[Pw_forum] From davcio: error #10
Ngoc Linh Nguyen
nnlinh at sissa.it
Sat Feb 20 15:02:07 CET 2010
Patrick Holvey wrote:
> Thanks for all of the assistance everyone.
>
> Linh, I tried out your suggestions and it worked like a charm. I was
> wondering if you would explain to me how you arrived at those numbers
I suppose that you have been not familiar with Xcrysen package :D.
Firstly, you should find the lattice constants of the given slab, then
calculate the positions of atoms belong to these parameters.
By assuming that the values of the positions of atoms are right and
present in your input file, I visualize the input file by Xcrysden
package .
- Then, we displayed the Crystal cells (Display -> Crystal Cells).
Here, you can be seen that, with the celldm(1)=30, the atoms are located
just at the conner of hole supercell.
- You duplicate the supercell be long to Ox or Oy (Modify -> Number
of unit drawn), you can see that your slab is not continuous belong to
Ox and Oy axis because the supercell sides are to lager. Thus, I should
decrease celldm(1) to keep continuousness of the slab. Of couse, my
values maybe not precise completely, so you should recalculate so that
the atom positions agree with periodicity.
Moreover, you should also recalculate the Celldm(3) value associate with
the new Celldm(1) one. (I suppose you've known how to get a suitable of
Celldm(3))
> and why they worked while the prior ones did not.
You can see that when Celldm(1) is too large and a wrong value, the G
cutoff , FFT grid values are very larger, and an insufficient virtual
memory could be happened.
> Further, I'm going to be moving the ion closer to the surface in
> future calculations. Will I have to recalculate those numbers or am I
> ok to keep them as they are now?
The Celldm(1) value should be fixed, because it does not relate to ion
moving, but Celldm(3) maybe changed if you move too far from surface
with respect to the Oz side of supercell.
Linh
> Many thanks,
>
> Patrick Holvey
> University of Notre Dame
>
> On Thu, Feb 18, 2010 at 12:19 PM, Ngoc Linh Nguyen <nnlinh at sissa.it
> <mailto:nnlinh at sissa.it>> wrote:
>
> Patrick Holvey wrote:
> > Good morning everyone! I'm new at this so I hope this posts
> properly.
> >
> > I'm attempting to perform an SCF calculation on an Au slab with a
> > single polarized ion above it. However, every instance crashes with
> > the error from davcio: error #10.
> That error is induced by either error in writing or reading to/from
> output files or corruption of job. It seems to be 2nd case in your
> problem.
>
> I have a look on your input file, and find out that the value of
> celldm(1) is too large. It not only makes that supercell does not
> present the slab model in the right way but also stops running of pw.x
> because of needed too much memory of RAM.
>
> Let recalculate celldm(1) and celldm(3), I assume celldm(1) = 10.50
> Bohr and celldm(3) = 4.979, You will have a right slab model and
> the run
> will work well.
>
> Linh
>
> > I've included both the input and output files below. This error
> > results from, according to what I've found in this forum results
> from
> > corrupted wavefiles? I have all permissions necessary on this
> > environment and the disk is not dying, so those options are out.
> Any
> > help in the matter would be greatly appreciated.
