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Dear Giovanni and Giuseppe,<br>
<br>
Thank you very much for taking the discussion. <span tabindex="-1"
id="result_box" class="short_text" lang="en"><span class="hps">I
think</span> <span class="hps">it</span> <span class="hps">will
benefit</span> <span class="hps">many beginners</span><span>. </span></span><span
tabindex="-1" id="result_box" class="" lang="en"><span class="hps">I
try to</span> <span class="hps">read</span> <span class="hps">as
much as possible</span> <span class="hps">but</span> <span
class="hps">some important</span> <span class="hps">things</span>
<span class="hps">escape</span> <span class="hps">me</span> <span
class="hps">at the</span> <span class="hps">accumulation of</span>
<span class="hps">a lot of information</span>, <span class="hps">not
yet</span> <span class="hps">know how to</span> <span
class="hps">sift</span><span> it.<br>
<br>
</span></span><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps">The answers</span> <span class="hps">given
by</span> <span class="hps">you</span> <span class="hps">are
very</span> <span class="hps">kind</span><span>, and after</span>
<span class="hps">reading them</span> <span class="hps">I</span>
<span class="hps">raise</span> <span class="hps">further
questions</span><span>:<br>
<br>
</span></span><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps">1.If</span> <span class="hps">different
potentials</span> <span class="hps">have</span> <span
class="hps">different</span> <span class="hps">cutoff</span> <span
class="hps">energies, </span></span><span tabindex="-1"
id="result_box" class="" lang="en"><span class="hps atn">is it "</span><span>safe</span><span
class="">"</span> to<span class="hps"></span> <span class="hps
alt-edited">overestimate</span> <span class="hps">them
(ecutwfc)</span><span>, losing</span> <span class="hps">only</span>
<span class="hps">the time</span> <span class="hps">of
calculation</span><span> but maintaining good quality?<br>
<br>
</span></span>2. "I guess (but maybe I’m wrong!) that you are
wondering whether it is possible to mix spin polarised and non spin
polarised pseudo potentials because
you are mislead by the “sp “ and “nsp” found in the pseudo file
name." - yes. Of course it was clearly my mistake. Question was
about spin polarization and I've also mistaken name conventions...
sorry for that. <span tabindex="-1" id="result_box" class=""
lang="en"><span><br>
<br>
</span></span><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps">3. I understand</span> <span
class="hps">that the various</span> <span class="hps">"pp"</span>
<span class="hps">for the same</span> <span class="hps">elements</span>
<span class="hps">have a different</span> number of electrons<span
class="hps"></span><span>.</span> <span class="hps">How do I
know</span> wchich<span class="hps"></span> <span class="hps">PP
I "want"</span> <span class="hps">to use</span><span>?</span> <span
class="hps"><-</span> <span class="hps">Perhaps this</span>
<span class="hps">question is</span> <span class="hps">more</span>
in <span class="hps">physics</span> <span class="hps">than</span>
<span class="hps">QE<br>
<br>
4. </span></span><span id="result_box" class="" lang="en"><span
class="hps alt-edited">This will be</span> <span class="hps">a
very basic question</span><span>:</span> <span class="hps">If I</span>
<span class="hps">want to do</span> <span class="hps">to optimize</span>
<span class="hps">the positions of</span> <span class="hps">the
atoms in</span> <span class="hps">the unit cell</span> <span
class="hps">should</span> I <span class="hps">calculate the</span>
<span class="hps atn">'</span><span>relax</span><span class="atn">'
or '</span><span class="atn">vc-</span><span>relax</span><span>'?</span>
<span class="hps">If</span> <span class="hps">I want to</span> <span
class="hps">optimize</span> <span class="hps">for example</span><span></span>
<span class="hps">'a' and 'c</span>' cell width <span class="hps">parameters</span>
<span class="hps">I have to</span> <span class="hps">use the</span>
<span class="hps atn">'</span><span>vc</span><span class="">-relax</span><span>'
and if I</span> <span class="hps">do not</span> want to <span
class="hps">optimize</span> <span class="hps">the size of</span>
<span class="hps">the unit cell</span> <span class="hps">but </span><span
class="hps">only</span> <span class="hps">atomic positions</span>
<span class="hps">I do the</span> <span class="hps atn">'</span><span
class="">relax</span><span class="">' calculation? What when I
need to do both atomic positions and cell parameters?<br>
<br>
5.</span></span> "But, introducing an even small perturbation to
the linear geometry [...]"<span id="result_box" class="" lang="en"><span
class=""></span></span>
- <span tabindex="-1" id="result_box" class="" lang="en"><span
class="hps">In optimizing</span> <span class="hps">the geometry</span>
<span class="hps">should</span> I always <span class="hps">slightly</span>
<span class="hps atn">"</span><span class="">move</span><span>"</span>
<span class="hps">atoms</span> <span class="hps alt-edited">from</span>
<span class="hps">theoretical (Wyckoff) positions?</span></span>
<div class="moz-cite-prefix"><br>
6. <span tabindex="-1" id="result_box" class="" lang="en"><span
