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

Yves Ferro yves.ferro at univ-amu.fr
Tue Nov 12 16:01:39 CET 2019


Yes but for calculation I can read scf instead of vc-relax. 

It should be:
&control
      calculation      = vc-relax
…..

&cell
      cell_dofree = « volume » or « ibrav »

Fixing force_conv_thr  is useless and you should have a warning in the output.
It seems that you are only running a scf calculation, which is valid for a single atom, not for the bulk.

The a and c parameter you will compute will be another way to compare to experimental values.

Yves



> Le 12 nov. 2019 à 15:45, Ajmal Ghan <ajmalghan1991 at gmail.com> a écrit :
> 
> Thank you for your email,
> 
> I have performed convergence studies ( both on 1x1 and 2x2 unit cell) for k-point, wave-function cutoff, smearing. 
> 
> Here is the input for Ti bulk,
> 
> &control
>    calculation      = 'scf'
>    restart_mode     = 'from_scratch'
>    pseudo_dir       = '/work/shared/s-tih/pseudo/'
>    prefix           = 'Ti2_deg4_40_8k'
>    wf_collect       = .true.
>    tstress          = .true.
>    tprnfor          = .true.
>    forc_conv_thr    = 1.0d-5
>    verbosity        = 'high'
>  /
> &system
>    ibrav            = 4
>    a = 2.950,b=2.950,c=4.81735,cosbc=0,cosac=0,cosab=-0.5
>    nat              = 2
>    ntyp             = 1
>    ecutwfc          = 40
>    ecutrho          = 320
>    occupations      = 'smearing',  smearing='mp', degauss=0.04D0
>  /
> &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     0.666 0.333 0.7500
>    Ti     0.333 0.666 0.2500
> 
> K_POINTS {automatic}
>   8  8  5  0  0  0
> 
> And the output, 
> 
> ..................................................................................................................
>     bravais-lattice index     =            4
>      lattice parameter (alat)  =       5.5747  a.u.
>      unit-cell volume          =     245.0076 (a.u.)^3
>      number of atoms/cell      =            2
>      number of atomic types    =            1
>      number of electrons       =        24.00
>      number of Kohn-Sham states=           16
>      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)=   5.574692  celldm(2)=   1.000000  celldm(3)=   1.633000
>      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
> 
>      crystal axes: (cart. coord. in units of alat)
>                a(1) = (   1.000000   0.000000   0.000000 )
>                a(2) = (  -0.500000   0.866025   0.000000 )
>                a(3) = (   0.000000   0.000000   1.633000 )
> 
>      reciprocal axes: (cart. coord. in units 2 pi/alat)
>                b(1) = (  1.000000  0.577350  0.000000 )
>                b(2) = (  0.000000  1.154701  0.000000 )
>                b(3) = (  0.000000  0.000000  0.612370 )
> 
> 
>      PseudoPot. # 1 for Ti read from file:
>      /work/shared/s-tih/pseudo/Ti.pbe-spn-rrkjus_psl.1.0.0.UPF
>      MD5 check sum: e281089c08e14b8efcf92e44a67ada65
>      Pseudo is Ultrasoft + core correction, Zval = 12.0
>      Generated using "atomic" code by A. Dal Corso v.6.2.2
>      Using radial grid of 1177 points,  6 beta functions with:
>                 l(1) =   0
>                 l(2) =   0
>                 l(3) =   1
>                 l(4) =   1
>                 l(5) =   2
>                 l(6) =   2
>      Q(r) pseudized with 0 coefficients
> 
> 
>      atomic species   valence    mass     pseudopotential
>         Ti            12.00    47.86700     Ti( 1.00)
> 
>       8 Sym. Ops., with inversion, found ( 6 have fractional translation)
> ..................................................................................................................
> 
>      the Fermi energy is    12.6981 ev
> 
> !    total energy              =    -239.45976063 Ry
>      Harris-Foulkes estimate   =    -239.45976064 Ry
>      estimated scf accuracy    <          6.2E-09 Ry
> 
>      The total energy is the sum of the following terms:
> 
>      one-electron contribution =     -84.68427794 Ry
>      hartree contribution      =      49.69752058 Ry
>      xc contribution           =     -36.99691545 Ry
>      ewald contribution        =    -167.48081236 Ry
>      smearing contrib. (-TS)   =       0.00472453 Ry
> 
>      convergence has been achieved in   7 iterations
> 
> 
> cohesive Energy  = -239.45976063/2 - -119.34098597 = -0.388894345 Ry = -5.29 eV.   (0.44 eV difference from experimental value).
> 
> I am attaching the i/o files also with this, but most of the important details of the calculation are above.
> 
> Thanks for any help.
> 
> ------------------------------------------------------------------------------------------------------
> 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 <mailto:ajmalghan.muthali at u-bourgogne.fr>
> 
> On Tue, Nov 12, 2019 at 12:25 PM Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it <mailto:giuseppe.mattioli at ism.cnr.it>> wrote:
> 
> Dear Ajmalghan
> Sorry for asking a possibly stupid question, but you are focusing on  
> the calculation of isolated Ti, and the error might be contained in  
> the calculation of hcp metal Ti... Are you sure that everything is  
> correct in that case?
> HTH
> Giuseppe
> 
> Quoting Ajmal Ghan <ajmalghan1991 at gmail.com <mailto:ajmalghan1991 at gmail.com>>:
> 
> > 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 <mailto:ajmalghan.muthali at u-bourgogne.fr>
> >
> >
> > On Sun, Nov 10, 2019 at 3:52 PM Ari P Seitsonen <Ari.P.Seitsonen at iki.fi <mailto: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 <mailto:Ari.P.Seitsonen at iki.fi> / http://www.iki.fi/~apsi/ <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 <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 <mailto:ajmalghan.muthali at u-bourgogne.fr>
> >> >
> >> >_______________________________________________
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> 
> 
> 
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
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> E-mail: <giuseppe.mattioli at ism.cnr.it <mailto:giuseppe.mattioli at ism.cnr.it>>
> 
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