[CP2K-user] [CP2K:22349] Troubleshooting: changing periodicity and index to radix array not found

[Johann Pototschnig]

Which version due you use?
 $ cp2k.psmp --version
 CP2K version 2026.2 (Development Version)
 Source code revision 170fc5735f
 cp2kflags: omp libint fftw3 libxc elpa parallel scalapack mpi_f08 cosma 
libxs libxsmm spglib libdftd4 dftd4_v4_2 s_dftd3 mctc-lib tblite libvori 
libbqb
 compiler: GCC version 13.3.0


On Wednesday, July 29, 2026 at 3:00:44 PM UTC+2 Johann Pototschnig wrote:

> I tried running it with a smaller coordinate file and got 
> Ga_solvent_geoopt-RESTART.wfn. 
>
> For using it you need to add:
> ...
> &DFT
>      WFN_RESTART_FILE_NAME Ga_solvent_geoopt-RESTART.wfn
> ...
>
> The restart files are written after finishing one SCF optimization. 
>
> How do run it? If run on a cluster does it use a temporary directory? 
>
> best,
> Johann
>
> On Tuesday, July 28, 2026 at 4:56:15 PM UTC+2 Michela Cavalieri wrote:
>
>> Hello CP2K community, happy Tuesday! I am sorry to message about this 
>> issue again. Is there something obvious I am missing?
>> Thank you,
>> Michela
>>
>> On Monday, July 27, 2026 at 4:37:09 PM UTC-4 Michela Cavalieri wrote:
>>
>>> 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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