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<p>Ok, so you have this:</p>
<p><br>
</p>
<p></p>
<div>atom 1 Tr[ns(na)]= 6.2349321 -> Fe1<br>
atom 2 Tr[ns(na)]= 6.2349321 -> Fe1<br>
atom 3 Tr[ns(na)]= 6.2349321 -> Fe1<br>
atom 4 Tr[ns(na)]= 6.2348428 -> Fe1<br>
atom 5 Tr[ns(na)]= 6.1942515 -> Fe2<br>
atom 6 Tr[ns(na)]= 6.1942515 -> Fe2</div>
<p></p>
<p><br>
</p>
<p>Just use find_atpert=1 and <span>docc_thr</span>=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
<span>docc_thr</span>=5.d-2: in this case the code will perturb only Fe1 atom.</p>
<p><br>
</p>
<p>HTH</p>
<p><br>
</p>
<p>Iurii<br>
</p>
<p><br>
</p>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">--<br>
<span style="font-family:Cambria,Georgia,serif">Dr. Iurii TIMROV</span><br>
<span style="font-family:Cambria,Georgia,serif">Senior Research Scientist</span></font></div>
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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 Dr. K. C. Bhamu <kcbhamu85@gmail.com><br>
<b>Sent:</b> Wednesday, November 24, 2021 3:31:30 PM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Query for skip_type and equiv_type for DFT+U+V</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div class="gmail_quote">
<div class="gmail_default" style="font-size:large">Thanks Iurii,</div>
<div class="gmail_default" style="font-size:large">I find that <span class="gmail_default" style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif">"</span><span style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:16px">find_atpert"
is by default set at 1.</span></div>
<div class="gmail_default" style="font-size:large"><span class="gmail_default">With the setting mention in my previous mail, I got the below error:</span></div>
Error in routine hp_find_inequiv_sites (1):<br>
skip_type must not be setup from the input when find_atpert=1<span class="gmail_default" style="font-size:large">.</span></div>
<div class="gmail_quote"><span class="gmail_default" style="font-size:large"></span></div>
<div class="gmail_quote"><font size="4"><span class="gmail_default" style="font-size:large">For magnetite structure (Fe3O4), Fe has two states: Fe2+ and Fe3+.</span><br>
</font></div>
<div class="gmail_quote"><font size="4"><br>
</font>
<div class="gmail_default" style="font-size:large"><span style="font-size:small"> </span><span style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif">Here is the Tr[ns(na)] and input file</span></div>
<div><span class="gmail_default" style="font-size:large"></span>atom 1 Tr[ns(na)]= 6.2349321</div>
atom 1 Mag[ns(na)]= 3.5251042<br>
atom 2 Tr[ns(na)]= 6.2349321<br>
atom 2 Mag[ns(na)]= 3.5251042<br>
atom 3 Tr[ns(na)]= 6.2349321<br>
atom 3 Mag[ns(na)]= 3.5251042<br>
atom 4 Tr[ns(na)]= 6.2348428<br>
atom 4 Mag[ns(na)]= 3.5251547<br>
atom 5 Tr[ns(na)]= 6.1942515<br>
atom 5 Mag[ns(na)]= <span class="gmail_default" style="font-size:large"></span>-3.5314272<br>
atom 6 Tr[ns(na)]= 6.1942515<br>
atom 6 Mag[ns(na)]= -3.5314272<br>
atom 7 Tr[ns(na)]= 5.0802986<br>
atom 7 Mag[ns(na)]= 0.0754368<br>
atom 8 Tr[ns(na)]= 5.0802986<br>
atom 8 Mag[ns(na)]= 0.0754368<br>
atom 9 Tr[ns(na)]= 5.0802986<br>
atom 9 Mag[ns(na)]= 0.0754368<br>
atom 10 Tr[ns(na)]= 5.0802986<br>
atom 10 Mag[ns(na)]= 0.0754368<br>
atom 11 Tr[ns(na)]= 5.0802986<br>
atom 11 Mag[ns(na)]= 0.0754368<br>
atom 12 Tr[ns(na)]= 5.0802986<br>
atom 12 Mag[ns(na)]= 0.0754368<br>
atom 13 Tr[ns(na)]= 5.0802792<br>
atom 13 Mag[ns(na)]= 0.0754401<br>
atom 14 Tr[ns(na)]= 5.0802792<br>
atom 14 Mag[ns(na)]= 0.0754401<br>
<div><span class="gmail_default" style="font-size:large"><br>
</span></div>
<div><span class="gmail_default" style="font-size:large">Input file:</span></div>
<div><span class="gmail_default" style="font-size:large"><br>
</span></div>
<div><span class="gmail_default" style="font-size:large">&CONTROL<br>
calculation = 'vc-relax'<br>
restart_mode='from_scratch',<br>
etot_conv_thr = 0.0001<br>
forc_conv_thr = 0.001<br>
outdir = './temp/'<br>
prefix = 'pwscf'<br>
pseudo_dir = '~/PP/'<br>
tprnfor = .true.<br>
