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?<br /><br />
<span style="color: rgb(0, 0, 0); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial; overflow-wrap: break-word; white-space: pre-wrap;">&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</span>
<br /><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, July 23, 2026 at 2:03:41 PM UTC-4 Michela Cavalieri wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>Johann, thank you so much for your response. I think I have those sections already as:</div><div><br></div><div>&MOTION</div><div>
<span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap"> &PRINT
&RESTART SILENT
ADD_LAST NUMERIC
&EACH
QS_SCF 1
&END EACH
&END RESTART
&END PRINT</span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap">(...)</span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap"><br></span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap">and under FORCE_EVAL section:</span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap"> &PRINT
&RESTART ON
&END RESTART
&END PRINT
&END SCF
</span><br></div><div>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.<br><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap">
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.<br><br>Thank you very much,</span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap"><br></span></div><div><span style="color:rgb(0,0,0);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;white-space:pre-wrap">Michela</span></div><div><br>
<br></div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, July 23, 2026 at 9:53:20 AM UTC-4 Johann Pototschnig wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Have you tried the explicit keywords? </div><div><br></div><div><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/SCF/PRINT/RESTART.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/SCF/PRINT/RESTART.html&source=gmail&ust=1785270982427000&usg=AOvVaw08NJ4EMVqv8xC81kxSfJIG">https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/SCF/PRINT/RESTART.html</a></div><div><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/PRINT/RESTART.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/PRINT/RESTART.html&source=gmail&ust=1785270982427000&usg=AOvVaw0rdDFMuxY_afIDhP17p_BG">https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/PRINT/RESTART.html</a></div><div><br></div><div><br></div><div>Also:</div><div><a href="https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red.inp" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red.inp&source=gmail&ust=1785270982427000&usg=AOvVaw1o5WrGF63c77kmQA5wv3yk">https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red.inp</a></div><div><a href="https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red_restart.inp" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red_restart.inp&source=gmail&ust=1785270982427000&usg=AOvVaw0i6fTpB2MqqFBv9kF9SfX1">https://github.com/cp2k/cp2k/blob/master/tests/QS/regtest-kp-1/h_sym_red_restart.inp</a></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, July 22, 2026 at 11:16:22 PM UTC+2 Michela Cavalieri wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hello Dr. Stein, it is actually not printing a restart yet despite running after I changed the STRESS_TENSOR to NUMERICAL.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
In the meantime, is there anything else that jumps out to you as a culprit?</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thank you!<br>
<br>
Michela</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div></div>
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> <a rel="nofollow">cp...@googlegroups.com</a> <<a rel="nofollow">cp...@googlegroups.com</a>> on behalf of Frederick Stein <<a rel="nofollow">f.s...@hzdr.de</a>><br>
<b>Sent:</b> Wednesday, July 15, 2026 12:16 PM<br>
<b>To:</b> cp2k <<a rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject:</b> Re: [CP2K:22326] Troubleshooting: changing periodicity and index to radix array not found</font>
<div> </div>
</div>
<div></div></div><div dir="ltr"><div>
<div>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.</div>
<div><br>
</div>
<div>An alternative would be to describe your system as a 3D-periodic system if the boy in the non-periodic direction carries enough vacuum.</div>
<div>Best</div>
<br>
<div>
<div dir="auto">Michela Cavalieri schrieb am Mittwoch, 15. Juli 2026 um 18:01:49 UTC+2:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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 :)<br>
<br>
<div>
<div dir="auto">On Wednesday, July 15, 2026 at 12:00:17 PM UTC-4 Michela Cavalieri wrote:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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?<br>
<br>
<div>Funnily enough, while I was trying to understand this, I found this <a href="https://groups.google.com/g/cp2k/c/-pJubMFm70Y" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/g/cp2k/c/-pJubMFm70Y&source=gmail&ust=1785270982427000&usg=AOvVaw1WYdoS_S-TFbmUcut-frE5">
thread from last year where the two of spoke about a similar issue</a>! I am now trying NUMERICAL stress tensor following your advice (left the system in 2D for now).</div>
<div><br>
</div>
<div>Thank you,</div>
<div>
<div dir="auto">On Wednesday, July 15, 2026 at 9:44:24 AM UTC-4 Frederick Stein wrote:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Dear Michela,</div>
<div>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.</div>
<div>Best,</div>
<div>Frederick</div>
<br>
<div>
<div dir="auto">Michela Cavalieri schrieb am Mittwoch, 15. Juli 2026 um 15:35:46 UTC+2:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Good morning Dr. Stein and CP2K community!</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>The changes I made, as mentioned earlier, include the new library you suggested + PRINT_LEVEL HIGH.<br>
<br>
The files that were generated include:<br>
- .out and .err (attached)<br>
- a number of localLog.out files<br>
- a number of nonbonded_nl.out files<br>
- ELF, efield, hartree, ELECTRON_DENSITY, TOTAL_DENSITY, WFN cubes<br>
- a restart.wfn file</div>
<div><br>
</div>
<div>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.<br>
<br>
</div>
<div>Notably for the output and error files,</div>
<div>1. The .err reports an OpenFabrics error.</div>
<div>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".</div>
<div></div>
<div><br>
Kindly let me know if I should upload anything else!</div>
<div><br>
</div>
<div>Thank you, </div>
<div><br>
</div>
<div>Michela</div>
<div>
<div dir="auto">On Tuesday, July 14, 2026 at 9:40:29 AM UTC-4 Michela Cavalieri wrote:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>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.</div>
<div><br>
</div>
<div>Thank you very much!<br>
Michela</div>
<br>
<div>
<div dir="auto">On Thursday, July 9, 2026 at 11:25:07 AM UTC-4 Stein, Dr. Frederick wrote:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear Michela, <br>
Sorry for the long time to respond. I guess it is just a very special <br>
question. <br>
Your system may be too large for the internal FFT library. Please consider <br>
PREFERRED_FFT_LIBRARY FFTW3. I have just run the calculation with FFTW3 but <br>
replaced your system with hydrogen such that the underlying FFT-grids should <br>
be the same. If you still observe an error, could you increase the print <br>
level and send a suitable output file. <br>
Best, <br>
Frederick <br>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
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