[QE-users] pw.x stuck.
Hud Wahab
hudwahab at gmail.com
Thu May 9 22:40:54 CEST 2019
Hi
ok, even if I try with ibrav == 0, specify cell_parameters, and use cartesian coordinates for all as such:
&control
calculation = 'scf'
prefix = 'graphene'
pseudo_dir = '/gscratch/hwahab/DFT-code/psp/'
outdir = './'
restart_mode = 'from_scratch'
etot_conv_thr = 1.d-6
forc_conv_thr = 1.d-5
/
&system
ibrav = 0
nat = 48
ntyp = 1
ecutwfc = 80
occupations = 'smearing'
smearing = 'gaussian'
degauss = 0.1
vdw_corr='grimme-d2'
/
&electrons
diagonalization = 'david'
diago_thr_init = 1.d-4
mixing_mode = 'local-TF'
mixing_beta = 0.7
conv_thr = 1.d-8
/
&ions
/
ATOMIC_SPECIES
C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS angstrom
C -0.005594637 0.710607728 17.606217811
C -0.007113039 2.128152101 17.584272182
C 1.224800757 0.002792887 17.613037723
C 1.220781849 2.833821539 17.553802163
C 2.453370565 0.710361709 17.588200291
C 2.452466724 2.129238290 17.551425829
C 3.684434744 0.001530538 17.594476170
C 3.684438920 2.839550201 17.533796214
C 4.915544062 0.711333118 17.590036280
C 4.915853909 2.129726547 17.558981625
C 6.143486600 0.002227196 17.614492659
C 6.144397239 2.838931198 17.567937591
C -0.009386173 4.969207674 17.562655171
C -0.007017413 6.394548846 17.533586100
C 1.221221723 4.253471766 17.548052411
C 1.198574699 7.115165393 17.592468497
C 2.446729939 4.945634289 17.560357556
C 2.429014083 6.377364466 17.843730988
C 3.679896901 4.258356417 17.551643715
C 3.704632453 7.115561848 17.867361404
C 4.916336515 4.974358812 17.564482071
C 4.935632583 6.385210475 17.597930230
C 6.145763199 4.260558789 17.557531939
C 6.139436097 7.104085900 17.546822753
C -0.008057730 9.237466939 17.548881513
C -0.005309676 10.658828114 17.540319093
C 1.220546640 8.524488204 17.583337938
C 1.225791434 11.368226350 17.566890173
C 2.458810059 9.240431880 17.612862514
C 2.454941023 10.659162890 17.592221246
C 3.688725076 8.555854012 17.643635937
C 3.683918063 11.368771580 17.603925777
C 4.910904632 9.244786635 17.581661741
C 4.913395819 10.664333371 17.573847419
C 6.143923926 8.528771033 17.556446236
C 6.142987294 11.370161820 17.555480374
C -0.004309434 13.496944454 17.583281339
C -0.004505934 14.915030012 17.613620426
C 1.226582522 12.786684076 17.587667221
C 1.224762481 15.623384029 17.618836753
C 2.455170254 13.495545076 17.620810601
C 2.455394258 14.913895553 17.626574694
C 3.684071873 12.787455574 17.618041427
C 3.684499812 15.622198165 17.627916140
C 4.913552069 13.495405863 17.614905357
C 4.913417489 14.913710743 17.621452935
C 6.142676777 12.788081224 17.582175333
C 6.143988489 15.623015254 17.616347215
K_POINTS automatic
4 2 1 0 0 0
CELL_PARAMETERS angstrom
7.378073983 0.000000000 0.0000000000
0.000000000 17.038932 0.0000000000
0.000000000 0.000000000 25.00
I still get it stuck here in output:
Estimated max dynamical RAM per process > 9360.31MB
Check: negative/imaginary core charge= -0.000003 0.000000
Initial potential from superposition of free atoms
Check: negative starting charge= -0.001323
starting charge 191.99800, renormalised to 192.00000
negative rho (up, down): 1.323E-03 0.000E+00
Starting wfc are 192 randomized atomic wfcs
total cpu time spent up to now is 1474.4 secs
per-process dynamical memory: 1195.0 Mb
Self-consistent Calculation
iteration # 1 ecut= 80.00 Ry beta=0.70
Davidson diagonalization with overlap
This code has worked previously with qe/5.4.0, but gets stuck with 6.1 serial.
-Hud
On 5/9/2019 1:23:39 PM, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it> wrote:
You are mixing two different ways to indicate cell parameters
///---
EITHER:
+--------------------------------------------------------------------
Variable: celldm(i), i=1,6
Type: REAL
See: ibrav
Description: Crystallographic constants - see the "ibrav" variable.
Specify either these OR
"A","B","C","cosAB","cosBC","cosAC" NOT both.
Only needed values (depending on "ibrav") must
be specified
alat = "celldm"(1) is the lattice parameter "a"
(in BOHR)
If "ibrav"==0, only "celldm"(1) is used if present;
cell vectors are read from card "CELL_PARAMETERS"
+--------------------------------------------------------------------
OR:
+--------------------------------------------------------------------
Variables: A, B, C, cosAB, cosAC, cosBC
Type: REAL
See: ibrav
Description: Traditional crystallographic constants:
a,b,c in ANGSTROM
cosAB = cosine of the angle between axis a
and b (gamma)
cosAC = cosine of the angle between axis a
and c (beta)
cosBC = cosine of the angle between axis b
and c (alpha)
The axis are chosen according to the value of
@ref ibrav.
