<div dir="ltr"><div>Look into lambda.f90 and figure out where and why it gives NaN. Most likely there is a division by zero or a square root of a negative quantity. <br></div><div>Once upon the time, one needed to get rid of acoustic phonons at q=0 in lambda.x in order to get sensible results. This was done by simply skipping the first three phonons. I don't know how it works now (if it works)</div><div><br></div><div>Paolo<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jun 15, 2020 at 2:53 PM Maciej Szary <<a href="mailto:maciej.szary@put.poznan.pl">maciej.szary@put.poznan.pl</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>
<font face="Courier New, Courier, monospace">Dear Professor
Giannozzi,<br>
<br>
sorry if I didn't specify. "NaN" referred explicitly to Tc
calculations done by lambda.x. I do a pw.x calculation and I get a
convergence, ph.x run is rather long, still it produces </font><font face="Courier New, Courier, monospace"><font face="Courier New,
Courier, monospace">positive </font>frequencies e.g.<br>
<i><br>
</i><i> **************************************************************************</i><i><br>
</i><i> freq ( 1) = 0.819632 [THz] = 27.339964
[cm-1]</i><i><br>
</i><i> freq ( 2) = 0.914078 [THz] = 30.490364
[cm-1]</i><i><br>
</i><i>...</i><i><br>
</i><i> freq ( 18) = 2.063295 [THz] = 68.824112
[cm-1]</i><br>
<i> **************************************************************************</i><br>
<br>
Next I use q2r.x. I do get some warnings e.g.:<br>
<br>
<i> Broadening = 0.005</i><i><br>
</i><i> q-space grid ok, #points = 36</i><i><br>
</i><i><br>
</i><i> fft-check warning: sum of imaginary terms =
3.497134E-06</i><br>
<br>
but based on the previous forum posts, this seems acceptable.<br>
<br>
<br>
Subsequently I use matdyn.x and get lambda file containing:<br>
<i><br>
</i><i> Broadening 0.0050 lambda 1.7637 dos(Ef) 21.5379
omega_ln [K] 49.4388</i><i><br>
</i><i> Broadening 0.0100 lambda 1.7028 dos(Ef) 21.2277
omega_ln [K] 49.7600</i><i><br>
</i><i>...</i><i></i><i><br>
</i><i> Broadening 0.0500 lambda 1.7499 dos(Ef) 22.1428
omega_ln [K] 48.1738</i><br>
<br>
<br>
(shouldn't this be enough to calculate Tc using McMillan formula?)<br>
<br>
<br>
Finally I use lambda.x and get:<br>
<i><br>
</i><i> lambda = NaN ( NaN ) <log w>=
NaN K N(Ef)= 21.537940 at degauss= 0.005</i><i><br>
</i><i> lambda = NaN ( NaN ) <log w>=
NaN K N(Ef)= 21.227733 at degauss= 0.010</i><i><br>
</i><i>...</i><i><br>
</i><i> lambda = NaN ( NaN ) <log w>=
NaN K N(Ef)= 22.142765 at degauss= 0.050</i><i><br>
</i><i>lambda omega_log T_c</i><i><br>
</i><i> NaN NaN NaN</i><i><br>
</i><i> NaN NaN NaN</i><i><br>
</i><i>...</i><i><br>
</i><i> NaN NaN NaN</i></font><br>
<font face="Courier New, Courier, monospace"><br>
<br>
I've been redoing this procedure, with different parameters listed
in my previous email.<br>
<br>
Regards,<br>
Maciej Szary</font><br>
<pre cols="72">--
Research Assistant,
Institute of Physics,
Poznan University of Technology
Piotrowo 3A, 61-138 Poznan</pre>
<br>
<br>
<div>On 6/14/20 3:50 PM, Maciej Szary wrote:<br>
</div>
<blockquote type="cite">
<font face="Courier New, Courier, monospace">Dear QE users,<br>
<br>
I'm trying to calculate electron-phonon coefficient and the
critical superconducting temperature of Pb(111). As an
introduction I've done the [PHonon/examples/example03] (bulk
Al), and I've reproduced the results successfully. However, in
case of Pb(111), I can't get Tc for the system. I only get
"NaN". I understand that, this is often a result of imaginary
components in the dynamical matrices, thus I've been redoing the
calculations with different sets of parameters, however, to no
avail. <br>
<br>
In scf I've been changing:<br>
<br>
1. ecutwfc, and ecutrho (current values 80, and 650 Ry,
respectively)<br>
2. conv_thr (currently 1.0d-14)<br>
3. k-point mesh (currently 36x36x1)<br>
4. Pb pseudopotentials (currently Pb.rel-pbe-n-nc.UPF,
