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harveydevereuxalinelenaElliottKasoar
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Md cli tutorial (#477)
* Add extended MD CLI tutorial * Add data for md cli tutorial * Adds help and units mentioned * Update docs/source/tutorials/cli/md.ipynb Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com> --------- Co-authored-by: Alin Marin Elena <alin@elena.re> Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
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Lattice="11.83989160297016 0.0 0.0 0.0 12.348523833072429 0.0 0.0 0.0 12.08318025690884" Properties=species:S:1:pos:R:3:momenta:R:3:masses:R:1:forces:R:3:mace_mp_forces:R:3 units="_JSON {\"energy\": \"eV\", \"forces\": \"ev/Ang\", \"stress\": \"ev/Ang^3\", \"time\": \"fs\", \"real_time\": \"s\", \"temperature\": \"K\", \"pressure\": \"GPa\", \"density\": \"g/cm^3\", \"momenta\": \"(eV*u)^0.5\"}" time=36999.99999997435 step=37000 density=1.757776024984141 model_path=small arch=mace_mp mace_mp_energy=-206.10633613898372 mace_mp_stress="0.004931976289420984 0.0039352739684786935 0.005098898746989619 -0.00016578679108218003 -0.0010645130482978384 0.001027458099499788" system_name=NaCl temperature=900.0 pressure=0.000101325 energy=-206.10633613898372 free_energy=-206.10633613898372 stress="0.004931976289420984 0.001027458099499788 -0.0010645130482978384 0.001027458099499788 0.0039352739684786935 -0.00016578679108218003 -0.0010645130482978384 -0.00016578679108218003 0.005098898746989619" pbc="T T T"
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Na 0.04494746 0.29202366 0.00704524 -1.73403039 -0.16012705 0.90924477 22.98976928 -0.08287087 0.05037538 0.20190083 -0.08287087 0.05037538 0.20190083
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Cl 2.59383988 0.19351230 0.30652469 1.38066514 -2.47315128 -0.36160175 35.45000000 -0.11939689 0.23031775 -0.43511370 -0.11939689 0.23031775 -0.43511370
5+
Na 0.15427668 2.90592937 3.24574557 -0.65745917 2.13294681 0.48136523 22.98976928 -0.17044386 0.10974167 -0.47683330 -0.17044386 0.10974167 -0.47683330
6+
Cl 3.03711169 3.10363327 2.52588016 0.84747665 0.18250892 0.49803759 35.45000000 0.14421429 -0.12947583 0.33996014 0.14421429 -0.12947583 0.33996014
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Na 3.05939302 0.06839530 2.85615993 0.74401070 -0.81141227 -1.78310798 22.98976928 0.19912566 0.03192598 0.05504395 0.19912566 0.03192598 0.05504395
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Cl 0.44156677 -0.19905651 3.10285537 -2.07103898 -1.57341736 1.74732103 35.45000000 -0.42190928 0.22192375 -0.25131679 -0.42190928 0.22192375 -0.25131679
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Na 3.07593610 2.76636294 -0.16361868 1.13947567 -0.55622519 2.95403437 22.98976928 0.05002485 0.22644381 0.46347654 0.05002485 0.22644381 0.46347654
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Cl -0.23352687 3.38639212 0.35113753 1.62876854 -0.68630295 0.43197286 35.45000000 -0.06315827 -0.39465504 -0.12871554 -0.06315827 -0.39465504 -0.12871554
