| 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2013 University of Bonn
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| 4 | # Copyright (C) 2013 Frederik Heber
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| 5 | #
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| 6 | # This program is free software: you can redistribute it and/or modify
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| 7 | # it under the terms of the GNU General Public License as published by
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| 8 | # the Free Software Foundation, either version 3 of the License, or
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| 9 | # (at your option) any later version.
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| 10 | #
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| 11 | # This program is distributed in the hope that it will be useful,
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| 12 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 14 | # GNU General Public License for more details.
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| 15 | #
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| 16 | # You should have received a copy of the GNU General Public License
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| 17 | # along with this program. If not, see <http://www.gnu.org/licenses/>.
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| 18 | #
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| 19 | ### fit some potentials
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| 20 |
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| 21 | AT_SETUP([Potential - Fit morse potential to water])
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| 22 | AT_KEYWORDS([potential parse-homologies fit-potential morse])
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| 23 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 24 | # homology files probably originate from Labspace/PotentialFitting/WaterAngle
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| 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
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| 26 |
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| 27 | file=length_homology.dat
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| 28 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 29 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 30 | AT_CHECK([../../molecuilder \
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| 31 | --parse-homologies $file \
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| 32 | --set-random-number-engine "lagged_fibonacci607" \
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| 33 | --random-number-engine-parameters "seed=1;" \
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| 34 | --set-random-number-distribution "uniform_real" \
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| 35 | --random-number-distribution-parameters "min=0;max=1;" \
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| 36 | --fit-potential \
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| 37 | --potential-type "morse" \
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| 38 | --potential-charges 8 1 \
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| 39 | --fragment-charges 1 8 1 \
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| 40 | --set-threshold 5e-6 \
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| 41 | --save-potentials length.potentials], 0, [stdout], [ignore])
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| 42 | # check that L_2 error is below 1e-6
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| 43 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
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| 44 | # check parameters to printed precision
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| 45 | AT_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])
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| 46 |
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| 47 | AT_CLEANUP
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| 48 |
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| 49 | AT_SETUP([Potential - Fit harmonic potential to water])
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| 50 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
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| 51 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 52 | # homology files probably originate from Labspace/PotentialFitting/Water
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| 53 | # see morse fitting
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| 54 |
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| 55 | file=length_homology.dat
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| 56 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 57 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 58 | AT_CHECK([../../molecuilder \
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| 59 | --parse-homologies $file \
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| 60 | --set-random-number-engine "lagged_fibonacci607" \
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| 61 | --random-number-engine-parameters "seed=1;" \
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| 62 | --set-random-number-distribution "uniform_real" \
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| 63 | --random-number-distribution-parameters "min=0;max=1;" \
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| 64 | --fit-potential \
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| 65 | --potential-type "harmonic_bond" \
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| 66 | --potential-charges 8 1 \
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| 67 | --fragment-charges 1 8 1 \
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| 68 | --set-threshold 6e-4 \
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| 69 | --save-potentials harmonic.potentials], 0, [stdout], [ignore])
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| 70 | # check that L_2 error is below 6e-4
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| 71 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore])
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| 72 | # check parameters to printed precision
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| 73 | AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
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| 74 |
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| 75 | AT_CLEANUP
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| 76 |
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| 77 | AT_SETUP([Potential - Fit harmonic_angle potential to water])
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| 78 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
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| 79 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 80 | # homology files probably originate from Labspace/PotentialFitting/WaterAngle
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| 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
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| 82 |
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| 83 | file=angle_homology.dat
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| 84 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 85 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 86 | AT_CHECK([../../molecuilder \
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| 87 | --parse-homologies $file \
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| 88 | --set-random-number-engine "lagged_fibonacci607" \
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| 89 | --random-number-engine-parameters "seed=1;" \
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| 90 | --set-random-number-distribution "uniform_real" \
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| 91 | --random-number-distribution-parameters "min=0;max=1;" \
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| 92 | --fit-potential \
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| 93 | --potential-type "harmonic_angle" \
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| 94 | --potential-charges 1 8 1 \
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| 95 | --fragment-charges 1 8 1 \
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| 96 | --set-threshold 1e-6 \
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| 97 | --save-potentials angle.potentials], 0, [stdout], [ignore])
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| 98 | # check that L_2 error is below 1e-6
