Examples¶
Before running these examples, you need to install the appropriate backends.
See also the Python example for M3GNet.
AIMNet2¶
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task SinglePoint
Properties
Gradients Yes
DipoleMoment Yes
Charges Yes
End
System
Atoms
C -3.1168071304396 -3.303815558265976 0.0
C -1.981697818585937 -4.344278296437102 -0.02375164458614451
H -2.786224865835057 -2.422406202569603 0.5293702995256127
H -3.978089852534168 -3.72201295092763 0.4997029251388921
H -3.382157359184612 -3.037352354271593 -1.012416227162533
H -1.120415096491369 -3.926080903775447 -0.5234545697250367
H -2.312280083190481 -5.225687652133474 -0.5531219441117571
H -1.716347589840925 -4.610741500431485 0.9886645825763885
End
Charge 0
End
Engine MLPotential
Model AIMNet2-B973c
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
C 0.0 1.402 0.0
C 1.214 0.701 0.0
C 1.214 -0.701 0.0
C 0.0 -1.402 0.0
C -1.214 -0.701 0.0
C -1.214 0.701 0.0
C 0.0 2.902 0.0
H 2.156 1.244 0.0
H 2.156 -1.244 0.0
H 0.0 -2.49 0.0
H -2.156 -1.244 0.0
H -2.156 1.244 0.0
H 0.891 3.302 -0.515
H -0.891 3.302 -0.515
End
End
Engine MLPotential
Model AIMNet2-NSE
Unrestricted Yes
UnpairedElectrons 1
Backend AIMNet2
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
Pd 0.00 0.00 0.00
Br 0.00 -2.50 0.00
P 2.30 0.00 0.00
H 2.90 1.20 0.50
H 2.90 -0.60 1.10
H 2.90 -0.60 -1.10
P -2.30 0.00 0.00
H -2.90 1.20 0.50
H -2.90 -0.60 1.10
H -2.90 -0.60 -1.10
C 0.00 2.05 0.00
C 1.21 2.75 0.00
C 1.21 4.15 0.00
C 0.00 4.85 0.00
C -1.21 4.15 0.00
C -1.21 2.75 0.00
H 2.16 2.20 0.00
H 2.16 4.70 0.00
H 0.00 5.94 0.00
H -2.16 4.70 0.00
H -2.16 2.20 0.00
End
End
Engine MLPotential
Model AIMNet2-Pd
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task NEB
Properties
PESPointCharacter Yes
End
System
Atoms
N 1.88630912 -0.34204867 -1.59424245
N 1.14203025 -1.15084766 -1.95458206
O 0.07639739 -1.27682918 -1.40578886
C 0.74766633 1.24132374 1.29097263
C -0.52735637 0.87051548 1.20080269
H 1.08791192 2.15092371 0.80682956
H -1.23438622 1.47569873 0.64278673
H -0.86675778 -0.04061999 1.68265930
H 1.45534611 0.63457332 1.84647164
End
End
System final
Atoms
N 1.44280525 0.39326405 0.02115802
N 0.56588608 -0.32983790 -0.53167497
O -0.68785300 -0.26603404 -0.00725496
C 0.86550207 1.12517445 1.10513146
C -0.57889386 0.65549932 1.05974328
H 0.94852175 2.21696742 0.91684905
H -1.26384434 1.51200042 0.88137995
H -0.85746564 0.15513847 2.01191277
H 1.35845740 0.84559176 2.06071421
End
End
Engine MLPotential
Model AIMNet2-Rxn
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
O 0.04860755606500984 0.0971372577526642 -0.081354537305321
H -0.2328162516007876 -1.012116503978655 -2.117604862050755
O -1.992446973426099 1.712464866670328 -3.330034755237272
O -3.886353329581932 0.5968586270252267 -2.863868435457037
C -1.111627081458342 1.94297050610809 -1.090239107451721
C -1.961868140766307 2.359189025341761 -2.093441335756647
C -2.720117650745908 3.498067972911344 -1.967905712702122
H -3.48333901851376 3.716125358774957 -2.70832297458963
C -2.471695653588654 4.337084339803085 -0.8962610415481828
H -2.919010982741548 5.314382023683942 -0.8784403312444639
C -1.606962158860589 3.956938547674243 0.1105001463660947
H -1.433768794470819 4.624926919116493 0.9359854124562355
C -0.9455324014004485 2.753353766947446 0.02232804689121052
H -0.2774419458680448 2.435561158038573 0.8046195241750883
C -0.477900381329607 0.5657480988236798 -1.064767148009391
