Incorrect Parsing of OSZICAR with VASP 6.3.2

[YunyeongChoi]

Python version

python 3.9.12

Pymatgen version

2024.3.1

Operating system version

Rocky Linux release 8.9

Current behavior

I know this is related to the VASP error, but thought worth reporting the issue.

In some static calculations using VASP version 6.3.2, when the energy difference (dE) is extremely small, OSZICAR writes the dE value incorrectly. This issue arises in cases where dE is not represented in scientific notation with a very small exponent. For instance:

1 F= -.16497036E+04 E0= -.16497036E+04 d E =-.302333-128 mag= 13.9998

Here, the correct representation of dE should be d E =-.302333E-128, but it is mistakenly written as -302333-128, which leads to parsing errors when attempting to read the outputs using Oszicar in pymatgen.

For instance, Error when I use Oszicar to read outputs:

from pymatgen.io.vasp.outputs import Oszicar
Oszicar('/home/yychoi/ts_static/0.0833_0.5833/4/2/OSZICAR')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[2], line 1
----> 1 Oszicar('/home/yychoi/ts_static/0.0833_0.5833/4/2/OSZICAR')

File ~/miniconda3/envs/mace/lib/python3.9/site-packages/pymatgen/io/vasp/outputs.py:3934, in Oszicar.__init__(self, filename)
   3931         elif line.strip() != "":
   3932             # remove space first and apply field agnostic extraction
   3933             matches = re.findall(ionic_general_pattern, re.sub(r"d E ", "dE", line))
-> 3934             ionic_steps.append({key: float(value) for key, value in matches})
   3936 self.electronic_steps = electronic_steps
   3937 self.ionic_steps = ionic_steps

File ~/miniconda3/envs/mace/lib/python3.9/site-packages/pymatgen/io/vasp/outputs.py:3934, in <dictcomp>(.0)
   3931         elif line.strip() != "":
   3932             # remove space first and apply field agnostic extraction
   3933             matches = re.findall(ionic_general_pattern, re.sub(r"d E ", "dE", line))
-> 3934             ionic_steps.append({key: float(value) for key, value in matches})
   3936 self.electronic_steps = electronic_steps
   3937 self.ionic_steps = ionic_steps

ValueError: could not convert string to float: '-.302333-128'

Expected Behavior

The OSZICAR file should correctly represent the energy difference in scientific notation, allowing for accurate parsing using Oszicar in pymatgen.

Or it will be great if pymatgen support exception-handling for these cases.

Minimal example

No response

Relevant files to reproduce this bug

   N       E                     dE             d eps       ncg     rms          rms(c)

