[QE-users] Too many r-vectors error while running cp.x
Hello, I'm trying to run the Car-Parrinello dynamics on a pentacene-fullerene system. When I run the electronic minimization with cp.x, it shows the error, "too many r-vectors." This error is always reproducible when I use the van der Waals correction, 'dft-d'. I guess that the electronic minimization without the vdw correction is probably reliable because the ions are fixed, but eventually I need to run the molecular dynamics with the option. (I found out that the same error also occurs in the md option.) So, how can I solve this problem? Any help is greatly appreciated. Thank you. Daeho Han Here's the input file: calculation = 'cp', restart_mode = 'from_scratch' pseudo_dir = '/home/dhhan/program/qe-6.3/pseudo/', outdir = './', prefix = 'x', tprnfor = .true. disk_io = 'low', ndw = 50 nstep = 10 dt = 2.5 iprint=1 isave = 100 etot_conv_thr = 1.d-9 ekin_conv_thr = 1.d-4 / ibrav = 0, celldm(1) = 1.89 , nat = 96, ntyp = 2, nspin = 1, nbnd = 200, ecutwfc = 50, tot_charge = 0.0, nr1b = 10, nr2b = 10, nr3b = 10, vdw_corr = 'dft-d' / electron_dynamics = 'sd' emass = 400.d0 / $IONS ion_dynamics = 'none' / $CELL cell_dynamics = 'none' press = 0.0d0 / ATOMIC_SPECIES C 12.01 c_pbe_v1.2.uspp.F.UPF H 1.008 h_pbe_v1.4.uspp.F.UPF CELL_PARAMETERS {alat} 30.0000.0000.000 0.000 30.0000.000 0.0000.000 30.000 ATOMIC_POSITIONS {alat} C-3.620019680 -1.596664767 -2.981088793 C-5.049446573 -1.551957644 -2.955719388 H-5.550242110 -1.531945305 -1.981688934 C-5.773877596 -1.521724485 -4.118155337 C-5.113314586 -1.543823352 -5.386022394 C-3.746249846 -1.598321275 -5.458279948 H-3.235876507 -1.613352411 -6.427434150 C-2.947413637 -1.623340762 -4.272153533 C 0.711467886 -1.297048188 -0.731337101 C-0.681004135 -1.450567531 -0.684622495 H-1.188646096 -1.415069620 0.286226517 C-1.448496595 -1.570983559 -1.850510970 C-0.773974552 -1.606764345 -3.143573693 C 0.624803034 -1.523543426 -3.185386085 H 1.130607036 -1.539147286 -4.157616134 C 1.386147130 -1.333864744 -2.023964228 H 5.501737273 0.131789158 2.326306574 C 4.932192343 -0.130321082 1.429616510 C 3.599383930 -0.431413616 1.525858698 H 3.088198215 -0.413607385 2.494648776 C 2.834738057 -0.763753469 0.363647824 C 3.506845025 -0.788914066 -0.927490969 C 4.901012359 -0.474472537 -0.977381056 H 5.401262401 -0.489054724 -1.951679285 C 5.591546399 -0.150689817 0.161194947 H 6.655448371 0.097458132 0.105475937 C 2.775571895 -1.092116620 -2.072233651 C 1.471725180 -1.035054217 0.428251941 C-2.859620257 -1.589702670 -1.816319912 C-1.556829295 -1.648461975 -4.317425599 H-6.866387935 -1.476959384 -4.082946616 H-5.710282815 -1.514110422 -6.302383669 H-3.365609741 -1.562799799 -0.844115136 H-1.051325976 -1.666342639 -5.290100609 H 3.281517719 -1.106238988 -3.044716269 H 0.963211455 -1.006611265 1.399081785 C-0.513273424 6.385540559 0.645143886 C-1.684255282 5.529884159 0.642596711 C-1.232546111 4.151635345 0.640753255 C 0.217273101 4.154931930 0.642235014 C 0.662171269 5.535796350 0.644345310 C 1.791785119 5.907237005 -0.089593407 C 2.519160733 4.911448331 -0.853855057 C 2.090321693 3.580903795 -0.856042131 C 0.917587645 3.195443892 -0.094499559 C 0.195304399 2.196897077 -0.858740117 C-1.201784605 2.193288767 -0.860281083 C-1.927907483 3.189338378 -0.097079156 C-3.102118197 3.569516795 -0.859113865 C-3.537469491 4.897345340 -0.856060062 C-2.815325479 5.896019655 -0.091384560 C-2.819230145 7.131371389 -0.851267102 C-3.544097170 6.896056651 -2.085379579 C-3.988198258 5.515340327 -2.087857262 C-3.986382454 4.781958166 -3.277291825 C-3.536275201 3.403038206 -3.280301332 C-3.101477979 2.807540389 -2.093038977 C-1.927775755 1.956038993 -2.093737695 C-1.228673483 1.734470822 -3.282392101 C 0.221199780 1.740407794 -3.280758005 C 0.920410155 1.966792484 -2.093041655 C 2.091247837 2.820536599 -2.091463512 C 2.524135295 3.417735819 -3.279291856 C 2.968491525 4.798694298 -3.276987984 C 2.966345651 5.532053762 -2.086567670 C 2.514296188 6.910346651 -2.084569182 C 2.081635913 7.507035534 -3.272766097 C 2.084051019 6.746476570 -4.508346479 C 2.519065478 5.417523089 -4.510238633 C 1.795668169 4.418189088 -5.274193365 C 1.798791742 3.182704328 -4.513220249 C 0.668797905 2.358585627 -4.513405104 C-0.505696107 2.738310163 -5.275979917 C-1.678466595 2.352184004 -4.514278903 C-2.811525902 3.170728513 -4.514359178 C-2.813492548 4.406743522 -5.273955466 C
