[CP2K-user] [CP2K:22343] Troubleshooting: changing periodicity and index to radix array not found

[Michela Cavalieri]

Even after changing it to this, the result did not change. No restart got 
printed and I am unable to continue geo_opt. Any suggestions?

&GLOBAL PROJECT "Ga_solvent_geoopt" RUN_TYPE GEO_OPT PRINT_LEVEL HIGH 
WALLTIME 23:30:00 SAVE_MEM T PREFERRED_FFT_LIBRARY FFTW3 
EXTENDED_FFT_LENGTHS T PREFERRED_DIAG_LIBRARY ScaLAPACK &END GLOBAL 
&FORCE_EVAL METHOD QS STRESS_TENSOR NUMERICAL &SUBSYS &CELL ABC 30 27 70 
MULTIPLE_UNIT_CELL 1 1 1 PERIODIC XY &END CELL &KIND Ga BASIS_SET 
DZVP-MOLOPT-SR-GTH ELEMENT Ga POTENTIAL GTH-PBE-q13 &END KIND &KIND C 
BASIS_SET DZVP-MOLOPT-SR-GTH ELEMENT C POTENTIAL GTH-PBE-q4 &END KIND &KIND 
S BASIS_SET DZVP-MOLOPT-GTH ELEMENT S POTENTIAL GTH-PBE-q6 &END KIND &KIND 
H BASIS_SET DZVP-MOLOPT-GTH ELEMENT H POTENTIAL GTH-PBE-q1 &END KIND &KIND 
Br BASIS_SET DZVP-MOLOPT-SR-GTH ELEMENT Br POTENTIAL GTH-PBE-q7 &END KIND 
&KIND O BASIS_SET DZVP-MOLOPT-GTH ELEMENT O POTENTIAL GTH-PBE-q6 &END KIND 
&TOPOLOGY COORD_FILE_NAME Ga_solvent.xyz COORD_FILE_FORMAT XYZ 
MULTIPLE_UNIT_CELL 1 1 1 &END TOPOLOGY &END SUBSYS &DFT BASIS_SET_FILE_NAME 
/anvil/projects/x-che250203/CP2K_Files/BASIS_MOLOPT POTENTIAL_FILE_NAME 
/anvil/projects/x-che250203/CP2K_Files/POTENTIAL &QS EPS_DEFAULT 
1.0000000000000000E-10 EXTRAPOLATION USE_PREV_WF METHOD GPW &END QS &MGRID 
CUTOFF 400 NGRIDS 5 REL_CUTOFF 40 &END MGRID &SCF MAX_SCF 300 EPS_SCF 
3.0000000000000002E-05 SCF_GUESS ATOMIC ADDED_MOS -1 &DIAGONALIZATION T 
ALGORITHM STANDARD &END DIAGONALIZATION &SMEAR T METHOD FERMI_DIRAC 
ELECTRONIC_TEMPERATURE 303.15 &END SMEAR &MIXING T METHOD BROYDEN_MIXING 
ALPHA 5.0000000000000002E-02 &END MIXING &PRINT &RESTART ON &END RESTART 
&END PRINT &END SCF &XC #should I add cutoffs? &VDW_POTENTIAL 
&PAIR_POTENTIAL R_CUTOFF 10 TYPE DFTD3 PARAMETER_FILE_NAME dftd3.dat 
REFERENCE_FUNCTIONAL "PBE" CALCULATE_C9_TERM T &END PAIR_POTENTIAL &END 
VDW_POTENTIAL &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &POISSON 
POISSON_SOLVER MT PERIODIC XY &END POISSON &END DFT &END FORCE_EVAL &MOTION 
&GEO_OPT TYPE MINIMIZATION MAX_DR 1.0E-03 MAX_FORCE 1.0E-03 RMS_DR 1.0E-03 
RMS_FORCE 1.0E-03 MAX_ITER 200 OPTIMIZER CG &END GEO_OPT &PRINT &TRAJECTORY 
SILENT &EACH QS_SCF 1 &END EACH &END TRAJECTORY &VELOCITIES SILENT &EACH MD 
50 &END EACH &END VELOCITIES &FORCES SILENT &EACH QS_SCF 1 &END EACH &END 
FORCES &STRESS SILENT &EACH QS_SCF 1 &END EACH &END STRESS &RESTART LOW 
ADD_LAST NUMERIC &EACH QS_SCF 1 &END EACH &END RESTART &END PRINT &END 
MOTION 

