[Pw_forum] MD calculations result in errors due to ions

Darshana Wickramaratne dwick004 at ucr.edu
Mon Oct 6 20:43:52 CEST 2014


Shenna,

In your input file the &ions namelist has not been closed.  Insert a
forward slash on a new line before the ATOMIC_SPECIES line of your input
file and this should work.

-- 
Darshana Wickramaratne
PhD Candidate
Laboratory for Terascale and Terahertz Electronics (LATTE)
Department of Electrical Engineering

On Mon, Oct 6, 2014 at 11:25 AM, shenna shearin <smsheari at gmail.com> wrote:

> Hello!
>
> I am trying to run a MD calculation on silica supported copper cluster in
> supercell. I have went through the archives to find similar problems but I
> havent come across any. I continue to get this error:
>
>  task #        36      from  read_namelists  : error #        19
> reading namelist ions
>
> Its very clear that my error is a result of the ions but I am unsure how
> to rectify this problem.
> My input reads:
>
> &control
>     calculation='md',
>     title='SiO2 edingtonite strcture:(100)surface + Cu7 using MD',
>     restart_mode='from_scratch',
>     prefix='sio2_01_Cu7'
>     outdir='tempdir',
>     pseudo_dir='/student/chemistry/shenna/QE/pseudo',
>    tstress=.true.,
>     tprnfor=.true.,
>     dt=20,
>     nstep=100,
>     disk_io='high'
>  /
>  &system
>     ibrav= 8,
>     celldm(1)=24.415132d0,
>     celldm(2)= 1.068111d0
>     celldm(3)= 1.500000d0,
>     nat=75,
>     ntyp=4,
>     ecutwfc =40.0,
>     ecutrho =400.0,
>     occupations='smearing',
>     smearing='gaussian',
>     degauss=0.02,
>     nosym=.true.
>  /
>  &electrons
>     conv_thr=1.0d-8,
>     mixing_beta=0.7,
>     mixing_mode='local-TF',
>  /
>  &ions
>    ! pot_extrapolation='second-order'
>    ! wfc_extrapolation='second-order'
> ATOMIC_SPECIES
>    Si    28.0855  Si.pbe-n-van.UPF
>     O    15.9994   O.pbe-rrkjus.UPF
>     H     1.0079   H.pbe-rrkjus.UPF
>    Cu    63.546   Cu.pbe-d-rrkjus.UPF
> ATOMIC_POSITIONS alat
> Si      -0.000244108   0.234531476   0.382996575
> Si       0.500780933   0.246371521   0.349771956
> Si      -0.003085319   0.774396819   0.373068753
> Si       0.495440733   0.773655800   0.322613709
> Si       0.197752462   0.092397624   0.396252391
> Si       0.684103131   0.096240992   0.372099296
> Si       0.182139825   0.627586534   0.336701790
> Si       0.687781801   0.630167356   0.314750098
> Si       0.182148836   0.381561889   0.344493517
> Si       0.698371972   0.382440164   0.314380735
> Si       0.192627183   0.911737253   0.404108539
> Si       0.683247159   0.917639875   0.363603039
> Si       0.320853610   0.269581729   0.507578952
> Si       0.797601301   0.262138922   0.502124058
> Si       0.324582074   0.740987442   0.495878923
> Si       0.786654016   0.747136655   0.500637614
> Si       0.294603013   0.212841434   0.221585440
> Si       0.821864850   0.213175735   0.215785040
> Si       0.287855418   0.796162508   0.212270581
> Si       0.825759493   0.802737034   0.214689603
> O        0.195319211  -0.031090285   0.420505869
> O        0.679945602  -0.027828709   0.388119015
> O        0.179284804   0.503698198   0.318138398
> O        0.693743373   0.506686187   0.294876743
> O        0.080299620   0.138902014   0.402308784
> O        0.565163376   0.139655493   0.362945676
> O        0.064556761   0.669697917   0.354843247
> O        0.570858666   0.673672529   0.297597948
> O        0.065236393   0.341459880   0.368434920
> O        0.578110278   0.342015865   0.320731154
> O        0.072966973   0.868731033   0.409736448
> O        0.567111094   0.876334905   0.336802140
> O        0.274199920   0.155429456   0.476006604
> O        0.739773382   0.153439797   0.469040984
> O        0.251999037   0.654288055   0.437023821
> O        0.718865837   0.650031669   0.438674820
> O        0.256420213   0.358806206   0.443855995
> O        0.755183578   0.355264815   0.423050693
> O        0.262296512   0.852599437   0.491693574
> O        0.729320938   0.853979378   0.462624430
> O        0.243788152   0.112921583   0.279682590
> O        0.746188229   0.124781782   0.265872313
> O        0.233139378   0.684624238   0.235771569
> O        0.770559394   0.691791040   0.244354113
> O        0.227914938   0.317745337   0.245041535
> O        0.761042921   0.324872652   0.221624418
> O        0.240626796   0.884130208   0.290248128
> O        0.756332693   0.896255274   0.262721208
> O        0.444953862   0.280516666   0.460880830
> O        0.921618106   0.246426282   0.480421546
> O        0.431996953   0.752339064   0.427838127
> O        0.905243768   0.750287996   0.456365177
> O        0.412690570   0.232608522   0.262666382
> O        0.931221684   0.214554786   0.278679886
> O        0.413656458   0.789218346   0.228110033
> O        0.942025906   0.805528078   0.263275790
> O        0.325211873   0.289353927   0.629055365
> O        0.772241487   0.294394065   0.618478326
> O        0.778439837   0.721480026   0.620635393
> O        0.294866944   0.185365142   0.098956770
> O        0.842369489   0.191465677   0.093905236
> O        0.261679850   0.823707650   0.092427869
> O        0.830294911   0.816050437   0.089967999
> O        0.354967999   0.699459413   0.608417960
> H        0.321404868   0.236116240   0.050789137
> H        0.901148972   0.149383109   0.074620786
> H        0.296678525   0.881770613   0.060664272
> H        0.895210417   0.802526613   0.055248268
> Cu       0.394368353   0.405710166   0.679412999
> Cu       0.521771611   0.405464658   0.546127201
> Cu       0.627834896   0.572637974   0.545887048
> Cu       0.562617084   0.511102070   0.712542993
> Cu       0.704923984   0.417041107   0.645125500
> Cu       0.428454601   0.575829299   0.604122799
> Cu       0.737663540   0.601590361   0.693735563
> K_POINTS (gamma)
>
> ______________________________________________________________________________________
>
> Your help is greatly appreciated!
> --
> Shenna Shearin
> PhD candidate
> Department of Computational Science & Engineering,
> North Carolina A & T State University
> Greensboro, NC 27411
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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