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deepmodeling / dpdata

Manipulating multiple atomic simulation data formats, including DeePMD-kit, VASP, LAMMPS, ABACUS, etc.
https://docs.deepmodeling.com/projects/dpdata/
GNU Lesser General Public License v3.0
188 stars 128 forks source link

the structure file lammps.lmp can not be transformed to lammps.dump #664

Open MumuMaster2021 opened 1 month ago

MumuMaster2021 commented 1 month ago

Bug summary

import dpdata

读取 LAMMPS 数据文件

system = dpdata.System('minimized_structure.output', fmt='lammps/lmp')

写出为 LAMMPS dump 文件

system.to_dump('lammps/dump', 'output.dump')

but occurs the error "NotImplementedError: LAMMPSDumpFormat doesn't support [System.to]"

dpdata Version

dpdata v0.2.18

Input Files, Running Commands, Error Log, etc.

LAMMPS data file via write_data, version 2 Aug 2023, timestep = 118, units = metal

216 atoms 3 atom types

-0.007919750161445126 15.115135509784455 xlo xhi -0.006528523477168591 15.110924597197704 ylo yhi -0.00634830214778237 14.691225008947782 zlo zhi

Masses

1 28.085 2 15.999 3 167.25

Atoms # atomic

9 1 2.570979738903111 2.151563688770844 3.255213656021737 0 0 0 131 2 2.0398432298939677 0.7699249234843454 2.5502112958515557 0 0 0 172 2 1.5157938840609564 3.3670151774784873 2.881684210209688 0 0 0 73 2 0.27996392372699563 3.482366162145133 0.6117126504005249 0 0 0 86 2 4.059289692135854 2.4614656930372507 2.6527183945760764 0 0 0 124 2 6.2624508346490355 3.0163198326653506 1.2851557016871669 0 0 0 3 1 5.345516690658251 3.4734632904380955 2.585308061335011 0 0 0 30 1 7.478219789600731 1.9327468954516531 0.8905711246455857 0 0 0 119 2 7.273072340802053 0.5367792778586831 1.7566542859234087 0 0 0 62 1 10.228570409617246 3.6286137537061167 1.0859193109173548 0 0 0 156 2 8.89423382911003 2.6812259694961824 1.229224333247987 0 0 0 49 1 0.15154502769581485 3.850904676409534 2.180438865771083 1 0 0 8 1 12.624188025446676 2.2187691249263786 2.7935025104062103 0 0 0 72 2 13.143061026492258 0.7410814732153949 2.2909694778837144 0 0 0 83 2 13.865599122098338 3.361259541595296 2.788633479218313 0 0 0 133 2 11.440570512703138 2.822995166170715 1.8428408985717672 0 0 0 167 2 0.3421515961703198 5.718215405198208 2.150445120699587 0 0 0 36 1 3.991673419193116 6.280071964673193 3.280383162519047 0 0 0 58 1 0.6881629368009633 6.445105613965724 0.5833783392755357 0 0 0 13 1 0.8818221626545912 6.508104092552748 3.715588142193891 0 0 0 137 2 4.733628673889022 5.016979628282846 2.518285154802884 0 0 0 121 2 3.8563097040366117 7.625863144749836 2.3850448060361473 0 0 0 92 2 5.925186048895728 7.690450802017303 0.8018141177197377 0 0 0 47 1 9.061832735538164 6.093690483983847 2.7902234780314146 0 0 0 171 2 8.362018739976465 7.32731875837776 1.9252601554985613 0 0 0 199 2 9.954003754029488 5.077597541649206 1.8482357870434056 0 0 0 55 1 7.554903867547055 7.774833868546047 0.5380293612238797 0 0 0 173 2 0.7974719581792953 8.096564166065425 0.6210146954786123 0 0 0 212 2 0.5953336566261354 8.114666994333042 3.725011000064728 0 0 0 182 2 0.5652385937097131 10.987713038089982 3.4567175868785838 0 0 0 40 1 4.6239609430812365 8.54257848760724 1.2819482679214274 