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Dear Toshiharu</div>
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If you compute the ILDOS of a system with spherical symmetry, such as the H atom, you should get a spherically symmetric distribution. For example, the 3 p orbitals will have the same energy, and when computing the ILDOS in their energy span, you will get the
contributions of p_x, p_y, and p_z, thus creating an isotropic plot.</div>
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You may try to get something different, breaking the spherical symmetry, such as an atom with partially filled shells. You might find a case like that in the pw_atom directory of the QE test suite.</div>
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Otherwise, plot the charge density contribution of single orbitals with plot_num = 7. An example of this for molecules is here:</div>
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<a href="https://gitlab.com/pietrodelugas/materials-for-max-qe2021-online-school/-/tree/master/Day-1?ref_type=heads" id="LPlnk913768">https://gitlab.com/pietrodelugas/materials-for-max-qe2021-online-school/-/tree/master/Day-1?ref_type=heads</a></div>
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best regards</div>
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Pietro</div>
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<div id="divRplyFwdMsg" dir="ltr" class="elementToProof"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Toshiharu Higuchi via users <users@lists.quantum-espresso.org><br>
</span></div>
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<b>Sent:</b> Friday, October 11, 2024 14:10<br>
<b>To:</b> "'Quantum ESPRESSO users Forum'" <users@lists.quantum-espresso.org>; "'ROBERT MIKHAIL GUZMAN ARELLANO'" <rguzmana@unmsm.edu.pe><br>
<b>Subject:</b> Re: [QE-users] The orbitals of a hydrogen atom</div>
<div style="direction: ltr;"> </div>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">Dear Professor Robert,</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">thank you very much for your helpful comment.</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">According to your explanation, a pseudopotential only reproduces the valence states (occupied) and the lowest energy unoccupied states. If
you open the pseudopotential used in your input file, you will see that it reproduces only the *s* and *p* states of hydrogen atoms.</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">However, in my calculations, the orbit is spherical even in the *p* state.</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">Could you please tell me the reason for this?</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;"> </span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">Best regard,</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;">Toshiharu Higuchi</span></p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: 游ゴシック; font-size: 10.5pt;"> </span></p>
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<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"><span style="font-family: "Calibri", sans-serif; font-size: 11pt;"><b>From:</b> ROBERT MIKHAIL GUZMAN ARELLANO <rguzmana@unmsm.edu.pe><br>
<b>Sent:</b> Friday, October 11, 2024 5:11 AM<br>
<b>To:</b> toshi1higu@docomo.ne.jp; Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Subject:</b> Re: [QE-users] The orbitals of a hydrogen atom</span></p>
</div>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"> </p>
<p>Dear Toshiharu,</p>
<p>Thank you very much for sharing your input files for <span style="font-family: "ＭＳ Ｐゴシック";">
<b>pw.x</b></span> and <span style="font-family: "ＭＳ Ｐゴシック";"><b>pp.x</b></span>.</p>
<p>I believe this might be the information you're looking for regarding how to plot a specific Kohn-Sham orbital:
<span style="color: blue;"><u><a href="https://www.youtube.com/watch?v=FrY8Sj0zUus" id="OWA1d9eb2cc-b320-083b-3dd0-a04e1365fa49" class="OWAAutoLink" style="color: blue; margin-top: 0px; margin-bottom: 0px;" data-auth="NotApplicable">https://www.youtube.com/watch?v=FrY8Sj0zUus</a></u></span></p>
<p>On another note, pseudopotentials do not include all atomic orbitals of the atoms. A pseudopotential only reproduces the valence states (occupied) and the lowest energy unoccupied states. If you open the pseudopotential used in your input file, you will
