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<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 class="moz-cite-prefix">I fail to understand what is your
problem and what you would like to compute/understand <br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">stefano<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 26/08/22 13:52, Jayraj Anadani
wrote:<br>
</div>
<blockquote type="cite" cite="mid:CAFZg28u1+=R-ZiqxiYdm4_Q+K=Qj-4KrZac51rBo4KtGbJ1EnQ@mail.gmail.com">
<div dir="ltr">Thank you sir, for your reply
<div>but <span style="font-family:"arial
narrow",sans-serif">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 style="font-family:"arial narrow",sans-serif">(for
a non-periodic system)</span><span style="font-family:"arial narrow",sans-serif"> of
around 15 Angstrom to converge properly. </span><b style="font-family:"arial narrow",sans-serif">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" moz-do-not-send="true" class="moz-txt-link-freetext">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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<pre class="moz-quote-pre" wrap="">_______________________________________________
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 class="moz-txt-link-abbreviated" href="http://www.max-centre.eu">www.max-centre.eu</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
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