6
102AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
103# check parameters to printed precision
104AT_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])
105
106AT_CLEANUP
107
108AT_SETUP([Potential - Fit torsion potential to butane])
109AT_KEYWORDS([potential parse-homologies fit-potential torsion])
110AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
111AT_XFAIL_IF([/bin/true])
112# homology files probably originate from Labspace/PotentialFitting/Butane
113# 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
114
115file=torsion_homology.dat
116AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
117AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
118AT_CHECK([../../molecuilder \
119 --parse-homologies $file \
120 --set-random-number-engine "lagged_fibonacci607" \
121 --random-number-engine-parameters "seed=1;" \
122 --set-random-number-distribution "uniform_real" \
123 --random-number-distribution-parameters "min=0;max=1;" \
124 --fit-potential \
125 --potential-type "torsion" \
126 --potential-charges 6 6 6 6 \
127 --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
128 --set-threshold 1e-9 \
129 --save-potentials torsion.potentials], 0, [stdout], [ignore])
130# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
131AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
132AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
133#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])
134
135AT_CLEANUP
136
137AT_SETUP([Potential - Fit improper potential to ammonia])
138AT_KEYWORDS([potential parse-homologies fit-potential improper])
139AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
140AT_XFAIL_IF([/bin/true])
141# homology files probably originate from Labspace/PotentialFitting/Ammonia
142# 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
143
144file=improper_homology.dat
145AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
146AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
147AT_CHECK([../../molecuilder \
148 --parse-homologies $file \
149 --set-random-number-engine "lagged_fibonacci607" \
150 --random-number-engine-parameters "seed=1;" \
151 --set-random-number-distribution "uniform_real" \
152 --random-number-distribution-parameters "min=0;max=1;" \
153 --fit-potential \
154 --potential-type "improper" \
155 --potential-charges 1 7 1 1 \
156 --fragment-charges 7 1 1 1 \
157 --set-threshold 3e-4 \
158 --save-potentials improper.potentials], 0, [stdout], [ignore])
159# check that L_2 error is below 3e-4
160AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
161# check parameters to printed precision
162AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
163#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])
164
165AT_CLEANUP
166
167AT_SETUP([Potential - Fit LJ potential to argon])
168AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
169AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
170AT_XFAIL_IF([/bin/true])
171# homology files probably originate from Labspace/PotentialFitting/Argon
172# 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
173
174file=lj_homology.dat
175AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
176AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
177AT_CHECK([../../molecuilder \
178 --parse-homologies $file \
179 --set-random-number-engine "lagged_fibonacci607" \
180 --random-number-engine-parameters "seed=5;" \
181 --set-random-number-distribution "uniform_real" \
182 --random-number-distribution-parameters "min=0;max=1;" \
183 --fit-potential \
184 --potential-type "lennardjones" \
185 --potential-charges 18 18 \
186 --fragment-charges 18 18 \
187 --set-threshold 7e-8 \
188 --save-potentials lj.potentials], 0, [stdout], [ignore])
189# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
190AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
191# check parameters to printed precision
192AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
193#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
194
195AT_CLEANUP
Note: See TracBrowser for help on using the repository browser.