C -3.013307587354709 0.8899843974898011 -3.628814548368718
C -2.917758626030059 0.3049792827325661 -4.992856797019101
H -3.095485688863513 -0.7497282828641882 -4.884045502594899
H -1.957590247815937 0.5216039739518978 -5.42262803640245
H -3.691343276341748 0.7090023230556253 -5.626838362711566
O -0.5953680605986843 -0.09867939000258648 -2.208687942174689
O 4.153216050034641 -3.875121736047424 -4.986041732991893
H 3.452860783499417 -4.579541839725793 -4.992428000054845
O 3.549738026038415 -3.715902936804428 -7.106350683482868
O 5.824900486810316 -2.07891608681996 -3.964168981115234
O 7.052543720808461 -3.84093210101215 -4.654871775045835
C 4.993336077874257 -2.026296302115845 -6.250441083192826
C 5.722558854826387 -1.490806426783637 -5.196210488076954
C 6.310042718924956 -0.2445290721400035 -5.307519986664454
H 6.862173754669996 0.1498389722883224 -4.467880390090206
C 6.204476721675038 0.4710019979683366 -6.48346956360509
H 6.606906600665488 1.462439822344561 -6.557960748335873
C 5.568529650215559 -0.09845404381886513 -7.57210089740888
H 5.533026182460117 0.4510368622664166 -8.488528495774009
C 4.959946673921331 -1.325463767296543 -7.447737763442552
H 4.4375540711267 -1.793968058413551 -8.267211625642116
C 4.180033923748099 -3.273600522530777 -6.162938473438507
C 6.39327178367673 -3.298427331617188 -3.811288232269865
C 6.158179080381492 -3.819363430787541 -2.457856227734333
H 6.748791897513932 -4.703229196015649 -2.285558341024863
H 5.104412906983105 -4.072453684375849 -2.397820915862852
H 6.362745019342372 -3.040342090298716 -1.728266433620813
O 1.732496386385789 4.236982928898501 0.2767479840391089
H 1.411996985137334 5.16869993936862 0.1941449812142532
O 1.121531426885298 4.087747016240419 -1.87209238528084
O 2.98838774618863 2.295091321788915 1.434737494721474
O 4.845987066968565 3.422661526164751 0.8301782891778253
C 2.244605302023779 2.234420847277881 -0.8908822985549013
C 2.849800477372665 1.649213444384081 0.2017147905484604
C 3.269877499307138 0.3425253540132174 0.149152261829114
H 3.570391746580956 -0.1476559576402316 1.057441054290178
C 3.211931622895864 -0.3379101018117979 -1.05163141669188
H 3.509216407876044 -1.369617930834089 -1.086476863960742
C 2.699831442514809 0.2706383563817227 -2.183432104363085
H 2.622091028461363 -0.2906164257984604 -3.10437087348455
C 2.224968887988104 1.554494339881022 -2.095690355416437
H 1.828543335843002 2.069811594721093 -2.953563268303134
C 1.635726337679244 3.604217612424756 -0.889138608060218
C 3.981398251988346 3.185981376569374 1.622539933016375
C 3.901168091278184 3.868225266101988 2.941465443116195
H 4.371502865534048 4.827155831853814 2.84452829591938
H 2.889290215632452 3.945594161134201 3.278560600124816
H 4.424544104686254 3.252292529396907 3.649394852165159
O -3.027077382899881 1.403072419282251 2.895419635585404
H -2.283478846370985 2.059917327560114 2.893104550363308
O -2.549341773844509 1.299905666970184 5.049336869342522
O -4.780761001044501 -0.3758063222242925 1.913576471428827
O -5.887797090494168 1.438672108086009 2.674670150088357
C -3.961355624591603 -0.4073461430834393 4.196929914232208
C -4.687632840278613 -0.9570812822080812 3.1495087590424
C -5.297790200384086 -2.191955162203467 3.268197139288474
H -5.849197323192125 -2.580175057306502 2.426396720515461
C -5.202698637142281 -2.894606688684493 4.455123558458713
H -5.618691438774545 -3.874664955129813 4.546256399815655
C -4.555029343404314 -2.316006331196987 5.534557362332546