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Na 0.38921930 0.07496074 5.63636833 0.23145982 1.01065181 -0.98826925 22.98976928 -0.15486733 0.01227276 0.62303330 -0.15486733 0.01227276 0.62303330
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Cl 3.21865779 0.18749746 5.46488002 -1.05737805 0.67675488 -0.80674588 35.45000000 -0.01678268 -0.13184801 0.46125890 -0.01678268 -0.13184801 0.46125890
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Na -0.12729041 2.71569252 9.40606559 0.60869974 0.20996356 0.15294480 22.98976928 -0.13793691 0.34260160 -0.13798850 -0.13793691 0.34260160 -0.13798850
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Cl 2.59976867 2.70304967 9.39460714 -1.52513939 3.06426864 -0.97122791 35.45000000 0.06327157 0.33754445 -0.16541703 0.06327157 0.33754445 -0.16541703
15+
Na 3.01320227 0.12053047 8.81162895 -0.50666204 0.66141201 0.93594711 22.98976928 0.01492688 0.07120196 -0.18958437 0.01492688 0.07120196 -0.18958437
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Cl -0.24762892 -0.39855155 8.35608297 0.86849017 -0.28491316 0.28485304 35.45000000 0.09291385 0.69377717 0.40201054 0.09291385 0.69377717 0.40201054
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Na 3.41716364 2.85921410 5.04212473 -1.28314778 -2.85652011 1.84564066 22.98976928 -0.13292715 -0.07277626 0.91171742 -0.13292715 -0.07277626 0.91171742
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Cl 0.15610541 2.95796548 5.85080968 -0.02573286 -1.76009375 1.32225449 35.45000000 -0.04690073 -0.07930203 0.10519965 -0.04690073 -0.07930203 0.10519965
19+
Na 0.21631718 6.60278373 0.34970947 -1.04085097 -0.50179717 0.63375503 22.98976928 0.01132537 -0.51647534 0.04075809 0.01132537 -0.51647534 0.04075809
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Cl 3.14209467 5.90432329 0.35723276 0.81349360 0.15754446 0.65281465 35.45000000 -0.05770919 0.09209656 -0.38990950 -0.05770919 0.09209656 -0.38990950
21+
Na 0.86302613 9.69122608 2.62202442 -0.09241110 2.03373896 -0.97002162 22.98976928 -0.38100247 -0.40032772 -0.05829608 -0.38100247 -0.40032772 -0.05829608
22+
Cl 3.16600203 8.75292297 3.08023862 0.05919137 0.90651845 1.29412597 35.45000000 0.24243399 0.04205274 0.09488601 0.24243399 0.04205274 0.09488601
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Na 2.79548039 5.60227205 3.29007882 -0.15399371 -2.11709666 -1.00855231 22.98976928 -0.11762554 0.70324788 -0.11879366 -0.11762554 0.70324788 -0.11879366
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Cl -0.01348386 6.14457832 3.17952219 -1.59598951 -0.73521554 0.36310226 35.45000000 0.10723348 -0.09168749 -0.19007629 0.10723348 -0.09168749 -0.19007629
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Na 3.43948725 10.29684477 -0.31024386 0.49589895 0.49128418 1.26250479 22.98976928 -0.17616439 -0.37774646 -0.24614947 -0.17616439 -0.37774646 -0.24614947
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Cl 0.01582821 9.24935066 0.01338857 -1.96995670 -1.25540697 2.74779105 35.45000000 0.05772164 0.02373058 0.02162407 0.05772164 0.02373058 0.02162407
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Na -0.20293552 5.83554837 5.87256124 0.48015181 0.77358222 1.11213324 22.98976928 0.30548988 0.21519595 0.30117386 0.30548988 0.21519595 0.30117386
