Hi, when using Xdatcar from pymatgen I get an error apparently related to parsing the XDATCAR. Looks like for a few coordinates, the minus sign is separated by numbers to the left with no space in between…verified that in the XDATCAR, which is from VASP 6.5.0. Has anyone found a fix for this? Here is the error output:
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[11], line 1 ----> 1 xd = Xdatcar(‘/data1/projects/20250214-AN1-diffusivity/aimd/LiCoO2-ICSD-91773/supercell-441/train-mlff-m24Li-1100K-multistep-moresteps/rescale_job_HkbSpe/continue-from-800_850/rescale_job_OzRsDe/continue_from_900_950/refit-1100K/NVE-1000K/XDATCAR’) File ~/miniconda3/envs/pymatgen_ase_recent_1/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py:4204, in Xdatcar.init(self, filename, ionicstep_start, ionicstep_end, comment) 4202 preamble.append(line) 4203 elif line == “” or “Direct configuration=” in line: → 4204 p = Poscar.from_string(“\n”.join([*preamble, “Direct”, *coords_str])) 4205 if ionicstep_end is None: 4206 if ionicstep_cnt >= ionicstep_start: File ~/miniconda3/envs/pymatgen_ase_recent_1/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:403, in Poscar.from_string(data, default_names, read_velocities) 401 tokens = lines[ipos + 1 + i].split() 402 crd_scale = scale if cart else 1 → 403 coords.append([float(j) * crd_scale for j in tokens[:3]]) 404 if has_selective_dynamics: 405 selective_dynamics.append([tok.upper()[0] == “T” for tok in tokens[3:6]]) File ~/miniconda3/envs/pymatgen_ase_recent_1/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:403, in (.0) 401 tokens = lines[ipos + 1 + i].split() 402 crd_scale = scale if cart else 1 → 403 coords.append([float(j) * crd_scale for j in tokens[:3]]) 404 if has_selective_dynamics: 405 selective_dynamics.append([tok.upper()[0] == “T” for tok in tokens[3:6]]) ValueError: could not convert string to float: ‘-9.24461682-10.00739829’
Hey @kirklew, there were issues parsing XDATCARs for unaries in older versions of pymatgen, can you make sure you’re running a newer version of pymatgen first?
Also if you can share the XDATCAR, or a relevant snippet from it, I’ll try to reproduce the error and and submit a PR for it
Hi @Aaron_Kaplan , thanks so much for your reply.
I will definitely check that out, though I’m pretty sure its not that old a version.
I don’t seem to be able to upload attachments as a “new” user so is there another way to get the file to you. Also, its like 250 MB zipped…maybe I need to cut it down regardless?
Thanks much!
Kirk
Couple options: you can send me a DM, post a relevant snippet of the XDATCAR here as a code block, or post / submit the XDATCAR as an issue to pymatgen’s github
Hi Aaron
How is this XDATCAR, which reproduces the error for me?:
unknown system
1
11.229396 0.023689 0.646390
-5.626997 9.760219 0.091869
0.026928 -0.047380 14.914223
Li Co O
24 48 96
Direct configuration= 10
0.22763001 0.85377520 0.18961835
0.23334233 0.60268760 0.22140627
0.50370077 0.62726279 0.21664055
0.55570392 0.12729342 0.20142812
0.42630951 0.38742370 0.19587398
0.18758412 0.07065382 0.20016995
0.76951945 0.54923323 0.20581355
0.93323613 0.86470051 0.19297605
1.00278653 0.52461186 0.52874224
