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 nisid...@iwate-u.ac.jp kazume.nishid...@gmail.com
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