[QE-users] Missing Hubbard atoms from ATOMIC_POSITIONS card

[Timrov Iurii]

Dear Hooman,


You need to put Mn1 and Mn2 first in the atomic list and then the remaining atoms, like this:


ATOMIC_POSITIONS {crystal}

Mn1      0.000000000   0.000000000   0.000000000

Mn1      0.500000000   0.500000000   0.000000000

Mn2     -0.000000000   0.500000000  -0.000000000

Mn2      0.500000000   0.000000000   0.000000000
O        0.138178100   0.392913471   0.233700489
O        0.361767139   0.106848852   0.766122199
Li       0.250095079   0.250498471   0.500248603
O        0.138177233   0.892913211   0.233699914
O        0.361766394   0.606847636   0.766121721
Li       0.250092166   0.750492217   0.500245834
O        0.638233606   0.393152364   0.233878279
O        0.861822767   0.107087789   0.766300086
Li       0.749907834   0.249508783   0.499754166
O        0.638233861   0.893152148   0.233877801
O        0.861822900   0.607086529   0.766299511
Li       0.749905921   0.749501529   0.499751397


This is so because the HP code expects that in the list of atoms you first have Hubbard atoms (i.e. with U) and then all the rest (no U). This is just how the code works.


> looks like you are applying U twice for Mn atom. what's the difference between Mn1 and Mn2 site?. different symmetry?


As Hooman said, Mn1 has a starting magnetization positive, and Mn2 has a starting magnetization negative. This means that essentially we are having two sub-lattices, which is needed to model the antiferromagnetic ordering. In this case I think that Mn1 and Mn2 are crystallographically equivalent, so the U values will be the same for both types of Mn, as Human said. But in general, in other cases, Mn1 and Mn2 may also be crystallographically slightly different and hence the resulting U will also be somewhat different.


If you are interested, you may have a look at these two papers about site-dependent U values (e.g. when there are O vacancies):

https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.094102
https://arxiv.org/abs/2001.06540


Greetings,

Iurii


--
Dr. Iurii Timrov
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
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 Hooman Yaghoobnejad Asl <hynr8 at mst.edu>
Sent: Friday, February 21, 2020 10:05:52 PM
To: Manu Hegde
Cc: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Missing Hubbard atoms from ATOMIC_POSITIONS card

The two U terms applied to the two crystallographically distinct Mn atoms (opposite spin arrangement). Still, I'm expecting to get similar values for both as they are in chemically identical environments, similar to the NiO reference.
Thanks,
Hooman

On Fri, Feb 21, 2020 at 2:29 PM Manu Hegde <mhegde at sfu.ca<mailto:mhegde at sfu.ca>> wrote:
looks like you are applying U twice for Mn atom. what's the difference between Mn1 and Mn2 site?. different symmetry?. you may have to think  about it.

Manu

On Fri, Feb 21, 2020 at 2:45 PM Hooman Yaghoobnejad Asl <hynr8 at mst.edu<mailto:hynr8 at mst.edu>> wrote:
Dear all,
The following must be an easy fix. I just started to use hp.x for LiMnO2 (hypothetical structure), which is a magnetic (AFM) insulator. I followed the example02 of the HP code (NiO U parameter) and it worked as expected. I do the same sequence for the above structure (i.e., magnetic metal, magnetic insulator, linear response), but at the last step, hp.x stops with the following error:
"     WARNING! All Hubbard atoms must be listed first in the ATOMIC_POSITIONS card of PWscf
     Stopping..."
Any hint to show me what I'm doing wrong is highly appreciated.
I'm using QE 6.4.1
Input for the second step (magnetic insulator) is pasted below:

 &SYSTEM
    ibrav = 0
    celldm(1) = 10.52955401,
    nat   = 16
    ntyp  = 4
    nbnd  = 72
                     ecutwfc = 50 ,
                     ecutrho = 400 ,
                 occupations = 'fixed' ,
                 nspin = 2 ,
tot_magnetization = 0.00
    lda_plus_u = .true.,
    lda_plus_u_kind = 0,
    U_projection_type = 'ortho-atomic',
    Hubbard_U(2) = 1.d-8
    Hubbard_U(3) = 1.d-8
 /
 &ELECTRONS
    electron_maxstep = 500,
    conv_thr =  1.d-15
    mixing_beta = 0.7 ,
    startingpot = 'file'
    startingwfc = 'file'
 /
ATOMIC_SPECIES
    O       15.99     O.pbe-n-kjpaw_psl.0.1.upf
    Mn1     54.93805  Mn.pbe-spn-kjpaw_psl.0.3.1.UPF
    Mn2     54.93805  Mn.pbe-spn-kjpaw_psl.0.3.1.UPF
    Li       6.94100  Li.pbe-s-kjpaw_psl.0.2.1.upf
ATOMIC_POSITIONS {crystal}
O        0.138178100   0.392913471   0.233700489
O        0.361767139   0.106848852   0.766122199
Mn1      0.000000000   0.000000000   0.000000000
Li       0.250095079   0.250498471   0.500248603
O        0.138177233   0.892913211   0.233699914
O        0.361766394   0.606847636   0.766121721
Mn2     -0.000000000   0.500000000  -0.000000000
Li       0.250092166   0.750492217   0.500245834
O        0.638233606   0.393152364   0.233878279
O        0.861822767   0.107087789   0.766300086
Mn2      0.500000000   0.000000000   0.000000000
Li       0.749907834   0.249508783   0.499754166
O        0.638233861   0.893152148   0.233877801
O        0.861822900   0.607086529   0.766299511
Mn1      0.500000000   0.500000000   0.000000000
Li       0.749905921   0.749501529   0.499751397
CELL_PARAMETERS (alat)
   0.994008748   0.006054947   0.149445159
  -0.494775805   0.989385379  -0.097973510
   0.114248343  -0.030106079   0.902638553
K_POINTS automatic
4 4 5   0 0 0

--
Hooman Yaghoobnejad
PhD, Department of Chemistry
Missouri University of Science and Technology
Rolla, MO 65409
USA


--
Hooman Yaghoobnejad
PhD, Department of Chemistry
Missouri University of Science and Technology
Rolla, MO 65409
USA
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