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<p>Dear Jibiao Li,</p>
<p>I think D3 is not implemented in the phonon code - at least if I
look at the beginning of<br>
the phonon.f90 which summarized what is possible:</p>
<p><a class="moz-txt-link-freetext" href="https://gitlab.com/QEF/q-e/-/blob/develop/PHonon/PH/phonon.f90?ref_type=heads">https://gitlab.com/QEF/q-e/-/blob/develop/PHonon/PH/phonon.f90?ref_type=heads</a></p>
<p>There I can read:</p>
<p> !! Not implemented in \(\texttt{ph.x}\): <br>
!! [6] [5] + constraints on the magnetization <br>
!! [7] Tkatchenko-Scheffler, DFT-D3 <br>
<br>
Sorry, but for D3 you probably need to use another code which is
interfaced with QE.<br>
Phonopy is working with QE.</p>
<p>Kind regards</p>
<p>Thomas<br>
</p>
<div class="moz-cite-prefix">On 8/6/23 04:12, Jibiao Li via users
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:tencent_FBD8E878D106EDE3FA1B9ACA66656FF5FF05@qq.com">
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<div style=" ; ; ;; ">Dear All,</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">I try to perform phonon calculations
in the develop version of QE, but I got an error message
below</div>
<div style=" ; ; ;; "><br>
</div>
<div style="">
<div style="">... ...</div>
<div style=""> Alpha used in Ewald sum = 2.8000</div>
<div style=""><br>
</div>
<div style=""> Reading Grimme-D3 Hessian from file:
./atop.hess</div>
<div style="">forrtl: severe (24): end-of-file during
read, unit 1, file
/home/jibiaoli/calc/monomers/first/./atop.hess</div>
<div style="">Image PC
Routine Line Source </div>
<div style="">ph.x 00000000010A6DD8
Unknown Unknown Unknown</div>
<div style="">ph.x 00000000010E1F7A
Unknown Unknown Unknown</div>
<div style="">ph.x 00000000005ECAFD
d2ionq_dispd3_ 51 d2ionq_disp.f90</div>
<div style="">ph.x 00000000005762F6
dynmat0_new_ 61 dynmat0.f90</div>
<div style="">ph.x 00000000004A7277
phq_init_ 407 phq_init.f90</div>
<div style="">ph.x 000000000047684F
initialize_ph_ 96 initialize_ph.f90</div>
<div style="">ph.x 000000000040C947
do_phonon_ 100 do_phonon.f90</div>
<div style="">ph.x 00000000004071C2
MAIN__ 78 phonon.f90</div>
<div style="">ph.x 0000000000407122
Unknown Unknown Unknown</div>
<div style="">libc-2.31.so 00007FA1520FC0B3
__libc_start_main Unknown Unknown</div>
<div style="">ph.x 000000000040702E
Unknown Unknown Unknown</div>
<div style=""><br>
</div>
<div style="">===================================================================================</div>
<div style="">= BAD TERMINATION OF ONE OF YOUR
APPLICATION PROCESSES</div>
<div style="">= RANK 1 PID 145409 RUNNING AT ubuntue</div>
<div style="">= KILLED BY SIGNAL: 9 (Killed)</div>
</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">Any suggestion to resolve this
problem?</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">I look forward to receiving your
reply.</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">Sincerely</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">Jibiao Li</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; ">phonons at Gamma</div>
<div style=" ; ; ;; "> &inputph</div>
<div style=" ; ; ;; "> tr2_ph=1.0d-14,</div>
<div style=" ; ; ;; "> prefix='atop',</div>
<div style=" ; ; ;; "> alpha_mix=0.15,</div>
<div style=" ; ; ;; "> fildyn='phG.dyn',</div>
<div style=" ; ; ;; "> amass(1)=15.999</div>
<div style=" ; ; ;; "> amass(2)=1.0079</div>
<div style=" ; ; ;; "> amass(3)=106.4</div>
<div style=" ; ; ;; "> outdir='./'</div>
<div style=" ; ; ;; "> nat_todo=3,</div>
<div style=" ; ; ;; "> /</div>
<div style=" ; ; ;; ">0.0 0.0 0.0</div>
<div style=" ; ; ;; ">1 2 3</div>
</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; "><br>
</div>
<div style=" ; ; ;; "> &CONTROL</div>
<div style=" ; ; ;; "> calculation = 'scf' ,</div>
<div style=" ; ; ;; "> restart_mode =
'from_scratch' ,</div>
<div style=" ; ; ;; "> outdir = './' ,</div>
<div style=" ; ; ;; "> pseudo_dir =
'/home/jibiaoli/pseudo/PAW' ,</div>
<div style=" ; ; ;; "> prefix = 'atop'
,</div>
<div style=" ; ; ;; "> tstress = .true.