0.12289906 0.98539743 0.51715652
0.38611900 0.44577619 0.52680803
0.73933058 0.27417079 0.54740408
0.63708409 0.89095788 0.52304407
0.42731465 0.22590139 0.53652574
0.35038925 0.80980233 0.52880796
0.76216176 0.70970991 0.57220302
0.14622579 0.85857335 0.85677580
0.65733493 0.30658346 0.86336702
0.61784763 0.57672471 0.87922407
0.34667744 0.57327046 0.87354316
0.84392089 0.07418890 0.86502047
0.33368270 0.23405545 0.85899010
0.10498873 0.30592628 0.87884220
0.88748805 0.55432002 0.86510629
0.53596013 0.39383319 0.70198884
0.55366586 0.66311734 0.71696333
0.54274721 0.91088703 0.71740552
0.54417728 0.15168685 0.70685332
0.80473444 0.42248951 0.71153872
0.79999785 0.66138282 0.71067143
0.80371597 0.91614033 0.70526983
0.80913831 0.16691342 0.70586395
0.04207285 0.40114399 0.70974248
0.05835912 0.67057875 0.70118925
0.04830267 0.92142556 0.69971909
0.04319330 0.15216112 0.69867901
0.29453879 0.41794898 0.70289614
0.29790132 0.66243210 0.71625880
0.29882449 0.90475573 0.70691985
0.30619571 0.16020973 0.70279573
0.43457497 0.72718478 0.03690382
0.41884688 0.96486626 0.03016788
0.42646279 0.20436475 0.02943887
0.42215291 0.46971416 0.03241687
0.68622486 0.71299405 0.04125167
0.68507105 0.96660490 0.03021407
0.67877979 0.21628269 0.01518676
0.67162203 0.46114123 0.02191093
0.93164518 0.71765048 0.01916358
0.93053718 0.95284322 0.02482680
0.91800098 0.20627110 0.03882883
0.91962740 0.45309314 0.03049058
0.16874693 0.70481362 0.01973816
0.16887363 0.96347611 0.02045196
0.17548593 0.22412591 0.04229906
0.16976794 0.45726426 0.03579611
0.81514328 0.78397153 0.36899135
0.79990642 0.02855450 0.35300448
0.79431456 0.27485697 0.34422261
0.80820843 0.53651973 0.37058946
0.07303936 0.78978624 0.36093162
0.05535263 0.03207160 0.36383109
0.05857164 0.28669373 0.36062611
0.05808026 0.53055039 0.34787703
0.31667795 0.78414336 0.36544314
0.31387113 0.03981889 0.34924707
0.31027547 0.29271766 0.36519330
0.29897231 0.53497938 0.37435132
0.56440894 0.77800494 0.36138992
0.53608901 0.00927090 0.36920330
0.55692059 0.28583467 0.36275432
0.54445351 0.52265677 0.38200763
0.84086039 0.79020522 0.09476630
0.83198911 0.04760359 0.09681889
0.82165357 0.27692347 0.07837857
0.83524082 0.54478881 0.08728686
0.09416758 0.79491913 0.08896492
0.06373313 0.01633407 0.10406076
0.06529631 0.27467657 0.10601137
0.07310874 0.53269113 0.09059379
0.63817040 0.58237386 0.63537921
0.63990886 0.83084087 0.65363639
0.65206320 0.08964302 0.65037435
0.62722585 0.32372929 0.64088034
0.89306114 0.59013265 0.62962624
0.88363926 0.83979070 0.64448142
0.88692151 0.07435950 0.62857581
0.89641951 0.33612616 0.63028165
0.13994390 0.59436460 0.63878419
0.13594874 0.83864326 0.63495071
0.11838109 0.08441354 0.62824495
0.13450627 0.32796501 0.65368088
0.38534198 0.58915373 0.65285109
0.38854582 0.82716927 0.64471413
0.37873976 0.06961998 0.64060957
0.40612214 0.33025997 0.62786229
0.70924662 0.60620530 0.44747956
0.74136060 0.86415244 0.43062278
0.71394436 0.10825031 0.42516046
0.72202686 0.35166015 0.42220767
0.98198185 0.60309598 0.42504588
0.97380818 0.87087070 0.43648076
0.94471378 0.10605816 0.41723926
0.94335982 0.36535682 0.41058463
0.21586798 0.61654140 0.43021936
0.24090188 0.88276345 0.42543032