>
>
> >
> > Many Thanks,
> >
> > Patrick Holvey
> > University of Notre Dame
> >
> > INPUT:
> > ----------------------------------------------------------
> > &CONTROL
> > calculation = 'scf' ,
> > restart_mode = 'from_scratch' ,
> > outdir = '/dscratch/pholvey/espresso/tmp3' ,
> > pseudo_dir =
> > '/afs/crc.nd.edu/group/gezelter/espresso/4.1.2/peudo
> <http://crc.nd.edu/group/gezelter/espresso/4.1.2/peudo>
> > <http://crc.nd.edu/group/gezelter/espresso/4.1.2/peudo>' ,
> > prefix = 'AuSlab-li+-10.5' ,
> > nstep = 200 ,
> > tstress = .true. ,
> > tprnfor = .true. ,
> > wf_collect = .true. ,
> > /
> > &SYSTEM
> > ibrav = 4,
> > celldm(1) = 30.0,
> > celldm(3) = 2.979,
> > nat = 13,
> > ntyp = 2,
> > ecutwfc = 30 ,
> > ecutrho = 300 ,
> > tot_charge = 1.000000,
> > occupations = 'smearing' ,
> > degauss = 0.02 ,
> > smearing = 'methfessel-paxton' ,
> > nspin = 2 ,
> > starting_magnetization(1) = 0.2,
> > starting_magnetization(2) = 0.5,
> > starting_magnetization(3) = 1.0,
> > /
> > &ELECTRONS
> > conv_thr = 1.D-6 ,
> > mixing_beta = 0.4D0 ,
> > diagonalization = 'david' ,
> > /
> > &IONS
> > ion_dynamics = 'bfgs' ,
> > /
> > ATOMIC_SPECIES
> > Au 196.96569 Au.pbe-nd-rrkjus.UPF
> > Li 6.941 Li.pbe-s-mt.UPF
> > ATOMIC_POSITIONS angstrom
> > Li 2.774511948 0.000118907 15.44640680 1 1 1
> > Au 2.775000000 1.602000000 0.000000000 0 0 0
> > Au 0.000000000 3.204000000 2.265000000 0 0 0
> > Au 0.000095442 0.000159091 4.946851613 0 0 0
> > Au 1.387000000 4.005000000 0.000000000 0 0 0
> > Au 1.387000000 0.801000000 2.265000000 0 0 0
> > Au -1.387039610 2.402849200 4.946626283 0 0 0
> > Au -1.387000000 4.005000000 0.000000000 0 0 0
> > Au 4.162000000 0.801000000 2.265000000 0 0 0
> > Au 1.387455156 2.402979759 4.946182797 0 0 0
> > Au 0.000000000 1.602000000 0.000000000 0 0 0
> > Au 2.775000000 3.204000000 2.265000000 0 0 0
> > Au 2.774511948 0.000118907 4.946406801 0 0 0
> > K_POINTS automatic
> > 4 4 1 1 1 1
> >
> >
> > OUTPUT:
> > -------------------------------------------------------------------
> > Program PWSCF v.4.1.2 starts ...
> > Today is 15Feb2010 at 23:39:52
> >
> > Parallel version (MPI)
> >
> > Number of processors in use: 16
> > R & G space division: proc/pool = 16
> >
> > For Norm-Conserving or Ultrasoft (Vanderbilt)
> Pseudopotentials or PAW
> >
> > Current dimensions of program pwscf are:
> > Max number of different atomic species (ntypx) = 10
> > Max number of k-points (npk) = 40000
> > Max angular momentum in pseudopotentials (lmaxx) = 3
> > Waiting for input...
> > Warning: card &IONS ignored
> > Warning: card ION_DYNAMICS = 'BFGS' , ignored
> > Warning: card / ignored
> >
> > Subspace diagonalization in iterative solution of the
> eigenvalue
> > problem:
> > a parallel distributed memory algorithm will be used,
> > eigenstates matrixes will be distributed block like on
> > ortho sub-group = 4* 4 procs
> >
> >
> > Planes per process (thick) : nr3 =500 npp = 32 ncplane =32400
> > Planes per process (smooth): nr3s=320 npps= 20 ncplanes=11664
> >
> > Proc/ planes cols G planes cols G columns G
> > Pool (dense grid) (smooth grid) (wavefct grid)
> > 1 32 1162 382028 20 465 96661 123 13177
> > 2 32 1163 382035 20 465 96645 123 13177
> > 3 32 1163 382035 20 465 96625 122 13172
> > 4 32 1163 382037 20 465 96639 122 13172
> > 5 31 1162 382022 20 465 96633 122 13172
> > 6 31 1162 382022 20 465 96641 122 13172
> > 7 31 1162 382022 20 465 96633 124 13176
> > 8 31 1162 382022 20 465 96643 124 13176
> > 9 31 1162 382022 20 465 96623 124 13176
> > 10 31 1162 382022 20 466 96666 123 13173
> > 11 31 1163 382035 20 466 96688 123 13173
> > 12 31 1163 382035 20 466 96694 123 13175
> > 13 31 1163 382035 20 466 96680 123 13175
> > 14 31 1163 382035 20 466 96662 124 13172
> > 15 31 1163 382035 20 466 96688 124 13172
> > 16 31 1163 382035 20 466 96684 123 13175
> > tot 500 18601 6112477 320 7447 1546505 1969 210785
> >
> >
> >
> > bravais-lattice index = 4
> > lattice parameter (a_0) = 30.0000 a.u.
