<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    <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 class="moz-txt-link-freetext" href="http://www.quantum-environ.org/">http://www.quantum-environ.org/</a>)  to
      minimize boundary effects<br>
    </p>
    <p>stefano<br>
    </p>
    <div class="moz-cite-prefix">On 26/08/22 15:01, Jayraj Anadani
      wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:CAFZg28vFaBWupbRLy5SmLf9_QdkpMPXoVs1eXNfLrXy34JUaKw@mail.gmail.com">
      
      <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" moz-do-not-send="true" class="moz-txt-link-freetext">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 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" target="_blank" rel="noreferrer" 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>
                  > _______________________________________________<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" moz-do-not-send="true">www.max-centre.eu</a>)<br>
                  > users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" rel="noreferrer" moz-do-not-send="true" class="moz-txt-link-freetext">users@lists.quantum-espresso.org</a><br>
                  > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
                  _______________________________________________<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" moz-do-not-send="true">www.max-centre.eu</a>)<br>
                  users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" rel="noreferrer" moz-do-not-send="true" class="moz-txt-link-freetext">users@lists.quantum-espresso.org</a><br>
                  <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
              </div>
              <br>
              <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" moz-do-not-send="true">www.max-centre.eu</a>)
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" rel="noreferrer" moz-do-not-send="true" class="moz-txt-link-freetext">users@lists.quantum-espresso.org</a>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank" rel="noreferrer" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.quantum-espresso.org/mailman/listinfo/users</a></pre>
            </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" target="_blank" moz-do-not-send="true">www.max-centre.eu</a>)<br>
          users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank" rel="noreferrer" moz-do-not-send="true" class="moz-txt-link-freetext">users@lists.quantum-espresso.org</a><br>
          <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
      </div>
      <br>
      <fieldset class="moz-mime-attachment-header"></fieldset>
      <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>
    </blockquote>
  </body>
</html>