DAV: 1 0.198644808263E+05 0.19864E+05 -0.76814E+05 7928 0.168E+03
DAV: 2 0.177691351143E+04 -0.18088E+05 -0.17054E+05 8024 0.484E+02
DAV: 3 -0.158070428665E+04 -0.33576E+04 -0.31537E+04 8544 0.214E+02
DAV: 4 -0.185134065799E+04 -0.27064E+03 -0.26453E+03 9944 0.651E+01
DAV: 5 -0.186458040528E+04 -0.13240E+02 -0.12993E+02 11408 0.140E+01 0.199E+02
RMM: 6 -0.171792907794E+04 0.14665E+03 -0.41106E+02 10187 0.207E+01 0.156E+02
RMM: 7 -0.186567247463E+04 -0.14774E+03 -0.57820E+02 11347 0.221E+01 0.179E+02
RMM: 8 -0.200888091592E+04 -0.14321E+03 -0.41272E+02 12538 0.179E+01 0.186E+02
RMM: 9 -0.172173427404E+04 0.28715E+03 -0.15493E+02 11854 0.119E+01 0.111E+02
RMM: 10 -0.172721147766E+04 -0.54772E+01 -0.12930E+02 11881 0.113E+01 0.120E+02
RMM: 11 -0.166575073031E+04 0.61461E+02 -0.65747E+01 11794 0.827E+00 0.977E+01
RMM: 12 -0.164740753637E+04 0.18343E+02 -0.32006E+01 12129 0.547E+00 0.902E+01
RMM: 13 -0.165350176003E+04 -0.60942E+01 -0.23500E+01 11251 0.461E+00 0.772E+01
RMM: 14 -0.163630171606E+04 0.17200E+02 -0.11769E+01 11244 0.367E+00 0.634E+01
RMM: 15 -0.163637944591E+04 -0.77730E-01 -0.79722E+00 11729 0.284E+00 0.666E+01
RMM: 16 -0.164663534176E+04 -0.10256E+02 -0.92111E+00 12202 0.295E+00 0.595E+01
RMM: 17 -0.164339719732E+04 0.32381E+01 -0.10554E+01 13078 0.333E+00 0.528E+01
RMM: 18 -0.163817383042E+04 0.52234E+01 -0.66205E+00 12744 0.277E+00 0.547E+01
RMM: 19 -0.163712705594E+04 0.10468E+01 -0.17954E+00 11950 0.205E+00 0.545E+01
RMM: 20 -0.163489256685E+04 0.22345E+01 -0.23296E+00 12214 0.173E+00 0.453E+01
RMM: 21 -0.163365787593E+04 0.12347E+01 -0.18720E+00 11993 0.143E+00 0.467E+01
RMM: 22 -0.163141557443E+04 0.22423E+01 -0.90062E-01 11655 0.111E+00 0.385E+01
RMM: 23 -0.163006244580E+04 0.13531E+01 -0.78896E-01 11753 0.103E+00 0.356E+01
RMM: 24 -0.163062486964E+04 -0.56242E+00 -0.27859E-01 12192 0.635E-01 0.358E+01
RMM: 25 -0.163063925046E+04 -0.14381E-01 -0.86328E-02 13600 0.381E-01 0.353E+01
RMM: 26 -0.163179352136E+04 -0.11543E+01 -0.37317E-01 13143 0.578E-01 0.344E+01
RMM: 27 -0.163191489821E+04 -0.12138E+00 -0.17332E-01 12543 0.523E-01 0.333E+01
RMM: 28 -0.163267026577E+04 -0.75537E+00 -0.18145E-01 12901 0.561E-01 0.323E+01
RMM: 29 -0.163262153019E+04 0.48736E-01 -0.29732E-02 11393 0.279E-01 0.323E+01
RMM: 30 -0.163257433804E+04 0.47192E-01 -0.80352E-03 13906 0.116E-01 0.323E+01
RMM: 31 -0.163278255682E+04 -0.20822E+00 -0.32646E-02 13066 0.173E-01 0.323E+01
RMM: 32 -0.163275490340E+04 0.27653E-01 -0.11181E-02 11316 0.168E-01 0.325E+01
RMM: 33 -0.163286732541E+04 -0.11242E+00 -0.28791E-02 13384 0.182E-01 0.319E+01
RMM: 34 -0.163283337826E+04 0.33947E-01 -0.21117E-02 12740 0.254E-01 0.321E+01
RMM: 35 -0.163320443626E+04 -0.37106E+00 -0.40264E-02 13666 0.215E-01 0.324E+01
RMM: 36 -0.163407413708E+04 -0.86970E+00 -0.39321E-01 15282 0.701E-01 0.414E+01
RMM: 37 -0.163382760380E+04 0.24653E+00 -0.12642E-01 13926 0.625E-01 0.363E+01
RMM: 38 -0.163390006478E+04 -0.72461E-01 -0.22931E-02 13255 0.259E-01 0.364E+01
RMM: 39 -0.163412675124E+04 -0.22669E+00 0.95263E-01 12973 0.332E-01 0.368E+01
RMM: 40 -0.163420021903E+04 -0.73468E-01 -0.11880E-01 12487 0.207E-01 0.368E+01
