<div dir="auto">I appreciate your help<div dir="auto">Thank you very much sir.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 26 Aug, 2022, 7:16 pm Stefano de Gironcoli, <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<p>I would take out small clusters from your 10000 cells (possibly
saturate with H atoms if you cut covalent bonds), not relax (with
the exception of relaxing the extra H atoms you added to
saturate), compute atomic PDOS of the central atom(s) and verify
that for increasing number of atoms in the clusters these
quantities stabilize and converge.</p>
<p>if a significant size dependence results you may want to play
with the environ feature (<a href="http://www.quantum-environ.org/" target="_blank" rel="noreferrer">http://www.quantum-environ.org/</a>) to
minimize boundary effects<br>
</p>
<p>stefano<br>
</p>
<div>On 26/08/22 15:01, Jayraj Anadani
wrote:<br>
</div>
<blockquote type="cite">
<div dir="auto">I have one amorphorse metallic system of 10000
atoms in which several clusters are in it. I want to calculate
atomic bonding and electronic interaction through finding
DOS/PDOS and Charge analysis of a small cluster part of a large
amorphorse metallic system.
<div dir="auto">My cluster size is upto 13 to 25 atoms which is
part of large md simulation.</div>
<div dir="auto"><br>
</div>
<div dir="auto">So can i have to do relaxation or i can directly
do scf calculation with restricted parameter ?</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thank you </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, 26 Aug, 2022, 6:04 pm
Stefano de Gironcoli, <<a href="mailto:degironc@sissa.it" target="_blank" rel="noreferrer">degironc@sissa.it</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<p>I dont think that a 10-20 atom cluster configuration
extracted from a 10000 condensed phase has anything to do
with the same system at 300 K.</p>
<p>possibly some electronic properties of the central
molecule may be similar to the corresponding properties in
the condensed phase but no guarantee. <br>
</p>
<p>if you relax or perform md for the cluster you loose your
(tiny) connection with the original cell. <br>
</p>
<div>I fail to understand what is your problem and what you
would like to compute/understand <br>
</div>
<div><br>
</div>
<div>stefano<br>
</div>
<div><br>
</div>
<div>On 26/08/22 13:52, Jayraj Anadani wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thank you sir, for your reply
<div>but <span>I have one particular molecular system of
10-20 atoms which I am getting from a simulation of
a large atom (around 10000 atoms) at a 300K
temperature from a molecular dynamic simulation
(LAMMPS). and I also did optimization of that MD
structure which is amorphous metallic glass. Now,</span>
<div>
<div><font face="arial narrow, sans-serif"> Can I do
dft study of a small part of a single molecule
of a large MD simulation(~10000 atoms) ?</font></div>
<div><font face="arial narrow, sans-serif">till now
i did below things but i am bit confused which
way is best way to study DFT . i also dis
AIMD/CPMD but for metallic glass CPMD doesn't
work good with PAW PP.</font></div>
<div><font face="arial narrow, sans-serif">so,</font></div>
<div><font face="arial narrow, sans-serif">1. Can I
do direct SCF calculation(without relax) by
giving a condition of <b>forc_conv_thr</b> and <b>tot_conv_thr</b> with
creating a vacuum</font><span>(for a non-periodic
system)</span><span> of around 15 Angstrom
to converge properly. </span><b>OR</b></div>
<div><font face="arial narrow, sans-serif">2. I
should do the RELAX calculation with vacuum and
then go to the <b>scf</b> calculation to find
the total energy and then <b>nscf</b>. </font></div>
<div><font face="arial narrow, sans-serif"><br>
</font></div>
<div><font face="arial narrow, sans-serif">***questions:</font></div>
<div><font face="arial narrow, sans-serif">1. what
if I relax a system and position is changed a
bit(which is obvious) to minimize the total
energy but that energy is at zero kelvin dft
calculation and I want to study the system at
300K. So how can small parts of a
structure reflect large MD simulation structural
properties?</font></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">
</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">Thank you</span></div>
</div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">regards </span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">
</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">
</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">jayraj anadani</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">Ph.D. Research scholar
