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Dear VASP team and forum members,

I am encountering an issue when trying to run a molecular dynamics (MD) simulation with my system. The electronic structure of the initial configuration converges properly, and I am using the associated WAVECAR for restarting.

However, after starting the MD, the calculation fails with NaN values in the output:
running 448 mpi-ranks, on 4 nodes
distrk: each k-point on 448 cores, 1 groups
distr: one band on 28 cores, 16 groups
vasp.6.4.2 20Jul23 (build Apr 19 2024 10:32:06) complex
POSCAR found type information on POSCAR CeO NiC H
POSCAR found : 5 types and 74 ions
Reading from existing POTCAR
scaLAPACK will be used
Reading from existing POTCAR
LDA part: xc-table for Pade appr. of Perdew
found WAVECAR, reading the header
number of bands has changed, file: 384 present: 352
trying to continue reading WAVECAR, but it might fail
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ... GRIDC
FFT: planning ... GRID_SOFT
FFT: planning ... GRID
reading WAVECAR
the WAVECAR file was read successfully
initial charge from wavefunction
prediction of wavefunctions initialized - no I/O
entering main loop
N E dE d eps ncg rms rms(c)
DAV: 1 -0.527568627644E+03 -0.52757E+03 -0.81138E+02 8032 0.609E+01
DAV: 2 -0.540560574349E+03 -0.12992E+02 -0.12975E+02 8496 0.216E+01 0.426E+00
RMM: 3 -0.541024279373E+03 -0.46371E+00 -0.51897E+00 6952 0.622E+00 0.400E+00
RMM: 4 -0.541319483494E+03 -0.29520E+00 -0.32932E+00 8298 0.232E+00 0.382E+00
RMM: 5 -0.541398151909E+03 -0.78668E-01 -0.85378E-01 8734 0.108E+00 0.354E+00
RMM: 6 -0.541419207433E+03 -0.21056E-01 -0.28110E-01 8848 0.636E-01 0.281E+00
RMM: 7 -0.541431974964E+03 -0.12768E-01 -0.17055E-01 8361 0.635E-01 0.113E+00
RMM: 8 -0.541438457288E+03 -0.64823E-02 -0.68590E-02 8766 0.311E-01 0.816E-01
RMM: 9 -0.541432934412E+03 0.55229E-02 -0.26985E-02 8210 0.244E-01 0.453E-01
RMM: 10 -0.541432346220E+03 0.58819E-03 -0.34306E-02 8602 0.255E-01 0.251E-01
RMM: 11 -0.541432482007E+03 -0.13579E-03 -0.45541E-03 8338 0.100E-01 0.213E-01
RMM: 12 -0.541432104582E+03 0.37743E-03 -0.21683E-03 7979 0.777E-02 0.143E-01
RMM: 13 -0.541432004552E+03 0.10003E-03 -0.34869E-03 8616 0.831E-02 0.855E-02
RMM: 14 -0.541432040614E+03 -0.36063E-04 -0.71923E-04 8264 0.379E-02 0.736E-02
RMM: 15 -0.541432044817E+03 -0.42031E-05 -0.39131E-04 8134 0.305E-02 0.545E-02
RMM: 16 -0.541432055486E+03 -0.10669E-04 -0.27745E-04 8119 0.252E-02 0.385E-02
RMM: 17 -0.541432069575E+03 -0.14088E-04 -0.10809E-04 6630 0.162E-02 0.352E-02
RMM: 18 -0.541432071658E+03 -0.20838E-05 -0.81830E-05 7320 0.199E-02 0.208E-02
RMM: 19 -0.541432079161E+03 -0.75029E-05 -0.37040E-05 6119 0.854E-03 0.177E-02
RMM: 20 -0.541432080762E+03 -0.16008E-05 -0.12172E-05 4571 0.745E-03 0.161E-02
RMM: 21 -0.541432083454E+03 -0.26915E-05 -0.94331E-06 4637 0.631E-03 0.137E-02
RMM: 22 -0.541432084720E+03 -0.12662E-05 -0.56463E-06 3932 0.564E-03 0.117E-02
RMM: 23 -0.541432085388E+03 -0.66843E-06 -0.36501E-06 3666 0.539E-03
1 T= NaN E= NaN F= -.54772306E+03 E0= -.54772262E+03 EK= NaN SP= 0.00E+00 SK= 0.00E+00 mag= 4.000
bond charge predicted

and the following error message in the stderr file:

I have tested the same setup with VASP 5.4.4 and encountered the same issue.