On Thursday, July 23, 2026 at 2:03:41 PM UTC-4 Michela Cavalieri wrote:

> Johann, thank you so much for your response. I think I have those sections 
> already as:
>
> &MOTION
> &PRINT &RESTART SILENT ADD_LAST NUMERIC &EACH QS_SCF 1 &END EACH &END 
> RESTART &END PRINT
> (...)
>
> and under FORCE_EVAL section:
> &PRINT &RESTART ON &END RESTART &END PRINT &END SCF 
> I have not needed to change these specific settings in a while, and have 
> ran multiple MD and GEO_OPT jobs in the past without this issue.
> Is that what you meant? I am aware that I have RESTART SILENT in the 
> MOTION block, but so far it has never been a problem for other MD or 
> GEO_OPT. It would always print a restart regardless. I am now trying 
> RESTART LOW under MOTION.
>
> Thank you very much,
>
> Michela
>
>
>
> On Thursday, July 23, 2026 at 9:53:20 AM UTC-4 Johann Pototschnig wrote:
>
>> Have you tried the explicit keywords? 
>>
>>
>> https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/SCF/PRINT/RESTART.html
>> https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/PRINT/RESTART.html
>>
>>
>> Also:
>>
>> https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red.inp
>>
>> https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red_restart.inp
>> On Wednesday, July 22, 2026 at 11:16:22 PM UTC+2 Michela Cavalieri wrote:
>>
>>> Hello Dr. Stein, it is actually not printing a restart yet despite 
>>> running after I changed the STRESS_TENSOR to NUMERICAL.
>>>
>>> Any suggestions? I think part of the problem is that I was printing the 
>>> restart EACH GEO_OPT 1, and since it did not complete GEO_OPT it did not 
>>> print a restart. I am now trying to run it after changing that part of the 
>>> print section to EACH QS_SCF 1.
>>>
>>> In the meantime, is there anything else that jumps out to you as a 
>>> culprit?
>>>
>>> Thank you!
>>>
>>> Michela
>>>
>>>
>>> ------------------------------
>>> *From:* cp... at googlegroups.com <cp... at googlegroups.com> on behalf of 
>>> Frederick Stein <f.s... at hzdr.de>
>>> *Sent:* Wednesday, July 15, 2026 12:16 PM
>>> *To:* cp2k <cp... at googlegroups.com>
>>> *Subject:* Re: [CP2K:22326] Troubleshooting: changing periodicity and 
>>> index to radix array not found 
>>>  
>>> No, your output file states that the given Poisson solver doesn't 
>>> implement stress tensors for 2D-periodic systems. I am pretty sure that all 
>>> Poisson solvers implement stress tensors for 3D-periodic systems but not 
>>> necessarily for 1D or 2D systems. In a few cases, this has changed over the 
>>> years.
>>>
>>> An alternative would be to describe your system as a 3D-periodic system 
>>> if the boy in the non-periodic direction carries enough vacuum.
>>> Best
>>>
>>> Michela Cavalieri schrieb am Mittwoch, 15. Juli 2026 um 18:01:49 UTC+2:
>>>
>>> Please scrap the first part of my question. I am seeing now that they 
>>> should match. I will leave it at this: trying NUMERICAL stress tensor. Will 
>>> update here if it works or if I get an updated error message. Thanks :)
>>>
>>> On Wednesday, July 15, 2026 at 12:00:17 PM UTC-4 Michela Cavalieri wrote:
>>>
>>> Hello Dr. Stein, thank you for your reply! I am actually a little 
>>> confused about this comment you made: " I am not sure which Poisson solver 
>>> implements stress tensors with PERIODIC XY. ". I thought MT, IMPLICIT and 
>>> WAVELET solvers were available for 2D systems. Does this only refer to the 
>>> electrostatics? In other words, could I use PERIODIC XY unit cell (CELL) 