0.21573591 0.10356612 0.41939769
0.20792453 0.35967683 0.43935091
0.45485913 0.59919022 0.43718154
0.48452513 0.85969268 0.43832004
0.45634092 0.11734812 0.41734563
0.46641076 0.34883906 0.43498679
0.26976982 0.61865967 0.96736006
0.25478924 0.88041689 0.95417601
0.27349444 0.15065285 0.96125537
0.25579496 0.37934897 0.97191253
0.52167608 0.64735993 0.96729148
0.51022066 0.88589053 0.97564975
0.50498317 0.11925602 0.96159108
0.51735521 0.39001524 0.95740019
0.76556340 0.63478736 0.95372770
0.75837246 0.87943492 0.97249989
0.76278963 0.12404130 0.95426547
0.77147849 0.38624477 0.94977415
0.01382683 0.63307322 0.96635021
0.01551288 0.88323818 0.95820427
0.02123433 0.13763454 0.95966042
0.02641598 0.37434841 0.96410541
0.70804022 0.48446141 0.77059877
0.72128343 0.74048809 0.77592436
0.71711217 0.00240929 0.77604198
0.71058589 0.24794097 0.75614420
0.96058551 0.49765201 0.76905169
0.97515119 0.76240364 0.76799185
0.94603112 -0.00471359 0.78380709
0.94485832 0.22803930 0.77108820
0.19417538 0.47751468 0.78961282
0.20366196 0.74576739 0.78259292
0.20794202 0.99115929 0.76847655
0.20533889 0.23560273 0.76588805
0.45413622 0.47906139 0.77214226
0.45717671 0.74553938 0.78267066
0.44449482 0.98011903 0.77212923
0.44841161 0.22098856 0.78384543
0.90187522 0.69392692 0.30373519
0.89908211 0.95076417 0.29903389
0.88631807 0.19503041 0.28583227
0.89266758 0.45978436 0.28288147
0.16972564 0.70387659 0.29219349
0.14210190 0.95214083 0.30185230
0.15144967 0.20929396 0.28941708
0.15274819 0.45052943 0.29588341
0.40130495 0.68896391 0.29560116
0.39444094 0.94429525 0.28001858
0.39979217 0.22944069 0.28979505
0.40643370 0.46621299 0.29611089
0.64548904 0.68980350 0.29925066
0.63874143 0.95142779 0.30717645
0.61188917 0.18889572 0.30276962
0.64177555 0.45528599 0.30777267
0.32810335 0.80007068 0.09502046
0.33924137 0.05312884 0.09867931
0.31667662 0.27665386 0.10098106
0.33685957 0.56086064 0.10249255
0.60084021 0.78859768 0.10807503
0.57656316 0.06243628 0.09441478
0.56952465 0.29714999 0.09706308
0.57271855 0.54832331 0.09475617
Direct configuration= 20
0.23885661 0.85545215 0.18161529
0.22966776 0.59326957 0.21190577
0.50856962 0.63884351 0.20921887
0.54002177 0.11054416 0.20319362
0.41872875 0.36867968 0.19612536
0.18562531 0.07807695 0.19844288
0.77845886 0.56003606 0.19712379
0.90856395 0.86133215 0.19849583
1.01679777 0.53212293 0.52618958
0.13000078 0.98727063 0.52159210
0.38643043 0.44115656 0.52312622
0.74046329 0.27698378 0.54065969
0.65772697 0.90909268 0.52086053
0.42636070 0.21685109 0.54340375
0.35396170 0.80919676 0.52342667
0.75588465 0.70615166 0.56163347
0.12769569 0.84539102 0.86163972
0.63868953 0.29999624 0.85860814
0.62648149 0.57376067 0.88079434
0.36205681 0.59440282 0.86416995
0.84347135 0.08556974 0.86431812
0.32599193 0.23839071 0.86238707
0.10765061 0.31861655 0.88246294
0.90647754 0.56749721 0.86082321
0.53956461 0.39763130 0.70082756
0.55149371 0.65810877 0.71640358
0.54239723 0.90859936 0.71964367
0.54185273 0.14713936 0.70432043
0.80493429 0.42169200 0.70834233
0.80420426 0.65981360 0.71301690
0.81190878 0.92102272 0.70487469
0.80324163 0.16304772 0.70589133
0.04515813 0.40430186 0.71083538
0.05440603 0.66536674 0.70139924
