def add(monte_carlo, steps_per, proc="", log="log.txt", tolerance=1e-8):
"""Add Log, Movie, CheckEnergy and Tuner to monte_carlo
steps_per -- perform analysis every this many steps
proc -- append movie file name with proc
log -- set the log file (default empty: standard output)
"""
monte_carlo.add(
feasst.MakeLog(
feasst.args({
"steps_per": str(steps_per),
"file_name": str(log),
"clear_file": "true"
})))
monte_carlo.add(
feasst.MakeMovie(
feasst.args({
"steps_per": str(steps_per),
"file_name": "movie" + str(proc) + ".xyz"
})))
monte_carlo.add(
feasst.MakeCheckEnergy(
feasst.args({
"steps_per": str(steps_per),
"tolerance": str(tolerance)
})))
monte_carlo.add(
feasst.MakeTuner(feasst.args({"steps_per": str(steps_per)})))
def mc(
target_acceptance=0.25,
tunable_param=0.1,
density=0.85,
cutoff=4,
temperature=0.88,
steps_per=int(1e6),
):
box_length = 2 * cutoff
file_app = "_a" + str(target_acceptance) + "_r" + str(cutoff)
num_particles = int(density * box_length**3)
print('num_particles', num_particles)
print('target_acceptance', target_acceptance)
print('tunable_param', tunable_param)
monte_carlo = feasst.Prefetch(feasst.args({"steps_per_check": "10000000"}))
monte_carlo.activate_prefetch(False)
monte_carlo.set(lj_system(box_length=box_length, cutoff=cutoff))
monte_carlo.set(
feasst.MakeMetropolis(
feasst.args({
"beta": str(1. / temperature),
"chemical_potential": "1.",
})))
monte_carlo.add(
feasst.MakeTrialTranslate(
feasst.args({
"weight": "1.",
"tunable_param": str(tunable_param),
"tunable_target_acceptance": str(target_acceptance),
"tunable_percent_change": "0.01",
# "num_steps": "4",
# "reference_index": "0",
})))
feasst.SeekNumParticles(num_particles).with_trial_add().run(monte_carlo)
monte_carlo.add(
feasst.MakeLog(
feasst.args({
"steps_per": str(steps_per),
"file_name": "log" + file_app + ".txt",
"clear_file": "true"
})))
monte_carlo.add(
feasst.MakeCheckEnergy(
feasst.args({
"steps_per": str(steps_per),
"tolerance": str(1e-8)
})))
monte_carlo.add(feasst.MakeTune(feasst.args({"steps_per":
str(steps_per)})))
#equilibrate
monte_carlo.attempt(int(1e7))
if not args.nopipe:
monte_carlo.activate_prefetch(True)
monte_carlo.add(
feasst.MakeMeanSquaredDisplacement(
feasst.args({
"steps_per_update": "10000",
"updates_per_origin": "1000",
"file_name": "msd" + file_app + ".txt",
"steps_per_write": str(int(1e5))
})))
monte_carlo.add(
feasst.MakeCPUTime(
feasst.args({
"steps_per_update": str(steps_per),
"steps_per_write": str(steps_per),
"file_name": "cpu" + file_app + ".txt",
})))
#h0 = feasst.cpu_hours()
monte_carlo.attempt(int(1e8))
feasst.args(
{"particle_type": feasst.install_dir() + "/forcefield/data.lj"})))
monte_carlo.add(feasst.Potential(feasst.MakeLennardJones()))
monte_carlo.add(feasst.Potential(feasst.MakeLongRangeCorrections()))
monte_carlo.add(feasst.MakeMetropolis(feasst.args({"beta": "1.5"})))
monte_carlo.add(
feasst.MakeTrialTranslate(
feasst.args({
"tunable_param": "2.",
"tunable_target_acceptance": "0.2"
})))
steps_per = int(1e3)
monte_carlo.add(feasst.MakeTuner(feasst.args({"steps_per": str(steps_per)})))
feasst.SeekNumParticles(50)\
.with_metropolis(feasst.args({"beta": "0.1", "chemical_potential": "10"}))\
.with_trial_add().run(monte_carlo)
monte_carlo.add(feasst.MakeLog(feasst.args({"steps_per": str(steps_per)})))
monte_carlo.add(
feasst.MakeMovie(
feasst.args({