H -4.507378014126695 -2.85747791053825 6.455065404658908
C -3.949446072188962 -1.086233519693823 5.408405715972387
H -3.447626399502241 -0.604360666529781 6.229728949802511
C -3.128855150824052 0.8332158440493268 4.086831462902356
C -5.320480170244285 0.8594818669827639 1.789252148803322
C -5.164464447002681 1.357863591426992 0.4203240088699552
H -5.99388837302361 2.005826941635436 0.182339724034313
H -4.237605337881823 1.917252430710591 0.4060775355378243
H -5.090603507498863 0.5184013743642466 -0.2606445492514907
O 0.1762245280361211 6.457312796098446 -0.01073193780308378
H -0.1919149076493603 5.220293385940322 -1.96063012092157
O -1.85019084582747 8.159107271252854 -3.347530472239347
O -3.802600333595072 7.228104398894319 -2.711932910329611
C -1.059240385434579 8.21953742011857 -1.032967668636604
C -1.677622785551121 8.813321272383027 -2.11860658201186
C -2.126987174035799 10.1117246640261 -2.037312338792584
H -2.465400915185731 10.61303255498974 -2.925998141968857
C -2.083188246890862 10.78254780058413 -0.8257233193387451
H -2.414143520912608 11.80371528682515 -0.7779449260377012
C -1.576375529111633 10.16254636661535 0.3014103890486781
H -1.569203991157636 10.67559662332674 1.249695215133801
C -1.062705636584219 8.892306275762866 0.1815972703522505
H -0.6651630140508134 8.365816147769246 1.034671824934235
C -0.4674480414962085 6.83431339134635 -0.9677066419584488
C -2.906306673820291 7.330464324521373 -3.502270816060985
C -2.86834207177452 6.496325612275228 -4.736468837855148
H -3.522915617041895 5.665136871753607 -4.564972579617495
H -1.874524938837096 6.154306936128693 -4.93159002102877
H -3.212310736335396 7.050421048455125 -5.592873000700019
O -0.7145165646008548 6.064707869777963 -2.022702886060319
O 3.710226087654821 2.854723207216134 -4.988274394125551
H 2.960869677522876 2.200967574674578 -4.991456135884804
O 3.291751253574205 2.986678162639616 -7.157180288259031
O 5.579738613017749 4.401987451268157 -3.936891616532034
O 6.977763212382649 2.780349349489539 -4.661183064970384
C 4.828843561327379 4.565506034986035 -6.223260926713717
C 5.568989698343653 5.043112747802413 -5.151941688436318
C 6.332738680524367 6.192096251930075 -5.230947973281959
H 6.847716724337805 6.576785366620904 -4.36468619441556
C 6.420735900712467 6.859960929345805 -6.440385331718218
H 6.994385808539304 7.76418142743556 -6.525774633339944
C 5.716312907442233 6.381003373632971 -7.531250200910872
H 5.712247846580635 6.954589942156929 -8.43592789219487
C 4.962241542699106 5.233651950025776 -7.42957381328034
H 4.472742135151824 4.79825322198111 -8.280624399797318
C 3.879060519625544 3.399327746437082 -6.179249422832465
C 6.357933833092463 3.315827754345507 -3.782023886532138
C 6.373715069547195 2.875062638038403 -2.373694567605715
H 7.121886032228725 2.108007184474804 -2.242915293243826
H 5.381018511715214 2.504005182815525 -2.122386579895904
H 6.590091964094448 3.727888828634314 -1.740343126862026
O 1.620683628752857 10.79600233245452 0.3064697491718397
H 1.244974371254131 11.70311864348044 0.2256989166094444
O 1.016815761508278 10.6514581544184 -1.834205368575327
O 2.896841657424981 8.872059977067853 1.455519634956904
O 4.800642039740612 9.94405412720532 0.9278836180517643
C 2.095436486724464 8.766570391394207 -0.835461505028147
C 2.824732462405849 8.230598545162666 0.2112673613126501
C 3.447113556763085 7.011950307427099 0.1171488982558159
H 4.099287097982017 6.67270496160664 0.9182717285815637