0.04879893 0.91302113 0.70077295
0.04161005 0.15541759 0.70260617
0.28760534 0.41413373 0.70491396
0.29983225 0.65718149 0.71648885
0.29605435 0.90617402 0.70855955
0.30523477 0.15658588 0.70239342
0.43074439 0.72754958 0.03524031
0.41553517 0.96055728 0.03007788
0.42545618 0.20281368 0.02953989
0.42377537 0.47254648 0.03145432
0.68289566 0.71183550 0.03818072
0.68366508 0.96697364 0.02988283
0.67722267 0.21600044 0.01503919
0.67459744 0.46166222 0.02142763
0.92855111 0.72269633 0.01878150
0.93215367 0.96082700 0.02698431
0.91514038 0.20167710 0.03789993
0.92193858 0.45300622 0.02399409
0.17162143 0.70119558 0.01654289
0.16710379 0.96389125 0.01825051
0.17298774 0.22105983 0.04255247
0.17249781 0.46149488 0.03561392
0.81854868 0.78614117 0.37018843
0.79881696 0.03361004 0.35231680
0.79253087 0.27518225 0.34705799
0.81363023 0.54112667 0.37307115
0.07453298 0.78852483 0.36139207
0.05630539 0.03962741 0.36091543
0.06011286 0.28544658 0.36280141
0.05553212 0.52765405 0.34727359
0.31467519 0.78069641 0.36264717
0.30814742 0.03648560 0.34934411
0.31211920 0.29560865 0.36690309
0.30460081 0.54166235 0.37240917
0.56414101 0.77854222 0.36137906
0.53812121 0.01355349 0.36776658
0.55689580 0.28594489 0.36353018
0.54745381 0.52830874 0.38186789
0.84743597 0.77840763 0.09943654
0.82869712 0.03324939 0.09815004
0.83290193 0.28809234 0.08445468
0.83724377 0.53892477 0.08698477
0.09772567 0.79995822 0.08234318
0.07644816 0.02420070 0.10396044
0.07246568 0.27890135 0.10534976
0.07627295 0.52334019 0.08489604
0.63601280 0.57707028 0.65092580
0.64015248 0.83428737 0.65327474
0.64901027 0.09214096 0.64118159
0.62643874 0.31825661 0.63486987
0.88404077 0.58570273 0.63388243
0.88015265 0.83119682 0.64133094
0.88590773 0.07690678 0.63103367
0.89709794 0.33788877 0.63768929
0.13210817 0.58792810 0.64954498
0.14102646 0.85022135 0.63494096
0.12742650 0.08747865 0.62732351
0.12877868 0.31969495 0.64806910
0.39456866 0.59894431 0.63902604
0.38915218 0.82880380 0.64412588
0.37675543 0.06702445 0.63161670
0.40129587 0.33005371 0.63017417
0.70356079 0.60621423 0.44195800
0.73613305 0.86759116 0.43524228
0.71053998 0.11213331 0.42174424
0.71970864 0.36232066 0.43173397
0.98165766 0.60269187 0.42242588
0.97030240 0.85208148 0.44211299
0.96485466 0.11951782 0.42414123
0.94467786 0.36255448 0.41611582
0.21785481 0.61484548 0.43206828
0.25102677 0.88468622 0.42709666
0.21959596 0.11776826 0.42388414
0.20656622 0.36922249 0.44131594
0.46321553 0.59646706 0.44079885
0.48994627 0.86799623 0.44282519
0.45737994 0.11902712 0.41180243
0.45191715 0.35026539 0.43784427
0.26955627 0.61984134 0.96395846
0.25162763 0.87604115 0.95300501
0.26649635 0.15193530 0.96991063
0.25970438 0.36978926 0.97081870
0.52385947 0.64968093 0.96197930
0.51842853 0.89333622 0.97843445
0.48946828 0.11753454 0.95723614
0.50962429 0.38945870 0.95945084
0.76705976 0.63179939 0.95370433
0.76184458 0.88083258 0.97488917
0.76470499 0.13354152 0.95969410
0.76703203 0.39438763 0.94921872
0.00941404 0.62680622 0.96707780
0.01527241 0.87913836 0.94990479
0.01895737 0.14826938 0.96390183
0.01783824 0.36235031 0.96756563
0.70907769 0.49124020 0.77496958
0.71630453 0.73753051 0.78766701
0.71995931 -0.00447302 0.76600915
