[QE-users] Query for skip_type and equiv_type for DFT+U+V
Dr. K. C. Bhamu
kcbhamu85 at gmail.com
Wed Nov 24 15:43:12 CET 2021
Thank you so much Dr. Timrov
Regards
Bhamu
On Wed, Nov 24, 2021 at 8:11 PM Iurii TIMROV via users <
users at lists.quantum-espresso.org> wrote:
> Ok, so you have this:
>
>
> atom 1 Tr[ns(na)]= 6.2349321 -> Fe1
> atom 2 Tr[ns(na)]= 6.2349321 -> Fe1
> atom 3 Tr[ns(na)]= 6.2349321 -> Fe1
> atom 4 Tr[ns(na)]= 6.2348428 -> Fe1
> atom 5 Tr[ns(na)]= 6.1942515 -> Fe2
> atom 6 Tr[ns(na)]= 6.1942515 -> Fe2
>
>
> Just use find_atpert=1 and docc_thr=1.d-4. This will perturb one Fe1 atom
> and one Fe2 atom, because they have different occupations. If you want to
> have the same U for both Fe1 and Fe2 then set docc_thr=5.d-2: in this
> case the code will perturb only Fe1 atom.
>
>
> HTH
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> ------------------------------
> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of Dr.
> K. C. Bhamu <kcbhamu85 at gmail.com>
> *Sent:* Wednesday, November 24, 2021 3:31:30 PM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Query for skip_type and equiv_type for DFT+U+V
>
> Thanks Iurii,
> I find that "find_atpert" is by default set at 1.
> With the setting mention in my previous mail, I got the below error:
> Error in routine hp_find_inequiv_sites (1):
> skip_type must not be setup from the input when find_atpert=1.
> For magnetite structure (Fe3O4), Fe has two states: Fe2+ and Fe3+.
>
> Here is the Tr[ns(na)] and input file
> atom 1 Tr[ns(na)]= 6.2349321
> atom 1 Mag[ns(na)]= 3.5251042
> atom 2 Tr[ns(na)]= 6.2349321
> atom 2 Mag[ns(na)]= 3.5251042
> atom 3 Tr[ns(na)]= 6.2349321
> atom 3 Mag[ns(na)]= 3.5251042
> atom 4 Tr[ns(na)]= 6.2348428
> atom 4 Mag[ns(na)]= 3.5251547
> atom 5 Tr[ns(na)]= 6.1942515
> atom 5 Mag[ns(na)]= -3.5314272
> atom 6 Tr[ns(na)]= 6.1942515
> atom 6 Mag[ns(na)]= -3.5314272
> atom 7 Tr[ns(na)]= 5.0802986
> atom 7 Mag[ns(na)]= 0.0754368
> atom 8 Tr[ns(na)]= 5.0802986
> atom 8 Mag[ns(na)]= 0.0754368
> atom 9 Tr[ns(na)]= 5.0802986
> atom 9 Mag[ns(na)]= 0.0754368
> atom 10 Tr[ns(na)]= 5.0802986
> atom 10 Mag[ns(na)]= 0.0754368
> atom 11 Tr[ns(na)]= 5.0802986
> atom 11 Mag[ns(na)]= 0.0754368
> atom 12 Tr[ns(na)]= 5.0802986
> atom 12 Mag[ns(na)]= 0.0754368
> atom 13 Tr[ns(na)]= 5.0802792
> atom 13 Mag[ns(na)]= 0.0754401
> atom 14 Tr[ns(na)]= 5.0802792
> atom 14 Mag[ns(na)]= 0.0754401
>
> Input file:
>
> &CONTROL
> calculation = 'vc-relax'
> restart_mode='from_scratch',
> etot_conv_thr = 0.0001
> forc_conv_thr = 0.001
> outdir = './temp/'
> prefix = 'pwscf'
> pseudo_dir = '~/PP/'
> tprnfor = .true.
> tstress = .true.
> verbosity = 'high'
> /
> &SYSTEM
> degauss = 0.022
> ecutrho = 320
> ecutwfc = 40
> occupations = 'smearing' , smearing = 'mp'
> ibrav = 0
> nat = 14
> nosym = .false.