see that it reproduces only the <span style="font-family: "ＭＳ Ｐゴシック";"><b>s</b></span> and
<span style="font-family: "ＭＳ Ｐゴシック";"><b>p</b></span> states of hydrogen atoms. If you are interested in
<span style="font-family: "ＭＳ Ｐゴシック";"><b>d</b></span> orbitals, you can use a pseudopotential for elements like Nickel or Cobalt.</p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;">Best regards, </p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;"> </p>
<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;">El mié, 9 oct 2024 a las 20:57, Toshiharu Higuchi via users (<<span style="color: blue;"><u><a href="mailto:users@lists.quantum-espresso.org" id="OWA5dfc81f7-d3c4-af11-db1f-b5e766c001f9" class="OWAAutoLink" style="color: blue; margin-top: 0px; margin-bottom: 0px;">users@lists.quantum-espresso.org</a></u></span>>)
escribió:</p>
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<p style="margin: 0mm; font-family: "ＭＳ Ｐゴシック"; font-size: 12pt;">Dear members of Quantum-Espresso,<br>
I am a beginner of Quantum-Espresso. My question is about the orbital of a<br>
hydrogen atom. I calculated the orbital of a hydrogen atom using<br>
Quantum-Espresso. The orbitals of the hydrogen atom have already been<br>
analytically solved. These orbitals are (1) s-orbital is a spherically<br>
symmetric orbital, (2) p-orbitals have two lobes with a node located at the<br>
nucleus, and (3) d-orbitals have two types of orbitals, one kind of orbitals<br>
consist of a cloverleaf shape, with four electron-dense lobes, and another<br>
type of orbital has two lobes oriented in the z-axis with a donut-shaped<br>
ring in the x-y plane.<br>
<br>
However, the orbitals obtained with Quantum-Espresso (assuming the ILDOS<br>
pattern as the orbital) were all spherically symmetric orbitals from the<br>
first orbital to the tenth orbital. I was not able to obtain a pattern with<br>
a shape like p-orbital or d-orbital.<br>
Could someone tell me why the orbital turned out like this?<br>
<br>
My input data is as follows.<br>
<br>
[1] pw.x input<br>
&CONTROL<br>
title = 'QE_H_atom_Orbital_2' ,<br>
calculation = 'scf' ,<br>
restart_mode = 'from_scratch' ,<br>
wf_collect = .true. ,<br>
outdir = '/home/user/tmp/' ,<br>
pseudo_dir =<br>
'/home/user/user/espresso-5.0.1/espresso-5.0.1/pseudo/' ,<br>
prefix = 'QE_H_atom_Orbital_2' ,<br>
verbosity = 'high' ,<br>
tstress = .false. ,<br>
tprnfor = .false. ,<br>
tefield = .false. ,<br>
dipfield = .false. ,<br>
lelfield = .false. ,<br>
/<br>
&SYSTEM<br>
ibrav = 8,<br>
A = 20.0 ,<br>
B = 20.0 ,<br>
C = 45.0 ,<br>
nat = 1,<br>
ntyp = 1,<br>
ecutwfc = 26 ,<br>
ecutrho = 156 ,<br>
nbnd = 228,<br>
occupations = 'smearing' ,<br>
starting_spin_angle = .true. ,<br>
degauss = 0.003675 ,<br>
smearing = 'gaussian' ,<br>
nspin = 1 ,<br>
nr1 = 36 ,<br>
/<br>
&ELECTRONS<br>
electron_maxstep = 2000,<br>
conv_thr = 1.D-6 ,<br>
mixing_mode = 'plain' ,<br>
mixing_beta = 0.05 ,<br>
/<br>
ATOMIC_SPECIES<br>
H 1.00000 H.pz-rrkjus.UPF<br>
ATOMIC_POSITIONS angstrom<br>
H 10.000000000 10.000000000 22.500000000 <br>
K_POINTS gamma<br>
<br>
<br>
[2] pp.x input<br>
[a] 1st ILDOS<br>
&INPUTPP<br>
prefix = 'QE_H_atom_Orbital_2' ,<br>
outdir = '/home/user/tmp' ,<br>
filplot = '1st_QE_H_atom_Orbital_2' ,<br>
plot_num = 10,<br>
emin = -6.4009 ,<br>
emax = -6.3009 ,<br>
/<br>
&PLOT<br>
nfile = 1 ,<br>
weight(1) = 1.0,<br>
iflag = 3 ,<br>
output_format = 5 ,<br>
/<br>
<br>
<br>
[b] 2nd ILDOS<br>
&INPUTPP<br>
prefix = 'QE_H_atom_Orbital_2' ,<br>
outdir = '/home/user/tmp' ,<br>
filplot = '2nd_QE_H_atom_Orbital_2' ,<br>
plot_num = 10,<br>
emin = -0.2168 ,<br>
emax = -0.1168 ,<br>
/<br>
&PLOT<br>
nfile = 1 ,<br>
weight(1) = 1.0,<br>
iflag = 3 ,<br>
output_format = 5 ,<br>
/<br>
<br>
<br>
[c]10th ILDOS<br>
&INPUTPP<br>
prefix = 'QE_H_atom_Orbital_2' ,<br>
outdir = '/home/user/tmp' ,<br>
filplot = '10th_QE_H_atom_Orbital_2' ,<br>
plot_num = 10,<br>
emin = 0.1896 ,<br>
emax = 0.2896 ,<br>
/<br>
&PLOT<br>
nfile = 1 ,<br>
weight(1) = 1.0,<br>
iflag = 3 ,<br>
output_format = 5 ,<br>
/<br>
*************************<br>
Kind regards,<br>
Higuchi<br>
<br>
***************************<br>
Toshiharu Higuchi<br>
Yokohama, Japan<br>
***************************<br>
<br>
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