Specify either these OR @ref celldm but NOT both.
Only needed values (depending on @ref ibrav)
must be specified.
The lattice parameter alat = A (in ANGSTROM ).
If @ref ibrav == 0, only A is used if present, and
cell vectors are read from card @ref CELL_PARAMETERS.
+--------------------------------------------------------------------
\\\---
This might be the cause of the strange behavior, supposing that your
machine has the ~4GB of free RAM to perform the calculation indicated
in the output. However, in the case of a regular hcp supercell you
should not need at all to indicate the cosAB and cosAC values.
HTH
Giuseppe
Quoting "H1 at GMAIL" :
> Hi Giuseppe
>
> apologies. My input file:
>
> &control
> calculation = 'scf'
> prefix = 'graphene'
> pseudo_dir = '/gscratch/hwahab/DFT-code/psp/'
> outdir = './'
> restart_mode = 'from_scratch'
> etot_conv_thr = 1.d-6
> forc_conv_thr = 1.d-5
> /
> &system
> ibrav = 4
> celldm(1) = 9.84
> celldm(3) = 10
> cosAB = -0.5
> cosAC = 1
> nat = 32
> ntyp = 1
> ecutwfc = 80
> occupations = 'smearing'
> smearing = 'gaussian'
> degauss = 0.1
> vdw_corr='grimme-d2'
> /
>
> &electrons
> diagonalization = 'david'
> diago_thr_init = 1.d-4
> mixing_mode = 'local-TF'
> mixing_beta = 0.7
> conv_thr = 1.d-10
> /
>
> &ions
> /
>
> ATOMIC_SPECIES
> C 12.0107 C.pbe-mt_gipaw.UPF
>
> ATOMIC_POSITIONS crystal
> C 0.16667 0.08333 0.00000
> C 0.41667 0.08333 0.00000
> C 0.66667 0.08333 0.00000
> C 0.91667 0.08333 0.00000
> C 0.08333 0.16667 0.00000
> C 0.33333 0.16667 0.00000
> C 0.58333 0.16667 0.00000
> C 0.83333 0.16667 0.00000
> C 0.16667 0.33333 0.00000
> C 0.41667 0.33333 0.00000
> C 0.66667 0.33333 0.00000
> C 0.91667 0.33333 0.00000
> C 0.08333 0.41667 0.00000
> C 0.33333 0.41667 0.00000
> C 0.58333 0.41667 0.00000
> C 0.83333 0.41667 0.00000
> C 0.16667 0.58333 0.00000
> C 0.41667 0.58333 0.00000
> C 0.66667 0.58333 0.00000
> C 0.91667 0.58333 0.00000
> C 0.08333 0.66667 0.00000
> C 0.33333 0.66667 0.00000
> C 0.58333 0.66667 0.00000
> C 0.83333 0.66667 0.00000
> C 0.16667 0.83333 0.00000
> C 0.41667 0.83333 0.00000
> C 0.66667 0.83333 0.00000
> C 0.91667 0.83333 0.00000
> C 0.08333 0.91667 0.00000
> C 0.33333 0.91667 0.00000
> C 0.58333 0.91667 0.00000
> C 0.83333 0.91667 0.00000
>
>
> K_POINTS automatic
> 8 8 1 0 0 0
>
> And the end snippet of the output:
>
> Estimated max dynamical RAM per process > 3558.76MB
>
> Initial potential from superposition of free atoms
>
> starting charge 111.99996, renormalised to 128.00000
>
> negative rho (up, down): 5.479E-05 0.000E+00
> Starting wfc are 256 randomized atomic wfcs
>
> There is no error outputs, it just gets stuck there..
>
> Hope this makes sense.
>
> Hud Wahab
> University of Wyoming
> 1000 E University Ave
> Laramie WY, 82072
> Email: hwahab at uwyo.edu
> On 5/9/2019 12:50:50 PM, Giuseppe Mattioli
> wrote:
>
> Dear Hud (please sign always with full name and scientific affiliation
> the posts to this forum, we appreciate it)
> It is impossible to help you if you don't post the input of your
> calculation and the relevant part of your output (where does the code
> stop?). Is there any system error like a segfault printed, e.g., in a
> nohup.out file? It is primarily important to look into such kind of
> information, in order to see if the error is reproducible on different
> machines/architectures or by using different compilers/libraries.
> HTH
> Giuseppe
>
> Quoting "H1 at GMAIL" :
>
>> Hello
>> I run on 6.1-serial. My pw.x scf runs ok with small size systems 2
>> atoms, but nothing happens when scaled to 4x4 or 32 atoms. I let it
>> run for more than an hour and don't expect that the calculation
>> takes that long.
>>
>> From the troubleshooting in User Guide I see it might be a
>> floating-point error causing endless NaNs - how to handle for such
>> exceptions?
>>
>> As I can't provide the error output, I am not sure what details you
>> need to troubleshoot, but let me know if something is missing
>>
>> Cheers, Hud
>> Dept. Chemical Engineering
>> University of Wyoming
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail:
>
> _______________________________________________
> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
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GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail:
_______________________________________________
Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
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