0 0 0 48 1 5.801377210276767 10.817352256687471 3.0829071268850132 0 0 0 142 2 4.980769061416608 9.988907243840341 1.9529976517439656 0 0 0 125 2 11.988936097940543 10.307897748969358 1.7290595810659548 0 0 0 203 2 9.791067494436662 11.183839322205847 2.764586790056013 0 0 0 50 1 11.413883935293383 11.428205191126706 2.8267419813082335 0 0 0 21 1 0.35799058692802554 12.399283884057121 2.5631917913094417 0 0 0 22 1 2.6356240012256382 14.569140571844711 1.7405247277378062 0 0 0 74 2 1.7402686413806403 13.27535511429026 2.253363070870032 0 0 0 153 2 7.157984446105217 11.462286133473066 2.404130025779533 0 0 0 71 2 4.17797511200816 14.199692333265842 2.199590020915656 0 0 0 43 1 4.766569362494105 13.683969327017541 3.6455940400779827 0 0 0 108 2 6.247998277590597 14.338710203965267 3.884668841157727 0 0 0 41 1 7.60141243834228 14.874516046813598 3.147045659199766 0 0 0 157 2 8.597214315403516 13.574505835940512 3.002374698651513 0 0 0 64 1 8.466647288165637 11.96617631213189 3.2784574153435853 0 0 0 103 2 15.074390909964782 11.874777566703223 1.051248772207822 0 0 0 80 2 11.724609972834138 12.97339843334146 2.4734839307293646 0 0 0 20 1 12.948414459911612 14.165472442098347 2.644337907321658 0 0 0 91 2 13.322626785206362 13.88959718023826 0.8824330584857543 0 0 0 107 2 14.35965465601689 13.404276266471307 3.2605259876396366 0 0 0 10 1 1.719783289140115 2.693876986432604 6.136551843215417 0 0 0 81 2 2.6686016197291558 2.132242326153217 4.896501139410334 0 0 0 89 2 2.009293289209988 1.8516198259374692 7.474013820941815 0 0 0 135 2 6.236521412243012 3.27463166543602 3.9675732715184804 0 0 0 141 2 5.362602451935968 2.890300666679204 6.920388717781936 0 0 0 27 1 8.717767594588297 1.51328231767562 5.511825434575129 0 0 0 79 2 10.242611135059732 0.9622814823307527 5.838581757574883 0 0 0 151 2 7.532318844872086 1.1552384961151816 6.638030517290476 0 0 0 158 2 8.36553991934642 0.8189681508890662 4.087261739576531 0 0 0 184 2 8.672836479416201 3.1456206911557656 5.201659566217196 0 0 0 170 2 0.11523865340708471 2.869666927537414 5.573891941624753 1 0 0 65 1 11.807905655452533 0.7654957417075252 5.22211266536018 0 0 0 177 2 12.077890196133716 2.167145146102916 4.351029048467743 0 0 0 178 2 12.809052202336963 0.7173844342417794 6.534039566319016 0 0 0 112 2 2.41803715603508 5.990422035033145 3.693406030483289 0 0 0 111 2 1.765225622254512 4.371175102050542 6.421741434042876 0 0 0 46 1 4.374368408765811 6.979768131519109 6.183552478522904 0 0 0 75 2 4.813920336480518 6.6718923430968315 4.62971582632203 0 0 0 136 2 4.464584026235276 5.523031828217165 6.954191793856136 0 0 0 145 2 6.907696710646213 4.8642791613915275 6.083187154010017 0 0 0 38 1 5.719034649894773 4.481746517730648 7.163992136348682 0 0 0 168 2 7.8887059798672095 5.239841312080952 3.5841820557280144 0 0 0 213 2 9.991919391380426 6.719443974005766 3.9957388387879886 0 0 0 52 1 7.446624109682847 4.134195755415219 4.708463373990205 0 0 0 185 2 9.976034091333585 7.174393269752975 6.718208617719029 0 0 0 54 1 0.14446426502809215 4.503363592734187 5.985348801622846 1 0 0 169 2 15.096097021765749 5.601529048226245 4.742422567452675 0 0 0 197 2 14.116930594486547 4.818048353890171 