| [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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| 24 |
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| 25 | file=length_homology.dat
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| 26 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 27 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 28 | 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 1e-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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| 29 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 30 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 31 | # check that L_2 error is below 1e-6
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| 32 | # check parameters to printed precision
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| 33 | AT_CHECK([grep "morse:.*particle_type1=8,.*particle_type2=1,.*spring_constant=1.27.*,.*equilibrium_distance=1.78.*,.*dissociation_energy=0.19.*;" length.potentials], 0, [ignore], [ignore])
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| 34 |
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| 35 | AT_CLEANUP
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| 36 |
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| 37 | AT_SETUP([Potential - Fit harmonic potential to water])
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| 38 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
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| 39 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 40 |
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| 41 | file=harmonic_homology.dat
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| 42 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 43 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 44 | 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 1e-6 --save-potentials harmonic.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
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| 45 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 46 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 47 | # check that L_2 error is below 1e-6
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| 48 | # check parameters to printed precision
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| 49 | AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.29.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
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| 50 |
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| 51 | AT_CLEANUP
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| 52 |
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| 53 | AT_SETUP([Potential - Fit harmonic_angle potential to water])
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| 54 | AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
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| 55 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 56 |
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| 57 | file=angle_homology.dat
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| 58 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 59 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 60 | 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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| 61 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 62 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 63 | # check that L_2 error is below 1e-6
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| 64 | # check parameters to printed precision
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| 65 | AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.10.*,.*equilibrium_distance=-0.27.*;" angle.potentials], 0, [ignore], [ignore])
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| 66 |
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| 67 | AT_CLEANUP
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| 68 |
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| 69 | AT_SETUP([Potential - Fit torsion potential to butane])
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| 70 | AT_KEYWORDS([potential parse-homologies fit-potential torsion])
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| 71 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 72 |
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| 73 | file=torsion_homology.dat
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| 74 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 75 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 76 | 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 2e-10 --save-potentials torsion.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
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| 77 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 78 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 79 | # check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
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| 80 | 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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| 81 | #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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| 82 |
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| 83 | AT_CLEANUP
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| 84 |
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| 85 | AT_SETUP([Potential - Fit improper potential to ammonia])
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| 86 | AT_KEYWORDS([potential parse-homologies fit-potential improper])
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| 87 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 88 |
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| 89 | file=improper_homology.dat
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| 90 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 91 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 92 | 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 1 7 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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| 93 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 94 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 95 | # check that L_2 error is below 3e-4
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| 96 | # check parameters to printed precision
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| 97 | AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=7,.*particle_type3=1,.*particle_type4=1,.*spring_constant=.*,.*equilibrium_distance=.*;" improper.potentials], 0, [ignore], [ignore])
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| 98 | #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])
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| 99 |
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| 100 | AT_CLEANUP
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| 101 |
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| 102 | AT_SETUP([Potential - Fit LJ potential to argon])
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| 103 | AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
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| 104 | AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
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| 105 |
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| 106 | file=lj_homology.dat
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| 107 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
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| 108 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [599b32] | 109 | 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-9 --save-potentials lj.potentials --no-dry-run --store-session session-potential-fit-potential.py --session-type python], 0, [stdout], [ignore])
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| 110 | AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-potential.py >session-potential-fit-potential_new.py], 0, [ignore], [ignore])
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| 111 | AT_CHECK([../../molecuilderguitest session-potential-fit-potential_new.py], 0, [stdout], [ignore])
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| [dd6c07] | 112 | # check that L_2 error is below 7e-11 ... just 7e-9 otherwise test takes too long
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| 113 | # check parameters to printed precision
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| 114 | AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
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| 115 | #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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| 116 |
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| 117 | AT_CLEANUP
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