class="hps"><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps">And finally, the</span> <span
class="hps">last</span> <span class="hps">(sorry for the</span>
<span class="hps">number of questions</span><span>!)</span>
<span class="hps">question</span><span>:</span> <span
class="hps">I know what</span> <span class="hps">is </span><span
class="hps">google</span><span class="">,</span></span>
but</span></span><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps"><span tabindex="-1" id="result_box"
class="" lang="en"><span class="hps"></span> <span
class="hps">I would like to</span> <span class="hps">take
advantage</span> <span class="hps">of Your</span> <span
class="hps">experience</span></span>: Is there somewhere
a</span> <span class="hps atn">"</span><span>guide</span> <span
class="hps alt-edited">by the hand</span><span class="">"
which</span> <span class="hps">would allow me</span> <span
class="hps">to feel</span> <span class="hps">more confident</span><span
class="">,</span> <span class="hps">and more specifically</span>
have <span class="hps">less</span> <span class="hps">doubt</span>
<span class="hps"></span> <span class="hps">which solutions</span>
<span class="hps">are good</span> <span class="hps">and which
are not</span><span class="hps">? For now I'm trying to read
and understand "Electronic Structure" by Richard M. Martin</span></span>
and I feel that it is a very good quality book.<br>
<br>
<span tabindex="-1" id="result_box" class="" lang="en"><span
class="hps">The questions that</span> <span class="hps">I
asked</span> <span class="hps">clearly</span> <span
class="hps">show how</span> <span class="hps">much novice I
am</span><span class="hps">. </span></span><span
tabindex="-1" id="result_box" class="" lang="en"><span
class="hps"><span tabindex="-1" id="result_box" class=""
lang="en"><span class="hps">I hope</span> <span class="hps">that
my</span> <span class="hps alt-edited">lack of knowledge</span>
<span class="hps">is not very</span> <span class="hps">blatant</span><span>,
because</span> <span class="hps">my curiosity</span> <span
class="hps">in this topic</span> <span class="hps">sometimes</span>
<span class="hps">keeps me awake</span> <span class="hps">:)</span></span><br>
</span><span class="hps"></span><span class="hps alt-edited"></span><span
class="hps"></span><span class="hps"><br>
"</span></span>so it is hard to give the correct answer
without your input file(s)
[...] <br>
<span tabindex="-1" id="result_box" class="" lang="en"><span
class="hps">Below I attach</span> <span class="hps">the input
file</span> <span class="hps">with the</span> <span
class="hps atn">'</span><span>relax</span><span>' </span></span><span
tabindex="-1" id="result_box" class="" lang="en"><span
class="hps">calculation I was asking before</span></span> in
the "same Z cooridinate" question.<br>
<br>
<span tabindex="-1" id="result_box" class="" lang="en"><span
class="hps">With your permission</span><span class="">,</span>
<span class="hps">I would like to</span> <span class="hps">ask
for</span> <span class="hps">assistance how to </span><span
class="hps">take</span> <span class="hps">into account</span>
<span class="hps">that the</span> <span class="hps">below</span>
<span class="hps">system is</span> <span class="hps">magnetic</span>
<span class="hps atn">(</span><span class="">ferromagnetic</span><span>)
</span></span><br>
<br>
&control<br>
prefix='YFe52',<br>
restart_mode='from_scratch'<br>
calculation='relax'<br>
pseudo_dir='/home/darnok/qe/espresso-5.1.1/pseudo/'<br>
outdir = '/home/darnok/qe/espresso-5.1.2/tempdir/'<br>
tstress = .true.<br>
tprnfor = .true.<br>
nstep = 55<br>
etot_conv_thr = 1.0E-5<br>
forc_conv_thr = 1.0D-4<br>
verbosity = 'high'<br>
/<br>
&system <br>
ibrav= 4, celldm(1) =9.505, nat= 6, ntyp= 2, celldm(3)=
0.77,<br>
ecutwfc = 80.0, ecutrho = 900, smearing = 'gaussian',
occupations = "smearing", degauss=0.02,<br>
/<br>
&electrons<br>
mixing_mode = 'plain'<br>
mixing_beta = 0.7<br>
/<br>
<br>
&ions<br>
/<br>
ATOMIC_SPECIES<br>
Fe 55.845 Fe.pbe-sp-van.UPF<br>
Y 88.906 Y.pbe-nsp-van.UPF<br>
ATOMIC_POSITIONS {crystal}<br>
Y 0.00 0.00 0.00 <br>
Fe 0.3333 0.6666 0.00 <br>
Fe 0.6666 0.3333 0.00<br>
Fe 0.50 0.00 0.50<br>
Fe 0.00 0.50 0.50<br>
Fe 0.50 0.50 0.50<br>
K_POINTS {automatic}<br>
1 1 1 0 0 0<br>
<br>
Again, thank you in advance for your kindly answer,<br>
Konrad Gruszka, PhD.<br>
<br>
<br>
<div style="display: inline-block;" id="gt-input-tool">
<div id="gt-src-p"><br>
</div>
</div>
W dniu 10.04.2015 o 12:50, Giovanni Cantele pisze:<br>
</div>
<blockquote
cite="mid:2B05851B-F08D-4F04-B9F5-55BEB454562A@spin.cnr.it"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">On 10 Apr 2015, at 11:33, Konrad Gruszka <a class="moz-txt-link-rfc2396E" href="mailto:kgruszka@wip.pcz.pl"><kgruszka@wip.pcz.pl></a> wrote:
Dear Users,
Recently while making some tests on simple systems I've found very
strange behaviour of pw.x. It is obvious that choosing different pseudo
potentials should give to some extent different total energies. Since
I'm a beginner, I would therefore ask a few questions:
1. To what extent has the pseudopotentials of two different elements
must be the same? Can I use spin polarized together with none spin
polarized PP? Or can I for example use Fe.pbe-sp-van.upf with
Y.pbe-nsp-van.UPF? Or even combine for example Fe.pbe-sp-van.upf with
Y.pbe-mt_fhi.UPF ?