previously Pb.rel-pbe-dn-rrkjus_psl.0.2.2.UPF)<br>
5. Slab thickness (6-12 layers)<br>
<br>
In ph I've been testing:<br>
<br>
1. tr2_ph (currently 1.0d-16, and </font><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace">up to
</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace">1.0d-17</font></font></font> with
</font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">Pb.rel-pbe-dn-rrkjus_psl.0.2.2.UPF</font></font><font face="Courier New, Courier, monospace"><font face="Courier New,
Courier, monospace">)<br>
2. electron_phonon (interpolated, and simple)<br>
3. q mesh (form 2x2x1 to 6x6x1)<br>
<br>
As a first step I've done the vc-relax, to relax the lattice
constant of the slab. Next I perform relaxation with SOC
included (etot_conv_thr, and forc_conv_thr= both 1.0d-6). Next
I do the scf run e.g.:<br>
<br>
--------------------------------------------------------<br>
<i> &system</i><i><br>
</i><i> ibrav= 4, </i><i><br>
</i><i> a=3.503660834</i><i><br>
</i><i> c=40</i><i><br>
</i><i> nat= 6, ntyp= 1,</i><i><br>
</i><i> ecutwfc =80.0,</i><i><br>
</i><i> ecutrho = 650, </i><i><br>
</i><i> occupations='smearing', smearing='mv', degauss=0.05</i><i><br>
</i><i> lspinorb=.true., noncolin=.true.,
starting_spin_angle=.true., starting_magnetization=0.0,</i><i><br>
</i><i> la2F = .true.,</i><i><br>
</i><i> nbnd = 48 </i><i><br>
</i><i>/</i><i><br>
</i><i> &electrons</i><i><br>
</i><i> mixing_mode = 'plain'</i><i><br>
</i><i> mixing_beta = 0.5</i><i><br>
</i><i> conv_thr = 1.0d-14</i><i><br>
</i><i> /</i><i><br>
</i><i> ATOMIC_SPECIES</i><i><br>
</i><i> Pb 207.2 Pb.rel-pbe-n-nc.UPF</i><i><br>
</i><i>ATOMIC_POSITIONS angstrom</i><i><br>
</i><i>Pb 0.000000000 0.000000000 19.078230578</i><i><br>
</i><i>Pb 0.000000000 0.000000000 27.596055131</i><i><br>
</i><i>Pb 1.751830417 1.011419906 16.119173776</i><i><br>
</i><i>Pb 1.751830417 1.011419906 24.874997245</i><i><br>
</i><i>Pb 3.503661844 2.022839813 13.398232981</i><i><br>
</i><i>Pb 3.503661844 2.022839813 21.915874849</i><i><br>
</i><i>K_POINTS automatic</i><i><br>
</i><i>36 36 1 0 0 0</i><br>
</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
<br>
this is followed by ph.x run:<br>
</font></font><br>
<font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
</font></font><i>&inputph</i><i><br>
</i><i> outdir='Files/',</i><i><br>
</i><i> prefix='QE'</i><i><br>
</i><i> fildvscf='aldv',</i><i><br>
</i><i> tr2_ph = 1.0d-16</i><i><br>
</i><i> amass(1) = 207.2</i><i><br>
</i><i> fildyn = 'Pb.dyn'</i><i><br>
</i><i> alpha_mix=0.2</i><i><br>
</i><i> electron_phonon='interpolated',</i><i><br>
</i><i> el_ph_sigma=0.005, </i><i><br>
</i><i> el_ph_nsigma=10,</i><i><br>
</i><i> trans=.true.,</i><i><br>
</i><i> ldisp=.true.</i><i><br>
</i><i> nq1 = 6, nq2 = 6, nq3 = 1</i><i><br>
</i><i> nogg = .true.</i><i><br>
</i><i> asr = .true.</i><i><br>
</i><i>/</i><br>
</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
<br>
Next are q2r.x, <br>
<br>
</font></font><br>
<font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
</font></font><i>&input</i><i><br>
</i><i> fildyn = 'Pb.dyn'</i><i><br>
</i><i> zasr = 'crystal'</i><i><br>
</i><i> flfrc = 'Pb.q661.fc'</i><i><br>
</i><i> la2F=.true.</i><i><br>
</i><i>/</i><br>
</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
<br>
matdyn.x,<br>
<br>
</font></font><br>
<font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------</font></font></font></font><br>
<i>&input</i><i><br>
</i><i> asr= 'simple'</i><i><br>
</i><i> flfrc = 'Pb.q661.fc', flfrq='Pb.q661.freq',
la2F=.true., dos=.true.</i><i><br>
</i><i> fldos='phonon.dos', nk1=60, nk2=60, nk3=1, ndos=50</i><i><br>
</i><i> /</i></font></font><br>
<font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
<br>
</font></font></font></font></font></font>and
lambda.x <br>
</font></font><br>
<font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
</font></font></font></font></font></font><i>5
