[CP2K-user] [CP2K:22348] Troubleshooting: changing periodicity and index to radix array not found

Johann Pototschnig pototschnig.johann at gmail.com
Wed Jul 29 13:00:43 UTC 2026
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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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>>>>> To view this discussion visit 
>>>>> https://groups.google.com/d/msgid/cp2k/4ae1cd77-0937-4f79-9692-14aba1bac6f7n%40googlegroups.com 
>>>>> <https://groups.google.com/d/msgid/cp2k/4ae1cd77-0937-4f79-9692-14aba1bac6f7n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>>

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