Example: MD for a box of water¶
#!/bin/sh
# ===== H2O_nreac.run =====
# Performs a non-reactive run followed by another non-reactive run with seamless
# restart (preserving the bonds from the first run), and finally a reactive run.
# The MD is restarted both times, ensuring a continuous trajectory.
# ========================
AMS_JOBNAME=nonreactive-1 "$AMSBIN/ams" << EOF
Task MolecularDynamics
MolecularDynamics
nSteps 400
TimeStep 0.25
Thermostat Type=berendsen Tau=100 Temperature=298
Trajectory SamplingFreq=10
Checkpoint Frequency=10
Preserve Momentum=false
InitialVelocities
Type Input
Values
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End
End
End
System
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H 21.8407416020393 1.79904340242951 4.80012337771288
O 7.05554461920893 6.67775456137714 21.3546971712662
H 6.28016360685572 6.8544437061049 20.8183009629116
H 7.3049916649121 5.75979107718035 21.1128209204277
O 14.8336907073802 10.6630412108449 12.6072318997941
H 14.7506256175597 9.98315284030392 13.2899291208987
H 14.8137740742027 11.4964140350684 13.1469733255842
O 8.90815300181195 1.38508666079576 20.5816890077744
H 8.93243225394696 1.8998198822924 19.764605510403
H 8.30715101990454 1.77666606568653 21.2323673420309
O 20.6463935216196 12.292698040882 20.5584779862385
H 21.5431426408091 12.2743756448765 20.2336209142387
H 20.6696348679349 12.9602837555417 21.3312191510132
O 21.974314316387 22.9514836321718 7.77556267341818
H 21.0913859600873 22.503927569699 7.90508738699415
H 22.1387968866284 22.6575857931732 6.86155002920839
O 17.9437985794669 18.2563619443599 15.9017509240301
H 18.0781893266389 18.3957829359947 14.9166059900195
H 18.5797671305862 18.8397486431446 16.3126111607707
O 13.2204360711776 6.01733641107673 8.55289123096035
H 13.2418856394226 6.97191228923339 8.40416253423256
H 14.1194717112323 5.7537342869001 8.32103808377718
O 3.2157558245234 14.2326972743607 8.730637201063
H 4.16623066632119 14.090793688217 8.49961522749945
H 3.33541118326475 14.164224923847 9.68924547375713
O 13.1592937076171 16.2746870546764 4.84763440438379
H 12.5776193454182 17.1359088993769 4.76175821351409
H 12.9234711530047 15.8066967332435 4.03723922784956
O 16.9446160535301 17.1792883037562 23.1215919842314
H 16.5185209309693 16.8124719231077 22.3463368473969
H 16.3623350401673 17.9651078695936 23.2229975273288
O 8.98533136817734 17.3333599458382 13.8139357087676
H 9.24473286008242 16.7233390507329 14.53856627302
H 8.83065459868408 18.1257603500438 14.3466240920529
O 9.32387016024863 14.3483670396112 2.12417009474062
H 8.97151309294185 14.4877647815423 2.97675667878064
H 10.1388567947616 14.9042036024622 2.18269580790894
O 23.7683101618845 14.6595587487731 18.7817563867457
H 24.1925250802981 13.8380016295488 19.043294126813
H 23.3878829731716 15.0127074031882 19.6125377256408
O 4.08588761534507 11.3571820044855 19.2475173213952
H 4.76744888888501 11.0962774620962 19.9045410199008
H 4.57089887680176 11.9648655976551 18.5992169198358
O 7.91393070171295 23.282119792168 19.07512296051
H 8.30049001206536 23.3698796007987 18.1785378277928
H 8.58472424602532 23.6031850231446 19.6516171343676
O 1.9471435701967 12.5782823690504 6.84244775122621
H 2.04943874924866 12.5367512634908 5.89308121409883
H 2.85313297992373 12.7655456575699 7.21073289075899
O 18.0907535940492 13.5701679293044 7.33215015315415
H 17.807218972944 12.9819817275358 8.07222580600028
H 17.4970327282178 14.3638933520022 7.43743500304588
O 15.894779806636 17.5842408663724 18.7733264361332
H 15.6910948035464 17.2136402126368 19.6533793956882
H 16.8463968832189 17.4305982110207 18.6742164826548
O 8.94693809543397 2.43480972546733 18.1008862789738
H 8.32346872501585 3.1224298132047 17.9776165979274
H 8.56378402905623 1.78779892578609 17.4711410803544
O 12.1817799652194 7.10016419710073 23.4817645814998
H 12.5274922279258 6.224033382981 23.4583326953381
H 12.8562511944266 7.62294820208728 23.0056556402493
O 13.737952440683 2.24832066529994 4.26308611554172
H 14.5552230772886 2.30203758459937 3.74118588852657
H 13.6269961250027 3.14645513389914 4.69545413631204
O 3.86747288766335 15.3898985491233 21.5952787720415
H 3.36618175086107 16.1759421748795 21.8664496980337
H 3.8478410217748 15.4427577776753 20.6317599001101
O 4.5514611990981 16.0796874972966 2.48824499173794
H 4.49063764483434 17.0022436434432 2.49625691718619