,</div>
<div style=" ; ; ;; "> tprnfor = .true.
,</div>
<div style=" ; ; ;; "> /</div>
<div style=" ; ; ;; "> &SYSTEM</div>
<div style=" ; ; ;; "> ibrav = 4,</div>
<div style=" ; ; ;; "> celldm(1) =
15.6677255,</div>
<div style=" ; ; ;; "> celldm(3) = 3.4,</div>
<div style=" ; ; ;; "> nat = 48,</div>
<div style=" ; ; ;; "> ntyp = 3,</div>
<div style=" ; ; ;; "> ecutwfc = 49 ,</div>
<div style=" ; ; ;; "> ecutrho = 411 ,</div>
<div style=" ; ; ;; "><span style="white-space: pre;"> </span> occupations
= 'smearing' ,</div>
<div style=" ; ; ;; "> degauss = 0.02D0
,</div>
<div style=" ; ; ;; "> smearing =
'marzari-vanderbilt' ,</div>
<div style=" ; ; ;; "><span style="white-space: pre;"> </span>
vdw_corr = 'DFT-D3',</div>
<div style=" ; ; ;; ">/</div>
<div style=" ; ; ;; "> &ELECTRONS</div>
<div style=" ; ; ;; "> electron_maxstep = 299,</div>
<div style=" ; ; ;; "> mixing_beta = 0.2D0 ,</div>
<div style=" ; ; ;; "> diagonalization = 'david'
,</div>
<div style=" ; ; ;; "> /</div>
<div style=" ; ; ;; ">ATOMIC_SPECIES</div>
<div style=" ; ; ;; "> O 15.999
O.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div style=" ; ; ;; "> H 1.0079
H.pbe-kjpaw_psl.1.0.0.UPF</div>
<div style=" ; ; ;; "> Pd 106.40
Pd.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div style=" ; ; ;; ">ATOMIC_POSITIONS angstrom</div>
<div style=" ; ; ;; ">H 2.1703819667
3.1677699191 11.4894189267</div>
<div style=" ; ; ;; ">O 1.5740335760
2.3936195417 11.4400536939</div>
<div style=" ; ; ;; ">H 2.1702795024
1.6192086817 11.4893627144</div>
<div style=" ; ; ;; ">Pd -0.0045915754
-0.0102383957 9.0266998715</div>
<div style=" ; ; ;; ">Pd -2.7651688140
4.7874278555 9.0360251883</div>
<div style=" ; ; ;; ">Pd 5.5259827527
-0.0001828639 9.0387617051</div>
<div style=" ; ; ;; ">Pd 2.7689931581
4.7956210226 9.0246308039</div>
<div style=" ; ; ;; ">Pd -1.3946621870
2.3938110685 9.0271708745</div>
<div style=" ; ; ;; ">Pd 4.1536116232
2.3931749457 9.0252316830</div>
<div style=" ; ; ;; ">Pd 1.3691550331
2.3939966336 9.0670107322</div>
<div style=" ; ; ;; ">Pd 2.7694105684
-0.0086872195 9.0249397450</div>
<div style=" ; ; ;; ">Pd -0.0054827549
4.7974751761 9.0269897862</div>
<div style=" ; ; ;; ">Pd 0.0066605988
3.1870668155 6.7670981200</div>
<div style=" ; ; ;; ">Pd 5.5283163914
3.1928013873 6.7495035331</div>
<div style=" ; ; ;; ">Pd 1.3818262753
0.8042230686 6.7653225775</div>
<div style=" ; ; ;; ">Pd -1.3828050324
5.5824639267 6.7487397927</div>
<div style=" ; ; ;; ">Pd 6.9077402952
0.7968151976 6.7553886260</div>
<div style=" ; ; ;; ">Pd 4.1480097045
5.5845055762 6.7479017041</div>
<div style=" ; ; ;; ">Pd 4.1467102526
0.7971898792 6.7545181138</div>
<div style=" ; ; ;; ">Pd 1.3813552626
5.5860818516 6.7546258538</div>
<div style=" ; ; ;; ">Pd 2.7589306780
3.1885119775 6.7642409667</div>
<div style=" ; ; ;; ">Pd 2.7636561440
1.5955976180 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 0.0000000000
6.3823904740 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 1.3818280720
3.9889940460 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd -1.3818280720
3.9889940460 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 4.1454842150
3.9889940460 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 0.0000000000
1.5955976180 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd -2.7636561440
6.3823904740 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 5.5273122870
1.5955976180 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd 2.7636561440
6.3823904740 4.5130315840 0 0 0</div>
<div style=" ; ; ;; ">Pd -0.0000000000
4.7867928550 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 1.3818280720
2.3933964280 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 2.7636561400