Below are the input files (INCAR, KPOINTS, and POSCAR) I am using:
SYSTEM = 3CO2gas + 3H2gas + Ni6/CeO2-x

Start parameter for this run:
ISTART = 1 ! start job from scratch (see INIWAV)

Electronic relaxation:
ENCUT = 415.0 ! Cutoff energy for plane waves basis set in eV
ALGO = F
LSUBROT = .FALSE.
NELMIN = 8 ! Minimum number of eletronic selfconsistency (SC) steps
NELM = 1000 ! Maximum number of electronic SC steps
NELMDL = 2 ! Number of NON-SCF steps (SHOULD be NEGATIVE)
EDIFF = 1E-6 ! Global-break condition for the electronic SC-loop (ELM)
#IMIX = 1
AMIX = 0.050
BMIX = 0.0001
AMIX_MAG = 0.20
BMIX_MAG = 0.0001

Calculation mode:
PREC = Medium ! Calculation level (Changes FFT-grids)
ISPIN = 2 ! spin-polarized calculations
MAGMOM = -1 0 -1 1 0 -1 68*0
##NUPDOWN = 16
LMAXMIX = 6 ! PAW flag
ADDGRID = .TRUE. ! PAW flag
LASPH = .TRUE. ! PAW flag
ISYM = 0
###POMASS = 196.966 196.966 196.966 196.966

#PBE+U calculation:
LDAU = .TRUE.
LDAUTYPE = 2
LDAUL = 3 -1 -1 -1 -1
LDAUU = 4.50 0.00 0.00 0.00 0.00
LDAUJ = 0.00 0.00 0.00 0.00 0.00
LDAUPRINT = 0

Integration over the Brillouin zone (BZ):
ISMEAR = 0 ! Gaussian smearing
SIGMA = 0.05

Ionic relaxation:
NSW = 1000 ! Number of ionic steps
EDIFFG = -0.01 ! stop if all forces are smaller than |EDIFFG|
MDALGO = 2
IBRION = 0
##IWAVPR = 11
ISIF = 2 ! Calculate FORCE and Relax Ions
POTIM = 0.2
TEBEG = 673
TEEND = 673
SMASS = 0
LREAL = Auto
NBLOCK = 10
LREAL = Auto
LDIAG = T

Van der Waals Correction
vdW-D3

IVDW=11

DOS calculation:
LORBIT = 11 ! Calculate the DOS without providing the Wigner Seitz radius
NEDOS = 3001 ! Number of points to calculate the DOS

VASP OUTPUTs
NWRITE = 2 ! Determines how much information will be written in OUTCAR
LCHARG = .TRUE.
LWAVE = .TRUE.

Key for parallel mode calculation:
NPAR = 16 ! Con 64 proc NPAR = 8 con 32 NPAR = 4
EOF

