libatoms / extxyz Goto Github PK

55
Lattice="20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 20.0" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 Energy=-47.004771 eV=T energy=-272.0659427345163 free_energy=-272.0659427345163 pbc="F F F"
Na 0.86364636 1.57812167 -2.18684227 -0.00109982 -0.00089096 0.00315033 -3.41207940
Na 2.02204820 2.25161453 0.29239011 -0.00883164 0.00056004 0.00687033 -4.67235435
Na 2.16881205 2.05651489 -0.81436795 -0.00250120 0.00091068 -0.00663141 -4.67237035
Na 1.18067198 2.24384074 -1.33712900 0.00517875 0.00717914 0.00100301 -4.67237169
Na -0.63997632 2.19533722 -0.63110435 0.00200118 -0.00425127 0.00164094 -3.41209255
Na 0.90890203 1.20186707 -1.16572989 -0.00280419 0.00532541 -0.00654315 -7.06116635
Na 2.69216839 1.40404231 -0.04962184 0.02173881 0.00016219 0.00286750 -4.67236183
Na -0.64627451 1.14204885 -1.02669889 0.01855016 0.01686871 0.01851100 -4.67239222
Na 1.19011066 0.52321876 -1.97155977 0.00057942 0.00548648 -0.01021530 -4.67228224
Na 0.10550238 1.89459571 -1.41814906 0.00084719 -0.00381055 -0.00281982 -4.67242921
Na 0.43842073 -0.22926985 -1.57994659 0.00136771 0.00126323 0.00160386 -4.67245124
Na -0.79301085 1.33727705 0.08019330 0.00692566 -0.00353563 -0.00279138 -4.67236207
Na -0.78718413 0.27385028 -0.31190345 -0.00434216 -0.00472311 0.00442282 -4.67232279
Na 0.99614157 0.47588599 0.80426980 0.00019905 0.01540941 0.00171245 -7.06121974
Na -0.27303877 1.34206056 1.08733340 0.00011782 0.00070267 0.00378639 -4.67238746
Na -0.62847218 0.08430324 -1.40948095 -0.00059519 0.00054557 0.00147847 -3.41204690
Na 0.17064184 1.50495764 -0.40181675 -0.02848364 -0.00564580 -0.01621290 -7.06161847
Na 0.67740403 1.50956084 0.57977885 -0.00763431 0.01305644 0.01640567 -7.06141632
Na 0.99604557 0.47591205 0.80418967 0.00878027 0.03677974 0.06941770 -7.06246103
Na 1.85103404 1.39634308 -1.67913266 -0.00013937 -0.00009266 -0.00405013 -4.67241176
Na 1.73446106 0.17291627 0.04041680 0.00407331 -0.00153765 -0.00918292 -7.06143340
Na 1.51301737 -0.52693701 -1.72959828 0.00029979 -0.00546992 -0.00314927 -3.41200768
Na 0.05401403 0.28155283 1.31769487 -0.00648140 0.00116106 0.00139537 -4.67236738
Na 0.99604557 0.47591205 0.80418967 0.00878027 0.03677974 0.06941770 -7.06246103
Na 1.46670008 1.90706004 1.21850229 -0.00046936 0.00623599 -0.00085697 -4.67233006
Na 2.55126113 0.53571217 0.66509619 -0.00194351 -0.00112889 -0.00035625 -4.67233183
Na 2.69806295 0.34062512 -0.44170481 -0.00222511 0.00079260 0.00057867 -4.67245435
Na -0.13199336 2.21030780 0.37268317 -0.00197369 0.00137359 0.00265287 -4.67240398
Na 0.99604557 0.47591205 0.80418967 0.00878027 0.03677974 0.06941770 -7.06246103
Na 2.03710096 -0.53243071 -0.73411187 0.00308901 -0.00101167 -0.00197997 -4.67237459
Na 0.39215155 2.20489941 1.36824523 0.00233747 -0.01435696 -0.01509974 -3.41209379
Na 0.41064598 -1.21075591 0.10874498 -0.00059049 -0.00707510 -0.00140736 -3.41206480