28+
Cl 2.74286036 5.83925722 6.01895905 -1.83628045 -2.28164044 -2.03706616 35.45000000 0.08131820 -0.01159592 0.07335268 0.08131820 -0.01159592 0.07335268
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Na 0.18882142 8.61880618 9.42801940 0.41711882 1.08958160 -0.63311678 22.98976928 -0.04849711 0.17217759 -0.55489986 -0.04849711 0.17217759 -0.55489986
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Cl 2.76575304 9.91983812 9.15590918 -0.91319978 1.83525753 1.05530033 35.45000000 0.24599238 -0.53372332 -0.05977138 0.24599238 -0.53372332 -0.05977138
31+
Na 2.88666785 5.55157544 9.53759845 1.09895390 -0.30858709 -1.68520309 22.98976928 -0.36189894 0.08826518 -0.15937884 -0.36189894 0.08826518 -0.15937884
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Cl -0.33359582 5.73658506 9.52448175 -3.42979345 -0.26275222 -1.50479871 35.45000000 0.49199629 0.42747375 0.12758737 0.49199629 0.42747375 0.12758737
33+
Na 3.15521665 9.07312134 5.76463168 0.94316885 -1.94017414 0.20187899 22.98976928 -0.07234384 -0.08153868 0.06736357 -0.07234384 -0.08153868 0.06736357
34+
Cl -0.29805494 8.94337064 6.51932613 0.30580390 2.71110037 1.80443249 35.45000000 0.24511374 -0.13554479 -0.25206010 0.24511374 -0.13554479 -0.25206010
35+
Na 7.10784611 0.14114333 -0.61268279 1.02595206 0.10160288 -0.27959215 22.98976928 -1.27968951 0.11998449 -0.23266816 -1.27968951 0.11998449 -0.23266816
36+
Cl 9.32497548 -0.19420224 0.22507710 0.28699237 -0.32816273 0.11449770 35.45000000 0.44562288 -0.20944098 0.18752551 0.44562288 -0.20944098 0.18752551
37+
Na 5.87639406 3.73908963 2.92909277 0.44865793 1.74589338 2.44731127 22.98976928 0.13510625 -1.10290459 -0.59005878 0.13510625 -1.10290459 -0.59005878
38+
Cl 8.57562011 3.32773398 2.95134075 1.46119085 -1.44495567 1.77650793 35.45000000 -0.08044987 -0.13240526 -0.00244838 -0.08044987 -0.13240526 -0.00244838
39+
Na 8.10125776 0.58515361 2.55919525 0.51310100 -0.89043582 -0.90146767 22.98976928 0.35250739 0.14500376 0.32613178 0.35250739 0.14500376 0.32613178
40+
Cl 5.63366927 -0.04955042 2.54643144 0.26844843 1.00596190 -1.92997732 35.45000000 0.39476233 0.08981199 0.03350706 0.39476233 0.08981199 0.03350706
41+
Na 8.80518162 4.12054368 -0.29949764 -0.39143049 -0.15326301 -1.89988686 22.98976928 0.36085594 -0.69105557 0.19754229 0.36085594 -0.69105557 0.19754229
42+
Cl 6.11094787 3.36531438 -0.08947758 -3.06527163 1.50678418 1.06431107 35.45000000 -0.13038925 0.09346453 0.06365319 -0.13038925 0.09346453 0.06365319
43+
Na 6.19661491 -0.13033951 5.82183385 -0.68353019 -1.54360124 0.15164459 22.98976928 -0.25088482 0.49841280 0.00923222 -0.25088482 0.49841280 0.00923222
44+
Cl 9.00056018 0.18958456 5.40515482 -1.42514644 -2.24148970 0.30976090 35.45000000 -0.26683234 0.68748673 0.14174374 -0.26683234 0.68748673 0.14174374
45+
Na 5.63053283 3.67194972 9.32793452 2.23509282 0.36413349 -1.50906072 22.98976928 0.26330072 -0.40142770 -0.16338249 0.26330072 -0.40142770 -0.16338249
46+
Cl 8.61771939 3.37775479 9.21298123 1.82689451 -0.11052157 1.85633820 35.45000000 0.09165083 -0.34624807 0.19424001 0.09165083 -0.34624807 0.19424001
47+
