[QE-users] [Pw_forum] input file for isolated atom
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Tue Nov 12 12:24:51 CET 2019
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>:
> 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)
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GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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E-mail: <giuseppe.mattioli at ism.cnr.it>
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