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testsuite-potential-fit-potential.at@ 1155ba

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Last change on this file since 1155ba was 1155ba, checked in by Frederik Heber <heber@…>, 8 years ago

Converted filterArguments... into faster filter, renamed other to ..ByBindingModel.

there are now two filters: One filters by list of particles types and is meant for simple pair potentials. The other one filters (and reorders) by the binding model. This takes more computation time but is required for more complex potentials.
TESTFIX: This allows morse and harmonic pair potentials tests to pass again, removed XFAIL from the corresponding regression tests.

Property mode set to 100644

File size: 10.4 KB

Rev	Line
[48d20d]	1	#
	2	# MoleCuilder - creates and alters molecular systems
	3	# Copyright (C) 2013 University of Bonn
[5aaa43]	4	# Copyright (C) 2013 Frederik Heber
[48d20d]	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
[f5724f]	21	AT_SETUP([Potential - Fit morse potential to water])
	22	AT_KEYWORDS([potential parse-homologies fit-potential morse])
[55feff5]	23	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]	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
[48d20d]	26
	27	file=length_homology.dat
[f5724f]	28	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[48d20d]	29	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	30	AT_CHECK([../../molecuilder \
	31	--parse-homologies $file \
	32	--set-random-number-engine "lagged_fibonacci607" \
	33	--random-number-engine-parameters "seed=1;" \
	34	--set-random-number-distribution "uniform_real" \
	35	--random-number-distribution-parameters "min=0;max=1;" \
	36	--fit-potential \
	37	--potential-type "morse" \
	38	--potential-charges 8 1 \
	39	--fragment-charges 1 8 1 \
[b8f2ea]	40	--set-threshold 5e-6 \
[0ea063]	41	--save-potentials length.potentials], 0, [stdout], [ignore])
[48d20d]	42	# check that L_2 error is below 1e-6
[b8f2ea]	43	AT_CHECK([grep "Best parameters with L2 error" stdout \| awk '{if ($8 > 5e-6) exit 1}'], 0, [ignore], [ignore])
[48d20d]	44	# check parameters to printed precision
[16c6f7]	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])
[48d20d]	46
	47	AT_CLEANUP
	48
[f5724f]	49	AT_SETUP([Potential - Fit harmonic potential to water])
	50	AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
[55feff5]	51	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]	52	# homology files probably originate from Labspace/PotentialFitting/Water
	53	# see morse fitting
[6550cf]	54
[16c6f7]	55	file=length_homology.dat
[f5724f]	56	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[6550cf]	57	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	58	AT_CHECK([../../molecuilder \
	59	--parse-homologies $file \
	60	--set-random-number-engine "lagged_fibonacci607" \
	61	--random-number-engine-parameters "seed=1;" \
	62	--set-random-number-distribution "uniform_real" \
	63	--random-number-distribution-parameters "min=0;max=1;" \
	64	--fit-potential \
	65	--potential-type "harmonic_bond" \
	66	--potential-charges 8 1 \
	67	--fragment-charges 1 8 1 \
[16c6f7]	68	--set-threshold 6e-4 \
[0ea063]	69	--save-potentials harmonic.potentials], 0, [stdout], [ignore])
[16c6f7]	70	# check that L_2 error is below 6e-4
	71	AT_CHECK([grep "Best parameters with L2 error" stdout \| awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore])
[6550cf]	72	# check parameters to printed precision
[16c6f7]	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])
[6550cf]	74
	75	AT_CLEANUP
	76
[f5724f]	77	AT_SETUP([Potential - Fit harmonic_angle potential to water])
	78	AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
[55feff5]	79	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[2124aa]	80	AT_XFAIL_IF([/bin/true])
[16c6f7]	81	# homology files probably originate from Labspace/PotentialFitting/WaterAngle
	82	# 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
[48d20d]	83
	84	file=angle_homology.dat
[f5724f]	85	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[48d20d]	86	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	87	AT_CHECK([../../molecuilder \
	88	--parse-homologies $file \
	89	--set-random-number-engine "lagged_fibonacci607" \
	90	--random-number-engine-parameters "seed=1;" \
	91	--set-random-number-distribution "uniform_real" \
	92	--random-number-distribution-parameters "min=0;max=1;" \
	93	--fit-potential \
	94	--potential-type "harmonic_angle" \
	95	--potential-charges 1 8 1 \
	96	--fragment-charges 1 8 1 \
	97	--set-threshold 1e-6 \
	98	--save-potentials angle.potentials], 0, [stdout], [ignore])
[48d20d]	99	# check that L_2 error is below 1e-6
	100	AT_CHECK([grep "\|\|e\|\|_2:" stdout \| awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])
	101	# check parameters to printed precision
