[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
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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
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