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Hi<div><br></div><div>ok, even if I try with ibrav == 0, specify cell_parameters, and use cartesian coordinates for all as such:</div><div><br></div><div><div>&control</div><div> calculation = 'scf'</div><div> prefix = 'graphene'</div><div> pseudo_dir = '/gscratch/hwahab/DFT-code/psp/' </div><div> outdir = './'</div><div> restart_mode = 'from_scratch'</div><div> etot_conv_thr = 1.d-6</div><div> forc_conv_thr = 1.d-5</div><div>/</div><div><br></div><div>&system</div><div> ibrav = 0</div><div> nat = 48</div><div> ntyp = 1</div><div> ecutwfc = 80</div><div> occupations = 'smearing'</div><div> smearing = 'gaussian'</div><div> degauss = 0.1</div><div> vdw_corr='grimme-d2'</div><div>/</div><div><br></div><div>&electrons</div><div> diagonalization = 'david'</div><div> diago_thr_init = 1.d-4</div><div> mixing_mode = 'local-TF'</div><div> mixing_beta = 0.7</div><div> conv_thr = 1.d-8</div><div>/<span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div>&ions</div><div> </div><div>/</div><div><br></div><div>ATOMIC_SPECIES</div><div>C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF </div><div><br></div><div>ATOMIC_POSITIONS angstrom</div><div>C -0.005594637 0.710607728 17.606217811</div><div>C -0.007113039 2.128152101 17.584272182</div><div>C 1.224800757 0.002792887 17.613037723</div><div>C 1.220781849 2.833821539 17.553802163</div><div>C 2.453370565 0.710361709 17.588200291</div><div>C 2.452466724 2.129238290 17.551425829</div><div>C 3.684434744 0.001530538 17.594476170</div><div>C 3.684438920 2.839550201 17.533796214</div><div>C 4.915544062 0.711333118 17.590036280</div><div>C 4.915853909 2.129726547 17.558981625</div><div>C 6.143486600 0.002227196 17.614492659</div><div>C 6.144397239 2.838931198 17.567937591</div><div>C -0.009386173 4.969207674 17.562655171</div><div>C -0.007017413 6.394548846 17.533586100</div><div>C 1.221221723 4.253471766 17.548052411</div><div>C 1.198574699 7.115165393 17.592468497</div><div>C 2.446729939 4.945634289 17.560357556</div><div>C 2.429014083 6.377364466 17.843730988</div><div>C 3.679896901 4.258356417 17.551643715</div><div>C 3.704632453 7.115561848 17.867361404</div><div>C 4.916336515 4.974358812 17.564482071</div><div>C 4.935632583 6.385210475 17.597930230</div><div>C 6.145763199 4.260558789 17.557531939</div><div>C 6.139436097 7.104085900 17.546822753</div><div>C -0.008057730 9.237466939 17.548881513</div><div>C -0.005309676 10.658828114 17.540319093</div><div>C 1.220546640 8.524488204 17.583337938</div><div>C 1.225791434 11.368226350 17.566890173</div><div>C 2.458810059 9.240431880 17.612862514</div><div>C 2.454941023 10.659162890 17.592221246</div><div>C 3.688725076 8.555854012 17.643635937</div><div>C 3.683918063 11.368771580 17.603925777</div><div>C 4.910904632 9.244786635 17.581661741</div><div>C 4.913395819 10.664333371 17.573847419</div><div>C 6.143923926 8.528771033 17.556446236</div><div>C 6.142987294 11.370161820 17.555480374</div><div>C -0.004309434 13.496944454 17.583281339</div><div>C -0.004505934 14.915030012 17.613620426</div><div>C 1.226582522 12.786684076 17.587667221</div><div>C 1.224762481 15.623384029 17.618836753</div><div>C 2.455170254 13.495545076 17.620810601</div><div>C 2.455394258 14.913895553 17.626574694</div><div>C 3.684071873 12.787455574 17.618041427</div><div>C 3.684499812 15.622198165 17.627916140</div><div>C 4.913552069 13.495405863 17.614905357</div><div>C 4.913417489 14.913710743 17.621452935</div><div>C 6.142676777 12.788081224 17.582175333</div><div>C 6.143988489 15.623015254 17.616347215</div><div><br></div><div><br></div><div>K_POINTS automatic</div><div>4 2 1 0 0 0</div><div><br></div><div>CELL_PARAMETERS angstrom</div><div>7.378073983 0.000000000 0.0000000000</div><div>0.000000000 17.038932 0.0000000000</div><div>0.000000000 0.000000000 25.00</div></div><div><br></div><div>I still get it stuck here in output: </div><div><br></div><div><div>Estimated max dynamical RAM per process > 9360.31MB</div><div><br></div><div> Check: negative/imaginary core charge= -0.000003 