def write_equilibrium_trajectory(trajectory: md.Trajectory,
trajectory_filename: str) -> float:
"""
Write the results of an equilibrium simulation to disk. This task will append the results to the given filename.
Arguments
----------
trajectory : md.Trajectory
the trajectory resulting from an equilibrium simulation
trajectory_filename : str
the name of the trajectory file to which we should append
Returns
-------
True
"""
if not os.path.exists(trajectory_filename):
trajectory.save_hdf5(trajectory_filename)
_logger.debug(
f"{trajectory_filename} does not exist; instantiating and writing to."
)
else:
_logger.debug(f"{trajectory_filename} exists; appending.")
written_traj = md.load_hdf5(trajectory_filename)
concatenated_traj = written_traj.join(trajectory)
concatenated_traj.save_hdf5(trajectory_filename)
return True
def write_equilibrium_trajectory(equilibrium_result: EquilibriumResult,
trajectory: md.Trajectory,
trajectory_filename: str) -> float:
"""
Write the results of an equilibrium simulation to disk. This task will append the results to the given filename.
Parameters
----------
equilibrium_result : EquilibriumResult namedtuple
the result of an equilibrium calculation
trajectory : md.Trajectory
the trajectory resulting from an equilibrium simulation
trajectory_filename : str
the name of the trajectory file to which we should append
Returns
-------
reduced_potential_final_frame : float
the reduced potential of the final frame
"""
if not os.path.exists(trajectory_filename):
trajectory.save_hdf5(trajectory_filename)
else:
written_traj = md.load_hdf5(trajectory_filename)
concatenated_traj = written_traj.join(trajectory)
concatenated_traj.save_hdf5(trajectory_filename)
return equilibrium_result.reduced_potential
def write_equilibrium_trajectory(equilibrium_result: EquilibriumResult, trajectory: md.Trajectory, trajectory_filename: str) -> float:
"""
Write the results of an equilibrium simulation to disk. This task will append the results to the given filename.
Parameters
----------
equilibrium_result : EquilibriumResult namedtuple
the result of an equilibrium calculation
trajectory : md.Trajectory
the trajectory resulting from an equilibrium simulation
trajectory_filename : str
the name of the trajectory file to which we should append
Returns
-------
reduced_potential_final_frame : float
the reduced potential of the final frame
"""
if not os.path.exists(trajectory_filename):
trajectory.save_hdf5(trajectory_filename)
else:
written_traj = md.load_hdf5(trajectory_filename)
concatenated_traj = written_traj.join(trajectory)
concatenated_traj.save_hdf5(trajectory_filename)
return equilibrium_result.reduced_potential
def write_nonequilibrium_trajectory(
nonequilibrium_result: NonequilibriumResult,
nonequilibrium_trajectory: md.Trajectory,
trajectory_filename: str) -> float:
"""
Write the results of a nonequilibrium switching trajectory to a file. The trajectory is written to an
mdtraj hdf5 file, whereas the cumulative work is written to a numpy file.
Parameters
----------
nonequilibrium_result : NonequilibriumResult namedtuple
The result of a nonequilibrium switching calculation
nonequilibrium_trajectory : md.Trajectory
The trajectory resulting from a nonequilibrium simulation
trajectory_filename : str
The full filepath for where to store the trajectory
Returns
-------
final_work : float
The final value of the work trajectory
"""
if nonequilibrium_trajectory is not None:
nonequilibrium_trajectory.save_hdf5(trajectory_filename)
return nonequilibrium_result.cumulative_work[-1]
def write_nonequilibrium_trajectory(nonequilibrium_result: NonequilibriumResult, nonequilibrium_trajectory: md.Trajectory, trajectory_filename: str) -> float:
"""
Write the results of a nonequilibrium switching trajectory to a file. The trajectory is written to an
mdtraj hdf5 file, whereas the cumulative work is written to a numpy file.
Parameters
----------
nonequilibrium_result : NonequilibriumResult namedtuple
The result of a nonequilibrium switching calculation
nonequilibrium_trajectory : md.Trajectory
The trajectory resulting from a nonequilibrium simulation
trajectory_filename : str
The full filepath for where to store the trajectory
Returns
-------
final_work : float
The final value of the work trajectory
"""
if nonequilibrium_trajectory is not None:
nonequilibrium_trajectory.save_hdf5(trajectory_filename)
return nonequilibrium_result.cumulative_work[-1]