C 3.260680281497434 6.26298945440832 -1.03294675043782
H 3.61203836078094 5.243867822061278 -1.072130776978642
C 2.572821839438208 6.793146421610337 -2.106933374876411
H 2.449861774833169 6.19910386567984 -2.990709417846023
C 2.026656091839281 8.049032743304929 -2.017587723107726
H 1.533585922248474 8.511445317970933 -2.86259181258779
C 1.511009844807591 10.14930857885686 -0.8499907507709529
C 3.955042930401036 9.659497863640361 1.727710680540356
C 3.932853134449287 10.24296554883757 3.092570139217483
H 4.147025494891217 11.29131469850891 2.983022184636803
H 2.981898860249081 10.07031472145477 3.556258412080108
H 4.708723454716195 9.804983026780027 3.701751626655497
O -2.93929294325435 7.96199285046685 3.242929814662677
H -2.152860481307227 8.557750298895494 3.140842390138013
O -1.960189092244857 7.39156597875531 5.138301929466556
O -4.709606666403765 6.257956943341605 2.162221098025118
O -6.270986653917533 7.789965187663544 2.791246859945085
C -3.813622676595064 6.067024782150596 4.406169188968828
C -4.634598242915302 5.617938335790974 3.384046268846401
C -5.355769459626017 4.446947962156086 3.503934106207474
H -5.879455671010743 4.036737823139527 2.657921093510495
C -5.368390750057744 3.77488321460016 4.710617000166378
H -5.888089830609816 2.839495704637321 4.805958326042291
C -4.662353037598126 4.284684750046861 5.780548147688033
H -4.729846520980134 3.814823000142925 6.734906900230896
C -3.85761321767941 5.385692962321408 5.614903747966862
H -3.280826068600533 5.787022265672467 6.428608654035133
C -2.821812494967769 7.19441906072857 4.305685495244704
C -5.607057886807037 7.240641007415478 1.950039250913551
C -5.660725254694074 7.535027320125071 0.5014962900068018
H -6.36908292638689 8.316326418681269 0.2870814759999322
H -4.670807267062709 7.81599670209993 0.1712758473781559
H -5.940879802664183 6.618637892935095 -0.003257980839910505
End
Lattice
4.13918313 -0.04768066 -10.24193922
-0.01325102 13.01907746 0.09994816999999999
12.17784537 -0.03532923999999999 -0.15399026
End
End
Engine MLPotential
Model AIMNet2-wB97MD3
Backend AIMNet2
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
C 1.1917 0.0037 0.0128
C 2.1539 1.0167 -0.0103
C -0.168 0.3408 0.0612
C -0.5446 1.6751 0.0858
C 1.7616 2.3374 0.0146
C 0.4166 2.6663 0.0625
C 1.604 -1.4116 -0.0198
O 0.7642 -2.2896 -0.0047
O 2.9122 -1.7313 -0.0664
O -1.1117 -0.6342 0.08359999999999999
C -2.4107 -0.3144999999999999 -0.0356
O -2.7326 0.8244 -0.2789
C -3.466699999999999 -1.3761 0.1341
H 3.2034 0.7649 -0.0473
H -1.591 1.9396 0.1227
H 2.506 3.119699999999999 -0.0029
H 0.1182 3.704 0.0818
H 3.1826 -2.6595 -0.0878
H -4.4532 -0.9316 0.003
H -3.3186 -2.1582 -0.6106
H -3.391999999999999 -1.8065 1.1328
End
End
Engine MLPotential
Model AIMNet2-wB97MD3
AIMNet2
UseEnsemble Yes
EnsembleSize 3
End
EndEngine
eor
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
C 0.000 0.000 0.000
N 0.000 0.000 1.520
H 1.030 0.000 -0.380
H -0.515 0.893 -0.380
H -0.515 -0.893 -0.380
H 0.943 0.000 1.920
H -0.471 0.817 1.920
H -0.471 -0.817 1.920
End
Charge 1
End
Engine MLPotential
Model AIMNet2-wB97MD3
EndEngine
eor
M3GNet-UP-2022¶
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" <<EOF
Task SinglePoint
Properties
Gradients True
StressTensor Yes
End
System
Atoms
C 1.1705 0.2287 -0.3792
C 0.0000 -0.6414 0.0001
C -1.1706 0.2288 0.3792
O -2.2331 0.0875 -0.1770
O 2.2330 0.0876 0.1771
H 1.0604 0.9753 -1.1517
H -0.2743 -1.2708 -0.8464
H 0.2743 -1.2705 0.8469
H -1.0592 0.9787 1.1484
End
Lattice