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| 99 | AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
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| 100 | # check parameters to printed precision
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| 101 | AT_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])
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| 102 |
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| 103 | AT_CLEANUP
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| 104 |
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| 105 | AT_SETUP([Potential - Fit torsion potential to butane])
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| 106 | AT_KEYWORDS([potential parse-homologies fit-potential torsion])
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| 107 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 108 | # homology files probably originate from Labspace/PotentialFitting/Butane
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| 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
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| 110 |
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| 111 | file=torsion_homology.dat
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| 112 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 113 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 114 | AT_CHECK([../../molecuilder \
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| 115 | --parse-homologies $file \
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| 116 | --set-random-number-engine "lagged_fibonacci607" \
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| 117 | --random-number-engine-parameters "seed=1;" \
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| 118 | --set-random-number-distribution "uniform_real" \
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| 119 | --random-number-distribution-parameters "min=0;max=1;" \
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| 120 | --fit-potential \
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| 121 | --potential-type "torsion" \
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| 122 | --potential-charges 6 6 6 6 \
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| 123 | --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
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| 124 | --set-threshold 1e-9 \
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| 125 | --save-potentials torsion.potentials], 0, [stdout], [ignore])
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| 126 | # check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
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| 127 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
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| 128 | AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=.*,.*equilibrium_distance=.*;" torsion.potentials], 0, [ignore], [ignore])
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| 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])
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| 130 |
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| 131 | AT_CLEANUP
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| 132 |
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| 133 | AT_SETUP([Potential - Fit improper potential to ammonia])
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| 134 | AT_KEYWORDS([potential parse-homologies fit-potential improper])
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| 135 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 136 | # homology files probably originate from Labspace/PotentialFitting/Ammonia
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| 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
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| 138 |
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| 139 | file=improper_homology.dat
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| 140 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 141 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 142 | AT_CHECK([../../molecuilder \
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| 143 | --parse-homologies $file \
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| 144 | --set-random-number-engine "lagged_fibonacci607" \
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| 145 | --random-number-engine-parameters "seed=1;" \
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| 146 | --set-random-number-distribution "uniform_real" \
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| 147 | --random-number-distribution-parameters "min=0;max=1;" \
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| 148 | --fit-potential \
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| 149 | --potential-type "improper" \
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| 150 | --potential-charges 7 1 1 1 \
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| 151 | --fragment-charges 7 1 1 1 \
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| 152 | --set-threshold 3e-4 \
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| 153 | --save-potentials improper.potentials], 0, [stdout], [ignore])
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| 154 | # check that L_2 error is below 3e-4
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| 155 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
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| 156 | # check parameters to printed precision
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| 157 | AT_CHECK([grep "improper:.*particle_type1=7,.*particle_type2=1,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
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| 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])
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| 159 |
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| 160 | AT_CLEANUP
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| 161 |
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| 162 | AT_SETUP([Potential - Fit LJ potential to argon])
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| 163 | AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
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| 164 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 165 | # homology files probably originate from Labspace/PotentialFitting/Argon
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| 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
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| 167 |
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| 168 | file=lj_homology.dat
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| 169 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 170 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| 171 | AT_CHECK([../../molecuilder \
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| 172 | --parse-homologies $file \
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| 173 | --set-random-number-engine "lagged_fibonacci607" \
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| 174 | --random-number-engine-parameters "seed=5;" \
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| 175 | --set-random-number-distribution "uniform_real" \
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| 176 | --random-number-distribution-parameters "min=0;max=1;" \
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| 177 | --fit-potential \
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| 178 | --potential-type "lennardjones" \
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| 179 | --potential-charges 18 18 \
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| 180 | --fragment-charges 18 18 \
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| 181 | --set-threshold 7e-8 \
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| 182 | --save-potentials lj.potentials], 0, [stdout], [ignore])
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| 183 | # check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
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| 184 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
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| 185 | # check parameters to printed precision
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| 186 | AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
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| 187 | #AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])
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| 188 |
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| 189 | AT_CLEANUP
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