0.70290943 0.24732300 0.76640840
0.96562781 0.50297479 0.77010536
0.96905672 0.75492478 0.76693264
0.95655666 -0.01086567 0.78082002
0.95646161 0.21878786 0.77703326
0.20324062 0.47754045 0.79195260
0.19527755 0.74681290 0.77905515
0.20560842 0.99405124 0.76696845
0.20730409 0.24648824 0.76756170
0.46159337 0.48785338 0.77578606
0.45159966 0.73010185 0.78323774
0.43937321 0.98618172 0.78158163
0.44921369 0.22748235 0.77925677
0.90995110 0.69650409 0.29838505
0.90257131 0.94389394 0.29841242
0.87453190 0.20002013 0.28520688
0.89079561 0.45333317 0.28211454
0.16850639 0.69879182 0.29471895
0.12910445 0.93677479 0.29889867
0.15681246 0.21005386 0.29132972
0.15036210 0.45322372 0.29845669
0.39792686 0.69326173 0.29481124
0.38686546 0.94182916 0.28374384
0.40462925 0.22651417 0.28984713
0.40324064 0.47129318 0.29715966
0.64640627 0.69146677 0.29911700
0.62732130 0.94830730 0.31015784
0.61893826 0.17782215 0.30511343
0.64534217 0.45879220 0.30782806
0.32822466 0.79709858 0.09513080
0.33776783 0.04762165 0.09380380
0.31972050 0.27701818 0.10304208
0.33715061 0.55460354 0.10828388
0.59856750 0.78904935 0.10003265
0.57647584 0.05908233 0.09500071
0.57495626 0.29868619 0.09507485
0.57767448 0.54157095 0.09320561
Direct configuration=30
0.51163844 0.58046753 0.18234814
5.82808788 3.54517856 0.18172823
2.45025367 -0.71280508 0.19892265
2.10930349 0.46146234 0.18439601
-1.68874936 -6.14753249 0.18735395
0.65241264 0.07598806 0.20251400
-3.86474534 -5.99299934 0.20132227
-1.10240819 -3.00236673 0.21075616
-1.11684206 7.62872249 0.53675090
-0.49211057 2.25898096 0.53011703
0.32991886 -0.53364685 0.55007695
-1.91319000 -3.90018608 0.54467731
-1.24370616 1.25535188 0.54302551
-4.69574132 -2.19593515 0.52947138
0.53015502 -1.23343320 0.52449508
-0.17575027 1.04305092 0.54177175
-7.49736533 -4.65356280 0.86721406
-1.08240106 0.83233534 0.86649901
-3.93188216 -3.60166556 0.86177030
-4.88527815 -4.84503847 0.87129431
-9.24468158 -9.98254155 0.88410189
-12.65153410 -0.10677269 0.87029345
-10.21720366 -4.60115912 0.88297836
-4.51593963 -3.28596821 0.86535916
0.09178516 -0.08776133 0.69579005
0.09853683 0.16763287 0.70242419
0.11373484 0.43974794 0.68185422
0.11100355 -0.32145015 0.70779142
0.35308617 -0.07816822 0.69268952
0.34640469 0.16494777 0.70489530
0.35092451 0.41449402 0.70528118
0.36354348 -0.31935915 0.68725070
-0.39439680 -0.06705666 0.69990882
-0.39848803 0.18485597 0.70365718
-0.39013327 0.43117539 0.70169399
-0.39317546 -0.33268811 0.69203104
-0.14160906 -0.08033540 0.69747131
-0.13447360 0.18290521 0.69810803
-0.14592008 0.42439085 0.69635664
-0.14405867 -0.32227706 0.70435414
0.81526840 0.60814000 0.03540485
0.79946931 0.84386296 0.04373876
0.80502525 0.10919215 0.04193071
0.80648020 0.33927240 0.03095451
1.06181027 0.59481808 0.03818544
1.06157829 0.85303114 0.04200737
1.02608517 0.08395782 0.04405921
1.06012686 0.33838132 0.03287568
1.30597445 0.59423371 0.03348919
1.31018623 0.85057831 0.02528468
1.28746621 0.10210656 0.01945993
1.29955317 0.35001579 0.02510322
0.55044334 0.59590617 0.01319444
0.56657578 0.84915951 0.04098368
0.55536305 0.12006607 0.02942682
0.55138168 0.36747884 0.03122369
1.21438127 1.62868891 0.36545395
