gabor1
commented
1 year ago this is really an ASE question. you load up the EXTXYZ file into an ASE list of atoms objects, modify whatever property you want, and then write out the list as an EXTXYZ file again
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