RMM: 41 -0.163419244801E+04 0.77710E-02 -0.87626E-03 11435 0.122E-01 0.368E+01
RMM: 42 -0.163422979439E+04 -0.37346E-01 -0.12047E-02 12961 0.121E-01 0.369E+01
RMM: 43 -0.163420973389E+04 0.20061E-01 -0.13444E-02 12503 0.200E-01 0.369E+01
RMM: 44 -0.163414792913E+04 0.61805E-01 0.16536E+00 10096 0.423E-01 0.369E+01
RMM: 45 -0.163431092130E+04 -0.16299E+00 -0.14911E-01 14545 0.210E-01 0.369E+01
RMM: 46 -0.163476010333E+04 -0.44918E+00 -0.48589E-02 15049 0.234E-01 0.367E+01
RMM: 47 -0.163553328218E+04 -0.77318E+00 -0.14279E-01 15271 0.389E-01 0.357E+01
RMM: 48 -0.163563315848E+04 -0.99876E-01 -0.59802E-02 14187 0.427E-01 0.357E+01
RMM: 49 -0.163680681603E+04 -0.11737E+01 -0.32732E-01 15673 0.653E-01 0.344E+01
RMM: 50 -0.163677475285E+04 0.32063E-01 -0.87467E-02 14518 0.508E-01 0.343E+01
RMM: 51 -0.164663442650E+04 -0.98597E+01 -0.34895E+00 15808 0.168E+00 0.505E+01
RMM: 52 -0.164373490958E+04 0.28995E+01 -0.75860E-01 15808 0.113E+00 0.413E+01
RMM: 53 -0.164374563210E+04 -0.10723E-01 -0.18761E-01 15598 0.580E-01 0.409E+01
RMM: 54 -0.164362725418E+04 0.11838E+00 0.51312E-01 15482 0.609E-01 0.405E+01
RMM: 55 -0.164192656489E+04 0.17007E+01 -0.28825E+00 15808 0.179E+00 0.398E+01
RMM: 56 -0.164037512926E+04 0.15514E+01 -0.15923E+00 15808 0.140E+00 0.349E+01
RMM: 57 -0.164064904725E+04 -0.27392E+00 -0.63695E-01 15775 0.819E-01 0.317E+01
RMM: 58 -0.164181445552E+04 -0.11654E+01 -0.29807E-01 15643 0.585E-01 0.304E+01
RMM: 59 -0.164243590281E+04 -0.62145E+00 -0.19136E-01 15629 0.461E-01 0.301E+01
RMM: 60 -0.164455757073E+04 -0.21217E+01 -0.13330E+00 15799 0.111E+00 0.353E+01
RMM: 61 -0.164747535058E+04 -0.29178E+01 -0.16120E+00 15808 0.140E+00 0.400E+01
RMM: 62 -0.164640894414E+04 0.10664E+01 -0.80572E-01 15804 0.109E+00 0.350E+01
RMM: 63 -0.164636500890E+04 0.43935E-01 -0.39001E-01 15497 0.679E-01 0.346E+01
RMM: 64 -0.164177603260E+04 0.45890E+01 -0.30958E+00 15751 0.137E+00 0.352E+01
RMM: 65 -0.164139491880E+04 0.38111E+00 -0.15321E-01 14624 0.416E-01 0.353E+01
RMM: 66 -0.162891181069E+04 0.12483E+02 -0.43915E+00 15799 0.182E+00 0.354E+01
RMM: 67 -0.162211815256E+04 0.67937E+01 -0.68494E-01 15553 0.804E-01 0.358E+01
RMM: 68 -0.161038008612E+04 0.11738E+02 -0.76532E-01 15598 0.765E-01 0.367E+01
RMM: 69 -0.161167553239E+04 -0.12954E+01 -0.48895E-02 13654 0.204E-01 0.366E+01
RMM: 70 -0.160826123439E+04 0.34143E+01 0.69323E-01 14348 0.510E-01 0.368E+01
RMM: 71 -0.160315436220E+04 0.51069E+01 -0.79457E-01 15773 0.960E-01 0.360E+01
RMM: 72 -0.160780389698E+04 -0.46495E+01 -0.29678E-01 15638 0.660E-01 0.350E+01
RMM: 73 -0.161087399804E+04 -0.30701E+01 -0.19747E+00 15808 0.148E+00 0.344E+01
RMM: 74 -0.161335160945E+04 -0.24776E+01 -0.37405E-01 15407 0.581E-01 0.360E+01
RMM: 75 -0.161429987608E+04 -0.94827E+00 -0.14368E-01 15253 0.386E-01 0.352E+01
RMM: 76 -0.162719321380E+04 -0.12893E+02 -0.23547E+00 15784 0.146E+00 0.332E+01
RMM: 77 -0.162651459802E+04 0.67862E+00 -0.72626E-01 15685 0.792E-01 0.312E+01
RMM: 78 -0.161661577101E+04 0.98988E+01 -0.17480E+00 15804 0.136E+00 0.286E+01
RMM: 79 -0.161617174415E+04 0.44403E+00 -0.38132E-01 15640 0.617E-01 0.278E+01