> > unit-cell volume = 69657.0213 (a.u.)^3
> > number of atoms/cell = 13
> > number of atomic types = 2
> > number of electrons = 134.00
> > number of Kohn-Sham states= 80
> > kinetic-energy cutoff = 30.0000 Ry
> > charge density cutoff = 300.0000 Ry
> > convergence threshold = 1.0E-06
> > mixing beta = 0.4000
> > number of iterations used = 8 plain mixing
> > Exchange-correlation = SLA PW PBE PBE (1434)
> >
> > celldm(1)= 30.000000 celldm(2)= 0.000000 celldm(3)=
> 2.979000
> > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)=
> 0.000000
> >
> > crystal axes: (cart. coord. in units of a_0)
> > a(1) = ( 1.000000 0.000000 0.000000 )
> > a(2) = ( -0.500000 0.866025 0.000000 )
> > a(3) = ( 0.000000 0.000000 2.979000 )
> >
> > reciprocal axes: (cart. coord. in units 2 pi/a_0)
> > b(1) = ( 1.000000 0.577350 0.000000 )
> > b(2) = ( 0.000000 1.154701 0.000000 )
> > b(3) = ( 0.000000 0.000000 0.335683 )
> >
> >
> > PseudoPot. # 1 for Au read from file Au.pbe-nd-rrkjus.UPF
> > Pseudo is Ultrasoft + core correction, Zval = 11.0
> > Generated by new atomic code, or converted to UPF format
> > Using radial grid of 1279 points, 3 beta functions with:
> > l(1) = 2
> > l(2) = 2
> > l(3) = 1
> > Q(r) pseudized with 0 coefficients
> >
> >
> > PseudoPot. # 2 for Li read from file Li.pbe-s-mt.UPF
> > Pseudo is Norm-conserving, Zval = 3.0
> > Generated by new atomic code, or converted to UPF format
> > Using radial grid of 881 points, 1 beta functions with:
> > l(1) = 0
> >
> > atomic species valence mass pseudopotential
> > Au 11.00 196.96569 Au( 1.00)
> > Li 3.00 6.94100 Li( 1.00)
> >
> > Starting magnetic structure
> > atomic species magnetization
> > Au 0.200
> > Li 0.500
> >
> > No symmetry!
