source: tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at@ 53a85a

#
#    MoleCuilder - creates and alters molecular systems
#    Copyright (C) 2017 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/>.
#
### testing potential fitting from an MD simulation of water

# perform test with PoolWorkers using molecuilder_poolworker
AT_SETUP([Potential Fitting - water with harmonic bond and angle potential])
AT_KEYWORDS([fit-potential water harmonic_bond harmonic_angle])

# check that ports are unique over all tests such that they may run in parallel
WORKERPORT=12300
CONTROLLERPORT=12301
WORKERLISTENPORT=12302

# start service in background
${AUTOTEST_PATH}/molecuilder_server --workerport $WORKERPORT --controllerport $CONTROLLERPORT --timeout 3 &
server_pid=$!
AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid])
AT_CHECK([kill -s 0 $server_pid], 0, [ignore], [ignore], [kill $server_pid])

# enlist a worker to work on jobs
../../molecuilder_poolworker -v 5 --server 127.0.0.1:${WORKERPORT} --hostname 127.0.0.1 --listen $WORKERLISTENPORT &
worker_script_pid=$!
worker_pid=`ps -ef | grep molecuilder_poolworker | grep $worker_script_pid | awk '{print $2}'`
AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
AT_CHECK([kill -s 0 $worker_pid], 0, [ignore], [ignore], [kill $server_pid $worker_pid])

# create jobs via molecuilder
molfile="water.pdb"
outputfile="water.data"
AT_CHECK([cp -f ${abs_top_srcdir}/tests/integration/PotentialFitting/pre/$molfile $molfile], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
AT_CHECK([chmod +rw $molfile], 0)
AT_CHECK([../../molecuilder \
        -i $molfile \
        -o tremolo \
        --set-tremolo-atomdata "Id type x=3 u=3 F=3 neighbors=2" \
        --select-all-atoms \
        --set-random-number-distribution "uniform_real" \
                --random-number-distribution-parameters "min=0;max=1;" \
        --set-random-number-engine "lagged_fibonacci607" \
                --random-number-engine-parameters "seed=5;" \
        --random-perturbation 0.1 \
        --center-in-box "10,0,10,0,0,10" \
        --set-boundary-conditions Wrap Wrap Wrap \
        --update-molecules \
        --set-parser-parameters mpqc \
                --parser-parameters "theory=CLHF;basis=3-21G;" \
        --molecular-dynamics \
                --keep-bondgraph 1 \
                --parse-state-files 0 \
                --deltat 0.5 \
                --steps 30 \
                --order 1 \
                --grid-level 4 \
                --server-address 127.0.0.1 \
                --server-port ${CONTROLLERPORT} \
                --DoLongrange 0 \
        --save-homologies water.homologies], 0, [stdout], [ignore], [kill $server_pid $worker_pid])

# send removeall to server such that all workers shutdown
AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command removeall], 0, [ignore], [ignore], [kill $server_pid $worker_pid])

# check that worker is truely down
AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
AT_CHECK([kill $worker_pid], 1, [ignore], [ignore], [kill $server_pid])

# shutdown controller socket 
AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command shutdown], 0, [stdout], [ignore], [kill $server_pid])

# check that server is truely down
AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $server_pid])
AT_CHECK([kill $server_pid], 1, [ignore], [ignore])

# NOTE that due the limited number of steps we will not get any good parameters
# This is mostly a test whether save-homologies afte the MD works, we can parse in
# all the steps we made (different configurations) and perform some potential to it.

# fit potential harmonic_bond
AT_CHECK([../../molecuilder \
        --parse-homologies water.homologies \
        --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], [kill $server_pid $worker_pid])
# check that L_2 error is below desired threshold
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 6e-4) exit 1}'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
# check parameters to printed precision
AT_CHECK([grep "harmonic_bond:.*particle_type1=8,.*particle_type2=1,.*spring_constant=0.22.*,.*equilibrium_distance=1.8.*;" harmonic.potentials], 0, [ignore], [ignore])

# fit potential harmonic_angle
AT_CHECK([../../molecuilder \
        --parse-homologies water.homologies \
        --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 4e-3 \
        --save-potentials angle.potentials], 0, [stdout], [ignore], [kill $server_pid $worker_pid])
# check that L_2 error is below threshold
AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 4e-3) exit 1}'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
# check parameters to printed precision
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])

AT_CLEANUP