2. I have noticed that combining some PP together gives very different
total energies: for example for the same system first run with Fe and Y
with ",pbe-mt_fhi.UPF" gives total = -200 Ry and when using
Fe.pbe-sp-van.upf with Y.pbe-nsp-van.upf gives total energy = -1333 Ry.
Why those two PP give so big difference?
3. The last one noob-like question: While doing a 'relax' calc. only
the X and Y coordinates change during calculation, the Z always is such
as set on the begining. Is that normal? (or maybe it is only fortuity
for my atomic system?)
The lecture of pwscf manual did not answer my questions. I regret to
note that the beginnings with QE are wery hard for novice...
Thank you in advice for your kindly answer
Konrad Gruszka, PhD.
Czestochowa University of Technology, Poland
-- dr inż. Konrad Gruszka Politechnika Częstochowska Instytut Fizyki
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</pre>
</blockquote>
<pre wrap="">
actually, the lecture of the pwscf documentation does answer your questions:
1. I guess (but maybe I’m wrong!) that you are wondering whether it is possible to mix spin polarised and non spin polarised pseudo potentials because
you are mislead by the “sp “ and “nsp” found in the pseudo file name. As you can read here:
<a class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/pseudopotentials/naming-convention/">http://www.quantum-espresso.org/pseudopotentials/naming-convention/</a>
the “s”, “p” and “n” stand for
• s: semicore state s in valence
• p: semicore state p in valence
• n: nonlinear core-correction
So you can mix the mentioned pseudos, provided you know the features of the pseudo you are using (norm conserving versus ultrasoft,
with versus without non linear core correction, ect.)
2. see here: <a class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/faq/pseudopotentials/#2.4">http://www.quantum-espresso.org/faq/pseudopotentials/#2.4</a>
as explained in the above link, mostly when two different pseudos of the same elements are built with a different number of electrons, the two total energies differ a lot. If you look carefully inside the pseudo files, you (not that hardly) discover that Y.pbe-mt_fhi.UPF has 3 valence electrons, with only 5s and 4d orbitals occupied,
5s 5 0 2.00 0.000 0.000 0.000000
5p 5 1 0.00 0.000 0.000 0.000000
4d 4 2 1.00 0.000 0.000 0.000000
4f 4 3 0.00 0.000 0.000 0.000000
whereas Y.pbe-nsp-van.UPF has 11 valence electrons with 4s and 4p orbitals occupied as well
Wavefunctions nl l occ
4S 0 2.00
4P 1 6.00
4D 2 1.00
5S 0 2.00
3. see here: <a class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/faq/self-consistency/#6.14">http://www.quantum-espresso.org/faq/self-consistency/#6.14</a>
so it is hard to give the correct answer without your input file(s), but what is likely going on is that you system has a symmetry that forces the z component of the forces to zero.
Beware: when finding a symmetry, pw.x always keeps that symmetry during the run. How? For example, all the forces that, consistently with the found symmetry, should be zero, are NOT calculated but set to zero. A typical example is try to run a relax run for an H2O molecule. If you start with the following positions:
ATOMIC_POSITIONS (angstrom)
H 0.0 0.0 -1.0
O 0.0 0.0 0.0
H 0.0 0.0 1.0
then pw.x relaxes to
H 0.000000000 0.000000000 -0.945242812
O 0.000000000 0.000000000 0.000000000
H 0.000000000 0.000000000 0.945242812
because the molecule initially starts with a linear geometry (in this case along the z axis). The found symmetry is such that any force between atoms cannot have either an x or an y component, so pw.x is able (unless otherwise instructed) to output a relaxed structure constrained to lie along the z axis (which in this case is not the lowest energy one!).
But, introducing an even small perturbation to the linear geometry, such as
ATOMIC_POSITIONS (angstrom)
H 0.0 0.1 -1.0
O 0.0 0.0 0.0
H 0.0 0.1 1.0
the right experimental geometry is found:
H 0.000000000 0.264981368 -0.771676756
O 0.000000000 -0.329962735 0.000000000
H 0.000000000 0.264981368 0.771676756
(OH bond: 0.97 A, H-O-H angle: 104.7)
In the first case 16 symmetry operations are found, whereas in the second only 4!
Giovanni
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
dr inż. Konrad Gruszka
Politechnika Częstochowska
Instytut Fizyki</pre>
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