>>> but PERIODIC XYZ electrostatics in POISSON_SOLVER?
>>>
>>> Funnily enough, while I was trying to understand this, I found this thread 
>>> from last year where the two of spoke about a similar issue 
>>> <https://groups.google.com/g/cp2k/c/-pJubMFm70Y>! I am now trying 
>>> NUMERICAL stress tensor following your advice (left the system in 2D for 
>>> now).
>>>
>>> Thank you,
>>> On Wednesday, July 15, 2026 at 9:44:24 AM UTC-4 Frederick Stein wrote:
>>>
>>> Dear Michela,
>>> These are great news! You may try to reduce the print level again to 
>>> have a less verbose CP2K. I guess that the missing restart file is related 
>>> to CP2K aborting before finishing the first optimization step. You will 
>>> need to employ PERIODIC XYZ instead of PERIODIC XY. I am not sure which 
>>> Poisson solver implements stress tensors with PERIODIC XY.
>>> Best,
>>> Frederick
>>>
>>> Michela Cavalieri schrieb am Mittwoch, 15. Juli 2026 um 15:35:46 UTC+2:
>>>
>>> Good morning Dr. Stein and CP2K community!
>>>
>>> I have an update. With the library you suggested, the job ran (thank 
>>> you!!). However, no .restart file was generated, so I am a little confused.
>>>
>>> The changes I made, as mentioned earlier, include the new library you 
>>> suggested + PRINT_LEVEL HIGH.
>>>
>>> The files that were generated include:
>>> - .out and .err (attached)
>>> - a number of localLog.out files
>>> - a number of nonbonded_nl.out files
>>> - ELF, efield, hartree, ELECTRON_DENSITY, TOTAL_DENSITY, WFN cubes
>>> - a restart.wfn file
>>>
>>> but no restart!!! Now, my geo_opt is not done, so I was planning on 
>>> restarting and I would normally write the file myself, but coordinates, 
>>> cell dimensions, velocities etc were not printed as individual files or as 
>>> part of the output. Is there anything I should fix in my original script to 
>>> ensure a restart gets printed? I could maybe just switch back to 
>>> PRINT_LEVEL LOW like I had before.
>>>
>>> Notably for the output and error files,
>>> 1. The .err reports an OpenFabrics error.
>>> 2. The .out reports some problems, such as: "Stress Tensor not tested 
>>> for 2D Systems" (aborted after); "Berry phase moments for non uniform MOs' 
>>> occupation numbers not implemented".
>>>
>>> Kindly let me know if I should upload anything else!
>>>
>>> Thank you, 
>>>
>>> Michela
>>> On Tuesday, July 14, 2026 at 9:40:29 AM UTC-4 Michela Cavalieri wrote:
>>>
>>> Dr. Stein, thank you so much for your help! Sorry for the long time to 
>>> respond on my end as well. For some reason, I did not receive an email 
>>> notification! I am trying FFTW3 now and increased the print level to HIGH. 
>>> I will update you as soon as possible.
>>>
>>> Thank you very much!
>>> Michela
>>>
>>> On Thursday, July 9, 2026 at 11:25:07 AM UTC-4 Stein, Dr. Frederick 
>>> wrote:
>>>
>>> Dear Michela, 
>>> Sorry for the long time to respond. I guess it is just a very special 
>>> question. 
>>> Your system may be too large for the internal FFT library. Please 
>>> consider 
>>> PREFERRED_FFT_LIBRARY FFTW3. I have just run the calculation with FFTW3 
>>> but 
>>> replaced your system with hydrogen such that the underlying FFT-grids 
>>> should 
>>> be the same. If you still observe an error, could you increase the print 
>>> level and send a suitable output file. 
>>> Best, 
>>> Frederick 
>>>
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>>> .
>>>
>>

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