RMM: 80 -0.161847125020E+04 -0.22995E+01 -0.17959E-01 15119 0.414E-01 0.272E+01
RMM: 81 -0.163769475276E+04 -0.19224E+02 -0.11793E+01 15808 0.282E+00 0.207E+01
RMM: 82 -0.163808508584E+04 -0.39033E+00 -0.14110E+00 15767 0.115E+00 0.193E+01
RMM: 83 -0.163869413723E+04 -0.60905E+00 -0.15923E+00 15798 0.112E+00 0.186E+01
RMM: 84 -0.163867223477E+04 0.21902E-01 -0.41028E-01 15645 0.642E-01 0.190E+01
RMM: 85 -0.163628001934E+04 0.23922E+01 -0.70656E-01 15525 0.691E-01 0.195E+01
RMM: 86 -0.164384211906E+04 -0.75621E+01 -0.35842E+00 15725 0.142E+00 0.174E+01
RMM: 87 -0.164461357137E+04 -0.77145E+00 -0.52838E-01 15509 0.641E-01 0.179E+01
RMM: 88 -0.164508951612E+04 -0.47594E+00 -0.32836E-01 15543 0.619E-01 0.167E+01
RMM: 89 -0.164482299107E+04 0.26653E+00 -0.27492E-01 15552 0.446E-01 0.157E+01
RMM: 90 -0.164557977706E+04 -0.75679E+00 -0.11055E+00 15751 0.934E-01 0.166E+01
RMM: 91 -0.164662397320E+04 -0.10442E+01 -0.93234E-01 15802 0.102E+00 0.124E+01
RMM: 92 -0.164707700994E+04 -0.45304E+00 -0.31632E-01 15695 0.560E-01 0.118E+01
RMM: 93 -0.164786025912E+04 -0.78325E+00 -0.33197E-01 15743 0.544E-01 0.139E+01
RMM: 94 -0.164776008156E+04 0.10018E+00 -0.67764E-02 14862 0.322E-01 0.127E+01
RMM: 95 -0.164771121456E+04 0.48867E-01 -0.90430E-02 15371 0.305E-01 0.154E+01
RMM: 96 -0.164717268247E+04 0.53853E+00 -0.66085E-01 15788 0.772E-01 0.107E+01
RMM: 97 -0.164780314441E+04 -0.63046E+00 0.61314E-01 15768 0.118E+00 0.957E+00
RMM: 98 -0.164849902279E+04 -0.69588E+00 -0.56142E-01 15721 0.731E-01 0.789E+00
RMM: 99 -0.164885610645E+04 -0.35708E+00 -0.19920E-01 15577 0.454E-01 0.676E+00
RMM: 100 -0.164900111963E+04 -0.14501E+00 -0.32632E-01 15748 0.619E-01 0.598E+00
RMM: 101 -0.164904270183E+04 -0.41582E-01 -0.24735E-01 15667 0.465E-01 0.588E+00
RMM: 102 -0.164914185453E+04 -0.99153E-01 -0.96764E-02 15391 0.266E-01 0.588E+00
RMM: 103 -0.164926857571E+04 -0.12672E+00 -0.13624E-01 15665 0.357E-01 0.599E+00
RMM: 104 -0.164948846432E+04 -0.21989E+00 -0.13529E-01 15555 0.337E-01 0.620E+00
RMM: 105 -0.164961448544E+04 -0.12602E+00 -0.40922E-02 14662 0.181E-01 0.615E+00
RMM: 106 -0.164966536267E+04 -0.50877E-01 -0.68155E-02 15269 0.266E-01 0.632E+00
RMM: 107 -0.164963085216E+04 0.34511E-01 -0.37160E-02 14819 0.223E-01 0.591E+00
RMM: 108 -0.164964484846E+04 -0.13996E-01 -0.32480E-02 14598 0.177E-01 0.576E+00
RMM: 109 -0.164963730638E+04 0.75421E-02 -0.22548E-02 14309 0.137E-01 0.562E+00
RMM: 110 -0.164956162428E+04 0.75682E-01 -0.90666E-02 15298 0.317E-01 0.521E+00
RMM: 111 -0.164957619375E+04 -0.14569E-01 -0.96677E-02 15332 0.307E-01 0.497E+00
RMM: 112 -0.164951639304E+04 0.59801E-01 -0.70438E-02 15139 0.258E-01 0.453E+00
RMM: 113 -0.164953123883E+04 -0.14846E-01 0.56095E-01 14700 0.410E-01 0.431E+00
RMM: 114 -0.164950881622E+04 0.22423E-01 -0.80654E-02 14361 0.216E-01 0.421E+00
RMM: 115 -0.164951009060E+04 -0.12744E-02 -0.58988E-03 13210 0.707E-02 0.420E+00
RMM: 116 -0.164953181144E+04 -0.21721E-01 -0.11229E-01 15228 0.411E-01 0.449E+00
RMM: 117 -0.164954797556E+04 -0.16164E-01 -0.23704E-02 14123 0.146E-01 0.438E+00
RMM: 118 -0.164950748133E+04 0.40494E-01 -0.19638E-02 14639 0.148E-01 0.404E+00