Na 1.21863339 1.84535196 -0.32287808 0.00031406 0.00484534 0.00528004 -7.06146548
Na 0.68643432 -0.16747765 -0.03850597 0.01088705 -0.00341485 -0.02240005 -7.06136267
Na 1.48177959 -0.87697301 0.19194542 0.00001972 0.00601112 0.00498680 -4.67240254
Na -0.26370256 -0.37863296 0.45295167 -0.01210330 0.00305186 -0.00073641 -4.67233353
Na -0.91995426 0.47176629 0.78762275 -0.00108466 -0.00392258 0.00166890 -3.41202944
Na 1.22777494 0.16830542 -0.94130290 -0.01755172 -0.00132628 0.03000281 -7.06133514
Na 0.99604557 0.47591205 0.80418967 0.00878027 0.03677974 0.06941770 -7.06246103
Na 0.71498841 1.15459891 1.61011524 -0.00153051 0.00379268 -0.00248538 -4.67243012
Na 1.49442213 2.88866871 -0.47018824 -0.00203612 -0.00370912 -0.00044805 -3.41206033
Na 0.03311784 0.65862137 0.29478301 0.00008574 0.00592482 -0.00750927 -7.06126391
Na 2.82504435 1.20618186 -1.14914117 -0.00122458 0.00115514 0.00215139 -3.41205329
Na 2.17819019 0.33587935 -1.44884275 0.00165523 -0.00278371 -0.00227842 -4.67227211
Na 1.79948754 -0.21677863 1.05671318 0.00569022 -0.00770154 0.00119627 -4.67233000
Na 2.54504085 -0.51749742 0.26957793 -0.00135083 -0.00039188 0.00475624 -3.41205969
Na 1.72886749 1.20942942 0.42253480 -0.01076587 -0.00776722 0.00696611 -7.06121271
Na 0.11133938 0.83115916 -1.81027222 -0.00334590 0.00268621 -0.00499022 -4.67238720
Na 2.53357612 1.59342018 1.04800222 0.00179006 0.00255676 -0.00217301 -3.41204576
Na 0.95253667 0.83891963 -0.18072666 0.00811409 -0.00728716 -0.00617682 -6.21355010
Na 1.04131731 0.09970361 1.82535307 0.00720225 -0.00216297 0.00583532 -3.41205920
Na 1.87195690 1.01925127 -0.65624703 -0.00789099 -0.00466256 0.00291142 -7.06132955
Na 0.17619642 0.46848003 -0.78401879 0.01095855 -0.00974251 -0.00279974 -7.06146824
Na -0.11686489 -0.57373666 -0.65387766 -0.00248716 0.00224791 0.00120585 -4.67241161
Na 0.72423665 -0.56610410 0.97576557 0.00810947 0.00213273 -0.00448133 -4.67222230
55
Lattice="20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 20.0" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 Energy=-47.004771 eV=T energy=-272.026088560666 free_energy=-272.026088560666 pbc="F F F"
Na 0.78669323 1.58866331 -2.17455167 0.14525328 -0.26323980 -0.53509492 -3.41153556
Na 1.96775066 2.29270488 0.28134106 0.23203043 0.11697440 -0.22520116 -4.67415016
Na 2.09980751 2.11436975 -0.83234348 -0.12663029 -0.02846175 0.21360804 -4.66948157
Na 1.09238146 2.25999617 -1.32966918 0.11990219 0.04967243 0.18642523 -4.67612462
Na -0.70879535 2.12870396 -0.58736342 0.47523876 -0.02729661 0.04000884 -3.41490069
Na 0.86741328 1.20523291 -1.16076135 0.65743020 -0.16400327 -0.38760378 -7.04877510
Na 2.66590582 1.47747609 -0.08398019 0.37144034 0.24076884 0.37390236 -4.66882075
Na -0.67762131 1.08063709 -0.98844817 0.21077886 -0.60214528 -0.34838786 -4.67341911
Na 1.16461436 0.54406974 -1.97805046 -0.12490173 0.18628366 0.01732160 -4.66994289
