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<p>Dear Hooman,</p>
<p><br>
</p>
<p>You need to put Mn1 and Mn2 first in the atomic list and then the remaining atoms, like this:</p>
<p><br>
</p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">ATOMIC_POSITIONS {crystal}</span></p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;"></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Mn1
0.000000000 0.000000000 0.000000000</span></p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;"></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Mn1
0.500000000 0.500000000 0.000000000</span></p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;"></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Mn2
-0.000000000 0.500000000 -0.000000000</span></p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;"></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Mn2
0.500000000 0.000000000 0.000000000</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.138178100 0.392913471 0.233700489</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.361767139 0.106848852 0.766122199</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Li 0.250095079 0.250498471 0.500248603</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.138177233 0.892913211 0.233699914</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.361766394 0.606847636 0.766121721</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Li 0.250092166 0.750492217 0.500245834</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.638233606 0.393152364 0.233878279</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.861822767 0.107087789 0.766300086</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Li 0.749907834 0.249508783 0.499754166</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.638233861 0.893152148 0.233877801</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">O 0.861822900 0.607086529 0.766299511</span><br style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif, serif, EmojiFont; font-size: 15px;">Li 0.749905921 0.749501529 0.499751397</span><br>
</p>
<p><br>
</p>
<p>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. </p>
<p><br>
</p>
<p><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: arial, helvetica, sans-serif, serif, EmojiFont; font-size: 15px;">> looks like you are applying U twice for Mn atom. what's the difference between Mn1 and Mn2 site?. different
symmetry?</span><br>
</p>
<p><br>
</p>
<p>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. </p>
<p><br>
</p>
<p>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):</p>
<p><a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.094102" class="OWAAutoLink" id="LPlnk295160" previewremoved="true">https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.094102</a><br>
<a href="https://arxiv.org/abs/2001.06540" class="OWAAutoLink" id="LPlnk62857" previewremoved="true">https://arxiv.org/abs/2001.06540</a><br>
</p>
<p><br>
</p>
<p>Greetings,</p>
<p>Iurii </p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Hooman Yaghoobnejad Asl <hynr8@mst.edu><br>
<b>Sent:</b> Friday, February 21, 2020 10:05:52 PM<br>
<b>To:</b> Manu Hegde<br>
<b>Cc:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Missing Hubbard atoms from ATOMIC_POSITIONS card</font>
<div> </div>
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<div>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.</div>
<div>Thanks,</div>
<div>Hooman</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Feb 21, 2020 at 2:29 PM Manu Hegde <<a href="mailto:mhegde@sfu.ca">mhegde@sfu.ca</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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.</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Manu</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Feb 21, 2020 at 2:45 PM Hooman Yaghoobnejad Asl <<a href="mailto:hynr8@mst.edu" target="_blank">hynr8@mst.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">Dear all,
<div>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: </div>
<div><font color="#351c75">" WARNING! All Hubbard atoms must be listed first in the ATOMIC_POSITIONS card of PWscf<br>
Stopping..."</font></div>
<div>Any hint to show me what I'm doing wrong is highly appreciated.</div>
<div>I'm using QE 6.4.1</div>
<div>Input for the second step (magnetic insulator) is pasted below:</div>
<div> <br>
&SYSTEM<br>
ibrav = 0<br>
celldm(1) = 10.52955401,<br>
nat = 16<br>
ntyp = 4<br>
nbnd = 72<br>
ecutwfc = 50 ,<br>
ecutrho = 400 ,<br>
occupations = 'fixed' ,<br>
nspin = 2 ,<br>
tot_magnetization = 0.00<br>
lda_plus_u = .true.,<br>
lda_plus_u_kind = 0,<br>
U_projection_type = 'ortho-atomic',<br>
Hubbard_U(2) = 1.d-8<br>
Hubbard_U(3) = 1.d-8<br>
/<br>
&ELECTRONS<br>
electron_maxstep = 500,<br>
conv_thr = 1.d-15<br>
mixing_beta = 0.7 ,<br>
startingpot = 'file'<br>
startingwfc = 'file'<br>
/<br>
ATOMIC_SPECIES<br>
O 15.99 O.pbe-n-kjpaw_psl.0.1.upf <br>
Mn1 54.93805 Mn.pbe-spn-kjpaw_psl.0.3.1.UPF<br>
Mn2 54.93805 Mn.pbe-spn-kjpaw_psl.0.3.1.UPF<br>
Li 6.94100 Li.pbe-s-kjpaw_psl.0.2.1.upf<br>
ATOMIC_POSITIONS {crystal}<br>
O 0.138178100 0.392913471 0.233700489<br>
O 0.361767139 0.106848852 0.766122199<br>
Mn1 0.000000000 0.000000000 0.000000000<br>
Li 0.250095079 0.250498471 0.500248603<br>
O 0.138177233 0.892913211 0.233699914<br>
O 0.361766394 0.606847636 0.766121721<br>
Mn2 -0.000000000 0.500000000 -0.000000000<br>
Li 0.250092166 0.750492217 0.500245834<br>
O 0.638233606 0.393152364 0.233878279<br>
O 0.861822767 0.107087789 0.766300086<br>
Mn2 0.500000000 0.000000000 0.000000000<br>
Li 0.749907834 0.249508783 0.499754166<br>
O 0.638233861 0.893152148 0.233877801<br>
O 0.861822900 0.607086529 0.766299511<br>
Mn1 0.500000000 0.500000000 0.000000000<br>
Li 0.749905921 0.749501529 0.499751397<br>
CELL_PARAMETERS (alat)<br>
0.994008748 0.006054947 0.149445159<br>
-0.494775805 0.989385379 -0.097973510<br>
0.114248343 -0.030106079 0.902638553<br>
K_POINTS automatic <br>
4 4 5 0 0 0 <br>
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<div><font size="1"><span style="color:rgb(153,153,153)"><b>Hooman Yaghoobnejad<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>PhD, Department of Chemistry<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>Missouri University of Science and Technology<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>Rolla, MO 65409<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>USA</b></span></font><br>
</div>
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-- <br>
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<div><font size="1"><span style="color:rgb(153,153,153)"><b>Hooman Yaghoobnejad<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>PhD, Department of Chemistry<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>Missouri University of Science and Technology<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>Rolla, MO 65409<br>
</b></span></font></div>
<font size="1"><span style="color:rgb(153,153,153)"><b>USA</b></span></font><br>
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