[16c6f7]	102	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])
[48d20d]	103
	104	AT_CLEANUP
[1413f4]	105
[f5724f]	106	AT_SETUP([Potential - Fit torsion potential to butane])
	107	AT_KEYWORDS([potential parse-homologies fit-potential torsion])
[55feff5]	108	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[2124aa]	109	AT_XFAIL_IF([/bin/true])
[16c6f7]	110	# homology files probably originate from Labspace/PotentialFitting/Butane
	111	# 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
[e2037e]	112
	113	file=torsion_homology.dat
[f5724f]	114	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[e2037e]	115	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	116	AT_CHECK([../../molecuilder \
	117	--parse-homologies $file \
	118	--set-random-number-engine "lagged_fibonacci607" \
	119	--random-number-engine-parameters "seed=1;" \
	120	--set-random-number-distribution "uniform_real" \
	121	--random-number-distribution-parameters "min=0;max=1;" \
	122	--fit-potential \
	123	--potential-type "torsion" \
	124	--potential-charges 6 6 6 6 \
	125	--fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 \
[b8f2ea]	126	--set-threshold 1e-9 \
[0ea063]	127	--save-potentials torsion.potentials], 0, [stdout], [ignore])
[1dbbeb]	128	# check that L_2 error is below 9e-12 ... just 2e-10 otherwise test takes tooo long
[b8f2ea]	129	AT_CHECK([grep "Best parameters with L2 error" stdout \| awk '{if ($8 > 1e-9) exit 1}'], 0, [ignore], [ignore])
[0ea063]	130	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])
	131	#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])
[e2037e]	132
	133	AT_CLEANUP
	134
[f5724f]	135	AT_SETUP([Potential - Fit improper potential to ammonia])
	136	AT_KEYWORDS([potential parse-homologies fit-potential improper])
[55feff5]	137	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[2124aa]	138	AT_XFAIL_IF([/bin/true])
[16c6f7]	139	# homology files probably originate from Labspace/PotentialFitting/Ammonia
	140	# 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
[791a12]	141
	142	file=improper_homology.dat
[f5724f]	143	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[791a12]	144	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	145	AT_CHECK([../../molecuilder \
	146	--parse-homologies $file \
	147	--set-random-number-engine "lagged_fibonacci607" \
	148	--random-number-engine-parameters "seed=1;" \
	149	--set-random-number-distribution "uniform_real" \
	150	--random-number-distribution-parameters "min=0;max=1;" \
	151	--fit-potential \
	152	--potential-type "improper" \
	153	--potential-charges 1 7 1 1 \
	154	--fragment-charges 7 1 1 1 \
	155	--set-threshold 3e-4 \
	156	--save-potentials improper.potentials], 0, [stdout], [ignore])
[791a12]	157	# check that L_2 error is below 3e-4
	158	AT_CHECK([grep "Best parameters with L2 error" stdout \| awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
	159	# check parameters to printed precision
[0ea063]	160	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])
	161	#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])
[791a12]	162
	163	AT_CLEANUP
	164
[f5724f]	165	AT_SETUP([Potential - Fit LJ potential to argon])
	166	AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
[55feff5]	167	AT_SKIP_IF([../../molecuilder --help fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
[16c6f7]	168	# homology files probably originate from Labspace/PotentialFitting/Argon
	169	# 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
[1413f4]	170
	171	file=lj_homology.dat
[f5724f]	172	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
[1413f4]	173	AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
[0ea063]	174	AT_CHECK([../../molecuilder \
	175	--parse-homologies $file \
	176	--set-random-number-engine "lagged_fibonacci607" \
	177	--random-number-engine-parameters "seed=5;" \
	178	--set-random-number-distribution "uniform_real" \
	179	--random-number-distribution-parameters "min=0;max=1;" \
	180	--fit-potential \
	181	--potential-type "lennardjones" \
	182	--potential-charges 18 18 \
	183	--fragment-charges 18 18 \
[b8f2ea]	184	--set-threshold 7e-8 \
[0ea063]	185	--save-potentials lj.potentials], 0, [stdout], [ignore])
[b8f2ea]	186	# check that L_2 error is below 7e-11 ... just 7e-8 otherwise test takes too long
	187	AT_CHECK([grep "Best parameters with L2 error" stdout \| awk '{if ($8 > 7e-8) exit 1}'], 0, [ignore], [ignore])
[1413f4]	188	# check parameters to printed precision
[0ea063]	189	AT_CHECK([grep "lennardjones:.particle_type1=18,.particle_type2=18,.epsilon=.,.sigma=.;" lj.potentials], 0, [ignore], [ignore])
	190	#AT_CHECK([grep "lennardjones:.particle_type1=18,.particle_type2=18,.epsilon=1.e-05,.sigma=8.2.;" lj.potentials], 0, [ignore], [ignore])
[1413f4]	191
	192	AT_CLEANUP

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