[QE-users] Atomic velocities units

[nisidate nisidate]

It is common to use Gaussian distribution for the initial velocities.
The purpose is to introduce specious randomness at the temperature T.

But off course it is not guaranteed that the system is in an
equilibrium state. I usually do three steps MD calculation to achieve
the equilibrium.

1. Specify the T and give the Gaussian distributed initial
  velocities to the system  (eg. tempw=300 in the QE) .

2. Calculate the MD upto a few thousands steps regulating the
  temperature (velocity scaling method in the QE,
  ion_temperature='rescaling').

3. Calculate the MD without the temperature regulation. In this case,
  the system is in the NVE microcanonical ensemble and the total
  energy will be conserved (with some fluctuations) during the MD
  calculation. We can check it by plotting the energies.  If it was
  not conserved, the system may far from the equilibrium state. We
  can go back to the step 2 or just modify the initial atomic
  geometries.

I wrote a perl script, qe-velocities.pl, which estimates the variation
of velocities from the output file of QE. You can download from here:

https://www.filemail.com/d/jbtzfobtxttkamj


It evaluates the velocities using the formula of
v = (r(t2)-r(t1))/dt
in the unit of (Angstrom/femto-second).

To run the script, save the file in a directory and
type the command of:
./qe-velocities.pl qe-md.out
where the file 'qe-md.out' is the output file of QE (MD
calculation of 64 H2O molecule in a cubic box).

Note that you must add the executable permission to the script
using the command
chmod 755 ./qe-velocities.pl
before the execution of it.

It creates three files; md.xyz, md-v-a-fs.dat, and md-v-au.dat.

* The file md-v-a-fs.dat contains the velocities in
(Angstrom/femto-second) unit at each MD time steps.

* The file md-v-au.dat contains the velocities in (a.u) unit at each
MD time steps and can be directory used as an input for the next MD
run (&ATOMIC_VELOCITIES section of the input file).

The file md.xyz is the position data of atoms (Angstrom) at each MD
time steps in the 'xyz' format and can be used as an input for the
general MD animation softwares such as the 'Ovito'.

Note also that the script, qe-velocities.pl, is not solely checked and
may contain some bugs. It is currently applicable only for the cubic
sytem (alpha=beta=gamma=90 degrees) due to the difficulty to handle
the cycric BC of the other systems (at least for me).

have fun!


best regards
kazume NISHIDATE
敬具 西館数芽

nisidate at iwate-u.ac.jp
kazume.nishidate at gmail.com
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