H 5.47718380607977 15.9372260459189 2.78328380545389
O 6.92741735516738 7.50453637524835 14.9698503993398
H 7.65426164809353 8.16338404885461 14.643951836378
H 7.04053486663875 6.70103381142342 14.3901363739914
O 20.6596705486836 12.3897506074602 12.7930329474224
H 20.1309226604344 12.7636641870273 12.0203649210193
H 20.4610077095223 11.426055940025 12.8045731959762
O 6.39544663416596 17.7712431635522 8.66698284622892
H 6.60741856936031 18.1866450421456 9.60180320312909
H 6.97250241127015 16.9969565237132 8.54291839637305
O 16.6433576789323 1.57323597421774 5.76423685580887
H 17.1673302260291 2.29062046113686 6.16926345373739
H 16.6115843957939 1.84608392193703 4.85738025697457
O 14.4709342610582 17.6346655436059 6.99718915964663
H 14.2488995837892 17.1945824992105 6.17512828733452
H 14.4098907325861 16.8994164806796 7.61362737995617
O 2.04499358279235 16.6316138898995 7.95474301448801
H 2.46562784048632 17.2207429793286 8.70335657280149
H 2.32562254361856 15.6622501481173 8.16104431905799
O 2.42593487303999 17.2987146363241 19.8838123166929
H 1.75136863575383 17.5262842845273 19.2400632752157
H 1.99780382901871 17.3021909816918 20.7009870808284
O 23.0492497885206 18.9881597847423 19.2156555635655
H 23.0694624402642 18.0487505301133 19.5757222280316
H 22.1514601714427 19.0575427313514 18.8577810061993
O 0.380122468791277 18.8823902595585 7.8793321975752
H 0.774420182650264 18.0420767550393 8.10847280059931
H -0.225487594040111 19.0843352296383 8.61381728865852
O 17.9481990687121 9.68003824288202 11.0571109552008
H 17.4888885027779 8.96638806434936 11.461185826768
H 18.8914528075 9.60447909497386 11.4758869389139
O 2.26828654780973 6.97637530097545 4.12992139586634
H 2.38516545540896 6.21916262180925 4.78597283740082
H 3.00897112890131 6.89574676413313 3.43948831884857
O 3.060396519791 2.7103712397421 12.9564805526564
H 2.81375873591907 2.64836992701821 13.9135105334626
H 3.49037149884967 3.58016536209759 12.8550557759661
O 13.9557102236056 23.7734759070336 12.5099866940474
H 13.6704314507593 23.8453993726844 13.4121304641479
H 14.9141852060649 23.6793639857439 12.6361434531209
O 9.33624067538513 15.8093516801567 11.4113115771699
H 9.01393593305819 16.4385559763422 12.0541340831743
H 10.2985631697983 15.9743558598379 11.4919008912435
O 19.0123721607196 17.9262754595125 4.20692553570937
H 18.2027155935977 17.6523552984061 4.60401450345876
H 19.0527678957264 18.7775522071305 4.61795716014284
O 21.8033499595358 7.65400131586474 16.8808660175919
H 21.6868561261467 7.22926235371191 17.7471272239381
H 20.901355209095 7.71186269960936 16.5990766831027
O 8.48207168373828 13.1317173562011 22.954915678683
H 7.47314470596222 13.1733436957379 22.9815966370404
H 8.71132115833836 12.1928060203038 23.1634504487795
O 10.2049157457924 7.33457239938852 9.22067706946937
H 10.3895058253218 8.11930619065367 9.76473495954057
H 10.3490911937328 6.55677038114947 9.79400205959616
O 5.90565815690294 22.0792939722276 2.42746295521207
H 6.61705670576304 22.1985620154302 1.75983065305629
H 5.2167656155614 22.6561645502677 2.07483118436487
End
Lattice
25.000000 0.000000 0.000000
0.000000 25.000000 0.000000
0.000000 0.000000 25.000000
End
End
Engine ReaxFF
ForceField Al-H2O.ff
NonReactive
EndEngine
EOF
AMS_JOBNAME=nonreactive-2 "$AMSBIN/ams" << EOF
Task MolecularDynamics
MolecularDynamics
Restart nonreactive-1.results/ams.rkf
nSteps 500
TimeStep 0.25
Thermostat Type=berendsen Tau=100 Temperature=298
Trajectory SamplingFreq=10
Checkpoint Frequency=10
Preserve Momentum=false
End
LoadSystem
File nonreactive-1.results/ams.rkf
End
EngineRestart nonreactive-1.results/MDStep400.rkf
Engine ReaxFF
ForceField Al-H2O.ff
Torsions 2013
NonReactive
EndEngine
EOF
AMS_JOBNAME=reactive "$AMSBIN/ams" << EOF
Task MolecularDynamics
MolecularDynamics
Restart nonreactive-2.results/ams.rkf
nSteps 800
TimeStep 0.25
Thermostat Type=berendsen Tau=100 Temperature=298
Trajectory SamplingFreq=10
Checkpoint Frequency=10
Preserve Momentum=false
End
LoadSystem
File nonreactive-2.results/ams.rkf
End
EngineRestart nonreactive-2.results/MDStep500.rkf
Engine ReaxFF
ForceField Al-H2O.ff
Torsions 2013
EndEngine
EOF
echo START OF TEST
for f in energylog thermolog; do
echo "Contents of $f"
for phase in nonreactive-1 nonreactive-2 reactive; do
"$AMSBIN/amspython" "$AMSHOME/scripting/standalone/reaxff-ams/$f.py" $phase.results
done
done
echo END OF TEST