> >
> > Cartesian axes
> >
> > site n. atom positions (a_0 units)
> > 1 Li tau( 1) = ( 0.1747689 0.0000075
> > 0.9729826 )
> > 2 Au tau( 2) = ( 0.1747997 0.1009114
> > 0.0000000 )
> > 3 Au tau( 3) = ( 0.0000000 0.2018228
> > 0.1426743 )
> > 4 Au tau( 4) = ( 0.0000060 0.0000100
> > 0.3116065 )
> > 5 Au tau( 5) = ( 0.0873683 0.2522784
> > 0.0000000 )
> > 6 Au tau( 6) = ( 0.0873683 0.0504557
> > 0.1426743 )
> > 7 Au tau( 7) = ( -0.0873708 0.1513576
> > 0.3115923 )
> > 8 Au tau( 8) = ( -0.0873683 0.2522784
> > 0.0000000 )
> > 9 Au tau( 9) = ( 0.2621680 0.0504557
> > 0.1426743 )
> > 10 Au tau( 10) = ( 0.0873970 0.1513658
> > 0.3115644 )
> > 11 Au tau( 11) = ( 0.0000000 0.1009114
> > 0.0000000 )
> > 12 Au tau( 12) = ( 0.1747997 0.2018228
> > 0.1426743 )
> > 13 Au tau( 13) = ( 0.1747689 0.0000075
> > 0.3115785 )
> >
> > number of k points= 48 gaussian broad. (Ry)= 0.0200
> > ngauss = 1
> > cart. coord. in units 2pi/a_0
> > k( 1) = ( 0.1250000 0.2165064 -0.1678416), wk =
> > 0.0416667
> > k( 2) = ( 0.1250000 0.5051815 -0.1678416), wk =
> > 0.0416667
> > k( 3) = ( 0.1250000 -0.3608439 -0.1678416), wk =
> > 0.0416667
> > k( 4) = ( 0.1250000 -0.0721688 -0.1678416), wk =
> > 0.0416667
> > k( 5) = ( 0.3750000 0.6495191 -0.1678416), wk =
> > 0.0416667
> > k( 6) = ( 0.3750000 -0.2165064 -0.1678416), wk =
> > 0.0416667
> > k( 7) = ( -0.1250000 0.2165064 0.1678416), wk =
> > 0.0416667
> > k( 8) = ( 0.2500000 0.0000000 -0.1678416), wk =
> > 0.0416667
> > k( 9) = ( -0.1250000 0.5051815 0.1678416), wk =
> > 0.0416667
> > k( 10) = ( -0.3750000 0.3608439 -0.1678416), wk =
> > 0.0416667
> > k( 11) = ( 0.5000000 0.1443376 -0.1678416), wk =
> > 0.0416667
> > k( 12) = ( -0.3750000 -0.3608439 0.1678416), wk =
> > 0.0416667
> > k( 13) = ( 0.5000000 -0.1443376 0.1678416), wk =
> > 0.0416667
> > k( 14) = ( -0.1250000 -0.3608439 0.1678416), wk =
> > 0.0416667
> > k( 15) = ( 0.3750000 -0.0721688 -0.1678416), wk =
> > 0.0416667
> > k( 16) = ( -0.2500000 -0.2886751 -0.1678416), wk =
> > 0.0416667
> > k( 17) = ( 0.3750000 0.0721688 0.1678416), wk =
> > 0.0416667
> > k( 18) = ( -0.2500000 0.2886751 0.1678416), wk =
> > 0.0416667
> > k( 19) = ( -0.1250000 -0.0721688 0.1678416), wk =
> > 0.0416667
> > k( 20) = ( 0.0000000 -0.1443376 -0.1678416), wk =
> > 0.0416667
> > k( 21) = ( -0.3750000 0.6495191 0.1678416), wk =
> > 0.0416667
> > k( 22) = ( 0.7500000 0.0000000 -0.1678416), wk =
> > 0.0416667
> > k( 23) = ( -0.3750000 -0.2165064 0.1678416), wk =
> > 0.0416667
> > k( 24) = ( 0.0000000 -0.4330127 -0.1678416), wk =
> > 0.0416667
> > k( 25) = ( 0.1250000 0.2165064 -0.1678416), wk =
> > 0.0416667
> > k( 26) = ( 0.1250000 0.5051815 -0.1678416), wk =
> > 0.0416667
> > k( 27) = ( 0.1250000 -0.3608439 -0.1678416), wk =
> > 0.0416667
> > k( 28) = ( 0.1250000 -0.0721688 -0.1678416), wk =
> > 0.0416667
> > k( 29) = ( 0.3750000 0.6495191 -0.1678416), wk =
> > 0.0416667
> > k( 30) = ( 0.3750000 -0.2165064 -0.1678416), wk =
> > 0.0416667
> > k( 31) = ( -0.1250000 0.2165064 0.1678416), wk =
