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Restarting molecular dynamics

Restarting molecular dynamics#

To restart a molecular dynamics (MD) calculation, such that the trajectory is continuous with the earlier calculation:

  • Set up a new calculation with the same model (hamiltonian, boundary conditions, …) parameters as the previous one.

  • Use the last geometry of the previous run as an initial geometry.

  • Copy the velocities (the last 3 columns) of the final geometry in the xyz-file of the last run and add them as the initial velocities into the dftb_in.hsd file of the new run. (Make sure you set the unit of the velocities to be [AA/ps]).

  • If you have a temperature profile (see Simulated annealing), you will have to adjust it to start from the right temperature in the new run.

Thermostats#

The internal state of the thermostat (if used) can affect the trajectory of the restart:

* Berendsen -- no internal state, so the restarted trajectory is
  continuous if restarted, if compared to a longer run from the
  initial conditions.

* Andersen -- stochastic thermostat, its internal state cannot
  currently be restarted, so the trajectory can be different
  depending on the `RandomSeed` used for the calculation. The
  *average* or ensemble behaviour is consistent however.

* NoseHoover -- internal state of the thermostat can be specified,
  see the `x`, `v` and `g` values printed in `md.out`. The values
  from the last step should be set in the new input::

    Thermostat = NoseHoover {
      x = { 0.9996930771E+00    0.9964985276E+00    0.9965061982E+00}
      v = {-0.5716463853E-05   -0.3655208165E-04   -0.3640230213E-04}
      g = {-0.7062330098E-07   -0.1886240308E-06   -0.1879742133E-06}
    }

Automating restarts#

There is a set of scripts provided by Dr. Takuro Hosomi (Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo) which can automate this process.

The output can be processed to produce suitable restart file(s), by running the script in the directory containing the files dftb_in.hsd, geo_end.xyz and charges.bin (if SCC) from the initial part of the MD trajectory

python3 ./restart_filemaker.py

This produces a directory called restart with the processed new input file. The script has options that customize its behaviour (see restart_filemaker.py -h). The

A second script, restart_collector.py, can be used to collect and join together the output of several restarted calculations

python3 ./restart_collector.py

This script should be run in the top directory of the calculation, and will recursively descend to find data

./geo_end.xyz
  ./restart/geo_end.xyz
    ./restart/restart/geo_end.xyz

and place it into ./collect/ as a combined output file. Again, see restart_collector.py -h for extra options.

Example of restarting#

[Input: recipes/moleculardynamics/thermalise/]

Stop a running MD calculation by

  • pressing ctrl + c on the attached terminal

  • in the DFTB+ working directory create a stop file

    touch stop_driver

    which cleanly halts DFTB+ (remove the file afterwards)

  • waiting for it to terminate after sufficent iterations

Then, in the working directory run the restart_collector.py script. Without any arguments, it will create a directory called restart containing the input to continue the trajectory. Compare the original dftb_in.hsd file and the restart/dftb_in.hsd.

You’ll notice that the generated dftb_in.hsd looks quite different, but contains the last structure, it’s final velocities, any thermostat state and ReadInitialCharges = Yes (as this is an SCC calculation).

This is now ready to restart in the directory (and can be nested to futher restarts inside this directory).

The resulting sections of trajectories can the be re-assembled using the restart_collector.py script. Run this in the top directory containing the first calculation in the set, and the resulting composite data is then placed in the subdirectory collect/.

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