def run_measurment(self, steps, sample):
assert not self.filament.attributes.magnetize, "you are running with the non-spara run funct !!!!!"
sys.integrator.run(steps=0)
dict_of_god = dict()
prop_dict = self.filter_part_properties()
for timestep in range(steps):
logging.info('integrating step: ' + str(timestep))
sys.integrator.run(steps=sample)
dict_of_god['timestep_%s' % timestep] = {
'pid_%s' % x.id: {y: getattr(x, y)
for y in prop_dict}
for x in sys.part[self.filament.attributes.realz_indices]
}
vtf.writevcf(sys, measurments_trj)
measurments_trj.flush()
pickle.dump(dict_of_god, gzip.open(path_to_custom_data, 'wb'),
pickle.HIGHEST_PROTOCOL)
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
def run_measurment_spara(self, steps, sample):
assert self.filament.attributes.magnetize, "you are running with the spara run funct but you shouldnt!!!!!"
sys.integrator.run(steps=0)
dict_of_god = dict()
prop_dict = self.filter_part_properties()
for timestep in range(steps):
logging.info('integrating step: ' + str(timestep))
for bla in range(sample):
self.filament.magnetize()
sys.integrator.run(0, recalc_forces=True)
sys.integrator.run(steps=1, reuse_forces=True)
dict_of_god['timestep_%s' % timestep] = {
'pid_%s' % x.id: {y: getattr(x, y)
for y in prop_dict}
for x in sys.part.select(lambda p: p.type == self.filament.
attributes.type_to_be_magnetized)
}
vtf.writevcf(sys, measurments_trj)
measurments_trj.flush()
pickle.dump(dict_of_god, gzip.open(path_to_custom_data, 'wb'),
pickle.HIGHEST_PROTOCOL)
#############################################################
# 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
while (act_min_dist < 0.95):
vtf.writevcf(system, outfile)
print("min_dist: {} \t force cap: {}".format(act_min_dist, lj_cap))
system.integrator.run(warm_steps)
system.part[:].v = [0, 0, 0]
# Warmup criterion
act_min_dist = system.analysis.min_dist()
lj_cap = lj_cap * 1.01
system.force_cap = lj_cap
#remove force cap
lj_cap = 0
system.force_cap = lj_cap
system.integrator.run(warm_steps * 10)
# restore simulation temperature
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
'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')
path_fluid_sacrifice = os.path.join(lokacija, 'you_cant_see_me.txt')
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
lj_cap += 1.0
system.force_cap = lj_cap
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)
