Modify a checkpoint file during restarting to run longer

In this example, the first simulation generates a checkpoint file. The second simulation runs from the checkpoint file after modification of the number of cycles to complete a simulation.

import sys
import pandas as pd
import subprocess

# Run a feasst simulation with the given parameters
def run_fst():
    with open("launch00.txt", "w") as myfile: myfile.write("""
MonteCarlo
Checkpoint checkpoint_file=lj.fst
RandomMT19937 seed=1572362164
Configuration cubic_side_length=55.0321208149104 particle_type=lj:/feasst/particle/lj_new.txt
Potential Model=LennardJones VisitModel=VisitModelCell
Potential VisitModel=LongRangeCorrections
ThermoParams beta=1.111111111111111 chemical_potential=-1
Metropolis
TrialTranslate tunable_param=2
Tune
CheckEnergy trials_per_update=1e4 decimal_places=8
TrialAdd weight=2 particle_type=lj
Run until_num_particles=500
Remove name=TrialAdd
Run num_trials=1e5
Remove name=Tune
Let [write]=trials_per_write=1e4 output_file=lj
Log [write].csv clear_file=true
Movie [write].xyz
Energy [write]_en.csv
Metropolis trials_per_cycle=1e4 cycles_to_complete=1e2
Run until=complete
WriteCheckpoint
""")
    syscode = subprocess.call("../../../build/bin/fst < launch00.txt", shell=True, executable='/bin/bash')
    if syscode > 0: sys.exit(1)

run_fst()
df = pd.read_csv('lj.csv')
assert len(df) == 101

# Write a second run script that restarts the simulation and adds a lot more trials. Too many. Try to clear those on a second restart.
with open('continue.txt', 'w') as myfile: myfile.write("""Restart lj.fst
Metropolis trials_per_cycle=1e8 cycles_to_complete=2e8
Checkpoint checkpoint_file=lj2.fst num_hours_terminate=0.01
Run until=complete
WriteCheckpoint
""")
syscode = subprocess.call("../../../build/bin/fst < continue.txt", shell=True, executable='/bin/bash')

# Write a third run script that restarts the simulation and the clears the previous arguments. Ask for a reasonable number of trials.
with open('continue2.txt', 'w') as myfile: myfile.write("""Restart lj2.fst clear_previous_arguments
Metropolis trials_per_cycle=1e4 cycles_to_complete=1e1
Run until=complete
WriteCheckpoint
""")
syscode = subprocess.call("../../../build/bin/fst < continue2.txt", shell=True, executable='/bin/bash')

df = pd.read_csv('lj.csv')
assert len(df) > 202

# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
MonteCarlo
Checkpoint checkpoint_file=lj.fst
RandomMT19937 seed=1572362164
# Initializing random number generator with seed: 1572362164
Configuration cubic_side_length=55.0321208149104 particle_type=lj:/feasst/particle/lj_new.txt
Potential Model=LennardJones VisitModel=VisitModelCell
Potential VisitModel=LongRangeCorrections
ThermoParams beta=1.111111111111111 chemical_potential=-1
Metropolis
TrialTranslate tunable_param=2
Tune
CheckEnergy decimal_places=8 trials_per_update=1e4
TrialAdd particle_type=lj weight=2
Run until_num_particles=500
Remove name=TrialAdd
Run num_trials=1e5
Remove name=Tune
Log clear_file=true output_file=lj.csv trials_per_write=1e4
Movie output_file=lj.xyz trials_per_write=1e4
Energy output_file=lj_en.csv trials_per_write=1e4
Metropolis cycles_to_complete=1e2 trials_per_cycle=1e4
Run until=complete
WriteCheckpoint
# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
# Restarting from file: lj.fst
Metropolis cycles_to_complete=2e8 trials_per_cycle=1e8
Checkpoint checkpoint_file=lj2.fst num_hours_terminate=0.01
Run until=complete

terminate called after throwing an instance of 'feasst::CustomException'
  what():  Throw on proc 0 : #Fatal error0 plugin/utils/include/checkpoint.h:88: Terminating because Checkpoint has reached the user input num_hours_terminate: 0.01. Detect this termination in Bash shell using "$? != 0"
/bin/bash: line 1: 839272 Aborted                 (core dumped) ../../../build/bin/fst < continue.txt

# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
# Restarting from file: lj2.fst
Metropolis cycles_to_complete=1e1 trials_per_cycle=1e4
Run until=complete
WriteCheckpoint

Did this tutorial work as expected? Did you find any inconsistencies or have any comments? Please contact us. Any feedback is appreciated!