source: tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at@ 0aae02

Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
Last change on this file since 0aae02 was 0aae02, checked in by Frederik Heber <frederik.heber@…>, 7 years ago

Added integration test molecular dynamics of a water molecule.

  • we test for forces (actually full state) in first two steps and the overall temperature profile.
  • Property mode set to 100644
File size: 3.8 KB
RevLine 
[0aae02]1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2017 Frederik Heber
4#
5# This program is free software: you can redistribute it and/or modify
6# it under the terms of the GNU General Public License as published by
7# the Free Software Foundation, either version 3 of the License, or
8# (at your option) any later version.
9#
10# This program is distributed in the hope that it will be useful,
11# but WITHOUT ANY WARRANTY; without even the implied warranty of
12# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13# GNU General Public License for more details.
14#
15# You should have received a copy of the GNU General Public License
16# along with this program. If not, see <http://www.gnu.org/licenses/>.
17#
18### testing molecular dynamics simulation of water
19
20# perform test with PoolWorkers using molecuilder_poolworker
21AT_SETUP([Integration - molecular dynamics of water])
22AT_KEYWORDS([molecular dynamics water])
23
24# check that ports are unique over all tests such that they may run in parallel
25WORKERPORT=12110
26CONTROLLERPORT=12111
27WORKERLISTENPORT=12112
28
29# start service in background
30${AUTOTEST_PATH}/molecuilder_server --workerport $WORKERPORT --controllerport $CONTROLLERPORT --timeout 3 &
31server_pid=$!
32AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid])
33AT_CHECK([kill -s 0 $server_pid], 0, [ignore], [ignore], [kill $server_pid])
34
35# enlist a worker to work on jobs
36../../molecuilder_poolworker -v 5 --server 127.0.0.1:${WORKERPORT} --hostname 127.0.0.1 --listen $WORKERLISTENPORT &
37worker_script_pid=$!
38worker_pid=`ps -ef | grep molecuilder_poolworker | grep $worker_script_pid | awk '{print $2}'`
39AT_CHECK([sleep 2], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
40AT_CHECK([kill -s 0 $worker_pid], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
41
42# create jobs via molecuilder
43molfile="water.pdb"
44outputfile="water.data"
45AT_CHECK([cp -f ${abs_top_srcdir}/tests/integration/MolecularDynamics/pre/$molfile $molfile], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
46AT_CHECK([chmod +rw $molfile], 0)
47AT_CHECK([../../molecuilder \
48 -i $molfile \
49 -o tremolo \
50 --set-tremolo-atomdata "Id type x=3 u=3 F=3 neighbors=2" \
51 --select-all-atoms \
52 --center-in-box "10,0,10,0,0,10" \
53 --set-boundary-conditions Wrap Wrap Wrap \
54 --update-molecules \
55 --set-parser-parameters mpqc \
56 --parser-parameters "theory=CLHF;basis=3-21G;" \
57 --molecular-dynamics \
58 --keep-bondgraph 1 \
59 --parse-state-files 0 \
60 --deltat 0.5 \
61 --steps 30 \
62 --order 1 \
63 --grid-level 4 \
64 --server-address 127.0.0.1 \
65 --server-port ${CONTROLLERPORT} \
66 --DoLongrange 0], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
67
68# send removeall to server such that all workers shutdown
69AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command removeall], 0, [ignore], [ignore], [kill $server_pid $worker_pid])
70
71# check that worker is truely down
72AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $worker_pid $server_pid])
73AT_CHECK([kill $worker_pid], 1, [ignore], [ignore], [kill $server_pid])
74
75# shutdown controller socket
76AT_CHECK([${AUTOTEST_PATH}/molecuilder_controller --server 127.0.0.1:$CONTROLLERPORT --command shutdown], 0, [stdout], [ignore], [kill $server_pid])
77
78# check that server is truely down
79AT_CHECK([sleep 1], 0, [ignore], [ignore], [kill $server_pid])
80AT_CHECK([kill $server_pid], 1, [ignore], [ignore])
81
82# check forces at initial two steps
83lines=`echo "2+3+1+3" | bc`
84AT_CHECK([head -n $lines $outputfile | diff - ${abs_top_srcdir}/tests/integration/MolecularDynamics/post/water_initial_steps.data], 0)
85
86# check average temperature
87tempfile="water.ekin"
88AT_CHECK([../../molecuilder \
89 -i $outputfile \
90 --select-all-atoms \
91 --save-temperature $tempfile], 0, [ignore], [ignore])
92AT_CHECK([diff $tempfile ${abs_top_srcdir}/tests/integration/MolecularDynamics/post/$tempfile], 0)
93
94AT_CLEANUP
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