Na 0.03320618 1.86713581 -1.39430123 -0.37790960 0.08785564 0.44290907 -4.66549855
Na 0.45704322 -0.24258270 -1.57630188 -0.23074308 0.23292616 0.03820999 -4.67446578
Na -0.80509270 1.26026096 0.11863514 -0.16046802 -0.16671038 0.12600800 -4.67613880
Na -0.76185776 0.19792946 -0.27818617 -0.37661530 -0.05045995 -0.18124428 -4.66498469
Na 1.03176978 0.47313142 0.79828897 0.42936625 -0.59953863 0.86801110 -7.05840531
Na -0.26643122 1.28054299 1.11374839 0.15111135 -0.10112576 0.27637930 -4.67293423
Na -0.62214908 0.02244676 -1.38020420 0.18250135 0.23446373 -0.00492988 -3.40972231
Na 0.13996784 1.47079343 -0.38358558 -0.75364635 0.55362283 0.38385177 -7.06367629
Na 0.66571148 1.49058474 0.58871714 -0.09464102 0.28874267 0.28487129 -7.06473947
Na 1.03136324 0.47331886 0.80023193 -0.58049383 -0.18814020 0.02105895 -7.06620063
Na 1.79008947 1.44030011 -1.68897404 0.05408873 0.44037550 -0.61661771 -4.67506940
Na 1.76713335 0.20658867 0.01792710 0.60766287 -0.60414512 0.45439722 -7.06511305
Na 1.54156613 -0.49300167 -1.74930769 -0.17569654 0.14501354 -0.14377541 -3.41178739
Na 0.11401990 0.23344465 1.33227977 -0.50440219 0.04179712 -0.28540159 -4.67101363
Na 1.03136324 0.47331886 0.80023193 -0.58049383 -0.18814020 0.02105895 -7.06620063
Na 1.44943142 1.91930248 1.21531700 0.16422419 -0.05086797 0.07437307 -4.67459336
Na 2.57799928 0.60165339 0.63368126 0.10460672 -0.34344286 -0.48837510 -4.67091392
Na 2.71217768 0.41926999 -0.48171960 0.07538365 0.21090761 -0.02493230 -4.66939086
Na -0.17575664 2.15490466 0.40407241 -0.18951972 0.36840817 -0.03687982 -4.67900513
Na 1.03136324 0.47331886 0.80023193 -0.58049383 -0.18814020 0.02105895 -7.06620063
Na 2.08462218 -0.48279420 -0.76779231 -0.04282637 0.24460212 0.36494813 -4.67209369
Na 0.36952494 2.17255732 1.38713542 -0.27578881 -0.39873625 0.09373478 -3.41458670
Na 0.50877444 -1.23303462 0.10458067 -0.18021722 -0.47769330 0.03061016 -3.41086705
Na 1.17059364 1.85551927 -0.32056598 0.26273633 0.72167845 -0.22455212 -7.07952180
Na 0.73565630 -0.18094597 -0.04222959 -0.46658964 0.27420808 0.64549027 -7.05236325
Na 1.56560740 -0.85726101 0.16632592 0.18193261 0.35085082 0.10294217 -4.67056838
Na -0.19535898 -0.43887467 0.47358532 0.34380069 0.67976830 -0.39815443 -4.67398078
Na -0.88239923 0.38386095 0.82020040 0.28001300 0.02544567 0.37392773 -3.41070586
Na 1.24179548 0.18680315 -0.95238548 -0.09687608 -0.58722261 -0.22018695 -7.05487123
Na 1.03136324 0.47331886 0.80023193 -0.58049383 -0.18814020 0.02105895 -7.06620063
Na 0.73976995 1.13392214 1.61707980 -0.07603502 -0.05203417 -0.14990068 -4.67402042
Na 1.39965937 2.91614673 -0.46723412 -0.23368506 -0.75711097 0.21514987 -3.41364790
Na 0.05187468 0.61515568 0.31111577 0.12095950 -0.46196103 0.32941639 -7.06298182
Na 2.78757999 1.29976676 -1.19081473 -0.37575702 -0.51421468 0.52787089 -3.40764008