7.11524013517582 0 0 0 24 1 0.3691483399648515 9.65524040712439 4.434830598924121 0 0 0 204 2 1.4575830303858608 9.795091251188689 5.656506481113254 0 0 0 2 1 2.1936280559775763 9.060348089218758 6.92733659415894 0 0 0 152 2 2.8930020720341227 7.680328652112619 6.331927521604483 0 0 0 154 2 6.289474063966945 9.80581746506807 4.304539953995428 0 0 0 114 2 7.18633711758583 9.949313305587575 6.855064217321352 0 0 0 45 1 7.6214977730131395 10.007349846721569 5.280498938871237 0 0 0 164 2 5.385035313041815 8.118490243613177 6.724033293930898 0 0 0 63 1 10.030039664842217 7.830437861989949 5.2029341760575925 0 0 0 208 2 8.759801473368052 8.868609764002864 4.953805407774037 0 0 0 126 2 11.48099698487476 8.573926022941315 5.0461196288476975 0 0 0 56 1 12.402308341271977 9.88374434986547 5.351263838329273 0 0 0 105 2 13.990457553671895 9.578411399820915 5.106882075133711 0 0 0 183 2 12.109166230416976 10.265081621488887 6.950706051177743 0 0 0 209 2 11.955653431134113 11.095212421879781 4.345800207922416 0 0 0 122 2 2.2056116305422235 14.66133436179624 6.8299484773082355 0 0 0 15 1 3.7529792777842172 14.306459395371496 6.494764565396183 0 0 0 146 2 3.9644982463403764 12.738751834715455 6.974977458731507 0 0 0 160 2 4.861910511377527 12.034757785095705 3.662970022627381 0 0 0 77 2 3.8248578635750374 14.237160930208466 4.845871428078339 0 0 0 188 2 8.224933527339736 11.515975153604344 4.873819707777509 0 0 0 201 2 12.18042233985904 14.596964299800733 4.2636142770790135 0 0 0 14 1 1.2622580657934541 0.3125940742832401 8.009908208705825 0 0 0 82 2 2.126566048469483 0.158479635081096 9.456777019451561 0 0 0 113 2 14.958694923080856 1.2278433507436124 8.16251844874996 -1 0 0 5 1 2.0731285336314986 0.611581387002004 11.011454903924285 0 0 0 84 2 4.96252407041671 0.20631644244384825 7.036507059368714 0 0 0 37 1 6.034197143552611 1.428375192962821 7.359228416231092 0 0 0 130 2 6.268449095485327 1.5971345457796913 8.981413969916433 0 0 0 42 1 7.438404461086113 1.7842282729306758 10.12904133966638 0 0 0 140 2 8.555665477694054 0.6154347939350612 9.715103760723322 0 0 0 120 2 8.116342520025464 3.3044937721111434 10.098026625198688 0 0 0 53 1 13.33704699107479 1.1085448185614857 8.039968890365577 0 0 0 60 1 12.157770694675921 3.1741990412717023 10.074955755915079 0 0 0 132 2 12.663217591169632 2.494071996253305 8.552067356874689 0 0 0 68 1 12.527123690708555 0.038092736729478834 10.671458312129973 0 1 0 180 2 11.92425840844823 1.5738236599741204 10.795744812749101 0 0 0 87 2 0.7767099825386166 5.6578123756758645 8.960801621053362 0 0 0 139 2 4.356508580504898 6.1727614186479425 10.159422865122806 0 0 0 144 2 6.247233217595924 4.735265025805787 8.715158303867867 0 0 0 33 1 5.903107867137601 5.421729106678803 10.140344730529165 0 0 0 179 2 6.84787185716757 6.66272478754763 10.68750453632606 0 0 0 148 2 10.677729083811641 3.7077711236116015 9.479285375831362 0 0 0 149 2 9.260386628900829 5.839289049918382 8.976493559757385 0 0 0 59 1 9.176332023319983 7.258845160528993 8.159281204909199 0 0 0 44 1 9.359205270806589 4.493189249182213 10.02760326784519 0 0 0 61 1 14.242025053893578 5.313446266234836 8.70854411178086 0 0 0 194 2 13.442927682500361 