Restarting your simulation

To collect sufficient statistic for the kinetic MonteCarlo simulation it may be important to restart MonteCoffee after a certain time has elapsed, especially on computer clusters with short queue times.

Thus, the user part can be adjusted in the following way, first in the main-run file:

real_t_end = 10 #Real end time of simulation to restart in s
# Instantiate simulator object, now including the simulation end time.
sim = NeighborKMC(system=p, tend=tend,
                  real_t_end = real_t_end,

In the ‘’ two new functions need to be defined, serialize and deserialize and the package pickle imported:

import pickle, os, time

def serialize(self,filename):
     """Ads the possibility to dump self object"""
     with open(filename, 'wb') as f:

 def deserialize(self,filename):
     """Reads the self object from the file"""
     with open(filename, 'rb') as f:
         self.__dict__ = pickle.load(f)

Additionally, the variable real_t_end has to be added to the __init__ of the simulation:

def __init__(self, system, tend, real_t_end = (96*60*60), parameters={}, events=[], rev_events={}): = [ev(parameters) for ev in events]
  self.reverses = None # Set later
  self.real_t_end = real_t_end

The time module is used to follow the real time of the simulation. To use the real time as second break condition of the simulation, it is included in the while-clause. At the end of the while-clause the self-object with the system state is dumped as pickle-file.

start_time = time.time()  # save start time of simulation
if os.path.exists('data.pck'):   # if restart file exists, load self-object

log.dump_point(self.stepNMC, self.t, self.evs_exec)
while  time.time() < start_time + self.real_t_end and self.t < self.tend:

self.serialize('data.pck') # dump self-object

Please notice: The time used here is the bare simulation time. Thus it must be reduced by any pre-process time to initialize the system.