7.0000 0.0000 0.0000
0.0000 7.0000 0.0000
0.0000 0.0000 7.0000
End
End
Engine MLPotential
Model M3GNET-UP-2022
EndEngine
EOF
MACE¶
#!/bin/sh
export NSCM=1
$AMSBIN/ams --delete-old-results << eor
Task GeometryOptimization
GeometryOptimization
OptimizeLattice Yes
End
System
Atoms
Ti 0.0 0.0 0.0
Ti 2.295 2.295 1.48
O 3.672 0.918 1.48
O 0.918 3.672 1.48
O 1.377 1.377 0.0
O -1.377 -1.377 0.0
End
Lattice
4.59 0.0 0.0
0.0 4.59 0.0
0.0 0.0 2.96
End
End
Engine MLPotential
Backend MACE
Model MACE-MPA-0
EndEngine
eor
#!/bin/sh
export NSCM=1
$AMSBIN/ams --delete-old-results <<EOF
Task SinglePoint
System
Atoms
Fe 1.668114040730352 0.1262520819109224 -0.2724347551151446
C 2.874773495523232 0.1245428246154846 1.415559348633178
C 2.864258443334903 0.1209340150334762 -1.968408033283078
C 2.045488061455903 -1.017035067242245 1.417327562237913
C 2.045319712526689 1.266012877626015 1.420696387814215
C 2.034996210818667 1.262513524978156 -1.970493441468708
C 2.03481947582235 -1.020501448939123 -1.962197066617627
C 0.7035387107772729 -0.5811263243586964 1.423538567180201
C 0.7034224460425285 0.8298589950221958 1.425623912376544
C 0.6930135800564622 0.8266219565708358 -1.965565890130913
C 0.6929106632695451 -0.5843873011438833 -1.960428837552032
H 3.953018521369533 0.1247117414887672 1.357511955640776
H 3.942916839876545 0.1210957019063513 -1.918153717773214
H 2.378591921119416 -2.042633565448724 1.360726469795222
H 2.378211455132701 2.291885187385673 1.368152852262757
H 2.368487649252263 2.288431948587419 -1.922729549563146
H 2.368164382464549 -2.046021823720774 -1.905595942151872
H -0.1692093008491947 -1.215015035830631 1.373284230500532
H -0.1693975768578689 1.463823066120819 1.377860052750967
H -0.1792940809531387 1.460901281003479 -1.913022353631542
H -0.1795070909127082 -1.218027215565519 -1.902381441905027
End
End
Engine MLPotential
Backend MACE
Model Custom
ParameterFile $AMSHOME/examples/MLPotential/MACE-Custom-MH-1/mace-mh-1.model
MACE
DataType float64
ModelHead OMOL
End
EndEngine
EOF
Note
The MACE-MH-1 model is licensed under ASL.
This means it can only be used free-of-charge in an academic (non-commercial) setting.
NequIP¶
#!/bin/sh
export NSCM=1
$AMSBIN/ams --delete-old-results <<EOF
Task SinglePoint
Properties
Gradients Yes
End
System
Atoms
O -1.239192986364078 0.7447630849670073 0.2053776714668624
C -0.4264399234121155 -0.3765076809707508 -0.005559613642175442
C 1.015520464999812 -0.00839542074865508 0.1578564463228227
O 1.445056954461275 0.3261487267553756 1.250054826420532
H -1.187895927300546 1.292145824840463 -0.6216000200358711
H -0.6908065725149979 -1.158618889736239 0.7362545961529634
H -0.5963066387066123 -0.7970408421468641 -1.022241368854639
H 1.680064628837262 -0.02249480296033578 -0.7001425378304952
End
End
Engine MLPotential
Backend NequIP
Model Custom
ParameterFile $AMSHOME/examples/MLPotential/NequIP-Custom/model.pth
MLEnergyUnit eV
MLDistanceUnit angstrom
EndEngine
EOF
UMA¶
#!/bin/sh
export NSCM=1
"$AMSBIN/ams" --delete-old-results << eor
Task GeometryOptimization
System
Atoms
O 0. 0. -0.6
H 0. 0. 0.6
End
Charge -1
End
Engine MLPotential
Model UMA-S-1.2-OMol
EndEngine
eor
#!/bin/sh
export NSCM=1
for unpaired_e in 0 2; do
AMS_JOBNAME=o2_unpaired_e_${unpaired_e} $AMSBIN/ams --delete-old-results -n 1 <<eor
Task GeometryOptimization
System
Atoms
O 0. 0. -0.6
O 0. 0. 0.6
End
End
Engine MLPotential
Model UMA-S-1.2-OMol
Unrestricted Yes
UnpairedElectrons ${unpaired_e}
EndEngine
eor
done