3H2gas + 3CO2gas + Ni/CeO2-x
1.00000000000000
11.6354420844246391 0.0000000000000000 0.0000000000000000
5.8177210422123204 10.0765884293742989 0.0000000000000000
0.0000000000000000 0.0000000000000000 34.7501493397576482
Ce O Ni C H
18 41 6 3 6
Selective dynamics
Direct
0.2191390473919385 0.2228710803232625 0.5479490009294556 T T T
0.2149807945088874 0.8918754632515161 0.5437044433922749 T T T
0.5478194797553833 0.5626130831703398 0.5424129704400478 T T T
0.8871510166761172 0.8888394106711714 0.5468054966121294 T T T
0.2133422057283126 0.5606597796296057 0.5435153126185500 T T T
0.5493099911413073 0.2142756384282381 0.5451368502405007 T T T
0.5617574329604071 0.8889869346736535 0.5445451457467417 T T T
0.9073521932796682 0.2146730543854734 0.5427189041372231 T T T
0.8949035733324675 0.5516094473651856 0.5446644684521683 T T T
0.1111111111111143 0.1111111111111143 0.4544352141404744 F F F
0.1111111111111142 0.4444444444444430 0.4544352141404744 F F F
0.1111111111111142 0.7777777777777789 0.4544352141404744 F F F
0.4444444444444429 0.1111111111111143 0.4544352141404744 F F F
0.4444444444444430 0.4444444444444430 0.4544352141404744 F F F
0.4444444444444428 0.7777777777777789 0.4544352141404744 F F F
0.7777777777779312 0.1111111111111143 0.4544352141404744 F F F
0.7777777777777785 0.4444444444444430 0.4544352141404744 F F F
0.7777777777777790 0.7777777777777789 0.4544352141404744 F F F
0.1163432527811895 0.1092323999285409 0.5209238024368454 T T T
0.0107136591323814 0.0059314095953497 0.5684224476788432 T T T
0.1163127105192256 0.4418767193256078 0.5218345647160829 T T T
0.9920509903182404 0.3364868517133157 0.5687139815121348 T T T
0.1133486308680512 0.7771942095812573 0.5201099624493960 T T T
0.0030755305743033 0.6546489438314633 0.5677562721769261 T T T
0.4399790184562261 0.1079458918499596 0.5227300873047394 T T T
0.3340332721995817 0.9884597964867887 0.5787811611327114 T T T
0.4412794957883194 0.4468080846330322 0.5214481627894423 T T T
0.3407875851902922 0.3668421047916488 0.5831080252375184 T T T
0.4427041606502383 0.7827393498120899 0.5221620021099215 T T T
0.3025381996542723 0.6835434955777521 0.5711272244242914 T T T
0.7728137693528538 0.1333391796913031 0.5264819518324440 T T T
0.6592152208463989 0.9890744167035229 0.5694492302064498 T T T
0.7751499387544799 0.4374282677467013 0.5233421701045757 T T T
0.7743584589077404 0.7704213991198059 0.5208389048143924 T T T
0.6832723856388281 0.6645958539656868 0.5759035759473404 T T T
0.0000000000000000 0.0000000000000000 0.4316528212107116 F F F
0.2222222222222215 0.2222222222222215 0.4772176070702372 F F F
0.0000000000000000 0.3333333333333358 0.4316528212107116 F F F
0.2222222222222214 0.5555555555555571 0.4772176070702372 F F F
0.0000000000000001 0.6666666666666643 0.4316528212107116 F F F
0.2222222222222214 0.8888888888888860 0.4772176070702372 F F F
0.3333333333333357 0.0000000000000000 0.4316528212107116 F F F
0.5555555555555574 0.2222222222222215 0.4772176070702372 F F F
0.3333333333333358 0.3333333333333358 0.4316528212107116 F F F
0.5555555555555571 0.5555555555555571 0.4772176070702372 F F F
0.3333333333333358 0.6666666666666643 0.4316528212107116 F F F
0.5555555555555569 0.8888888888888860 0.4772176070702372 F F F
0.6666666666666643 0.0000000000000000 0.4316528212107116 F F F
0.8888888888888860 0.2222222222222215 0.4772176070702372 F F F
0.6666666666666645 0.3333333333333358 0.4316528212107116 F F F
0.8888888888888860 0.5555555555555571 0.4772176070702372 F F F
0.6666666666666643 0.6666666666666643 0.4316528212107116 F F F
0.8888888888888860 0.8888888888888860 0.4772176070702372 F F F
0.1963120914471914 0.1703801938053585 0.6969126533235664 T T T
0.2282747240054286 0.2204271800449094 0.7602608639101541 T T T
0.4165659357318789 0.2871733535969459 0.7111129456021584 T T T
0.4775716951737509 0.3616224510166779 0.7662445048296983 T T T
0.6691021347852700 0.7408312474917801 0.7141143358024524 T T T
0.7436039552370448 0.7372094494107113 0.7773253219651441 T T T
0.3835544967821862 0.6647638056934020 0.6170319445243532 T T T
0.5862345041047526 0.6687285005875524 0.6170386374096167 T T T
0.5568812579397444 0.4918118530992673 0.6457161524512481 T T T
0.4581768396823742 0.7159344964920203 0.6712460178580603 T T T
0.3886225752606999 0.8680356694383907 0.6178325374506661 T T T
0.4210736779097204 0.4349286336182080 0.6137044421963530 T T T
0.2125104551865216 0.1956002951642214 0.7285083408463139 T T T
0.4469452096289631 0.3245088442696472 0.7386998153632406 T T T
0.7065952432441286 0.7391379097024512 0.7457360626161043 T T T
0.6820670268862918 0.0177587092843125 0.7151715447816740 T T T
0.7146753191473184 0.0118660871593893 0.7343283524421732 T T T
0.6336282455112405 0.5331770918557321 0.8058532566416431 T T T
0.5977320827749892 0.5198141918269596 0.8216154382248393 T T T
0.2102438537161850 0.7874396099048281 0.6954176242604335 T T T
0.1742724578459843 0.8011571973999519 0.7144873579379518 T T T