4.403520045071287 9.785208710198313 0 0 0 18 1 0.45821419903338084 7.314408036175525 9.015523815919217 0 0 0 90 2 1.049681964699687 8.43598343267749 7.964600871312902 0 0 0 99 2 0.6407361263669517 11.524063292034342 9.135132694365161 0 0 0 98 2 3.200102639417332 10.178196111913664 7.624188013469786 0 0 0 116 2 0.9147349171025486 7.82751965064742 10.502238522879363 0 0 0 70 1 6.481153112406039 8.728746936231412 7.774856875833418 0 0 0 129 2 5.838601653083093 8.940442944269414 9.249638031576637 0 0 0 163 2 9.730948939372704 8.663039254209052 8.974213241424389 0 0 0 101 2 7.602744352644803 7.525573861509922 7.864357617972148 0 0 0 39 1 9.411257653459733 10.141131543080887 9.61446042978674 0 0 0 102 2 9.50340361771485 10.00956525975281 11.242456799958536 0 0 0 186 2 13.939242891693702 6.994306545603588 8.788519540793338 0 0 0 57 1 12.406807501849721 10.788299057704371 8.453404019578018 0 0 0 181 2 13.01713990465064 9.667584091864645 9.486243818646463 0 0 0 11 1 13.218350129993306 9.404224789798715 11.115800808074209 0 0 0 66 1 1.7985251616131372 11.747279260997791 10.331082360522908 0 0 0 196 2 3.174527058945174 12.16529124981246 9.5143616564365 0 0 0 198 2 0.25877070932256196 13.946264960773858 8.122926275791777 0 0 0 23 1 6.748133790315116 11.937223958496322 9.419445473773793 0 0 0 26 1 3.910454061489225 11.599899805895538 8.148006135657381 0 0 0 192 2 5.491422674424191 11.391111036025196 8.544097197113196 0 0 0 162 2 7.160829787288338 13.44403596160208 8.794295195796142 0 0 0 97 2 10.805756709851908 11.289241017805919 9.217015250984527 0 0 0 128 2 8.025840624800646 10.869369799264978 9.214214222127149 0 0 0 32 1 10.537000960614815 12.994803419154538 9.7647173623497 0 0 0 34 1 8.538374123039736 14.156733948096434 9.316183676317205 0 0 0 143 2 9.933816039052566 13.789791777597856 8.421576587216183 0 0 0 176 2 13.254869956678473 12.170693435973634 8.349448743709944 0 0 0 214 2 12.921773679612741 14.976378698831407 9.055052908789238 0 0 0 25 1 14.678908233891667 12.789932774089774 8.991426183408432 0 0 0 150 2 14.216099022815502 13.072565142829852 10.538995004687898 0 0 0 200 2 11.557001312798347 13.757148962575965 10.747812717856913 0 0 0 29 1 3.444418321900753 0.6999563929810299 13.571429848777683 0 0 0 78 2 2.1027004872668607 2.2765500515915438 11.004556913733767 0 0 0 138 2 2.7962525757690933 2.2467290228121453 13.584637529026484 0 0 0 6 1 2.1039559677248616 3.164544908353489 12.381043519015217 0 0 0 109 2 3.285985096787774 0.09199793487180048 12.028441782081481 0 0 0 31 1 6.541896911066575 0.5472039231518803 13.017926727741889 0 0 0 94 2 6.749845448735417 1.2771045612869205 11.55228058804901 0 0 0 210 2 5.070831395252776 0.7479541120561097 13.742846639560653 0 0 0 76 2 7.530707767550268 1.3846479292187914 14.037542307647668 0 0 0 115 2 11.908551638131254 3.880713176727874 11.654982439682218 0 0 0 96 2 0.5541153672109553 3.618678932643079 12.716634848265151 0 0 0 166 2 2.8670376222001743 4.588943497724176 12.115743627486207 0 0 0 93 2 2.2386860614059954 6.321591900799035 14.657980346509625 0 0 0 88 2 5.489997839544587 4.511478390691299 11.485864723661708 0 0 0 35 1 4.143258275843667 5.518478818822473 11.767829351948885 