tstress = .true.<br>
verbosity = 'high'<br>
/<br>
&SYSTEM<br>
degauss = 0.022<br>
ecutrho = 320<br>
ecutwfc = 40<br>
occupations = 'smearing' , smearing = 'mp'<br>
ibrav = 0<br>
nat = 14<br>
nosym = .false.<br>
ntyp = 3<br>
nspin=2<br>
starting_magnetization(1) = 0.8<br>
starting_magnetization(2) = -0.8<br>
starting_magnetization(3) = 0.0<br>
<br>
lda_plus_u = .true.,<br>
lda_plus_u_kind = 2,<br>
U_projection_type = 'ortho-atomic',<br>
Hubbard_V(1,1,1) = 1.d-8<br>
Hubbard_V(5,5,1) = 1.d-8<br>
Hubbard_V(7,7,1) = 1.d-8<br>
!Hubbard_parameters = 'file'<br>
<br>
<br>
/<br>
&ELECTRONS<br>
conv_thr = 1.0000000000d-06<br>
electron_maxstep = 400<br>
mixing_beta = 1.5000000000d-01<br>
/<br>
&IONS<br>
ion_dynamics = 'bfgs'<br>
/<br>
&CELL<br>
/<br>
<br>
ATOMIC_SPECIES<br>
Fe1 55.845 Fe.pbe-nd-rrkjus.UPF<br>
Fe2 55.845 Fe.pbe-nd-rrkjus.UPF<br>
O 15.9994 O.pbe-rrkjus.UPF<br>
ATOMIC_POSITIONS (crystal)<br>
Fe1 0.0000000000 -0.0000000000 -0.0000000000<br>
Fe1 0.5000000000 0.0000000000 0.0000000000<br>
Fe1 0.9999999892 0.5000000216 -0.0000000000<br>
Fe1 0.9999999965 0.9999999956 0.5000000115<br>
Fe2 0.3749993721 0.3749993349 0.3750019210<br>
Fe2 0.6250006225 0.6250006532 0.6249981020<br>
O 0.2454868415 0.2454868399 0.2454949640<br>
O 0.7545131845 0.7545131098 0.7545050345<br>
O 0.7635313546 0.2454868399 0.2454949640<br>
O 0.2364686713 0.7545131098 0.7545050345<br>
O 0.2454868307 0.7635313746 0.2454949640<br>
O 0.7545132523 0.2364686217 0.7545050345<br>
O 0.2454908593 0.2454908222 0.7635274591<br>
O 0.7545090629 0.7545091741 0.2364725394<br>
<br>
CELL_PARAMETERS (angstrom)<br>
5.944682649 0.000000000 0.000000000<br>
2.972341325 5.148246192 0.000000000<br>
2.972341325 1.716082064 4.853885701<br>
<br>
K_POINTS automatic<br>
7 7 7 0 0 0<br>
</span></div>
<div><span class="gmail_default" style="font-size:large"><br>
</span></div>
<div><span class="gmail_default" style="font-size:large">Regards</span></div>
<div><span class="gmail_default" style="font-size:large">Bhamu</span></div>
<div><span class="gmail_default" style="font-size:large"><br>
</span></div>
<div><span class="gmail_default" style="font-size:large"></span> </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 id="gmail-m_7500084446782585102divtagdefaultwrapper" style="" dir="ltr">
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span class="gmail_default" style="font-size:large"></span><br>
</p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span>> As all Fe will have the same Hubbard parameter (as reported in the literature for the same system)...</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span><br>
</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span>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.</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span><br>
</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span>HTH</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span><br>
</span></p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<span>Iurii</span><br>
</p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<br>
</p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
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
<span style="font-family:Constantia,"Hoefler Text",serif">I</span>urii". Sorry, I don't want to bother you with this, but just to makes things clear
<span>😊</span><br>
</p>
<p style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif;font-size:12pt">
<br>
</p>
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<div name="divtagdefaultwrapper"><font size="3" face="'Times New Roman', Times, serif" color="808080">--<br>
<span style="font-family:Cambria,Georgia,serif">Dr. Iurii TIMROV</span><br>
<span style="font-family:Cambria,Georgia,serif">Senior Research Scientist</span></font></div>
<div name="divtagdefaultwrapper"><font size="3" face="'Times New Roman', Times, serif" color="808080"><span style="font-family:Cambria,Georgia,serif">Theory and Simulation of Materials (THEOS)</span></font></div>