0.12 1 ! emax (something more than highest phonon mode
in THz), degauss, smearing method </i><i><br>
</i><i> 7</i><i><br>
</i><i> 1 0.0000000 0.0000000 0.0000000 1.00</i><i><br>
</i><i> 2 0.1666667 0.0962250 0.0000000 6.00</i><i><br>
</i><i> 3 0.3333333 0.1924501 0.0000000 6.00</i><i><br>
</i><i> 4 0.5000000 0.2886751 0.0000000 3.00</i><i><br>
</i><i> 5 0.1666667 0.2886751 0.0000000 6.00</i><i><br>
</i><i> 6 0.3333333 0.3849002 0.0000000 12.00</i><i><br>
</i><i> 7 0.3333333 0.5773503 0.0000000 2.00</i><i><br>
</i><i>elph_dir/elph.inp_lambda.1 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.2 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.3 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.4 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.5 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.6 </i><i><br>
</i><i>elph_dir/elph.inp_lambda.7 </i><i><br>
</i><i>0.10</i> <br>
</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">--------------------------------------------------------<br>
</font></font></font></font></font></font><br>
The parameters I've used are relatively high in comparison to
the Pb fcc example given by S. Poncé in 2018. Output of ph.x
lacks negative frequencies, and DOS seems also fine:<br>
<br>
<i> # Frequency[cm^-1] DOS PDOS</i><i><br>
</i><i> 0.0000000000E+00 0.0000000000E+00 0.0000E+00
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00</i><i><br>
</i><i> 1.4306338313E+00 3.8122112950E-03 6.3283E-04
6.3953E-04 6.3336E-04 6.3251E-04 6.4093E-04 6.3306E-04</i><i><br>
</i><i> 2.8612676626E+00 6.7934053704E-03 1.1376E-03
1.1328E-03 1.1244E-03 1.1215E-03 1.1385E-03 1.1386E-03</i><i><br>
</i><i> 4.2919014939E+00 9.5022844921E-03 1.6112E-03
1.5734E-03 1.5628E-03 1.5658E-03 1.5730E-03 1.6162E-03</i><i><br>
</i><i> 5.7225353252E+00 1.2941007092E-02 2.2167E-03
2.1293E-03 2.1167E-03 2.1337E-03 2.1145E-03 2.2302E-03<br>
<br>
</i><i>...</i><br>
<br>
Also matdyn.x produces "lambda" file with:<br>
<br>
<i> Broadening 0.0050 lambda 1.7637 dos(Ef) 21.5379
omega_ln [K] 49.4388</i><i><br>
</i><i> Broadening 0.0100 lambda 1.7028 dos(Ef)
21.2277 omega_ln [K] 49.7600</i><i><br>
</i><i> Broadening 0.0150 lambda 1.6783 dos(Ef)
21.0885 omega_ln [K] 49.5935</i><i><br>
</i><i> Broadening 0.0200 lambda 1.6881 dos(Ef)
21.1817 omega_ln [K] 49.4624</i><i><br>
</i><i> Broadening 0.0250 lambda 1.7060 dos(Ef)
21.3799 omega_ln [K] 49.3380</i><i><br>
</i><i> Broadening 0.0300 lambda 1.7218 dos(Ef)
21.5945 omega_ln [K] 49.1667</i><i><br>
</i><i> Broadening 0.0350 lambda 1.7335 dos(Ef)
21.7888 omega_ln [K] 48.9500</i><i><br>
</i><i> Broadening 0.0400 lambda 1.7414 dos(Ef)
21.9474 omega_ln [K] 48.7041</i><i><br>
</i><i> Broadening 0.0450 lambda 1.7466 dos(Ef)
22.0647 omega_ln [K] 48.4423</i><i><br>
</i><i> Broadening 0.0500 lambda 1.7499 dos(Ef)
22.1428 omega_ln [K] 48.1738</i><br>
<br>
so shouldn't Tc be just a product of substitution into
McMillan formula using </font></font><font face="Courier New,
Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier
New, Courier, monospace">values of omega_ln and </font></font></font></font><font face="Courier New, Courier, monospace"><font face="Courier New,
Courier, monospace"><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">lambda</font></font><font face="Courier New, Courier, monospace"><font face="Courier New, Courier, monospace">?<br>
<br>
</font></font><font face="Courier New, Courier,
monospace"><font face="Courier New, Courier, monospace">Regards,<br>
Maciej Szary</font></font><i><font face="Courier New,
Courier, monospace"><font face="Courier New, Courier,
monospace"><i><br>
</i></font></font></i></font></font></font></font>
<pre cols="72">--
Research Assistant,
Institute of Physics,
Poznan University of Technology
Piotrowo 3A, 61-138 Poznan</pre>
</blockquote>
<br>
<pre cols="72"></pre>
</div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div></div>