[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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>
> _______________________________________________
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