source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ 1155ba

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Last change on this file since 1155ba was 1155ba, checked in by Frederik Heber <heber@…>, 8 years ago

Converted filterArguments... into faster filter, renamed other to ..ByBindingModel.

  • there are now two filters: One filters by list of particles types and is meant for simple pair potentials. The other one filters (and reorders) by the binding model. This takes more computation time but is required for more complex potentials.
  • TESTFIX: This allows morse and harmonic pair potentials tests to pass again, removed XFAIL from the corresponding regression tests.
  • Property mode set to 100644
File size: 10.4 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])
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
26
27file=length_homology.dat
28AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
29AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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 \
40 --set-threshold 5e-6 \
41 --save-potentials length.potentials], 0, [stdout], [ignore])
42# check that L_2 error is below 1e-6
43AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
44# check parameters to printed precision
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])
46
47AT_CLEANUP
48
49AT_SETUP([Potential - Fit harmonic potential to water])
50AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
51AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
52# homology files probably originate from Labspace/PotentialFitting/Water
53# see morse fitting
54
55file=length_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 \
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 \
68 --set-threshold 6e-4 \
69 --save-potentials harmonic.potentials], 0, [stdout], [ignore])
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])
72# check parameters to printed precision
73AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
74
75AT_CLEANUP
76
77AT_SETUP([Potential - Fit harmonic_angle potential to water])
78AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
79AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
80AT_XFAIL_IF([/bin/true])
81# homology files probably originate from Labspace/PotentialFitting/WaterAngle
82# 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
83
84file=angle_homology.dat
85AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
86AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
87AT_CHECK([../../molecuilder \
88 --parse-homologies $file \
89 --set-random-number-engine "lagged_fibonacci607" \
90 --random-number-engine-parameters "seed=1;" \
91 --set-random-number-distribution "uniform_real" \
92 --random-number-distribution-parameters "min=0;max=1;" \
93 --fit-potential \
94 --potential-type "harmonic_angle" \
95 --potential-charges 1 8 1 \
96 --fragment-charges 1 8 1 \
97 --set-threshold 1e-6 \
98 --save-potentials angle.potentials], 0, [stdout], [ignore])
99# check that L_2 error is below 1e-6
100AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
101# check parameters to printed precision
102AT_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])
103
104AT_CLEANUP
105
106AT_SETUP([Potential - Fit torsion potential to butane])
107AT_KEYWORDS([potential parse-homologies fit-potential torsion])
108AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
109AT_XFAIL_IF([/bin/true])
110# homology files probably originate from Labspace/PotentialFitting/Butane
111# 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
112
113file=torsion_homology.dat
114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
115AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
116AT_CHECK([../../molecuilder \
117 --parse-homologies $file \
118 --set-random-number-engine "lagged_fibonacci607" \
119 --random-number-engine-parameters "seed=1;" \
120 --set-random-number-distribution "uniform_real" \
121 --random-number-distribution-parameters "min=0;max=1;" \
122 --fit-potential \
123 --potential-type "torsion" \
124 --potential-charges 6 6 6 6 \
125 --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
126 --set-threshold 1e-9 \
127 --save-potentials torsion.potentials], 0, [stdout], [ignore])
128# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
129AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
130AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
131#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])
132
133AT_CLEANUP
134
135AT_SETUP([Potential - Fit improper potential to ammonia])
136AT_KEYWORDS([potential parse-homologies fit-potential improper])
137AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
138AT_XFAIL_IF([/bin/true])
139# homology files probably originate from Labspace/PotentialFitting/Ammonia
140# 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
141
142file=improper_homology.dat
143AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
144AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
145AT_CHECK([../../molecuilder \
146 --parse-homologies $file \
147 --set-random-number-engine "lagged_fibonacci607" \
148 --random-number-engine-parameters "seed=1;" \
149 --set-random-number-distribution "uniform_real" \
150 --random-number-distribution-parameters "min=0;max=1;" \
151 --fit-potential \
152 --potential-type "improper" \
153 --potential-charges 1 7 1 1 \
154 --fragment-charges 7 1 1 1 \
155 --set-threshold 3e-4 \
156 --save-potentials improper.potentials], 0, [stdout], [ignore])
157# check that L_2 error is below 3e-4
158AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
159# check parameters to printed precision
160AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
161#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])
162
163AT_CLEANUP
164
165AT_SETUP([Potential - Fit LJ potential to argon])
166AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
167AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
168# homology files probably originate from Labspace/PotentialFitting/Argon
169# 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
170
171file=lj_homology.dat
172AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
173AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
174AT_CHECK([../../molecuilder \
175 --parse-homologies $file \
176 --set-random-number-engine "lagged_fibonacci607" \
177 --random-number-engine-parameters "seed=5;" \
178 --set-random-number-distribution "uniform_real" \
179 --random-number-distribution-parameters "min=0;max=1;" \
180 --fit-potential \
181 --potential-type "lennardjones" \
182 --potential-charges 18 18 \
183 --fragment-charges 18 18 \
184 --set-threshold 7e-8 \
185 --save-potentials lj.potentials], 0, [stdout], [ignore])
186# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
187AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
188# check parameters to printed precision
189AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
190#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
191
192AT_CLEANUP
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