0.000000</div><div><br></div><div> Initial potential from superposition of free atoms</div><div> Check: negative starting charge= -0.001323</div><div><br></div><div> starting charge 191.99800, renormalised to 192.00000</div><div><br></div><div> negative rho (up, down): 1.323E-03 0.000E+00</div><div> Starting wfc are 192 randomized atomic wfcs</div><div><br></div><div> total cpu time spent up to now is 1474.4 secs</div><div><br></div><div> per-process dynamical memory: 1195.0 Mb</div><div><br></div><div> Self-consistent Calculation</div><div><br></div><div> iteration # 1 ecut= 80.00 Ry beta=0.70</div><div> Davidson diagonalization with overlap</div></div><div><br></div><div><br></div><div>This code has worked previously with qe/5.4.0, but gets stuck with 6.1 serial.</div><div><br></div><div>-Hud</div><div class="mb_sig"></div><blockquote class="history_container" type="cite" style="border-left-style:solid;border-width:1px; 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<p style="color: #AAAAAA; margin-top: 10px;">On 5/9/2019 1:23:39 PM, Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it> wrote:</p><div style="font-family:Arial,Helvetica,sans-serif"><br>You are mixing two different ways to indicate cell parameters<br><br> ///---<br> EITHER:<br><br> +--------------------------------------------------------------------<br> Variable: celldm(i), i=1,6<br><br> Type: REAL<br> See: ibrav<br> Description: Crystallographic constants - see the "ibrav" variable.<br> Specify either these OR <br>"A","B","C","cosAB","cosBC","cosAC" NOT both.<br> Only needed values (depending on "ibrav") must <br>be specified<br> alat = "celldm"(1) is the lattice parameter "a" <br>(in BOHR)<br> If "ibrav"==0, only "celldm"(1) is used if present;<br> cell vectors are read from card "CELL_PARAMETERS"<br> +--------------------------------------------------------------------<br><br> OR:<br><br> +--------------------------------------------------------------------<br> Variables: A, B, C, cosAB, cosAC, cosBC<br><br> Type: REAL<br> See: ibrav<br> Description: Traditional crystallographic constants:<br><br> a,b,c in ANGSTROM<br> cosAB = cosine of the angle between axis a <br>and b (gamma)<br> cosAC = cosine of the angle between axis a <br>and c (beta)<br> cosBC = cosine of the angle between axis b <br>and c (alpha)<br><br> The axis are chosen according to the value of <br>@ref ibrav.<br> Specify either these OR @ref celldm but NOT both.<br> Only needed values (depending on @ref ibrav) <br>must be specified.<br><br> The lattice parameter alat = A (in ANGSTROM ).<br><br> If @ref ibrav == 0, only A is used if present, and<br> cell vectors are read from card @ref CELL_PARAMETERS.<br> +--------------------------------------------------------------------<br><br> \\\---<br><br>This might be the cause of the strange behavior, supposing that your <br>machine has the ~4GB of free RAM to perform the calculation indicated <br>in the output. However, in the case of a regular hcp supercell you <br>should not need at all to indicate the cosAB and cosAC values.<br>HTH<br>Giuseppe<br><br><br>Quoting "H1@GMAIL" <hudwahab@gmail.com>:<br><br>> Hi Giuseppe<br>><br>> apologies. My input file:<br>><br>> &control<br>> calculation = 'scf'<br>> prefix = 'graphene'<br>> pseudo_dir = '/gscratch/hwahab/DFT-code/psp/'<br>> outdir = './'<br>> restart_mode = 'from_scratch'<br>> etot_conv_thr = 1.d-6<br>> forc_conv_thr = 1.d-5<br>> /<br>> &system<br>> ibrav = 4<br>> celldm(1) = 9.84<br>> celldm(3) = 10<br>> cosAB = -0.5<br>> cosAC = 1<br>> nat = 32<br>> ntyp = 1<br>> ecutwfc = 80<br>> occupations = 'smearing'<br>> smearing = 'gaussian'<br>> degauss = 0.1<br>> vdw_corr='grimme-d2'<br>> /<br>><br>> &electrons<br>> diagonalization = 'david'<br>> diago_thr_init = 1.d-4<br>> mixing_mode = 'local-TF'<br>> mixing_beta = 0.7<br>> conv_thr = 1.d-10<br>> / <br>><br>> &ions<br>> /<br>><br>> ATOMIC_SPECIES<br>> C 12.0107 C.pbe-mt_gipaw.UPF <br>><br>> ATOMIC_POSITIONS crystal<br>> C 0.16667 0.08333 0.00000<br>> C 0.41667 0.08333 0.00000<br>> C 0.66667 