Na 2.17351519 0.39700805 -1.47517034 0.06587412 0.08896647 -0.26164672 -4.66924391
Na 1.86855527 -0.18716900 1.03316586 0.29972424 0.11081265 -0.65549061 -4.67654114
Na 2.61257596 -0.44782900 0.22703075 -0.19726235 0.04991793 0.05378465 -3.41276894
Na 1.72400118 1.23914939 0.40927329 0.03534089 -0.17611916 0.00285107 -7.06347753
Na 0.07385242 0.80564361 -1.79285504 0.15225202 -0.17599590 0.23038656 -4.66869186
Na 2.52676754 1.65300821 1.02250611 -0.31539357 0.09077124 -0.33581985 -3.41173405
Na 0.95254864 0.83598418 -0.18192774 0.17437302 1.21421287 0.02517219 -6.18746713
Na 1.11675385 0.09169651 1.81653746 -0.12353138 0.05972797 0.07762995 -3.41501403
Na 1.85389631 1.06352319 -0.67405063 -0.46830067 -0.24431420 0.17143995 -7.05387822
Na 0.17855180 0.43787725 -0.76983030 0.21143603 0.17126417 -0.58574639 -7.05360607
Na -0.06289080 -0.61430894 -0.64085958 -0.27195765 -0.46142548 0.03431828 -4.66934292
Na 0.81390639 -0.58382768 0.96874382 -0.20537012 0.29906370 0.04117513 -4.67518401
55
Lattice="20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 20.0" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 Energy=-47.004771 eV=T energy=-271.98434756440173 free_energy=-271.98434756440173 pbc="F F F"
Na 0.60847616 1.57304948 -2.15918216 0.02935884 0.30340471 -0.25957587 -3.40994230
Na 1.89991629 2.35951528 0.22405544 0.11250853 -0.24481932 -0.32304378 -4.66765922
Na 1.96588683 2.18495313 -0.90339487 -0.19576868 0.07920588 0.61714325 -4.67410599
Na 0.92447482 2.26601855 -1.32973974 0.10888343 0.34867097 0.00811991 -4.66756261
Na -0.81181131 2.01931325 -0.46538743 0.22159921 -0.35128421 -0.15320891 -3.41458461
Na 0.78824536 1.20245959 -1.15353993 -0.70052683 -0.52755489 0.63153939 -7.06207408
Na 2.62478684 1.59817841 -0.19056969 -0.20844618 -0.44072679 -0.69044790 -4.67003865
Na -0.74048564 0.97498645 -0.87837089 0.13809326 -0.24202702 -0.05930543 -4.66416486
Na 1.06647430 0.55912709 -1.98701768 -0.13603725 0.52210378 -0.91367765 -4.66656296
Na -0.10677917 1.80400299 -1.31985548 -0.22960041 -0.14150310 -0.17685501 -4.67707867
Na 0.43826267 -0.26656094 -1.54968001 -0.69044126 0.14634622 0.79195783 -4.67920458
Na -0.80714831 1.14323152 0.23937454 0.25755978 -0.35187070 0.10566544 -4.68055648
Na -0.72523260 0.08685913 -0.16686708 0.29510130 0.29609157 -0.16667535 -4.66367449
Na 1.12058986 0.47461001 0.79238455 0.23696402 1.04611935 -0.31433345 -7.06281949
Na -0.20666358 1.19679581 1.19710994 0.00210472 -0.12550409 -0.07459660 -4.67330017
Na -0.63884914 -0.07352586 -1.27852405 -0.05127966 0.16214707 -0.11806696 -3.41092431
Na 0.08828136 1.41517922 -0.32147109 -0.67119495 0.37188578 -0.20021281 -7.04843513
Na 0.67237505 1.47073375 0.61257934 0.66134312 -0.96660613 0.25063859 -7.05525650
Na 1.11052683 0.47594710 0.79367167 0.34030300 0.24895047 -0.40285535 -7.05521028
Na 1.65271028 1.49678429 -1.75074444 -0.19729721 0.04013173 0.85107778 -4.66801344