> > 0.0416667
> > k( 32) = ( 0.2500000 0.0000000 -0.1678416), wk =
> > 0.0416667
> > k( 33) = ( -0.1250000 0.5051815 0.1678416), wk =
> > 0.0416667
> > k( 34) = ( -0.3750000 0.3608439 -0.1678416), wk =
> > 0.0416667
> > k( 35) = ( 0.5000000 0.1443376 -0.1678416), wk =
> > 0.0416667
> > k( 36) = ( -0.3750000 -0.3608439 0.1678416), wk =
> > 0.0416667
> > k( 37) = ( 0.5000000 -0.1443376 0.1678416), wk =
> > 0.0416667
> > k( 38) = ( -0.1250000 -0.3608439 0.1678416), wk =
> > 0.0416667
> > k( 39) = ( 0.3750000 -0.0721688 -0.1678416), wk =
> > 0.0416667
> > k( 40) = ( -0.2500000 -0.2886751 -0.1678416), wk =
> > 0.0416667
> > k( 41) = ( 0.3750000 0.0721688 0.1678416), wk =
> > 0.0416667
> > k( 42) = ( -0.2500000 0.2886751 0.1678416), wk =
> > 0.0416667
> > k( 43) = ( -0.1250000 -0.0721688 0.1678416), wk =
> > 0.0416667
> > k( 44) = ( 0.0000000 -0.1443376 -0.1678416), wk =
> > 0.0416667
> > k( 45) = ( -0.3750000 0.6495191 0.1678416), wk =
> > 0.0416667
> > k( 46) = ( 0.7500000 0.0000000 -0.1678416), wk =
> > 0.0416667
> > k( 47) = ( -0.3750000 -0.2165064 0.1678416), wk =
> > 0.0416667
> > k( 48) = ( 0.0000000 -0.4330127 -0.1678416), wk =
> > 0.0416667
> >
> > G cutoff = 6839.1799 (6112477 G-vectors) FFT grid:
> (180,180,500)
> > G cutoff = 2735.6720 (1546505 G-vectors) smooth grid:
> (108,108,320)
> >
> > Largest allocated arrays est. size (Mb) dimensions
> > Kohn-Sham Wavefunctions 14.81 Mb ( 12134, 80)
> > NL pseudopotentials 29.07 Mb ( 12134, 157)
> > Each V/rho on FFT grid 31.64 Mb (1036800, 2)
> > Each G-vector array 2.91 Mb ( 382028)
> > G-vector shells 1.02 Mb ( 133817)
> > Largest temporary arrays est. size (Mb) dimensions
> > Auxiliary wavefunctions 59.25 Mb ( 12134, 320)
> > Each subspace H/S matrix 1.56 Mb ( 320, 320)
> > Each <psi_i|beta_j> matrix 0.19 Mb ( 157, 80)
> > Arrays for rho mixing 126.56 Mb (1036800, 8)
> >
> > Check: negative/imaginary core charge= -0.000006 0.000000
> >
> > Initial potential from superposition of free atoms
> > Check: negative starting charge=(component1): -0.017143
> > Check: negative starting charge=(component2): -0.005642
> >
> > starting charge 134.96666, renormalised to 134.00000
> >
> > negative rho (up, down): 0.170E-01 0.560E-02
> > Starting wfc are 113 atomic wfcs
> >
> > total cpu time spent up to now is 273.74 secs
> >
> > Self-consistent Calculation
> >
> > iteration # 1 ecut= 30.00 Ry beta=0.40
> > Davidson diagonalization with overlap
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > from davcio : error # 10
> > error while writing to file
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > stopping ...
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
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>
>
>
>
> --
> Patrick Holvey
> pholvey at nd.edu <mailto:pholvey at nd.edu>
> 442 Siegfried Hall
> Notre Dame, IN 46556
> Cell: (865)-659-9908
> ------------------------------------------------------------------------
>
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