1.20533765 0.87895803 0.37340377
1.21903690 1.12424563 0.37767725
1.21521104 1.36724010 0.35572263
0.45225737 1.62050329 0.35217804
0.46207871 0.87221065 0.37763852
0.44758614 1.11437600 0.37486604
0.45857672 1.36495139 0.36416544
0.69333524 1.61233580 0.37146886
0.69973431 0.86656064 0.36383791
0.69770304 1.12278584 0.37629693
0.71155213 1.36904366 0.36135419
0.97187881 1.62181563 0.36546145
0.95872586 0.87472144 0.36765953
0.94488460 1.11878817 0.36400303
0.96629186 1.36968562 0.37006824
1.22815623 0.66837551 0.09903372
1.22410453 -0.07009190 0.09307479
1.21141707 0.17509604 0.09658563
1.21950307 0.41371463 0.09304127
0.45687823 0.66585081 0.09613174
0.48286674 -0.05176303 0.10524739
0.46086037 0.19623239 0.09409336
0.46312328 0.44519648 0.08608675
0.17978981 0.07198906 0.63435889
0.18096169 0.32757954 0.62611145
0.21276779 -0.39556373 0.62127563
0.18797446 -0.16796310 0.62929748
0.45831188 0.10135621 0.63120172
0.43098431 0.33133596 0.63944575
0.43614731 -0.41648254 0.63533135
0.45952004 -0.14398646 0.63448015
-0.29827175 0.10703823 0.63440494
-0.30871937 0.34829530 0.63263182
-0.29354824 -0.40001960 0.62642058
-0.30556004 -0.14982582 0.62681774
-0.05367090 0.07403428 0.63026684
-0.06861983 0.34213972 0.63751888
-0.05051835 -0.41033856 0.63875594
-0.06430565 -0.16575373 0.63595315
1.14221383 1.45481841 0.41512030
1.12319521 1.70851254 0.44887492
1.10804798 0.96092095 0.43695706
1.12626241 1.20591098 0.43023946
1.38900266 1.45931206 0.43028029
1.35952749 1.69198292 0.43867025
1.37372006 0.95811920 0.45026626
1.36433908 1.19674273 0.43460948
0.61466363 1.44384268 0.43450161
0.60249159 1.68926142 0.42953262
0.61521121 0.95170006 0.44447219
0.62265787 1.20089184 0.45645606
0.87429930 1.44234971 0.43476370
0.87437184 1.69459583 0.42627445
0.86442856 0.96141207 0.43078397
0.86710103 1.19204030 0.43076095
0.63333925 0.51322204 0.94599733
0.64510160 0.77236861 0.96308535
0.65984831 0.03722990 0.97398268
0.65409463 0.28123142 0.96085368
0.90815384 0.52283472 0.97436786
0.89172401 0.76400293 0.97396849
0.87695724 0.00351573 0.97254390
0.89244193 0.25699897 0.96597444
1.14476487 0.51011941 0.97039856
1.15119911 0.76689905 0.98033552
1.10823992 0.01042544 0.97039209
1.13033453 0.25268039 0.96460518
0.38433741 0.51594610 0.94955714
0.41259298 0.77325350 0.96600277
0.36094156 0.00158765 0.96874615
0.38208594 0.27463282 0.96220863
0.26417537 -0.00872318 0.76872090
0.25794956 0.24646478 0.76765113
0.25360519 -0.51397079 0.75537573
0.28586215 -0.24723448 0.76793757
0.51820968 0.02202672 0.77908872
0.50264071 0.24451260 0.76684524
0.50589385 -0.50856669 0.77300514
0.52648288 -0.24379537 0.75788904
-0.23512095 0.00078643 0.76379776
-0.23078786 0.26039960 0.76644708
-0.22860465 0.50482594 0.76501352
-0.22387550 -0.23885205 0.76866445
0.01200813 -0.00529452 0.76714557
0.01435285 0.25972757 0.75653784
0.01329586 0.51283401 0.76130620
0.02434804 -0.22720857 0.76476461
1.29884424 1.54728059 0.29388236
1.29226788 1.80727859 0.30172056
1.29839815 1.03140257 0.30545926
1.31963478 1.29299518 0.28721483
0.55684348 1.54628264 0.28931262
0.52765981 1.79071745 0.29191719
0.55044897 1.04722700 0.30637566
0.53003448 1.28012408 0.29825138
0.79724992 1.53869128 0.31139683
