def run(system, moves, run_type, run_length, temperature, **kwargs):
# Check that the user has the Cassandra binary on their PATH
# Also need library_setup.py on the PATH and python2
py2, fraglib_setup, cassandra = detect_cassandra_binaries()
# Sanity checks
# TODO: Write more of these
_check_system(system, moves)
# Write MCF files
write_mcfs(system)
# Write starting configs (if needed)
write_configs(system)
# Write input file
inp_file = write_input(system=system,
moves=moves,
run_type=run_type,
run_length=run_length,
temperature=temperature,
**kwargs)
# Write pdb files (this step will be removed when frag generation
# is incorporated into this workflow )
for isp, top in enumerate(system.species_topologies):
filename = "species{}.pdb".format(isp + 1)
write_pdb(top, filename)
log_file = "mosdef_cassandra_{}.log".format(
datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S.%f"))
# Run fragment generation (again, will be removed...)
print("Generating fragment libraries...")
successful_fraglib = _run_fraglib_setup(
py2,
fraglib_setup,
cassandra,
inp_file,
log_file,
len(system.species_topologies),
)
# Run simulation
if successful_fraglib:
print("Running Cassandra...")
_run_cassandra(cassandra, inp_file, log_file)
else:
raise ValueError("Cassandra failed due to unsuccessful "
"fragment generation")
def run(system, moveset, run_type, run_length, temperature, **kwargs):
"""Run the Monte Carlo simulation with Cassandra
The following steps are performed: write the molecular connectivity
files for each species to disk, write the starting structures
(if any) to disk, generate and write the Cassandra input file to disk,
call Cassandra to generate the required fragment libraries, and
call Cassandra to run the MC simulation.
Parameters
----------
system : mosdef_cassandra.System
the System to simulate
moveset : mosdef_cassandra.MoveSet
the MoveSet to simulate
run_type : "equilibration" or "production"
the type of run; in "equilibration" mode, Cassandra adaptively changes
the maximum translation, rotation, and volume move sizes to achieve
an acceptance ratio of 0.5
run_length : int
length of the MC simulation
temperature : float
temperature at which to perform the MC simulation
**kwargs : keyword arguments
any other valid keyword arguments, see
``mosdef_cassandra.print_valid_kwargs()`` for details
"""
# Check that the user has the Cassandra binary on their PATH
# Also need library_setup.py on the PATH and python2
py, fraglib_setup, cassandra = detect_cassandra_binaries()
# Sanity checks
# TODO: Write more of these
_check_system(system, moveset)
# Write MCF files
if "angle_style" in kwargs:
write_mcfs(system, angle_style=kwargs["angle_style"])
else:
write_mcfs(system)
# Write starting configs (if needed)
write_configs(system)
# Write input file
inp_file = write_input(
system=system,
moveset=moveset,
run_type=run_type,
run_length=run_length,
temperature=temperature,
**kwargs
)
# Write pdb files (this step will be removed when frag generation
# is incorporated into this workflow )
for isp, top in enumerate(system.species_topologies):
filename = "species{}.pdb".format(isp + 1)
write_pdb(top, filename)
log_file = "mosdef_cassandra_{}.log".format(
datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S.%f")
)
# Run fragment generation
print("Generating fragment libraries...")
_run_fraglib_setup(
py,
fraglib_setup,
cassandra,
inp_file,
log_file,
len(system.species_topologies),
)
# Run simulation
print("Running Cassandra...")
_run_cassandra(cassandra, inp_file, log_file)