Na 9.00990175 -0.36810870 8.68306028 -0.00069923 -0.13517667 -0.70930886 22.98976928 -0.03176172 -0.10538037 -0.22463738 -0.03176172 -0.10538037 -0.22463738
48+
Cl 5.74924028 0.03332394 9.17394212 -1.38690074 0.02478079 -1.58460071 35.45000000 0.26685792 -0.15204728 -0.01300211 0.26685792 -0.15204728 -0.01300211
49+
Na 8.72248006 3.02372538 6.57103405 -0.27164328 1.51840827 -0.98977926 22.98976928 0.08384134 -0.39361806 -0.14827360 0.08384134 -0.39361806 -0.14827360
50+
Cl 5.74438351 2.75852685 6.79431355 2.52305507 -1.28366531 0.86142831 35.45000000 0.09839959 0.30087696 -0.60504322 0.09839959 0.30087696 -0.60504322
51+
Na 5.79169042 6.38676943 0.26312832 0.08364223 -0.92381113 -2.27125830 22.98976928 -0.05746090 -0.06790282 -0.25124779 -0.05746090 -0.06790282 -0.25124779
52+
Cl 8.65397909 6.57617895 0.02162997 -0.00015258 -0.99164248 -2.31948311 35.45000000 -0.27036856 0.55829017 0.26917754 -0.27036856 0.55829017 0.26917754
53+
Na 6.11013265 8.49323450 2.71189517 0.40663531 -0.80396169 0.45360698 22.98976928 -0.07164277 0.59391483 0.33236438 -0.07164277 0.59391483 0.33236438
54+
Cl 8.88551126 8.68279923 3.25267305 -2.30583266 2.58441151 -3.81909399 35.45000000 -0.16757519 -0.22964204 -0.79436707 -0.16757519 -0.22964204 -0.79436707
55+
Na 9.16225899 5.86535490 3.53827812 -2.38804298 0.14044127 -0.57298456 22.98976928 -0.07856517 0.26676695 -0.01792601 -0.07856517 0.26676695 -0.01792601
56+
Cl 5.83442373 6.00292931 3.67249667 -1.08070793 0.23845779 1.22160806 35.45000000 -0.02439411 0.70907695 -0.17717965 -0.02439411 0.70907695 -0.17717965
57+
Na 9.17977855 9.35177038 0.46155207 0.97637592 0.33665291 -0.22878005 22.98976928 -0.12678202 -0.07802926 0.02792780 -0.12678202 -0.07802926 0.02792780
58+
Cl 5.79628255 9.54601145 -0.10293668 3.23002962 -0.65324323 1.33474722 35.45000000 0.69617311 -0.56099666 0.24045548 0.69617311 -0.56099666 0.24045548
59+
Na 6.43948662 5.73960432 6.17555206 -0.50034679 2.12682651 1.25092748 22.98976928 -0.44396332 0.07340750 0.38079905 -0.44396332 0.07340750 0.38079905
60+
Cl 8.97611920 5.56598951 6.43449472 3.85436633 -0.73018639 -2.61309797 35.45000000 0.06128541 0.36720913 -0.30312068 0.06128541 0.36720913 -0.30312068
61+
Na 5.84956804 9.32553552 8.78330843 0.46487636 0.87692170 1.13059641 22.98976928 -0.71582750 0.18842906 0.00491347 -0.71582750 0.18842906 0.00491347
62+
Cl 8.28321439 9.42392450 8.88882348 -1.82377185 0.14769413 -1.43861809 35.45000000 0.72880107 -0.15075342 0.32482886 0.72880107 -0.15075342 0.32482886
63+
Na 8.26340174 6.65148841 9.51471973 -0.09382947 -0.43474146 -0.44048677 22.98976928 0.31840492 -0.00155715 -0.51070613 0.31840492 -0.00155715 -0.51070613
64+
Cl 5.49440687 6.42550647 8.91947663 0.05450389 3.83757703 -2.21262425 35.45000000 0.06259702 -0.07718193 0.07082253 0.06259702 -0.07718193 0.07082253
65+
Na 9.11568816 10.06164034 5.31153307 2.28074918 0.67070936 1.43130989 22.98976928 0.19775648 -0.59809570 0.57643623 0.19775648 -0.59809570 0.57643623
66+
Cl 6.27569215 9.71958866 5.69764774 1.30697911 -1.93068002 0.37376126 35.45000000 -0.35200278 -0.52911863 0.17671785 -0.35200278 -0.52911863 0.17671785

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