"steps_per": str(steps_per),
"file_name": "movie.xyz"
})))
monte_carlo.add(
feasst.MakeCheckEnergy(
feasst.args({
"steps_per": str(steps_per),
"tolerance": "1e-8"
})))
monte_carlo.attempt(int(1e5))
def mc(thread, mn, mx):
steps_per = str(int(1e5))
mc = fst.MakeMonteCarlo()
#mc.set(fst.MakeRandomMT19937(fst.args({"seed": "12345"})))
#mc.set(fst.MakeRandomMT19937(fst.args({"seed": "1634926410"})))
chi = 0.7 # patch coverage
patch_angle = 2 * math.asin(math.sqrt(chi / 2)) * 180 / math.pi
print('patch_angle', patch_angle)
mc = fst.MonteCarlo()
config = fst.MakeConfiguration(
fst.args({
"cubic_box_length":
"8",
"particle_type0":
fst.install_dir() +
"/plugin/patch/forcefield/two_patch_linear.fstprt"
}))
config.add(fst.MakeGroup(fst.args({"site_type0": "0"})))
mc.add(config)
mc.add(
fst.MakePotential(
fst.MakeHardSphere(),
fst.MakeVisitModelCell(
fst.args({
"min_length": "1",
"cell_group": "1"
})), fst.args({"group_index": "1"})))
patch = fst.MakeVisitModelInnerPatch(
fst.args({"patch_degrees_of_type1": str(patch_angle)}))
mc.add(
fst.MakePotential(
fst.MakeSquareWell(),
fst.MakeVisitModel(patch),
#fst.MakeVisitModelCell(patch, fst.args({"min_length": "1.5", "cell_group": "1"})),
fst.args({"group_index": "1"})))
mc.set(
fst.MakeThermoParams(
fst.args({
"beta": str(1. / args.temperature),
"chemical_potential": str(args.mu)
})))
mc.set(
fst.MakeFlatHistogram(
fst.MakeMacrostateNumParticles(
fst.Histogram(
fst.args({
"width": "1",
"max": str(mx),
"min": str(mn)
}))),
# fst.MakeTransitionMatrix(fst.args({"min_sweeps": str(args.min_sweeps)})),
fst.MakeWLTM(
fst.args({
"collect_flatness": "18",
"min_flatness": "22",
"min_sweeps": str(args.min_sweeps)
}))))
mc.add(
fst.MakeTrialTranslate(
fst.args({
"weight": "0.5",
"tunable_param": "0.1"
})))
mc.add(
fst.MakeTrialRotate(fst.args({
"weight": "0.5",
"tunable_param": "20."
})))
mc.add(
fst.MakeTrialTransfer(fst.args({
"weight": "4",
"particle_type": "0"
})))
# mc.add(fst.MakeTrialGrow(fst.ArgsVector([{"translate": "true", "site": "0", "tunable_param": "1"}]),
# {"reference_index": ref, "num_steps": num_steps}))
# mc.add(fst.MakeTrialGrow(fst.ArgsVector([{"transfer": "true", "site": "0", "weight": "4"}]),
# {"reference_index": ref, "num_steps": num_steps}))
mc.add(
fst.MakeCheckEnergy(
fst.args({
"steps_per": steps_per,
"tolerance": "0.0001"
})))
mc.add(
fst.MakeTune(
fst.args({
"steps_per": steps_per,
"stop_after_phase": "0"
})))
mc.add(
fst.MakeLog(
fst.args({
"steps_per": steps_per,
"file_name": "clones" + str(thread) + ".txt",
"file_name_append_phase": "True"
})))
mc.add(
fst.MakeMoviePatch(
fst.args({
"steps_per": steps_per,
"file_name": "clones" + str(thread) + ".xyz",
"file_name_append_phase": "True"
})))
mc.add(
fst.MakeEnergy(
fst.args({
"steps_per_write": steps_per,
"file_name": "en" + str(thread) + ".txt",
"file_name_append_phase": "True",
"start_after_phase": "0",
"multistate": "True"
})))
mc.add(fst.MakeCriteriaUpdater(fst.args({"steps_per": steps_per})))
mc.add(
fst.MakeCriteriaWriter(
fst.args({
"steps_per": steps_per,
"file_name": "clones" + str(thread) + "_crit.txt",
"file_name_append_phase": "True"
})))
mc.set(
fst.MakeCheckpoint(
fst.args({
"file_name":
"checkpoint" + str(thread) + ".fst",
"num_hours":
str(0.1 * args.num_procs * args.num_hours),
"num_hours_terminate":
str(0.9 * args.num_procs * args.num_hours)
})))
return mc