[QE-users] Specific energy of the system increases with increase of supercell. Why?
I use wide-spread ribbon model for MoS2 edge. To ensure correctness of the model I calculated supercells with 2,3,4,6 periods (Mo atoms) along the edge. I expected that at least for one row of 2-4-6 or 3-6 I would see constant specific energy per edge Mo atom. Instead I see a slight, but constant increase in specific energy. The increase is small (~0.2 eV/period) but constant. It was observed for series with 2k points for all supercell sizes and for series where I used such number of K-point that product of supercell size and number of k-points were preserved. I could dismiss it, but ! That increase is observed for some structures in same model and not observed for others. If the increase was uniform between structures, I could dismiss it. As of now I need to understand where it comes from. What I should see for in my results and what could be the reason? Interestingly, when I run same calculation with Gamma-point, I saw different pattern, but this is of no importance now. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] qe-6.4: problem with fs.x
Dear Mr Giannozzi, Thank you for you reply and sincerely apologize for the wrong guess I have made.The problem appears with qe-6.4 compiled with intel v. 11 as well as with the one comming from Parallel Studio 2017. It does not appear with qe-6.3 compiled on the same machines. My example input files (problem appears also with other, more realistic inputs) are as follows: scf.in: calculation='scf' restart_mode='from_scratch', prefix='Nb', pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/', outdir='./tmp_dir/' / ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1, ecutwfc =50, ecutrho=600, occupations="smearing", smearing="m-v", degauss=0.02 / conv_thr = 1.0e-11 mixing_beta = 0.7 / ATOMIC_SPECIES Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS Nb 0.00 0.00 0.00 K_POINTS automatic 4 4 4 0 0 0 dos.in calculation='nscf' restart_mode='from_scratch', prefix='Nb', pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/', outdir='./tmp_dir/' / ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1, ecutwfc =50, ecutrho=600, occupations="tetrahedra" / conv_thr = 1.0e-11 mixing_beta = 0.7 / ATOMIC_SPECIES Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS Nb 0.00 0.00 0.00 K_POINTS automatic 4 4 4 0 0 0 fs.in outdir='./tmp_dir/' prefix='Nb' / Firstly I am running mpirun -np 4 pw.x scf.out and I can grep Fermi energy from *xml files: [student3 qe4]$ grep fermi tmp_dir/* tmp_dir/Nb.xml: 6.529259765371975e-1> Then I am running mpirun -np 4 pw.xdos.out and now I cannot see the Fermi energy in *xml: [student3 qe4]$ grep fermi tmp_dir/*(nothing appears) But for sure the Fermi energy is computed in nscf cycle, because I can grep it from dos.out file: [student3 qe4]$ grep Fermi * dos.out: the Fermi energy is18.0671 ev scf.out: the Fermi energy is17.7670 ev As I mentioned before, after running mpirun -np 4 fs.xfs.out I see in the fs.out file the line: 1 bands found crossing Ef =0.00 When I changed the fermisurface.f90 such that it is reading Fermi energy from dos.out, then the program fs.x works very well (in agreement with the results obtained with qe-6.3). I would like to thank you for your help in advance. Best regards, Sylwia >>> 03/16/19 12:02 PM >>> Send users mailing list submissions to users@lists.quantum-espresso.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.quantum-espresso.org/mailman/listinfo/users or, via email, send a message with subject or body 'help' to users-requ...