source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ f5dbea

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Last change on this file since f5dbea was 9c793c, checked in by Frederik Heber <heber@…>, 8 years ago

All ..Potentials now return BindingModel instead of HomologyGraph, Extractors::reorderArg..() uses it.

  • Extractors::filterArg..() and ::reorderArg..() expect BindingModel instead of HomologyGraph.
  • TESTFIX: Lennard Jones potential fitting regression test no longer fails because it is purely non-bonded.
  • 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])
170# homology files probably originate from Labspace/PotentialFitting/Argon
171# 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
172
173file=lj_homology.dat
174AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
175AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
176AT_CHECK([../../molecuilder \
177 --parse-homologies $file \
178 --set-random-number-engine "lagged_fibonacci607" \
179 --random-number-engine-parameters "seed=5;" \
180 --set-random-number-distribution "uniform_real" \
181 --random-number-distribution-parameters "min=0;max=1;" \
182 --fit-potential \
183 --potential-type "lennardjones" \
184 --potential-charges 18 18 \
185 --fragment-charges 18 18 \
186 --set-threshold 7e-8 \
187 --save-potentials lj.potentials], 0, [stdout], [ignore])
188# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
189AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
190# check parameters to printed precision
191AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
192#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
193
194AT_CLEANUP
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