Hi
I have run the in put on my mac with no problem.
The only change was the introducing the path for out directory.
outdir = '/Users/............................./tmp' ,
regards
Fariba
IASBS
On Fri, 24/08/2018 08:00 PM, Dan Gil <[email protected]> wrote:
>
Hi,
>
>
I am using pwscf v6.3, and running into some issues that I could not resolve.
>
I first ran simulations with hydroxylated sapphire (0001) surface with only 42
atoms successfully. Now I am trying to run an identical simulation with the
same surface with 168 atoms (2x2 supercell) and here is where I am running into
issues.
>
I've tried various settings, and I've gotten a variety of error messages. With
the input format shown below, I get the following error from the HPC.
>
- - - - -
/tmp/slurm/job8327489/slurm_script: line 11: 111713 Killed
pw.x < sapphire.pw.in > sapphire.pw.out
> slurmstepd: error: Exceeded step memory limit at some point.
- - - - -
>
When I run it on my personal computer, I get this error:
>
- - - - -
task # 0
> from diropn : error # 10
> error opening sapphire/pwscf.wfc1
>
- - - - -
>
And indeed, there is no pwscf.wfc1 to be seen.
>
Here is the input:
>
- - - - -
>
&control
> calculation='relax',
> wf_collect = .true. ,
> outdir = 'sapphire' ,
> restart_mode = 'from_scratch' ,
> pseudo_dir = 'pseudo' ,
> disk_io = 'low' ,
> verbosity = 'low' ,
> max_seconds = 72000 ,
> /
> &system
> ibrav = 4 ,
> celldm(1)=17.99085377,
> celldm(3)=10,
> nat = 168 ,
> ntyp = 3 ,
> ecutwfc =50,
> ecutrho =400,
> smearing='mp',
> occupations='smearing',
> degauss=0.03,
> /
> &electrons
> diagonalization='david',
> conv_thr = 1.d-9,
> mixing_mode = 'plain',
> /
> &ions
> /
> ATOMIC_SPECIES
> Al 26.981539 Al.pbe-n-rrkjus_psl.0.1.UPF
> O 15.999000 O.pbe-n-rrkjus_psl.0.1.UPF
> H 1.000800 H.pbe-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS crystal
> Al 0.000000000 0.000000000 0.095697893
> Al 0.000000000 0.000000000 0.177259148
> Al 0.000000000 0.000000000 0.040053860
> Al 0.000000000 0.000000000 0.232903158
> Al 0.333333311 0.166666621 0.187801968
> Al 0.333333311 0.166666621 0.270721823
> Al 0.333333311 0.166666621 0.131337383
> Al 0.333333311 0.166666621 0.045832216
> Al 0.166666682 0.333333364 0.002235215
> Al 0.166666682 0.333333364 0.085155073
> Al 0.166666682 0.333333364 0.227124825
> Al 0.166666682 0.333333364 0.141619636
> Al 0.500000000 0.000000000 0.095697893
> Al 0.500000000 0.000000000 0.177259148
> Al 0.500000000 0.000000000 0.040053860
> Al 0.500000000 0.000000000 0.232903158
> Al 0.833333311 0.166666621 0.187801968
> Al 0.833333311 0.166666621 0.270721823
> Al 0.833333311 0.166666621 0.131337383
> Al 0.833333311 0.166666621 0.045832216
> Al 0.666666682 0.333333364 0.002235215
> Al 0.666666682 0.333333364 0.085155073
> Al 0.666666682 0.333333364 0.227124825
> Al 0.666666682 0.333333364 0.141619636
> Al 0.500000000 0.500000000 0.095697893
> Al 0.500000000 0.500000000 0.177259148
> Al 0.500000000 0.500000000 0.040053860
> Al 0.500000000 0.500000000 0.232903158
> Al 0.833333311 0.666666621 0.187801968
> Al 0.833333311 0.666666621 0.270721823
> Al 0.833333311 0.666666621 0.131337383
> Al 0.833333311 0.666666621 0.045832216
> Al 0.666666682 0.833333364 0.002235215
> Al 0.666666682 0.833333364 0.085155073
> Al 0.666666682 0.833333364 0.227124825
> Al 0.666666682 0.833333364 0.141619636
> Al 0.000000000 0.500000000 0.095697893
> Al 0.000000000 0.500000000 0.177259148
> Al 0.000000000 0.500000000 0.040053860
> Al 0.000000000 0.500000000 0.232903158
> Al 0.333333311 0.666666621 0.187801968
> Al 0.333333311 0.666666621 0.270721823
> Al 0.333333311 0.666666621 0.131337383
> Al 0.333333311 0.666666621 0.045832216
> Al 0.166666682 0.833333364 0.002235215
> Al 0.166666682 0.833333364 0.085155073
> Al 0.166666682 0.833333364 0.227124825
> Al 0.166666682 0.833333364 0.141619636
> O 0.155404208 0.001886947 0.067662578
> O 0.344595898 -0.001886947 0.205294440
> O -0.001886987 0.153517181 0.067662578
> O 0.001886979 0.346482804 0.205294440
> O 0.346482772 0.344595857 0.067662578
> O 0.153517221 0.155404128 0.205294440
> O 0.171949672 0.170609214 0.023055667
> O 0.333498557 0.320107131 0.159438914
> O 0.329390758 0.001340470 0.023055667
> O 0.179892883 0.013391458 0.159438914
> O 0.328050321 0.329390771 0.249901352
> O 0.013391439 0.333498589 0.113518146
> O 0.166501497 0.179892975 0.113518146
> O 0.001340490 0.171949804 0.249901352
> O 0.320107118 -0.013391458 0.113518146
> O -0.013391447 0.166501396 0.159438914
