[QE-users] [Pw_forum] input file for isolated atom

Ajmal Ghan ajmalghan1991 at gmail.com
Tue Nov 12 12:01:57 CET 2019


Thanks all for the reply,

With all the inputs provided here and mail archives, I made some
significant changes ( fixed magnetization, increased the size of the cell,
Gamma point calculation, Mixing beta etc...).

*Input of isolated Ti atom*:

&control
   calculation      = 'scf'
   restart_mode     = 'from_scratch'
   pseudo_dir       = '/work/shared/s-tih/pseudo/'
   prefix           = 'Tifree_deg1_40_gk_1'
   wf_collect       = .true.
   forc_conv_thr    = 1.0d-5
   verbosity        = 'high'
 /
&system
   ibrav            = 1
   celldm(1)        = 30
   nat              = 1
   ntyp             = 1
   ecutwfc          = 40
   ecutrho          = 320
   nspin            = 2
   tot_magnetization = 2
   nosym            = .true
   nbnd             = 100
   occupations      = 'fixed'
 /
&electrons
   diagonalization  = 'cg'
   mixing_beta      = 0.3d00
   conv_thr         = 1.0d-7
/
ATOMIC_SPECIES
  Ti  47.8670  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF


ATOMIC_POSITIONS (crystal)
   Ti     0.5 0.5 0.5

K_POINTS GAMMA


And for bulk calculations, i used same forc_conv_thr, ecutwfc, &electrons
parameters. *But I am still getting 5.23 eV as cohesive energy for Ti*. is
it possible to get the experimental ( 4.85 eV) using DFT calculations as
reported in some of the journals?

The output of isolated Ti atom calculation looks like,

    bravais-lattice index     =            1
     lattice parameter (alat)  =      30.0000  a.u.
     unit-cell volume          =   27000.0000 (a.u.)^3
     number of atoms/cell      =            1
     number of atomic types    =            1
     number of electrons       =        12.00 (up:   7.00, down:   5.00)
     number of Kohn-Sham states=          100
     kinetic-energy cutoff     =      40.0000  Ry
     charge density cutoff     =     320.0000  Ry
     convergence threshold     =      1.0E-07
     mixing beta               =       0.3000
     number of iterations used =            8  plain     mixing
     Exchange-correlation      = PBE ( 1  4  3  4 0 0)

     celldm(1)=  30.000000  celldm(2)=   0.000000  celldm(3)=   0.000000
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000

etc..............................................................................................................

     Starting magnetic structure
     atomic species   magnetization
        Ti           0.000

     No symmetry found
etc..............................................................................................................
..................................................................................................................

     iteration # 23     ecut=    40.00 Ry     beta= 0.30
     CG style diagonalization
     ethr =  1.01E-09,  avg # of iterations =  3.1

     negative rho (up, down):  1.660E-02 1.306E-01

     Magnetic moment per site:
     atom:    1    charge:   11.9999    magn:    2.0000    constr:    0.0000

     total cpu time spent up to now is      108.5 secs

     End of self-consistent calculation

 ------ SPIN UP ------------

          k = 0.0000 0.0000 0.0000 ( 57657 PWs)   bands (ev):

   -62.1874 -38.4854 -38.4348 -38.4332  -4.4517  -4.4503  -4.4048  -3.5611
    -3.5610  -3.5153  -1.4572  -1.4565  -1.1485  -0.4725   0.0828   0.0992
     0.1709   0.1890   0.1914   0.2168   0.5306   0.5437   0.6058   0.6689
     0.6794   0.6917   0.7097   0.7127   0.8758   0.8811   0.9122   0.9174
     1.1513   1.1544   1.1806   1.2368   1.4025   1.4198   1.4417   1.4878
     1.5485   1.5709   1.9392   1.9444   1.9629   2.0040   2.0535   2.0683
     2.1492   2.1983   2.2084   2.3100   2.3235   2.3454   2.3845   2.4064
     2.4189   2.4639   2.4693   2.4865   2.4880   2.5054   2.5055   2.5179
     2.5188   2.5215   2.7061   2.7211   2.7420   2.7869   2.7963   2.8090
     2.8145   2.8304   2.9938   3.0003   3.0113   3.0175   3.0230   3.0259
     3.0280   3.0332   3.0529   3.0580   3.0645   3.0690   3.0757   3.0785
     3.0808   3.0898   3.5616   3.5684   3.6347   3.8452   3.9717   3.9774
     4.0381   4.0472   4.0540   4.0617

     occupation numbers
     1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000

 ------ SPIN DOWN ----------
          k = 0.0000 0.0000 0.0000 ( 57657 PWs)   bands (ev):

   -60.5692 -37.0219 -36.7521 -36.7481  -3.9282  -2.9464  -2.8480  -2.8461
    -2.0737  -2.0734  -1.3881  -0.9733  -0.9724  -0.4455   0.0983   0.1054
     0.2139   0.2301   0.2409   0.2476   0.5776   0.5939   0.6083   0.6823
     0.6922   0.7172   0.7202   0.7223   0.9007   0.9617   0.9637   0.9653
     1.1886   1.2019   1.2109   1.2572   1.4214   1.4579   1.4604   1.5175
     1.5802   1.6023   1.9618   1.9874   1.9882   2.0402   2.1348   2.1844
     2.2059   2.2275   2.2450   2.3219   2.3301   2.3507   2.4059   2.4124
     2.4170   2.4823   2.4877   2.4881   2.5037   2.5077   2.5266   2.5297
     2.5305   2.5376   2.7444   2.7669   2.7706   2.8302   2.8379   2.8443
     2.8558   2.8670   3.0199   3.0266   3.0335   3.0380   3.0397   3.0427
     3.0462   3.0493   3.0781   3.0795   3.0805   3.0813   3.0847   3.0869
     3.1009   3.1038   3.6043   3.6940   3.6955   3.9171   4.0363   4.0648
     4.0726   4.0791   4.0896   4.0980