<div name="divtagdefaultwrapper"><span style="font-size:12pt;color:rgb(128,128,128);font-family:Cambria,Georgia,serif">Swiss Federal Institute of Technology Lausanne (EPFL</span><font style="font-size:12pt;color:rgb(128,128,128);font-family:"Times New Roman",Times,serif" color="808080"><font face="'Times New Roman', Times, serif"><span style="font-family:Cambria,Georgia,serif">)</span></font></font><br>
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<div name="divtagdefaultwrapper"><span style="font-family:Cambria,Georgia,serif"></span><font size="3" face="'Times New Roman', Times, serif" color="808080"><span style="font-family:Cambria,Georgia,serif">CH-1015 Lausanne, Switzerland</span><br>
<span style="font-family:Cambria,Georgia,serif">+41 21 69 34 881</span></font></div>
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<div id="gmail-m_7500084446782585102divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>>
on behalf of Dr. K. C. Bhamu <<a href="mailto:kcbhamu85@gmail.com" target="_blank">kcbhamu85@gmail.com</a>><br>
<b>Sent:</b> Wednesday, November 24, 2021 1:00:13 PM<br>
<b>To:</b> Quantum Espresso users Forum<br>
<b>Subject:</b> [QE-users] Query for skip_type and equiv_type for DFT+U+V</font>
<div> </div>
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<div>
<div dir="ltr">
<div style="font-size:large">Dear Dr. Iurii (😊),</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">The ATOMIC_POSITIONS cart of my structure (ferrimagnetic system with ntyp = 3 ) is</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">ATOMIC_POSITIONS (crystal)<br>
Fe1 0.0000000000 -0.0000000000 -0.0000000000 (four times)<br>
Fe2 0.3749993721 0.3749993349 0.3750019210 (two times)<br>
O 0.2454868415 0.2454868399 0.2454949640 (eight times)</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Previously, based on ATOMIC_SPECIES cart, I defined my Hubbard tag as below</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large"> Hubbard_V(1,1,1) = 1.d-8<br>
Hubbard_V(2,2,1) = 1.d-8<br>
Hubbard_V(3,3,1) = 1.d-8</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">In the hp output file, I saw that only one Fe1 atom was perturbed.</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Then I defined below Hubbard tags according to ATOMIC_POSITIONS cart as</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large"> Hubbard_V(1,1,1) = 1.d-8<br>
Hubbard_V(5,5,1) = 1.d-8<br>
Hubbard_V(7,7,1) = 1.d-8<br>
</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">which perturbed four atoms <br>
</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large"> 1 Fe1 55.8450 tau( 1) = ( 0.00000 0.00000 0.00000 )<br>
4 Fe1 55.8450 tau( 4) = ( 1.75000 1.01036 0.40825 )<br>
5 Fe2 55.8450 tau( 5) = ( 0.75000 0.43301 0.30619 )<br>
7 O 15.9994 tau( 7) = ( 0.49098 0.28347 0.20045 )<br>
</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">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).</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Is it okay if I do so?</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">To skip the perturbation for Fe1(4) and Fe2(5), I have updated below tags in my hp input file:</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">skip_type(1)=.true.<br>
skip_type(2)=.true.<br>
equiv_type(1)=1<br>
equiv_type(2)=1</div>
<div style="font-size:large">disable_type_analysis=.true.,<br>
</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Could you please correct me if this modification is correct or not?</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">
<div>
<div>Sorry for the list of questions. But I am sure, my these queries will be helpful for others too.</div>
</div>
</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Thanks and regards</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">K C Bhamu</div>
<div style="font-size:large"><br>
</div>
<div style="font-size:large">Postdoctoral Fellow</div>
<div style="font-size:large">University of Ulsan</div>
<div style="font-size:large">South Korea</div>
<div style="font-size:large"><br>
</div>
</div>
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