> O -0.001340437 0.328050302 0.023055667
> O 0.170609242 -0.001340470 0.249901352
> O 0.181666250 0.166682692 0.300333049
> O 0.333317280 0.014983569 0.300333049
> O 0.485016464 0.318333724 0.300333049
> O 0.014983590 0.181666382 -0.027376009
> O 0.318333743 0.333317293 -0.027376009
> O 0.166682713 0.485016416 -0.027376009
> O 0.655404208 0.001886947 0.067662578
> O 0.844595898 -0.001886947 0.205294440
> O 0.498113014 0.153517181 0.067662578
> O 0.501886979 0.346482804 0.205294440
> O 0.846482772 0.344595857 0.067662578
> O 0.653517221 0.155404128 0.205294440
> O 0.671949672 0.170609214 0.023055667
> O 0.833498557 0.320107131 0.159438914
> O 0.829390758 0.001340470 0.023055667
> O 0.679892883 0.013391458 0.159438914
> O 0.828050321 0.329390771 0.249901352
> O 0.513391439 0.333498589 0.113518146
> O 0.666501497 0.179892975 0.113518146
> O 0.501340490 0.171949804 0.249901352
> O 0.820107118 -0.013391458 0.113518146
> O 0.486608554 0.166501396 0.159438914
> O 0.498659563 0.328050302 0.023055667
> O 0.670609242 -0.001340470 0.249901352
> O 0.681666250 0.166682692 0.300333049
> O 0.833317280 0.014983569 0.300333049
> O 0.985016464 0.318333724 0.300333049
> O 0.514983590 0.181666382 -0.027376009
> O 0.818333743 0.333317293 -0.027376009
> O 0.666682713 0.485016416 -0.027376009
> O 0.655404208 0.501886947 0.067662578
> O 0.844595898 0.498113054 0.205294440
> O 0.498113014 0.653517181 0.067662578
> O 0.501886979 0.846482804 0.205294440
> O 0.846482772 0.844595857 0.067662578
> O 0.653517221 0.655404128 0.205294440
> O 0.671949672 0.670609214 0.023055667
> O 0.833498557 0.820107131 0.159438914
> O 0.829390758 0.501340470 0.023055667
> O 0.679892883 0.513391458 0.159438914
> O 0.828050321 0.829390771 0.249901352
> O 0.513391439 0.833498589 0.113518146
> O 0.666501497 0.679892975 0.113518146
> O 0.501340490 0.671949804 0.249901352
> O 0.820107118 0.486608542 0.113518146
> O 0.486608554 0.666501396 0.159438914
> O 0.498659563 0.828050302 0.023055667
> O 0.670609242 0.498659531 0.249901352
> O 0.681666250 0.666682692 0.300333049
> O 0.833317280 0.514983569 0.300333049
> O 0.985016464 0.818333724 0.300333049
> O 0.514983590 0.681666382 -0.027376009
> O 0.818333743 0.833317293 -0.027376009
> O 0.666682713 0.985016416 -0.027376009
> O 0.155404208 0.501886947 0.067662578
> O 0.344595898 0.498113054 0.205294440
> O -0.001886987 0.653517181 0.067662578
> O 0.001886979 0.846482804 0.205294440
> O 0.346482772 0.844595857 0.067662578
> O 0.153517221 0.655404128 0.205294440
> O 0.171949672 0.670609214 0.023055667
> O 0.333498557 0.820107131 0.159438914
> O 0.329390758 0.501340470 0.023055667
> O 0.179892883 0.513391458 0.159438914
> O 0.328050321 0.829390771 0.249901352
> O 0.013391439 0.833498589 0.113518146
> O 0.166501497 0.679892975 0.113518146
> O 0.001340490 0.671949804 0.249901352
> O 0.320107118 0.486608542 0.113518146
> O -0.013391447 0.666501396 0.159438914
> O -0.001340437 0.828050302 0.023055667
> O 0.170609242 0.498659531 0.249901352
> O 0.181666250 0.666682692 0.300333049
> O 0.333317280 0.514983569 0.300333049
> O 0.485016464 0.818333724 0.300333049
> O 0.014983590 0.681666382 -0.027376009
> O 0.318333743 0.833317293 -0.027376009
> O 0.166682713 0.985016416 -0.027376009
> H 0.000000000 0.000000000 0.301962321
> H 0.333333311 0.166666621 0.311183904
> H 0.166666682 0.333333364 0.301819835
> H 0.000000000 0.000000000 -0.029005281
> H 0.333333311 0.166666621 -0.028862795
> H 0.166666682 0.333333364 -0.038226863
> H 0.500000000 0.000000000 0.301962321
> H 0.833333311 0.166666621 0.311183904
> H 0.666666682 0.333333364 0.301819835
> H 0.500000000 0.000000000 -0.029005281
> H 0.833333311 0.166666621 -0.028862795
> H 0.666666682 0.333333364 -0.038226863
> H 0.500000000 0.500000000 0.301962321
> H 0.833333311 0.666666621 0.311183904
> H 0.666666682 0.833333364 0.301819835
> H 0.500000000 0.500000000 -0.029005281
> H 0.833333311 0.666666621 -0.028862795
> H 0.666666682 0.833333364 -0.038226863
> H 0.000000000 0.500000000 0.301962321
> H 0.333333311 0.666666621 0.311183904
> H 0.166666682 0.833333364 0.301819835
> H 0.000000000 0.500000000 -0.029005281
> H 0.333333311 0.666666621 -0.028862795
> H 0.166666682 0.833333364 -0.038226863
> K_POINTS automatic
> 1 1 1 1 1 1
> - - - - -
>
>
Best Regards,
>
Dan Gil
PhD Candidate
Department of Chemical and Biomolecular Engineering
Case Western Reserve University
>
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