Hi,<br>I noticed that running molecular dynamic calculations , the time step (dt) cannot be changed if one restarts from a previous run (restart_mode='restart'). This happens at least in versions 4.0 and 3.2.<br>If it is done, pw.x runs without complain (see note below), but the velocities and the kinetic energies are not correctly calculated. Also, in the prefix.msd.dat file, the times are calculated as dt*istep, producing a jump in time if dt is changed. The time should be something like previous_final_time+(istep-previous_nstep)*dt. Note that the time is correctly reported in the standard output.<br>
<br>This can be tested with example04, running it mannually to avoid deletion of the temporary save, and restarting wiht a modified input file <br><a href="http://si.md8.in">si.md8.in</a> using <br> restart_mode='restart',<br>
dt=10,<br> nstep=150,<br><br>Note: There is also a warning message when restarting in example 4: RECOVER from restart file failed: file not found. <br><br>Here is my bash script (just one more) to extract the temperature and the energies from the output file. The jumps are seen plotting the dat files.<br>
<br>INFILE=si.md8.out<br>SUFFIX=si8.dat<br>grep kbar $INFILE |awk '{print $6}' >>p_${SUFFIX}<br>grep 'temperature =' $INFILE |awk '{print $3}' >>t_${SUFFIX}<br>grep 'Ekin + Etot (const)' $INFILE |awk '{print $6}' >>etotal_${SUFFIX}<br>
grep 'kinetic energy (Ekin) =' $INFILE |awk '{print $5}' >>ekin_${SUFFIX}<br>paste etotal_${SUFFIX} ekin_${SUFFIX}|awk '{printf("%7.7f \n", $1-$2)}' >epot_${SUFFIX}<br><br>Why change the time step? Maybe just to check the stability of the simulations. Or maybe a large dt is enough for driving the system to a certain temperature near equilibrium, but a smaller one is need after the thermostat is switched off.<br clear="all">
<br>-- <br>Eduardo Menendez