def print_dir_bops_to_dir(input_dir, pattern, output_dir, nf=None):
parser = parsers.Tip4pIceParser()
# we need a FullTrajectory (as opposed to a LazyTrajectory) because we later use systems as dictionary keys
trajectory = ba.FullTrajectory(parser)
trajectory.initialise_from_folder(input_dir, pattern, True)
if nf == None:
#nf = ba.CutoffFinder(1.3)
#nf = ba.SANNFinder(3.0, ba.SANNFinder.SYMMETRISE_BY_REMOVING)
nf = ba.FixedNumberFinder(16)
syst = trajectory.next_frame()
while syst != None:
nf.set_neighbours(syst.particles(), syst.box)
orders = {2, 4, 6, 8, 10, 12}
bop_obs = ba.BondOrderParameters(orders, compute_ws=True)
bop_obs.analyse_system(syst)
bops = bop_obs.result()
out_filename = os.path.join(output_dir, "bops_%d" % syst.time)
with open(out_filename, "w") as out_file:
print("# t=%d, orders=%s" %
(syst.time, ",".join(str(o) for o in orders)),
file=out_file)
for p_bops in bops:
print(" ".join([str(x) for x in p_bops]), file=out_file)
syst = trajectory.next_frame()
#!/usr/bin/python3
import baggianalysis as ba
import numpy as np
import sys
if len(sys.argv) < 3:
print("Usage is %s input N_attempts" % sys.argv[0], file=sys.stderr)
exit(0)
parser = ba.LAMMPSDumpParser()
trajectory = ba.FullTrajectory(parser)
trajectory.initialise_from_trajectory_file(sys.argv[1])
obs = ba.PoreSize(int(sys.argv[2]))
obs.analyse_trajectory(trajectory)
results = obs.result()
print("\n".join([str(x) for x in results]))