Automatic mesh
0
Gamma
2 2 1
0. 0. 0.

Any insights into what might be causing this issue or how to resolve it would be greatly appreciated.

Thank you for your time and support.

Best regards,

Pablo

Dear Pablo,

Thank you for your question. Which POTCAR files did you use? Then I can try to repeat the issue. Could you also upload the OUTCAR file as this will give a bit more context to the issue.

Many thanks,

Chris

Dear Chris,

Thank you for your response. Regarding the POTCAR files, these are the ones I am using:

POTCAR: PAW_PBE Ce_h 03Mar2005
POTCAR: PAW_PBE O 08Apr2002
POTCAR: PAW_PBE Ni_pv 06Sep2000
POTCAR: PAW_PBE C 08Apr2002
POTCAR: PAW_PBE H 15Jun2001
You can verify these details in the headers of the OUTCAR files I have attached. Additionally, I am including the results obtained from running the calculations with VASP 5.4.4 and VASP 6.4.2:

Please note that I used a different POSCAR file than the one shared previously. To facilitate convergence, I am also providing the WAVECAR, which you can find at the following link:
https://drive.google.com/file/d/1WDuyTe ... sp=sharing

I hope this helps clarify the issue. Please let me know if you need further details.

Best regards,
Pablo

Hi Pablo,

Thank you. I will try the calculations this afternoon.

Best wishes,

Chris

Hi Pablo,

The issue is in your POSCAR files. I link the other thread here for convenience (https://vasp.at/forum/viewtopic.php?p=30036). It is the same issue for both.

After the coordinates in POSCAR, the velocities are given. In your POSCAR files, these are "NaN NaN NaN" for each ion. These are read in so when the first ionic step is completed, these "NaN"s are the velocities used to calculate the next MD step, resulting in "NaN" appearing. Since they are strings, this causes the calculation to crash. I presume that whatever software you use to generate these structures inputs NaN as default if velocities are not provided. The solution is to remove these from the end of your POSCAR file, then the calculations run without issue.

Best wishes,

Chris

Hi Chris,

Thank you for pointing this out and linking the relevant thread. It’s the same issue as in the other post, as you mentioned. I hadn’t realized that the "NaN NaN NaN" entries at the end of the POSCAR files could cause such a problem, but your explanation makes perfect sense now.

I’ll remove those lines and rerun the calculations as suggested. Thanks again for your help and for catching this detail!

Best wishes,
Pablo

Hi Pablo,

I'm glad that it's now running. If this solves the problem, then I'll close the thread at the start of next week, unless you have any other questions?

Best wishes,

Chris