Use the IMP::misc::DecayPairContainerOptimizerState to gradually break the bonds in a bd simulation.
5 from __future__
import print_function
18 sys.argv,
"Use the IMP::misc::DecayPairContainerOptimizerState to gradually break the bonds in a bd simulation")
38 for i
in range(0, np):
39 p = m.add_particle(
"p")
43 d.set_coordinates_are_optimized(
True)
51 for i
in range(0, nb):
52 pp = random.sample(ps, 2)
53 if pp
not in bds
and [pp[1], pp[0]]
not in bds:
58 dos.set_period(period)
59 dos.set_log_level(IMP.SILENT)
69 dos.get_output_container(),
76 bd.set_maximum_time_step(1000)
77 bd.set_scoring_function(rs + [ev])
78 bd.add_optimizer_state(dos)
82 rmf = RMF.create_rmf_file(fn)
83 print(
"setting up file")
89 os.set_period(max(steps / 100, 1))
90 bd.add_optimizer_state(os)