0 0 0 134 2 4.310551551653694 6.899450876232896 12.595273192128335 0 0 0 85 2 9.353431895442615 5.2124232268798005 11.489541335695831 0 0 0 205 2 10.609858062560933 3.8674171460253697 14.198624295709124 0 0 0 215 3 8.529530438761878 7.028454645851022 12.085652623531697 0 0 0 207 2 7.984245652592954 6.789172586460315 14.039023797030062 0 0 0 206 2 13.197243129312103 3.6797650158140898 13.863452849052058 0 0 0 4 1 14.740073573881974 4.116556008929846 13.942866427730468 0 0 0 189 2 14.765168627998838 5.768407365003426 14.222139330134906 0 0 0 7 1 11.830561888277762 4.346340452130501 13.184958819670337 0 0 0 202 2 11.951394790214161 6.011852298637185 13.393308868922709 0 0 0 147 2 3.536635969695404 8.82105191318467 0.07738865440106496 0 0 1 193 2 2.13711008799745 10.235269165079542 10.965175415717495 0 0 0 17 1 2.206718860055964 8.001617296509025 14.328757789377304 0 0 0 16 1 1.0765044523431673 9.10546848250355 11.504964195447796 0 0 0 118 2 1.7210963394805305 8.494756330519227 12.862175127800253 0 0 0 216 3 5.31408185347401 8.227474367419296 11.130715786926983 0 0 0 159 2 6.938260296706383 9.008239267633186 12.327509874698674 0 0 0 67 1 7.174795002991346 10.189167513975528 13.48694327067446 0 0 0 161 2 5.849148865363319 11.272683904285417 13.47911628261609 0 0 0 127 2 7.775973574594662 9.402746455526094 0.1243677148061996 0 0 1 51 1 10.605339596252582 9.871906597125244 12.449232119369748 0 0 0 106 2 10.545236845471528 8.171519065102588 12.656328642257092 0 0 0 195 2 10.634730457672603 10.431297175431794 13.987733062981626 0 0 0 69 1 12.093859460318551 10.196497746469174 0.09039387347603645 0 0 1 191 2 12.559096514973273 8.632600095611313 14.328452789586693 0 0 0 12 1 12.099436857405262 7.589003295654277 13.105497480614602 0 0 0 95 2 12.972775624490476 7.876650296785476 11.721240285906022 0 0 0 100 2 14.715650932761598 9.817770028838412 11.650665086117767 0 0 0 187 2 12.030246111874805 10.344762189515862 11.76901236339727 0 0 0 110 2 2.735467170026763 14.948669669227804 0.11172582588869487 0 0 1 155 2 0.7407858410288639 0.13216330725387446 11.800201067458609 0 1 0 190 2 1.3809232469155812 12.816356675844892 11.488056911328943 0 0 0 28 1 14.975583041854808 13.82163271136555 11.857274461097445 -1 0 0 1 1 6.773879160622212 12.395504208439448 12.572210132077588 0 0 0 165 2 6.321214382020451 12.18417068283012 10.991816251554967 0 0 0 175 2 6.802898863477041 14.004854691925566 12.943803102667019 0 0 0 123 2 9.080749147059048 13.142367415485348 10.57498986874389 0 0 0 117 2 8.145835089053469 11.48588392879276 12.970870029678583 0 0 0 104 2 13.048026669435961 11.409414357402133 14.24487751081651 0 0 0 19 1 14.01531717445148 12.677548116932316 0.039818359446573144 0 0 1 174 2 14.782217545723704 13.194615497243582 13.388884220191287 0 0 0 211 2 13.549324973880799 14.921592988598025 11.906378226646305 0 0 0

Steps to Reproduce

import dpdata

读取 LAMMPS 数据文件

system = dpdata.System('minimized_structure.output', fmt='lammps/lmp')

写出为 LAMMPS dump 文件

system.to_dump('lammps/dump', 'output.dump')

Further Information, Files, and Links

No other information

njzjz commented 1 month ago

Not a bug, but no one has implemented this feature.