     occupation numbers
     1.0000   1.0000   1.0000   1.0000   1.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
     0.0000   0.0000   0.0000   0.0000

     highest occupied, lowest unoccupied level (ev):    -3.9282   -3.5611

!    total energy              =    -119.34098597 Ry
     Harris-Foulkes estimate   =    -119.34098367 Ry
     estimated scf accuracy    <       0.00000010 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =    -167.22501663 Ry
     hartree contribution      =      79.78699354 Ry
     xc contribution           =     -18.28393498 Ry
     ewald contribution        =     -13.61902790 Ry

     total magnetization       =     2.00 Bohr mag/cell
     absolute magnetization    =     2.44 Bohr mag/cell

     convergence has been achieved in  23 iterations


Waiting for reply. Thanks for all the inputs.

Thanks & Regards,
*------------------------------------------------------------------------------------------------------*
Ajmalghan MUTHALI

Post doctorate researcher
Laboratoire ICB
UMR 6303 CNRS-Université de Bourgogne
9 Avenue Alain Savary, BP 47870
F-21078 DIJON Cedex, France
Tel: +33-(0)7.69.28.19.91
Email : ajmalghan.muthali at u-bourgogne.fr


On Sun, Nov 10, 2019 at 3:52 PM Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
wrote:

>
> Dear Ajmalghan,
>
>    Some quick comments:
>
>   - Why do you use k point in the case of an isolated atom?? Well, that
> should not matter, just that you are wasting computing time
>
>   - I guess that the spherical symmetry of the atom is broken; thus I
> would
> use a non-cube cell, preferably the orthorhombic cell, with slightly
> different lengths of the basis vectors of the unit cell. Then to break the
> symmetry, you can use some randomisation of the initial wave functions.
> And still, the convergence is probably going to be very difficult... You
> can indeed try to fix the magnetisation; and I would reduce the
> 'mixing_beta' to something (very) small - in principle already at the
> first step the electron density should be close to the self-consistent
> one, bar the loss of sphericality and the randomised wave function
>
>   - Please remember that the scale of 'starting_magnetisation' is from -1
> to +1, meaning that all the electrons are spin-polarised either up or
> down, whereas in your case you only want to polarise the two valence
> electrons out of the valence of the pseudo potential that seems to be 12
> electrons
>
>    Well, Good Luck. :)
>
>      Greetings from Paris,
>
>         apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>    Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>
>
> On Sat, 9 Nov 2019, Ajmal Ghan wrote:
>
> > Hello all,
> >
> > I have gone through all the archived discussion about cohesive energy
> calculation.
> >
> > I am trying to calculate the cohesive energy of Ti which is  4.85eV. But
> I am getting 5.23 eV which is closer. But I have found from a previous
> discussion
> > here (
> https://www.mail-archive.com/users@lists.quantum-espresso.org/msg11410.html
> ) that, the final magnetization should be 2 Bohr mag/ cell at the end
> > of calculation for Ti and smearing contribution of energy should be
> 0.0Ry.
> > But I am getting to get 3.83 Bohr mag/cell and a significant smearing
> contribution = -0.03295688 Ry.
> >
> > Anyone help me to sort this. what should I change in the input?
> >
> >
> > here is my input,
> >
> > &control
> >    calculation      = 'scf'
> >    restart_mode     = 'from_scratch'
> >    pseudo_dir       = '/work/shared/s-tih/pseudo/'
> >    prefix           = 'Tifree_deg1_50_8k_1'
> >    wf_collect       = .true.
> >    tstress          = .true.
> >    tprnfor          = .true.
> >    forc_conv_thr    = 1.0d-6
> >    verbosity        = 'high'
> >  /
> > &system
> >    ibrav            = 1
> >    celldm(1)     = 20
> >    nat              = 1
> >    ntyp            = 1
> >    ecutwfc       = 50      //( I have performed convergence study. But
> since degauss is reduced to 0.01, i increased ecut)
> >    ecutrho       = 400
> >    nspin          = 2
> >    starting_magnetization(1) = 1        // I think, the final
> magnetisation should be 2 bohr mag/ cell at the end of calculation.
> >    nosym            = .true                    /// I hope this is enough
> to break the symmetry
> >    nbnd             = 100
> >    occupations      = 'smearing',  smearing='mp', degauss=0.01D0
> >  /
> > &electrons
> >    diagonalization  = 'cg'
> >    mixing_beta      = 0.7d00
> >    conv_thr         = 1.0d-8     // I used even higher convergence since
> smearing is reduced.
> > /
> > ATOMIC_SPECIES
> >   Ti  47.8670  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF
> >
> >
> > ATOMIC_POSITIONS (crystal)
> >    Ti     0.5 0.5 0.5
> >
> > K_POINTS {automatic}
> >   8  8  5  0  0  0
> >
> >
> > I don't really know this is the correct way to post a reply. All input
> is welcome.
> >
> > Thanks & Regards,
> >
> ------------------------------------------------------------------------------------------------------
> > Ajmalghan MUTHALI
> >
> > Post doctorate researcher
> > Laboratoire ICB
> > UMR 6303 CNRS-Université de Bourgogne
> > 9 Avenue Alain Savary, BP 47870
> > F-21078 DIJON Cedex, France
> > Tel: +33-(0)7.69.28.19.91
> > Email : ajmalghan.muthali at u-bourgogne.fr
> >
> >_______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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