Na 1.81842622 0.26039029 -0.03977207 0.02293193 -0.75620097 0.03139671 -7.05704330
Na 1.51475232 -0.45096467 -1.79737753 0.59535151 0.25025368 0.16778921 -3.41204603
Na 0.25524702 0.18411036 1.38328189 -0.31684392 -0.78464817 -0.00239194 -4.66779575
Na 1.11052683 0.47594710 0.79367167 0.34030300 0.24895047 -0.40285535 -7.05521028
Na 1.46599359 1.94546967 1.18491977 0.25059955 0.13396091 0.33917376 -4.67478985
Na 2.64478930 0.70970390 0.50722566 0.00451595 -0.44010325 1.10305591 -4.66232040
Na 2.71229051 0.53591937 -0.60097928 0.32400496 0.23134169 -0.37257811 -4.66380864
Na -0.21696107 2.07917502 0.48615698 -0.82263103 0.22440801 0.15039530 -4.67200769
Na 1.11052683 0.47594710 0.79367167 0.34030300 0.24895047 -0.40285535 -7.05521028
Na 2.12913230 -0.40396129 -0.85231918 -0.44790965 0.21976042 0.32276202 -4.67432247
Na 0.37958826 2.12233087 1.43427268 0.50059533 0.25412397 0.02400734 -3.41117011
Na 0.66735724 -1.25750850 0.12008622 -0.49962068 -0.15754300 -0.14743100 -3.41093434
Na 1.09612972 1.87067650 -0.32711102 0.26542052 -0.42846187 -0.45893057 -7.04909263
Na 0.81135864 -0.19006284 -0.03202584 0.25742727 -0.10321832 -0.48671705 -7.06866884
Na 1.69340005 -0.81334217 0.11564879 0.34877529 0.42421479 0.06767719 -4.66666652
Na -0.06493816 -0.50965082 0.53465462 0.16951974 0.22882839 0.14100081 -4.67029268
Na -0.77653641 0.25947503 0.94118512 0.14591877 0.33294935 -0.05774587 -3.41405224
Na 1.23231196 0.20903579 -0.97402726 -0.56761611 -1.05974927 0.89797812 -7.06780503
Na 1.11052683 0.47594710 0.79367167 0.34030300 0.24895047 -0.40285535 -7.05521028
Na 0.84083990 1.11520906 1.63308020 -0.04790713 0.34717494 -0.55538747 -4.67334946
Na 1.24245082 2.93806950 -0.48037824 -0.19960752 -0.10617856 -0.31059143 -3.40925727
Na 0.10500983 0.55532775 0.37042221 -0.71660815 0.10207928 0.18345487 -7.07219715
Na 2.67726364 1.42305078 -1.30328197 0.45085254 -0.81123478 0.18210368 -3.41117032
Na 2.11099536 0.47815777 -1.55732216 0.17752619 0.17052152 -0.36277891 -4.67051296
Na 2.00984299 -0.12662671 0.96230942 0.64815331 0.06444889 -0.40253589 -4.66557325
Na 2.71419551 -0.34272434 0.10464735 -0.12982016 0.35412542 0.29306130 -3.40982302
Na 1.73575154 1.28717371 0.35995898 -0.31739298 0.46188997 -0.06168128 -7.05106164
Na -0.02300870 0.75225478 -1.73267236 0.12206459 -0.28228719 0.90652009 -4.67757455
Na 2.54497349 1.75489867 0.91918582 -0.10517761 -0.10822104 0.07110485 -3.40899046
Na 0.95477965 0.84175609 -0.18043685 -0.74679836 -1.45754823 0.28473031 -6.21745934
Na 1.29632366 0.10557380 1.80327640 0.03430427 -0.38441775 -0.35275957 -3.40803217
Na 1.80348303 1.11754672 -0.73042923 0.35638234 1.69498188 -0.66427745 -7.05846262
Na 0.16667010 0.39266637 -0.71477904 1.25191492 0.19520477 -1.62862904 -7.07367483
Na 0.00696135 -0.67327142 -0.58461978 0.17868496 -0.74310706 0.22434805 -4.66893633
Na 0.97611882 -0.58985602 0.97102927 0.14715717 0.10323691 -0.00524228 -4.66635841