> ntyp = 3
> nspin=2
> starting_magnetization(1) = 0.8
> starting_magnetization(2) = -0.8
> starting_magnetization(3) = 0.0
>
> lda_plus_u = .true.,
> lda_plus_u_kind = 2,
> U_projection_type = 'ortho-atomic',
> Hubbard_V(1,1,1) = 1.d-8
> Hubbard_V(5,5,1) = 1.d-8
> Hubbard_V(7,7,1) = 1.d-8
> !Hubbard_parameters = 'file'
>
>
> /
> &ELECTRONS
> conv_thr = 1.0000000000d-06
> electron_maxstep = 400
> mixing_beta = 1.5000000000d-01
> /
> &IONS
> ion_dynamics = 'bfgs'
> /
> &CELL
> /
>
> ATOMIC_SPECIES
> Fe1 55.845 Fe.pbe-nd-rrkjus.UPF
> Fe2 55.845 Fe.pbe-nd-rrkjus.UPF
> O 15.9994 O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS (crystal)
> Fe1 0.0000000000 -0.0000000000 -0.0000000000
> Fe1 0.5000000000 0.0000000000 0.0000000000
> Fe1 0.9999999892 0.5000000216 -0.0000000000
> Fe1 0.9999999965 0.9999999956 0.5000000115
> Fe2 0.3749993721 0.3749993349 0.3750019210
> Fe2 0.6250006225 0.6250006532 0.6249981020
> O 0.2454868415 0.2454868399 0.2454949640
> O 0.7545131845 0.7545131098 0.7545050345
> O 0.7635313546 0.2454868399 0.2454949640
> O 0.2364686713 0.7545131098 0.7545050345
> O 0.2454868307 0.7635313746 0.2454949640
> O 0.7545132523 0.2364686217 0.7545050345
> O 0.2454908593 0.2454908222 0.7635274591
> O 0.7545090629 0.7545091741 0.2364725394
>
> CELL_PARAMETERS (angstrom)
> 5.944682649 0.000000000 0.000000000
> 2.972341325 5.148246192 0.000000000
> 2.972341325 1.716082064 4.853885701
>
> K_POINTS automatic
> 7 7 7 0 0 0
>
> Regards
> Bhamu
>
>
>
>>
>> > As all Fe will have the same Hubbard parameter (as reported in the
>> literature for the same system)...
>>
>>
>> In the literature people often use empirical U, so that's why they use a
>> single value of U for all Fe atoms. With the HP code you can do things
>> better, i.e. to find out if there are non-equivalent Fe atoms that require
>> their own first-principles U.
>>
>>
>> HTH
>>
>>
>> Iurii
>>
>>
>> P.S.: "Dr." is used with the last name not with the first name, so in my
>> case this will be "Dear Dr. Timrov". But if you want to address me using my
>> first name then just write "Dear Iurii". Sorry, I don't want to bother
>> you with this, but just to makes things clear 😊
>>
>>
>> --
>> Dr. Iurii TIMROV
>> Senior Research Scientist
>> Theory and Simulation of Materials (THEOS)
>> Swiss Federal Institute of Technology Lausanne (EPFL)
>> CH-1015 Lausanne, Switzerland
>> +41 21 69 34 881
>> http://people.epfl.ch/265334
>> ------------------------------
>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>> Dr. K. C. Bhamu <kcbhamu85 at gmail.com>
>> *Sent:* Wednesday, November 24, 2021 1:00:13 PM
>> *To:* Quantum Espresso users Forum
>> *Subject:* [QE-users] Query for skip_type and equiv_type for DFT+U+V
>>
>> Dear Dr. Iurii (😊),
>>
>> The ATOMIC_POSITIONS cart of my structure (ferrimagnetic system with ntyp
>> = 3 ) is
>>
>> ATOMIC_POSITIONS (crystal)
>> Fe1 0.0000000000 -0.0000000000 -0.0000000000 (four
>> times)
>> Fe2 0.3749993721 0.3749993349 0.3750019210 (two
>> times)
>> O 0.2454868415 0.2454868399 0.2454949640 (eight
>> times)
>>
>> Previously, based on ATOMIC_SPECIES cart, I defined my Hubbard tag as
>> below
>>
>> Hubbard_V(1,1,1) = 1.d-8
>> Hubbard_V(2,2,1) = 1.d-8
>> Hubbard_V(3,3,1) = 1.d-8
>>
>> In the hp output file, I saw that only one Fe1 atom was perturbed.
>>
>> Then I defined below Hubbard tags according to ATOMIC_POSITIONS cart as
>>
>> Hubbard_V(1,1,1) = 1.d-8
>> Hubbard_V(5,5,1) = 1.d-8
>> Hubbard_V(7,7,1) = 1.d-8
>>
>> which perturbed four atoms
>>
>> 1 Fe1 55.8450 tau( 1) = ( 0.00000 0.00000 0.00000 )
>> 4 Fe1 55.8450 tau( 4) = ( 1.75000 1.01036 0.40825 )
>> 5 Fe2 55.8450 tau( 5) = ( 0.75000 0.43301 0.30619 )
>> 7 O 15.9994 tau( 7) = ( 0.49098 0.28347 0.20045 )
>>
>> As all Fe will have the same Hubbard parameter (as reported in the
>> literature for the same system), I would like to skip the perturbation for
>> atom Fe1(4) and Fe2(5).
>>
>> Is it okay if I do so?
>>
>> To skip the perturbation for Fe1(4) and Fe2(5), I have updated below tags
>> in my hp input file:
>>
>> skip_type(1)=.true.
>> skip_type(2)=.true.
>> equiv_type(1)=1
>> equiv_type(2)=1
>> disable_type_analysis=.true.,
>>
>> Could you please correct me if this modification is correct or not?
>>
>> Sorry for the list of questions. But I am sure, my these queries will be
>> helpful for others too.
>>
>> Thanks and regards
>>
>> K C Bhamu
>>
>> Postdoctoral Fellow
>> University of Ulsan
>> South Korea
>>
>> _______________________________________________
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>
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