0.08333 0.00000<br>> C 0.91667 0.08333 0.00000<br>> C 0.08333 0.16667 0.00000<br>> C 0.33333 0.16667 0.00000<br>> C 0.58333 0.16667 0.00000<br>> C 0.83333 0.16667 0.00000<br>> C 0.16667 0.33333 0.00000<br>> C 0.41667 0.33333 0.00000<br>> C 0.66667 0.33333 0.00000<br>> C 0.91667 0.33333 0.00000<br>> C 0.08333 0.41667 0.00000<br>> C 0.33333 0.41667 0.00000<br>> C 0.58333 0.41667 0.00000<br>> C 0.83333 0.41667 0.00000<br>> C 0.16667 0.58333 0.00000<br>> C 0.41667 0.58333 0.00000<br>> C 0.66667 0.58333 0.00000<br>> C 0.91667 0.58333 0.00000<br>> C 0.08333 0.66667 0.00000<br>> C 0.33333 0.66667 0.00000<br>> C 0.58333 0.66667 0.00000<br>> C 0.83333 0.66667 0.00000<br>> C 0.16667 0.83333 0.00000<br>> C 0.41667 0.83333 0.00000<br>> C 0.66667 0.83333 0.00000<br>> C 0.91667 0.83333 0.00000<br>> C 0.08333 0.91667 0.00000<br>> C 0.33333 0.91667 0.00000<br>> C 0.58333 0.91667 0.00000<br>> C 0.83333 0.91667 0.00000<br>> <br>><br>> K_POINTS automatic<br>> 8 8 1 0 0 0<br>><br>> And the end snippet of the output:<br>><br>> Estimated max dynamical RAM per process > 3558.76MB<br>><br>> Initial potential from superposition of free atoms<br>><br>> starting charge 111.99996, renormalised to 128.00000<br>><br>> negative rho (up, down): 5.479E-05 0.000E+00<br>> Starting wfc are 256 randomized atomic wfcs<br>><br>> There is no error outputs, it just gets stuck there..<br>><br>> Hope this makes sense.<br>><br>> Hud Wahab<br>> University of Wyoming<br>> 1000 E University Ave<br>> Laramie WY, 82072<br>> Email: hwahab@uwyo.edu<br>> On 5/9/2019 12:50:50 PM, Giuseppe Mattioli <br>> <giuseppe.mattioli@ism.cnr.it> wrote:<br>><br>> Dear Hud (please sign always with full name and scientific affiliation<br>> the posts to this forum, we appreciate it)<br>> It is impossible to help you if you don't post the input of your<br>> calculation and the relevant part of your output (where does the code<br>> stop?). Is there any system error like a segfault printed, e.g., in a<br>> nohup.out file? It is primarily important to look into such kind of<br>> information, in order to see if the error is reproducible on different<br>> machines/architectures or by using different compilers/libraries.<br>> HTH<br>> Giuseppe<br>><br>> Quoting "H1@GMAIL" :<br>><br>>> Hello<br>>> I run on 6.1-serial. My pw.x scf runs ok with small size systems 2<br>>> atoms, but nothing happens when scaled to 4x4 or 32 atoms. I let it<br>>> run for more than an hour and don't expect that the calculation<br>>> takes that long.<br>>><br>>> From the troubleshooting in User Guide I see it might be a<br>>> floating-point error causing endless NaNs - how to handle for such<br>>> exceptions?<br>>><br>>> As I can't provide the error output, I am not sure what details you<br>>> need to troubleshoot, but let me know if something is missing<br>>><br>>> Cheers, Hud<br>>> Dept. Chemical Engineering<br>>> University of Wyoming<br>><br>><br>><br>> GIUSEPPE MATTIOLI<br>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>> Via Salaria Km 29,300 - C.P. 10<br>> I-00015 - Monterotondo Scalo (RM)<br>> Mob (*preferred*) +39 373 7305625<br>> Tel + 39 06 90672342 - Fax +39 06 90672316<br>> E-mail:<br>><br>> _______________________________________________<br>> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)<br>> users mailing list users@lists.quantum-espresso.org<br>> https://lists.quantum-espresso.org/mailman/listinfo/users<br><br><br><br>GIUSEPPE MATTIOLI<br>CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>Via Salaria Km 29,300 - C.P. 10<br>I-00015 - Monterotondo Scalo (RM)<br>Mob (*preferred*) +39 373 7305625<br>Tel + 39 06 90672342 - Fax +39 06 90672316<br>E-mail: <giuseppe.mattioli@ism.cnr.it><br><br>_______________________________________________<br>Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)<br>users mailing list users@lists.quantum-espresso.org<br>https://lists.quantum-espresso.org/mailman/listinfo/users</giuseppe.mattioli@ism.cnr.it></giuseppe.mattioli@ism.cnr.it></hudwahab@gmail.com></div></blockquote>
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