Hello,

Superficially, it seems like this should be a drop-in replacement for ase.io.read/write that just moves the parsing into C for speed (which is great!). Are there any pitfalls or other considerations, however, to be aware of when replacing ase.io.read/write with libextxyz?

Thanks!

Add this code to LAMMPS, to allow an extxyz dump style! I think it would be absolutely great to allow for dumping for a more powerful variant, similar to the custom dump style there, but formatting it according to this extended xyz format.

As reported at libAtoms/ExtXYZ.jl#12, this file contains a typo in the Lattice and should give an error:

[essswb@mnf144 ExtXYZ]$ cat test.xyz
8
Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.05.44" Properties=species:S:1:pos:R:3 Time=0.0
Si        0.00000000      0.00000000      0.00000000
Si        1.36000000      1.36000000      1.36000000
Si        2.72000000      2.72000000      0.00000000
Si        4.08000000      4.08000000      1.36000000
Si        2.72000000      0.00000000      2.72000000
Si        4.08000000      1.36000000      4.08000000
Si        0.00000000      2.72000000      2.72000000
Si        1.36000000      4.08000000      4.08000000

However, it is read successfully but gives a strange cell:

[essswb@mnf144 ExtXYZ]$ python3
Python 3.7.4 (default, Mar 26 2020, 11:57:44)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import extxyz
>>> extxyz.read("test.xyz")
Atoms(symbols='Si8', pbc=True, cell=[[5.44, 0.0, 0.0], [0.0, 5.44, 0.0], [0.0, 0.05, 0.44]])

For this to be the case there must be an error in the parser, or even in the grammar.

The original fortran libAtoms extxyz comment line parser was the same as the fortran command line parser. It would be nice to restore this compatibility by making the new extxyz comment line parser usable for the command line passed to a (fortran, but anything, really) program. This requires refactoring the new extxyz code so that the part that parses the comment line can be called with a string. independently of the rest of it, just returning a dict like info.

For example how should software interpret the value in key="a b c"? It could be either a string containing multiple spaces a b c or a backward compatible array of three strings (["a", "b", "c"]).

I think the easiest resolution of this ambiguity is to limit quoted arrays to only integer/real/boolean values, the same way '{' arrays are limited to string values. All the extxyz files I've seen in the wild use arrays in this way, so backward compatibility should be preserved. Do you agree @jameskermode?

Hello,

For some reason, I am unable to install extxyz by simply
pip install extxyz
I get the error:

ERROR: Could not find a version that satisfies the requirement extxyz (from versions: none)
ERROR: No matching distribution found for extxyz

I then tried to pip install git+https://github.com/libAtoms/extxyz
but this subsequently fails looking for the ftp server for ftp.pcre.org. This also seems to be the case when I try to use the setup.py from the source code.

Is anyone else having this issue or knows how to resolve it? My pip is perfectly fine as I installed packages just before it, the only added item I can give is I am on WSL2.

I realized I was not very clear in my last email, so here is a separate issue, hopefully clearer.

I'm wondering about the possibility to round-trip string values, i.e. store some data in extended XYZ and then be able to read it again.

In particular, there is some ambiguity here between string values and backward compatible arrays. If the user asks to store the string 1 3 4 5 (with spaces inside) with the string key in an extended XYZ comment line, simply writing it as a key="1 3 4 5" is not enough, since that will be read later as an array of 4 integers. It is possible to use a single element {} array instead, i.e. write this as key={"1 3 4 5"}, which will then be read as intended by the parser. The example from my email was about a string containing a single number or boolean value (True/...) which can not be written directly as key="3", but the same applies for string that would look like arrays.

This means that any extended XYZ writer must check all string values to ensure they would parse back as string, and otherwise use the {} array trick to make sure the type of the value is preserved in the extended XYZ comment line.

Do you agree with my reading of the spec and is this the intended behaviour?

I fear it will make writing to extended XYZ a bit more complex, since now every software that needs to write to this format also needs to implement a (partial) parser for it; but I also understand this is allowed for backward compatibility reasons.

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