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<p class="MsoNormal">Hello,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks Kazume and Lorenzo for your time.</p>
<p class="MsoNormal">I think having them printed would be great for users, in the meantime I will calculate them with what you gave me.</p>
<p class="MsoNormal">And Kazume, I took a look to the module you mentioned (thanks for that, it was really useful) and I could see that the starting velocities therefore follow a Maxwell-Boltzmann distribution. That means that the system is already thermalized?
I know this is not a technical question, but I was wondering so since when I run a MD simulation in pw.x in the past without inputting velocities, the variation in temperature was high at the beginning of the simulation.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,</p>
<p class="MsoNormal">Valeria</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:nisidate@iwate-u.ac.jp">Kazume NISHIDATE</a><br>
<b>Sent: </b>Monday, August 9, 2021 7:02 PM<br>
<b>To: </b><a href="mailto:users@lists.quantum-espresso.org">Quantum ESPRESSO users Forum</a><br>
<b>Subject: </b>Re: [QE-users] Atomic velocities units</p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hello Valeria:<br>
<br>
As the manual says that the 'dt’ is<br>
"time step for molecular dynamics, in Rydberg atomic units<br>
(1 a.u.=4.8378 * 10^-17 s : beware, the CP code uses<br>
Hartree atomic units, half that much!!!)”<br>
<a href="https://www.quantum-espresso.org/Doc/INPUT_PW.html">https://www.quantum-espresso.org/Doc/INPUT_PW.html</a><br>
<br>
If you did not supply the initial velocities, the initial velocities<br>
at the specified temperature are given by (dynamics_module.f90):<br>
<br>
! ... N.B. velocities must in a.u. units of alat and are zero <br>
! ... for fixed ions <br>
! <br>
vel(:,na) = DBLE( if_pos(:,na) ) * &<br>
gauss_dist( 0.D0, sigma, 3 ) / alat<br>
<br>
So the unit is a.u. divided by 'alat'.<br>
<br>
And the kinetic energy 'ekin' is calculated by (dynamics_module.f90):<br>
ekin = ekin + 0.5D0 * mass(na) * &<br>
( vel(1,na)**2 + vel(2,na)**2 + vel(3,na)**2 )<br>
<br>
then it is rescaled as<br>
ekin = ekin*alat**2<br>
to recover the atomic unit in the above vel**2 operation.<br>
<br>
<br>
> Another question; is there a way to grep or look for the velocities<br>
> in some kind of output file from a pw.x run?<br>
<br>
Possible. We can extract the atomic positions at each MD time steps<br>
from the output file. The velocities can be directly calculated by<br>
(r(t2)-r(t1))/dt.<br>
<br>
But I think QE may save the velocities at the final MD step in the<br>
working dir to make it possible the restart run. To check this<br>
you can calculate some short time MD run and investigate the directory<br>
if there is the final velocity data.<br>
<br>
<br>
<br>
> 2021/08/10 8:43<span style="font-family:"MS Gothic"">、</span>valeria arteaga muñiz <valitzelar@hotmail.com><span style="font-family:"MS Gothic"">のメール</span>:<br>
> <br>
> Hello Lorenzo,<br>
> <br>
> Thank you again. I don’t know how could I fix that bug since the version of QE I am currently using is installed on a supercomputer, and I don’t think I have access to the main directories.<br>
> Another question; is there a way to grep or look for the velocities in some kind of output file from a pw.x run?<br>
> <br>
<br>
best regards<br>
kazume NISHIDATE<br>
<span style="font-family:"MS Gothic"">敬具 西館数芽</span><br>
<br>
nisidate@iwate-u.ac.jp<br>
kazume.nishidate@gmail.com<br>
<br>
<br>
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