| [dd6c07] | 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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| [d50b91] | 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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| [dd6c07] | 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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| [af340c] | 30 | AT_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])
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| [599b32] | 31 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 32 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 33 | # check that L_2 error is below 1e-6
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| 34 | # check parameters to printed precision
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| [d50b91] | 35 | 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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| [dd6c07] | 36 |
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| 37 | AT_CLEANUP
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| 38 |
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| 39 | AT_SETUP([Potential - Fit harmonic potential to water])
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| 40 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
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| 41 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| [d50b91] | 42 | # homology files probably originate from Labspace/PotentialFitting/Water
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| 43 | # see morse fitting
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| [dd6c07] | 44 |
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| [d50b91] | 45 | file=length_homology.dat
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| [dd6c07] | 46 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 47 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 48 | AT_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])
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| [599b32] | 49 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 50 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [d50b91] | 51 | # check that L_2 error is below 6e-4
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| [dd6c07] | 52 | # check parameters to printed precision
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| [d50b91] | 53 | 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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| [dd6c07] | 54 |
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| 55 | AT_CLEANUP
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| 56 |
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| 57 | AT_SETUP([Potential - Fit harmonic_angle potential to water])
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| 58 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
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| 59 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| [d50b91] | 60 | # homology files probably originate from Labspace/PotentialFitting/WaterAngle
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| 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
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| [dd6c07] | 62 |
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| 63 | file=angle_homology.dat
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| 64 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 65 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 66 | AT_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])
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| 67 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 68 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 69 | # check that L_2 error is below 1e-6
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| 70 | # check parameters to printed precision
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| [d50b91] | 71 | 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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| [dd6c07] | 72 |
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| 73 | AT_CLEANUP
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| 74 |
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| 75 | AT_SETUP([Potential - Fit torsion potential to butane])
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| 76 | AT_KEYWORDS([potential parse-homologies fit-potential torsion])
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| 77 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| [d50b91] | 78 | # homology files probably originate from Labspace/PotentialFitting/Butane
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| 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
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| [dd6c07] | 80 |
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| 81 | file=torsion_homology.dat
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| 82 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 83 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [af340c] | 84 | AT_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])
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| [599b32] | 85 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 86 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 87 | # check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
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| 88 | 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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| 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])
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| 90 |
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| 91 | AT_CLEANUP
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| 92 |
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| 93 | AT_SETUP([Potential - Fit improper potential to ammonia])
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| 94 | AT_KEYWORDS([potential parse-homologies fit-potential improper])
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| 95 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| [d50b91] | 96 | # homology files probably originate from Labspace/PotentialFitting/Ammonia
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| 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
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| [dd6c07] | 98 |
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| 99 | file=improper_homology.dat
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| 100 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 101 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 102 | AT_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])
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| [599b32] | 103 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 104 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 105 | # check that L_2 error is below 3e-4
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| 106 | # check parameters to printed precision
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| [d50b91] | 107 | 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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| 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])
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| [dd6c07] | 109 |
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| 110 | AT_CLEANUP
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| 111 |
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| 112 | AT_SETUP([Potential - Fit LJ potential to argon])
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| 113 | AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
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| 114 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| [d50b91] | 115 | # homology files probably originate from Labspace/PotentialFitting/Argon
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| 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
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| [dd6c07] | 117 |
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| 118 | file=lj_homology.dat
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| 119 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 120 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [af340c] | 121 | AT_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])
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| [599b32] | 122 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 123 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [af340c] | 124 | # check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
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| [dd6c07] | 125 | # check parameters to printed precision
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| 126 | AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
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| 127 | #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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| 128 |
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| 129 | AT_CLEANUP
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