0.79452029 1.79072931 0.29800478
0.78640518 1.03595355 0.30869946
0.80192296 1.27913988 0.30186160
1.06791136 1.53934601 0.29631388
1.05691789 1.80446251 0.30309009
1.05395489 1.04024430 0.29215401
1.05739269 1.30081791 0.30733349
0.69521774 0.66568009 0.09734075
0.70848062 -0.07093332 0.11110180
0.71755962 0.19437097 0.10331056
0.70643984 0.42643763 0.08284622
0.96339535 0.67026709 0.10316293
0.96160851 -0.07203215 0.11303273
0.96417284 0.17725481 0.10476758
0.97073578 0.42973772 0.09492409
Direct configuration=40
0.54817033 0.61202428 0.17888002
5.83445270 3.53621363 0.18177156
2.44046539 -0.72690991 0.20304626
2.09713395 0.45823345 0.18694448
-1.68386737 -6.14359989 0.19594184
0.63664528 0.05471403 0.20881434
-3.86145819 -5.98608530 0.19086592
-1.09156572 -3.00131997 0.20328265
-1.11903817 7.62671631 0.53235968
-0.50177457 2.23764992 0.53384626
0.33162455 -0.53229079 0.53729832
-1.91162417 -3.90419684 0.54313918
-1.25755727 1.24142180 0.54313810
-4.68212776 -2.18245435 0.52933287
0.54248525 -1.21663581 0.53435578
-0.17377474 1.02671873 0.55291695
-7.49790972 -4.63620813 0.85913289
-1.08360686 0.82987134 0.86046644
-3.92905064 -3.61028604 0.86607767
-4.87273522 -4.84631238 0.87897387
-9.24461682-10.00739829 0.88276947
-12.63684997 -0.08228373 0.86119960
-10.23032481 -4.61247954 0.87403308
-4.52469306 -3.29807073 0.86770612
0.09305726 -0.09034005 0.69477155
0.09882447 0.16368235 0.70272286
0.11403924 0.43869281 0.68049946
0.11549972 -0.31752478 0.70917918
0.35443132 -0.07554414 0.69117531
0.33921076 0.16083433 0.70399505
0.35098282 0.41329622 0.70549891
0.36234152 -0.32159270 0.68911271
-0.39194832 -0.06774128 0.69885255
-0.40023832 0.18137127 0.70419028
-0.39099841 0.43055232 0.70108818
-0.39116295 -0.33824099 0.68823838
-0.14455557 -0.08066146 0.69895061
-0.13807907 0.17991013 0.70132249
-0.14466760 0.42861858 0.69354973
-0.14484935 -0.32289681 0.70484346
0.81364086 0.60678337 0.03241454
0.79827790 0.84022166 0.03657327
0.80395244 0.11341750 0.04489970
0.80258758 0.34124812 0.03049352
1.05642954 0.59328599 0.03681161
1.06086522 0.84405749 0.04391000
1.03202319 0.08963625 0.04259147
1.06047092 0.33465008 0.03306279
1.31332618 0.60298172 0.03284053
1.31201513 0.84929197 0.02707901
1.28695185 0.10219557 0.02201802
1.29927614 0.34991377 0.02599181
0.55328166 0.60360035 0.01446002
0.56469301 0.85327301 0.04030768
0.56151172 0.11923405 0.02801682
0.55786129 0.36746002 0.02580054
1.20729090 1.62596658 0.36443690
1.19777946 0.87511775 0.37542794
1.20852212 1.12021676 0.37901282
1.21896299 1.36781996 0.35320090
0.45112504 1.62106616 0.35601745
0.45346405 0.86555336 0.37459177
0.44990253 1.11490016 0.37227397
0.45854046 1.36352543 0.36376055
0.69892076 1.61661160 0.37445268
0.70370856 0.86815499 0.36659428
0.70021788 1.12689070 0.37636973
0.71615019 1.37054528 0.36516428
0.96972337 1.62132603 0.36167376
0.95541198 0.87460046 0.36916854
0.94215552 1.11427107 0.36456957
0.96645388 1.36935495 0.37202164
1.23959671 0.67991881 0.10230575
1.21852103 -0.07319132 0.09700157
1.20719906 0.17101682 0.09559361
1.21712756 0.41613951 0.09355969
0.46258051 0.67322420 0.09311990
0.47089140 -0.06116726 0.10469613
0.46688027 0.20184586 0.09476590
0.45924457 0.43530682 0.08822431