@lists.quantum-espresso.org You can reach the person managing the list at users-ow...@lists.quantum-espresso.org When replying, please edit your Subject line so it is more specific than "Re: Contents of users digest..." Today's Topics: 1. Negatively charged isolated molecule (Ernane de Freitas Martins) 2. qe-6.4: problem with fs.x (Sylwia Golab) 3. Re: Negatively charged isolated molecule (Giuseppe Mattioli) 4. Re: Negatively charged isolated molecule (Ernane de Freitas Martins) 5. Re: Negatively charged isolated molecule (Michal Krompiec) 6. Re: How to calculate water molecule energy at large cell size? (Paolo Giannozzi) 7. Re: qe-6.4: problem with fs.x (Paolo Giannozzi) 8. Re: Negatively charged isolated molecule (Nattino Francesco) 9. How can read constant velocity from input file when restart_mode= 'restart' (=?ISO-8859-1?B?THUgSGFpbGluIA==?=) -- Message: 1 Date: Fri, 15 Mar 2019 13:54:49 -0300 From: Ernane de Freitas Martins To: users@lists.quantum-espresso.org Subject: [QE-users] Negatively charged isolated molecule Message-ID: Content-Type: text/plain; charset="utf-8" Hello, I'm experiencing a problem to run a negatively charge molecule in quantum espresso. The system is CO32-. I try both vacuum and solvated (environ) calculations. The solvated one works fine. The problem is the calculation in vacuum. It never give the first ionic step because the SCF accuracy never reaches the convence criterion. I tried many different solutions (increase cutoffs and box size, use assume isolated, decreasing and changing the mixing scheme and etc) and nothing works. The unique calculation that works fine for vacuum is the one with a box size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for this specific box size. I ran several other charged systems (+1, +2 and -1 total charge) and all of them worked fine. The problem appears for -2 total charge in vacuum. Would some of you kindly help me in this? Cheers, Dr. Ernane de Freitas Martins Postdoctoral researcher IF - USP S?o Paulo, SP - Brazil -- next part -- An HTML attachment was scrubbed... URL: -- Message: 2 Date: Fri, 15 Mar 2019 18:56:38 +0100
Re: [QE-users] Problem with tetrahedra method: from tetra_init : error # 26, cannot remap grid on k-point list
Dear Pietro, I ran the scf calculation follows by the nscf calculation with occupation='smearing', smearing and degauss (with QE-6.3.0). I added bz_sum = 'tetrahedra_opt' in the dos.x input file and I ran it but, it crashed and I got the following error message task # 0 from dos : error #19 reading dos namelist Apparently, the tetrahedron method is used if - "the input data file has been produced by pw.x using the option occupations='tetrahedra', AND" - "a value for degauss is not given as input to namelist " read here https://gitlab.com/QEF/q-e/blob/qe-6.3/PP/Doc/INPUT_DOS.txt But pw.x (nscf) does not work in my case Further research on the internet led me to this website https://eamonnmurray.gitlab.io/modelling_materials/lab04/ where I could read that "Essentially this corresponds to doing a three dimensional linear interpolation from a regular grid of values."..."It’s important to note that in a real measurement of the density of states of a system the there is an implicit broadening that comes from 1. Electron-phonon coupling: the states are not simply at a fixed energy, but will have some distribution as the atoms vibrate. 2. Any measurement probe will have a finite energy width associated with it, which will limit how finely it can resolve density of states features. So while tetrahedron may seem the more accurate approach, you shouldn’t necessarily think of it as a more correct representation of a real system." I think I am just going to use the common way, that is, running the nscf calculation with smearing and degaus. Then, run this code prefix = '...', outdir = '...', fildos = 'dos.dat', / and plot the DOS. Regards - Pacome ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users