0.0000000000 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd -1.3818280720
2.3933964280 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 4.1454842150
2.3933964280 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 0.0000000000
0.0000000000 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd -2.7636561440
4.7867928550 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 5.5273122870
0.0000000000 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd 2.7636561440
4.7867928550 2.2565157920 0 0 0</div>
<div style=" ; ; ;; ">Pd -0.0000000000
3.1911952370 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 5.5273122870
3.1911952370 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 1.3818280720
0.7977988090 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd -1.3818280720
5.5845916650 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 6.9091403590
0.7977988090 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 4.1454842150
5.5845916650 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 4.1454842150
0.7977988090 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 1.3818280720
5.5845916650 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">Pd 2.7636561440
3.1911952370 0.0000000000 0 0 0</div>
<div style=" ; ; ;; ">K_POINTS automatic</div>
<div style=" ; ; ;; "> 6 6 1 0 0 0</div>
<div style=" ; ; ;; "><br>
</div>
</font></div>
</div>
<div><font size="2" face="Arial"><br>
</font></div>
<div>
<hr style="margin: 0 0 10px 0;border: 0;border-bottom:1px solid
#E4E5E6;height:0;line-height:0;font-size:0;padding: 20px 0 0
0;width: 50px;" align="left">
<div style="font-size:14px;font-family:Verdana;color:#000;">
<p><font size="2" face="Arial">Jibiao Li</font></p>
<p><font size="2" face="Arial">Department of Materials Science
and Engineering</font></p>
<p><font size="2" face="Arial">Yangtze Normal University</font></p>
<p><font size="2" face="Arial">Juxian Avenue 16, Fuling,
Chongqing, China 408100</font></p>
<p><font size="2" face="Arial">Scopus Research ID: <a
href="https://www.scopus.com/authid/detail.uri?authorId=54944118000"
moz-do-not-send="true"><font face="Arial"><font
face="Arial"><font face="Arial"><font face="Arial">54944118000</font></font></font></font></a></font></p>
<p><font size="2" face="Arial">Web of Science Research ID: <span style="letter-spacing: inherit; text-align: inherit; text-transform: inherit; white-space: pre-wrap;"><a class="moz-txt-link-freetext" href="http://www.webofscience.com/wos/author/record/">http://www.webofscience.com/wos/author/record/</a></span>GLS-7259-2022</font></p>
<p><font style="font-family: Arial; font-size: small; margin:
0px; padding: 0px; border: 0px; outline-style: initial;
outline-width: 0px; font-variant-numeric: inherit;
font-variant-east-asian: inherit; font-stretch: inherit;
line-height: inherit; vertical-align: top;
-webkit-font-smoothing: antialiased; white-space: normal;
color: rgb(0, 0, 0) !important;" size="2" face="Arial"><font
face="Arial"><font face="Arial"><span style="font-style:
inherit; font-variant: inherit; font-weight:
inherit; font-stretch: inherit; line-height:
inherit; margin: 0px; padding: 0px; border: 0px;
outline: 0px; vertical-align: top;
-webkit-font-smoothing: antialiased;"></span></font></font></font><br>
</p>
</div>
</div>
<div> </div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
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</blockquote>
<pre class="moz-signature" cols="72">--
Dr. rer. nat. Thomas Brumme
Theoretical chemistry
TU Dresden - KOE / 103
Bergstr. 66c
01069 Dresden
Tel: +49 (0)351 463 39449
email: <a class="moz-txt-link-abbreviated" href="mailto:thomas.brumme@tu-dresden.de">thomas.brumme@tu-dresden.de</a></pre>
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