def main(
trjfile: List[Path],
trj: bool = typer.Option(
False,
"-t",
help="Calculates the Lindemann-Index for the Trajectory file",
),
frames: bool = typer.Option(
False, "-f", help="Calculates the Lindemann-Index for each frame."
),
atoms: bool = typer.Option(
False,
"-a",
help="Calculates the Lindemann-Index for each atom for each frame.",
),
plot: bool = typer.Option(
False, "-p", help="Returns a plot Lindemann-Index vs. Frame."
),
lammpstrj: bool = typer.Option(
False,
"-l",
help="Saves the individual Lindemann-Index of each Atom in a lammpstrj, so it can be viewed in Ovito.",
),
version: bool = typer.Option(
None,
"-v",
"--version",
callback=version_callback,
is_eager=True,
help="Prints the version of the lindemann package.",
),
timeit: bool = typer.Option(
False, "-ti", "-timeit", help="Uses timeit module to show running time",
),
mem_useage: bool = typer.Option(
False,
"-m",
"-mem_use",
help="Calculates the memory use. Run it before you use any of the cli functionality despite the -t flag",
),
):
"""
lindemann is a python package to calculate the Lindemann index of a lammps trajectory as well as the progression of the Lindemann index per frame of temperature ramps for phase transition analysis.
"""
# frames = read.frames(trjfile)
# frames = lindemann.trajectory.read.frames(trjfile)
start = time.time()
n_cores = len(sched_getaffinity(0))
len_trjfiles = len(trjfile)
if len_trjfiles > n_cores:
n_cores = n_cores
else:
n_cores = len_trjfiles
if len(trjfile) == 1:
single_process = True
tjr_frames = read.frames(str(trjfile[0]))
else:
single_process = False
trjfile = [str(trjf) for trjf in trjfile]
tjr_frames = [read.frames(tf) for tf in trjfile]
if trj and single_process:
console.print(
f"[magenta]lindemann index for the Trajectory:[/] [bold blue]{per_trj.calculate(tjr_frames)}[/]"
)
raise typer.Exit()
if trj and not single_process:
with Pool(n_cores) as p:
console.print(f"Using {n_cores} cores")
res = p.map(per_trj.calculate, tjr_frames)
console.print(res)
raise typer.Exit()
if frames and single_process:
my_file_name = False
if my_file_name:
print("not implemented")
else:
filename = "lindemann_per_frame.txt"
np.savetxt(filename, per_frames.calculate(tjr_frames))
console.print(
f"[magenta]lindemann index per frame saved as:[/] [bold blue]{filename}[/]"
)
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
if atoms and single_process:
filename = "lindemann_per_atom.txt"
np.savetxt(filename, per_atoms.calculate(tjr_frames))
console.print(
f"[magenta]lindemann index per atoms saved as:[/] [bold blue]{filename}[/]"
)
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
if plot and single_process:
indices = per_frames.calculate(tjr_frames)
console.print(
f"[magenta]Saved file as:[/] [bold blue]{plt_plot.lindemann_vs_frames(indices)}[/]"
)
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
if lammpstrj and single_process:
indices_per_atom = per_atoms.calculate(tjr_frames)
console.print(f"[magenta]{save.to_lammps(trjfile,indices_per_atom)}[/]")
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
if timeit and single_process:
linde_for_time = per_trj.calculate(tjr_frames)
time_diff = time.time() - start
console.print(
f"[magenta]lindemann index for the Trajectory:[/] [bold blue]{linde_for_time}[/] \n[magenta]Runtime:[/] [bold green]{time_diff}[/]"
)
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
if mem_useage and single_process:
mem_use_in_gb = mem_use.in_gb(tjr_frames)
console.print(f"[magenta]memory use:[/] [bold blue]{mem_use_in_gb}[/]")
raise typer.Exit()
else:
print("multiprocessing is implemented only for the -t flag")
raise typer.Exit()
def test_atoms(trajectory, lindemannindex):
"""Example test with parametrization."""
frame = read.frames(trajectory)
assert (
np.round(np.mean(per_atoms.calculate(frame)[-1]), 12) == lindemannindex
)