0.18898345 0.08041344 0.63470605
0.17601875 0.33182244 0.63119893
0.19445779 -0.40612371 0.62470511
0.20294381 -0.15781009 0.63196455
0.44636952 0.09148745 0.63464248
0.44982603 0.34053208 0.63260143
0.43993906 -0.41342101 0.63489919
0.46434195 -0.13494235 0.62654502
-0.30530588 0.10189258 0.63371246
-0.30131737 0.34090706 0.63316624
-0.30456045 -0.40872924 0.63291426
-0.30331496 -0.15458201 0.62623234
-0.06149264 0.08031583 0.63526975
-0.07145903 0.33591314 0.63601032
-0.03752942 -0.40359600 0.63876327
-0.05246943 -0.15570390 0.62464402
1.13580410 1.45793309 0.41949332
1.12234658 1.70804153 0.44562968
1.10144675 0.95596886 0.43802781
1.13472090 1.21372710 0.42533984
1.38200348 1.45381206 0.43241959
1.35465593 1.68327848 0.43708599
1.37032702 0.94882342 0.44871664
1.38077016 1.20981132 0.43546886
0.61454754 1.43555785 0.43556995
0.60466454 1.68689124 0.43946831
0.61314634 0.94557450 0.44095320
0.62282523 1.20434204 0.44770881
0.86643269 1.43833551 0.43781252
0.87434594 1.68627985 0.42435414
0.86957325 0.95536244 0.43436577
0.85991668 1.19354800 0.42854513
0.63313762 0.51941005 0.94491251
0.65738243 0.78277420 0.96349183
0.65930494 0.02871223 0.97210600
0.65774929 0.28931317 0.95990564
0.90747699 0.52421461 0.97196312
0.90330531 0.77410095 0.97695806
0.88654282 0.01637594 0.96975703
0.89502851 0.25837486 0.96835272
1.14582608 0.50678545 0.96557972
1.14429699 0.75495877 0.98451169
1.12088853 0.01729490 0.97170968
1.13581036 0.26572599 0.96432703
0.39053013 0.52790986 0.95193074
0.41356819 0.77101289 0.96706221
0.36593728 0.00654925 0.95981734
0.39338896 0.27895725 0.95448784
0.26397767 -0.00528117 0.76516829
0.25588611 0.23982042 0.76355829
0.25556998 -0.49664598 0.76197045
0.28154862 -0.24075476 0.75330550
0.51461291 0.01557093 0.77653938
0.50455862 0.24574482 0.76922435
0.52132255 -0.49997925 0.77078850
0.51687246 -0.25107438 0.75549288
-0.23557290 0.00254273 0.76204345
-0.23274884 0.26337056 0.76940413
-0.23646133 0.49558334 0.76696076
-0.22079469 -0.24036681 0.76800343
0.00065352 -0.00561814 0.76462129
0.02134590 0.27513527 0.75653465
0.02371322 0.50579205 0.75913260
0.01504526 -0.23623614 0.77105982
1.30417447 1.55142379 0.29298608
1.29336438 1.80974997 0.31043441
1.30309706 1.03349696 0.30414969
1.31043706 1.29142607 0.29616467
0.54791787 1.55063379 0.29927009
0.53201409 1.79323718 0.30241014
0.55406433 1.05048674 0.30836279
0.52826644 1.28730793 0.29888870
0.78944657 1.52687635 0.31214589
0.79306191 1.79827817 0.29977038
0.78325160 1.03455809 0.30654570
0.81783982 1.29532293 0.30876449
1.06211370 1.53950924 0.30295100
1.05726319 1.80546090 0.30277636
1.04479912 1.04108561 0.29375349
1.05122629 1.30746807 0.30382745
0.69672553 0.67340502 0.09994608
0.71912407 -0.06362184 0.11660733
0.70339405 0.18670426 0.10227890
0.70590458 0.42732417 0.08836199
0.94832746 0.66793903 0.11237440
0.96273990 -0.07440730 0.11003209
0.95809031 0.17083289 0.10344434
0.96867151 0.42373580 0.08596164
Oh also, I updated to most recent pymatgen but no change in behavior.
Thanks, @kirklew. Confirming it was indeed the parsing of malformed floats. A fix was merged into pymatgen - you can pip install directly from the github repo until the next pymatgen release