source: tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at@ f5dbea

#
#    MoleCuilder - creates and alters molecular systems
#    Copyright (C) 2013 University of Bonn
#    Copyright (C) 2013 Frederik Heber
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
### fit some potentials

AT_SETUP([Potential - Fit morse potential to water])
AT_KEYWORDS([potential parse-homologies fit-potential morse])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
AT_XFAIL_IF([/bin/true])
# homology files probably originate from Labspace/PotentialFitting/WaterAngle
# 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

file=length_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 1e-6
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
# check parameters to printed precision
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])

AT_CLEANUP

AT_SETUP([Potential - Fit harmonic potential to water])
AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
AT_XFAIL_IF([/bin/true])
# homology files probably originate from Labspace/PotentialFitting/Water
# see morse fitting

file=length_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 6e-4
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore])
# check parameters to printed precision
AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.4.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])

AT_CLEANUP

AT_SETUP([Potential - Fit harmonic_angle potential to water])
AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
AT_XFAIL_IF([/bin/true])
# homology files probably originate from Labspace/PotentialFitting/WaterAngle
# 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

file=angle_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 1e-6
AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
# check parameters to printed precision
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])

AT_CLEANUP

AT_SETUP([Potential - Fit torsion potential to butane])
AT_KEYWORDS([potential parse-homologies fit-potential torsion])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
AT_XFAIL_IF([/bin/true])
# homology files probably originate from Labspace/PotentialFitting/Butane
# 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

file=torsion_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
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])
#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])

AT_CLEANUP

AT_SETUP([Potential - Fit improper potential to ammonia])
AT_KEYWORDS([potential parse-homologies fit-potential improper])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
AT_XFAIL_IF([/bin/true])
# homology files probably originate from Labspace/PotentialFitting/Ammonia
# 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

file=improper_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 3e-4
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
# check parameters to printed precision
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])
#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])

AT_CLEANUP

AT_SETUP([Potential - Fit LJ potential to argon])
AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
# homology files probably originate from Labspace/PotentialFitting/Argon
# 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

file=lj_homology.dat
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder \
        --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], 0, [stdout], [ignore])
# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
# check parameters to printed precision
AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=.*,.*sigma=.*;" lj.potentials], 0, [ignore], [ignore])
#AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" lj.potentials], 0, [ignore], [ignore])

AT_CLEANUP