Department of physics</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">sardar patel university</span></div>
<div><span style="font-family:"arial narrow",sans-serif;color:rgb(0,0,0);font-size:14px;white-space:pre-wrap">india</span></div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Aug 26, 2022
at 5:00 PM Stefano de Gironcoli <<a href="mailto:degironc@sissa.it" rel="noreferrer noreferrer" target="_blank">degironc@sissa.it</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">Dear JAYRAJ
ANADANI,<br>
<br>
calculation="scf" corresponds to a minimization of
the total energy <br>
at fixed atomic positions. you chose where to put the
ions. the code <br>
does its best to return the corresponding energy.<br>
<br>
calculaiton="relax" corresponds to a series of scf
calculations, <br>
followed by forces evaluation and geometry update to
minimize the energy <br>
of the system. The code does its best to converge to a
minimum (non <br>
necessarily the global minimum) in the GS potential
energy surface.<br>
<br>
there is no temperature in any of these
calculations.<br>
<br>
if you want to simulate the system at finite
(classical) temperature <br>
for the atoms you should perform MD simlations<br>
<br>
stefano<br>
<br>
On 26/08/22 05:02, Jayraj Anadani wrote:<br>
> Dear QE<br>
> I put H2O molecular atoms small far
apart from each <br>
> other within large supercell so that the periodic
image of the H2O do <br>
> not interact with each other and run a scf
calculation my convergence <br>
> done successfully with good amount of accuracy
upto 10^-9. But it is <br>
> not reflecting original H2O molecule at 300
Kelvin...but when i <br>
> relaxing these atoms and then did scf calculation
they are reflecting <br>
> H2O at 300k by observing bond angel and length..
how ? And my question is<br>
> 1) scf is also doing calculation using iteration
method algorithm by <br>
> using electronic densities at ground state so why
they converge when <br>
> two hydrogen atoms and one oxygen atom are not at
appropriate <br>
> distance.still scf converge how ?<br>
> 2) also by doing relax calculation all of sudden
two hydrogen and one <br>
> oxygen come closer and they formed a bond and
bond angel which is <br>
> reflect 300k H2O molecule structure. So how two
hydrogen and one <br>
> oxygen atoms knows during relaxation that i have
to make structure at <br>
> a room temperature?<br>
><br>
><br>
> Thank you<br>
> Regards<br>
><br>
> JAYRAJ ANADANI<br>
> Ph.D Research scholar<br>
> Department of physics<br>
> Sardar Patel University<br>
> Anand,Gujarat,<br>
> India<br>
><br>
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_______________________________________________<br>
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<pre>_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
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
_______________________________________________
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer noreferrer" target="_blank">www.max-centre.eu</a>)
users mailing list <a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a>
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</blockquote>
</div>
_______________________________________________<br>
The Quantum ESPRESSO community stands by the Ukrainian<br>
people and expresses its concerns about the devastating<br>
effects that the Russian military offensive has on their<br>
country and on the free and peaceful scientific, cultural,<br>
and economic cooperation amongst peoples<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer noreferrer noreferrer" target="_blank">www.max-centre.eu</a>)<br>
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<fieldset></fieldset>
<pre>_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
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
_______________________________________________
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" target="_blank" rel="noreferrer">www.max-centre.eu</a>)
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" rel="noreferrer">users@lists.quantum-espresso.org</a>
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</blockquote>
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_______________________________________________<br>
The Quantum ESPRESSO community stands by the Ukrainian<br>
people and expresses its concerns about the devastating<br>
effects that the Russian military offensive has on their<br>
country and on the free and peaceful scientific, cultural,<br>
and economic cooperation amongst peoples<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer noreferrer" target="_blank">www.max-centre.eu</a>)<br>
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