RMM: 119 -0.164947843591E+04 0.29045E-01 -0.14496E-02 14059 0.104E-01 0.380E+00
RMM: 120 -0.164944866460E+04 0.29771E-01 0.13877E-01 14449 0.215E-01 0.348E+00
RMM: 121 -0.164941830903E+04 0.30356E-01 -0.12918E-01 15619 0.358E-01 0.262E+00
RMM: 122 -0.164942381233E+04 -0.55033E-02 -0.12248E-01 15485 0.325E-01 0.199E+00
RMM: 123 -0.164944182374E+04 -0.18011E-01 -0.43971E-02 14977 0.182E-01 0.174E+00
RMM: 124 -0.164944624200E+04 -0.44183E-02 0.20644E-02 14882 0.232E-01 0.157E+00
RMM: 125 -0.164945611208E+04 -0.98701E-02 0.51711E-02 14323 0.218E-01 0.145E+00
RMM: 126 -0.164947951843E+04 -0.23406E-01 -0.40665E-02 14748 0.189E-01 0.132E+00
RMM: 127 -0.164949597337E+04 -0.16455E-01 -0.10958E-02 13978 0.107E-01 0.124E+00
RMM: 128 -0.164951648727E+04 -0.20514E-01 -0.11687E-02 14174 0.133E-01 0.106E+00
RMM: 129 -0.164952430584E+04 -0.78186E-02 -0.48139E-03 13401 0.720E-02 0.983E-01
RMM: 130 -0.164946890420E+04 0.55402E-01 0.18535E+00 14308 0.509E-01 0.910E-01
RMM: 131 -0.164956807462E+04 -0.99170E-01 -0.18192E-01 14784 0.333E-01 0.774E-01
RMM: 132 -0.164959091547E+04 -0.22841E-01 -0.23069E-02 14142 0.163E-01 0.713E-01
RMM: 133 -0.164961216925E+04 -0.21254E-01 -0.49191E-02 14889 0.272E-01 0.689E-01
RMM: 134 -0.164962308082E+04 -0.10912E-01 -0.76141E-03 13632 0.120E-01 0.609E-01
RMM: 135 -0.164963584602E+04 -0.12765E-01 -0.27528E-02 14350 0.210E-01 0.579E-01
RMM: 136 -0.164964378533E+04 -0.79393E-02 -0.52900E-02 14911 0.281E-01 0.616E-01
RMM: 137 -0.164965540757E+04 -0.11622E-01 -0.11630E-02 13882 0.172E-01 0.445E-01
RMM: 138 -0.164965885436E+04 -0.34468E-02 -0.24515E-03 12768 0.579E-02 0.437E-01
RMM: 139 -0.164966555807E+04 -0.67037E-02 -0.68158E-03 13439 0.107E-01 0.416E-01
RMM: 140 -0.164967230790E+04 -0.67498E-02 -0.85762E-03 13579 0.114E-01 0.400E-01
RMM: 141 -0.164967740655E+04 -0.50986E-02 -0.99055E-03 13760 0.121E-01 0.415E-01
RMM: 142 -0.164968617990E+04 -0.87734E-02 -0.82142E-03 13417 0.111E-01 0.325E-01
RMM: 143 -0.164969197857E+04 -0.57987E-02 -0.28990E-03 12884 0.648E-02 0.292E-01
RMM: 144 -0.164969591097E+04 -0.39324E-02 -0.19865E-03 12613 0.541E-02 0.286E-01
RMM: 145 -0.164969933345E+04 -0.34225E-02 -0.15448E-03 12115 0.455E-02 0.282E-01
RMM: 146 -0.164970213421E+04 -0.28008E-02 -0.10671E-03 11601 0.372E-02 0.279E-01
RMM: 147 -0.164970418696E+04 -0.20527E-02 -0.62262E-04 10701 0.282E-02 0.277E-01
RMM: 148 -0.164970446503E+04 -0.27807E-03 -0.12564E-04 7700 0.149E-02 0.278E-01
RMM: 149 -0.164970218098E+04 0.22840E-02 -0.35097E-04 8782 0.268E-02 0.277E-01
RMM: 150 -0.164970040620E+04 0.17748E-02 -0.48094E-04 9010 0.249E-02 0.274E-01
RMM: 151 -0.164969589843E+04 0.45078E-02 -0.19693E-03 11457 0.505E-02 0.277E-01
RMM: 152 -0.164969558382E+04 0.31460E-03 -0.92287E-04 10227 0.323E-02 0.269E-01
RMM: 153 -0.164969264490E+04 0.29389E-02 -0.29034E-03 12156 0.596E-02 0.265E-01
RMM: 154 -0.164968762446E+04 0.50204E-02 -0.12807E-02 13511 0.134E-01 0.265E-01
RMM: 155 -0.164969011294E+04 -0.24885E-02 -0.33286E-03 12120 0.595E-02 0.250E-01
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1 F= -.16497036E+04 E0= -.16497036E+04 d E =-.302333-128 mag= 13.9998