def setUpClass(cls):
"""Prepare a testsystem."""
cls.types_to_write = [2, 23]
with tempfile.TemporaryFile(mode='w+') as fp:
vtf.writevcf(cls.system, fp, types=cls.types_to_write)
fp.flush()
fp.seek(0)
cls.written_pos = np.loadtxt(fp, comments="t")
with tempfile.TemporaryFile(mode='w+') as fp:
vtf.writevsf(cls.system, fp, types=cls.types_to_write)
fp.flush()
fp.seek(0)
cls.written_bonds = np.loadtxt(
fp, skiprows=1, comments="a", delimiter=":",
usecols=[1]) # just the second bonded member
fp.seek(0)
cls.written_atoms = np.loadtxt(
fp, skiprows=1, comments="b",
usecols=[1, 7]) # just the part_ID and type_ID
cutoff=2**(1. / 6),
shift="auto")
fene = interactions.FeneBond(k=10, d_r_max=2)
system.bonded_inter.add(fene)
positions = polymer.positions(n_polymers=1,
beads_per_chain=50,
bond_length=1.0,
seed=3210)
for i, pos in enumerate(positions[0]):
id = len(system.part)
system.part.add(id=id, pos=pos)
if i > 0:
system.part[id].add_bond((fene, id - 1))
vtf.writevsf(system, outfile)
#############################################################
# Warmup #
#############################################################
warm_steps = 10
lj_cap = 1
system.force_cap = lj_cap
i = 0
act_min_dist = system.analysis.min_dist()
# warmp with zero temperature to remove overlaps
system.thermostat.set_langevin(kT=0.0, gamma=1.0)
# slowly ramp un up the cap
shift='auto')
system.non_bonded_inter[1, 1].lennard_jones.set_params(epsilon=lj_eps,
sigma=lj_sig,
cutoff=lj_cut,
shift='auto')
system.non_bonded_inter[0, 1].lennard_jones.set_params(epsilon=lj_eps,
sigma=lj_sig,
cutoff=lj_cut_mixed,
shift='auto')
system.force_cap = lj_cap
checkpoint.register("system.non_bonded_inter")
# write structure block as header
vtf.writevsf(system, fp, types='all')
# write initial positions as coordinate block
vtf.writevcf(system, fp, types='all')
# STEP 4 Warmup
warm_steps = 100
warm_n_time = 2000
min_dist = 0.87
i = 0
act_min_dist = system.analysis.min_dist()
while i < warm_n_time and act_min_dist < min_dist:
system.integrator.run(warm_steps)
act_min_dist = system.analysis.min_dist()
i += 1
path_fluid_save = os.path.join(os.path.join('/home/lv70806/', dir_path[14:]),
'fluid_field.txt')
path_fluid_compressed = os.path.join(
os.path.join('/home/lv70806/', dir_path[14:]), 'fluid_compressed.txt.gz')
path_fluid_sacrifice = os.path.join(
os.path.join('/home/lv70806/', dir_path[14:]), 'you_cant_see_me.txt')
core_inst = core()
sim_inst = Simulation(core_inst)
sim_inst.initialise_filament()
sim_inst.set_filament()
sim_inst.bond_rasp()
sim_inst.init_magnetic_inter()
sim_inst.set_steric()
vtf.writevsf(sys, measurments_trj)
vtf.writevcf(sys, measurments_trj)
sim_inst.set_rot_intertia_from_units()
print(sys.cuda_init_handle.device_list)
sys.cuda_init_handle.device = 0
lbb = sim_inst.init_lb_GPU(timestep=core.time_step)
sim_inst.create_flow_channel()
# //////////////////////////////////////////////////////////////////////////////////////////////
sys.part.clear()
lokacija = '/home/lv70806/deniz/upload/pypresso_testing/raspberry_filaments/shear_polymers/playground_magnetic_sphere'
path_fluid_save = os.path.join(lokacija, 'fluid_field.txt')
path_fluid_compressed = os.path.join(lokacija, 'fluid_compressed.txt.gz')
system.time_step = time_step
for p in system.part[novi_kolacici:]:
p.vs_auto_relate_to(0)
# make sure that the mean values bellow correspond to values you expect!!!
# also by tuning the nuber of partciles in the raspberry try to minimise the st_dev! you will see once you cant get better, doesnt take much time
slice_master = [x.id for x in system.part[:] if x.type == 1]
lister = [
np.linalg.norm(system.part[i].pos - system.part[j].pos)
for i, j in product(slice_master, slice_master) if i != j
]
lister.sort(reverse=False)
print('mean of shell: ', np.mean(lister[:n_col_part - 10]))
print('std dev of shell:', np.std(lister[:n_col_part - 10]))
slice_master = [x.id for x in system.part[:] if x.type == 2]
lister = [
np.linalg.norm(system.part[i].pos - system.part[j].pos)
for i, j in product(slice_master, slice_master) if i != j
]
lister.sort(reverse=False)
print('mean of core: ', np.mean(lister[:n_col_part - 10]))
print('std dev of core:', np.std(lister[:n_col_part - 10]))
system.part[0].pos = (0, 0, 0)
system.integrator.run(1)
custom_data = open('raspberry_visual.vtf', mode='w+t')
vtf.writevsf(system, custom_data)
vtf.writevcf(system, custom_data)
