source: tests/GuiChecks/Potential/FitPotential/testsuite-potential-fit-potential.at@ d50b91

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Last change on this file since d50b91 was d50b91, checked in by Frederik Heber <heber@…>, 8 years ago

Recreated all GuiChecks.
  • Property mode set to 100644
File size: 11.5 KB
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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 --dry-run --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 5e-6 --save-potentials length.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
31AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
32AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
33# check that L_2 error is below 1e-6
34# check parameters to printed precision
35AT_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])
36
37AT_CLEANUP
38
39AT_SETUP([Potential - Fit harmonic potential to water])
40AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
41AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
42# homology files probably originate from Labspace/PotentialFitting/Water
43# see morse fitting
44
45file=length_homology.dat
46AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
47AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
48AT_CHECK([../../molecuilder --dry-run --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 6e-4 --save-potentials harmonic.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
49AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
50AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
51# check that L_2 error is below 6e-4
52# check parameters to printed precision
53AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
54
55AT_CLEANUP
56
57AT_SETUP([Potential - Fit harmonic_angle potential to water])
58AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
59AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
60# homology files probably originate from Labspace/PotentialFitting/WaterAngle
61# 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
62
63file=angle_homology.dat
64AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
65AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
66AT_CHECK([../../molecuilder --dry-run --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 --save-potentials angle.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
67AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
68AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
69# check that L_2 error is below 1e-6
70# check parameters to printed precision
71AT_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])
72
73AT_CLEANUP
74
75AT_SETUP([Potential - Fit torsion potential to butane])
76AT_KEYWORDS([potential parse-homologies fit-potential torsion])
77AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
78# homology files probably originate from Labspace/PotentialFitting/Butane
79# 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
80
81file=torsion_homology.dat
82AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
83AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
84AT_CHECK([../../molecuilder --dry-run --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 1e-9 --save-potentials torsion.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
85AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
86AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
87# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
88AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
89#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])
90
91AT_CLEANUP
92
93AT_SETUP([Potential - Fit improper potential to ammonia])
94AT_KEYWORDS([potential parse-homologies fit-potential improper])
95AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
96# homology files probably originate from Labspace/PotentialFitting/Ammonia
97# 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
98
99file=improper_homology.dat
100AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
101AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
102AT_CHECK([../../molecuilder --dry-run --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 7 1 1 1 --fragment-charges 7 1 1 1 --set-threshold 3e-4 --save-potentials improper.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
103AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
104AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
105# check that L_2 error is below 3e-4
106# check parameters to printed precision
107AT_CHECK([grep "improper:.*particle_type1=7,.*particle_type2=1,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
108#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])
109
110AT_CLEANUP
111
112AT_SETUP([Potential - Fit LJ potential to argon])
113AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
114AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
115# homology files probably originate from Labspace/PotentialFitting/Argon
116# 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
117
118file=lj_homology.dat
119AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
120AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
121AT_CHECK([../../molecuilder --dry-run --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-8 --save-potentials lj.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
122AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
123AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
124# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
125# check parameters to printed precision
126AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
127#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
128
129AT_CLEANUP
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