| 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2017 Frederik Heber
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| 4 | #
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| 5 | # This program is free software: you can redistribute it and/or modify
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| 6 | # it under the terms of the GNU General Public License as published by
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| 7 | # the Free Software Foundation, either version 3 of the License, or
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| 8 | # (at your option) any later version.
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| 9 | #
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| 10 | # This program is distributed in the hope that it will be useful,
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| 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 13 | # GNU General Public License for more details.
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| 14 | #
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| 15 | # You should have received a copy of the GNU General Public License
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| 16 | # along with this program. If not, see <http://www.gnu.org/licenses/>.
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| 17 | #
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| 18 | ### testing potential fitting from an MD simulation of water
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| 19 |
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| 20 | # perform test with PoolWorkers using molecuilder_poolworker
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| 21 | AT_SETUP([Potential Fitting - water with harmonic bond and angle potential])
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| 22 | AT_KEYWORDS([fit-potential water harmonic_bond harmonic_angle])
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| 23 |
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| 24 | # check that ports are unique over all tests such that they may run in parallel
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| 25 | WORKERPORT=12300
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| 26 | CONTROLLERPORT=12301
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| 27 | WORKERLISTENPORT=12302
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| 28 |
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| 29 | # start service in background
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| 30 | ${AUTOTEST_PATH}/molecuilder_server --workerport $WORKERPORT --controllerport $CONTROLLERPORT --timeout 3 &
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| 31 | server_pid=$!
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| 32 | AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid])
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| 33 | AT_CHECK([kill -s 0 $server_pid], 0, [ignore], [ignore], [kill $server_pid])
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| 34 |
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| 35 | # enlist a worker to work on jobs
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| 36 | ../../molecuilder_poolworker -v 5 --server 127.0.0.1:${WORKERPORT} --hostname 127.0.0.1 --listen $WORKERLISTENPORT &
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| 37 | worker_pid=$!
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| 38 | AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 39 | AT_CHECK([kill -s 0 $worker_pid], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 40 |
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| 41 | # create jobs via molecuilder
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| 42 | molfile="water.pdb"
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| 43 | outputfile="water.data"
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| 44 | AT_CHECK([cp -f ${abs_top_srcdir}/tests/integration/PotentialFitting/pre/$molfile $molfile], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 45 | AT_CHECK([chmod +rw $molfile], 0)
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| 46 | AT_CHECK([../../molecuilder \
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| 47 | -i $molfile \
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| 48 | -o tremolo \
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| 49 | --set-tremolo-atomdata "Id type x=3 u=3 F=3 neighbors=2" \
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| 50 | --select-all-atoms \
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| 51 | --set-random-number-distribution "uniform_real" \
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| 52 | --random-number-distribution-parameters "min=0;max=1;" \
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| 53 | --set-random-number-engine "lagged_fibonacci607" \
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| 54 | --random-number-engine-parameters "seed=5;" \
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| 55 | --random-perturbation 0.1 \
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| 56 | --center-in-box "10,0,10,0,0,10" \
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| 57 | --set-boundary-conditions Wrap Wrap Wrap \
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| 58 | --update-molecules \
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| 59 | --set-parser-parameters mpqc \
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| 60 | --parser-parameters "theory=CLHF;basis=3-21G;" \
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| 61 | --molecular-dynamics \
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| 62 | --keep-bondgraph 1 \
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| 63 | --parse-state-files 0 \
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| 64 | --deltat 0.5 \
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| 65 | --steps 30 \
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| 66 | --order 1 \
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| 67 | --grid-level 4 \
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| 68 | --server-address 127.0.0.1 \
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| 69 | --server-port ${CONTROLLERPORT} \
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| 70 | --DoLongrange 0 \
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| 71 | --save-homologies water.homologies], 0, [stdout], [ignore], [kill $server_pid $worker_pid])
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| 72 |
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| 73 | # send removeall to server such that all workers shutdown
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| 74 | AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command removeall], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 75 |
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| 76 | # check that worker is truely down
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| 77 | AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
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| 78 | AT_CHECK([kill $worker_pid], 1, [ignore], [ignore], [kill $server_pid])
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| 79 |
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| 80 | # shutdown controller socket
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| 81 | AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command shutdown], 0, [stdout], [ignore], [kill $server_pid])
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| 82 |
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| 83 | # check that server is truely down
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| 84 | AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $server_pid])
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| 85 | AT_CHECK([kill $server_pid], 1, [ignore], [ignore])
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| 86 |
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| 87 | # NOTE that due the limited number of steps we will not get any good parameters
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| 88 | # This is mostly a test whether save-homologies afte the MD works, we can parse in
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| 89 | # all the steps we made (different configurations) and perform some potential to it.
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| 90 |
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| 91 | # fit potential harmonic_bond
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| 92 | AT_CHECK([../../molecuilder \
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| 93 | --parse-homologies water.homologies \
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| 94 | --set-random-number-engine "lagged_fibonacci607" \
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| 95 | --random-number-engine-parameters "seed=1;" \
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| 96 | --set-random-number-distribution "uniform_real" \
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| 97 | --random-number-distribution-parameters "min=0;max=1;" \
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| 98 | --fit-potential \
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| 99 | --potential-type "harmonic_bond" \
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| 100 | --potential-charges 8 1 \
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| 101 | --fragment-charges 1 8 1 \
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| 102 | --set-threshold 6e-4 \
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| 103 | --save-potentials harmonic.potentials], 0, [stdout], [ignore], [kill $server_pid $worker_pid])
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| 104 | # check that L_2 error is below desired threshold
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| 105 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 106 | # check parameters to printed precision
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| 107 | AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.22.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])
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| 108 |
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| 109 | # fit potential harmonic_angle
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| 110 | AT_CHECK([../../molecuilder \
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| 111 | --parse-homologies water.homologies \
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| 112 | --set-random-number-engine "lagged_fibonacci607" \
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| 113 | --random-number-engine-parameters "seed=1;" \
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| 114 | --set-random-number-distribution "uniform_real" \
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| 115 | --random-number-distribution-parameters "min=0;max=1;" \
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| 116 | --fit-potential \
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| 117 | --potential-type "harmonic_angle" \
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| 118 | --potential-charges 1 8 1 \
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| 119 | --fragment-charges 1 8 1 \
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| 120 | --set-threshold 4e-3 \
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| 121 | --save-potentials angle.potentials], 0, [stdout], [ignore], [kill $server_pid $worker_pid])
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| 122 | # check that L_2 error is below threshold
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| 123 | AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 4e-3) exit 1}'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
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| 124 | # check parameters to printed precision
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| 125 | AT_CHECK([grep "harmonic_angle:.*particle_type1=1,.*particle_type2=8,.*particle_type3=1,.*spring_constant=0.03.*,.*equilibrium_distance=-0.3.*;" angle.potentials], 0, [ignore], [ignore])
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| 126 |
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| 127 | AT_CLEANUP
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