def test_transition():
'''Test generic transitions'''
# labels are skipped in comparisons and hashing
t1 = Transition(IonType.S, 1, 0)
t2 = Transition(IonType.S,
1,
0,
label_ion='Yb',
label_i='ES',
label_f='GS')
assert t1 == t2
assert hash(t1) == hash(t2)
# different states yield different Transitions
t3 = Transition(IonType.S, 2, 0)
assert t3 != t1
assert t3 != t2
assert hash(t3) != hash(t1)
assert hash(t3) != hash(t2)
# different ions yield different Transitions
t4 = Transition(IonType.A, 1, 0)
assert t4 != t1
assert hash(t4) != hash(t1)
def test_optim_ok_proc(data_proc): # ok
data = data_proc[0] + '''optimization:
processes: [ETU53, {}]
'''.format(data_proc[1])
with temp_config_filename(data) as filename:
cte = settings.load(filename)
ETU53 = EneryTransferProcess([Transition(IonType.A, 5, 6), Transition(IonType.A, 3, 1)],
mult=6, strength=2.5e8, name='ETU53')
assert cte.optimization['processes'] == [ETU53, data_proc[2]]
def test_ET_process():
'''Test excitation transitions'''
strength = 1e9
t1 = Transition(IonType.S, 1, 0)
t2 = Transition(IonType.S, 0, 1)
et1 = EneryTransferProcess([t1, t2], mult=6, strength=strength)
et2 = EneryTransferProcess([t1, t2], mult=8, strength=strength)
assert et1 != et2
t3 = Transition(IonType.S, 0, 1, label_ion='Yb')
et3 = EneryTransferProcess([t1, t3], mult=6, strength=strength)
assert et1 == et3
assert et1.strength == strength
assert et1.strength_avg == strength
strength_avg = 1e3
et4 = EneryTransferProcess([t1, t2],
mult=8,
strength=strength,
strength_avg=strength_avg)
assert et4.strength_avg == strength_avg
def setup_cte_sim(setup_cte):
'''Load the settings for simulations'''
# test_sim_dyn_2S_2A was created with these settings
setup_cte['decay']['branching_A'].add(DecayTransition(IonType.A, 3, 2, branching_ratio=0.1))
setup_cte['energy_transfer'] = {
'CR50': EneryTransferProcess([Transition(IonType.A, 5, 3),
Transition(IonType.A, 0, 2)],
mult=6, strength=2893199540.0),
'ETU53': EneryTransferProcess([Transition(IonType.A, 5, 6),
Transition(IonType.A, 3, 1)],
mult=6, strength=254295690.0),
'BackET': EneryTransferProcess([Transition(IonType.A, 3, 0),
Transition(IonType.S, 0, 1)],
mult=6, strength=4502.20614),
'EM': EneryTransferProcess([Transition(IonType.S, 1, 0),
Transition(IonType.S, 0, 1)],
mult=6, strength=45022061400.0),
'ETU1': EneryTransferProcess([Transition(IonType.S, 1, 0),
Transition(IonType.A, 0, 2)],
mult=6, strength=10000.0)
}
return Settings.load_from_dict(setup_cte)
def test_decay_transition():
'''Test generic decay or branching transitions'''
# labels are skipped in comparisons and hashing
t1 = DecayTransition(IonType.S, 1, 0, branching_ratio=0.4)
t2 = DecayTransition(IonType.S,
1,
0,
branching_ratio=0.4,
label_ion='Yb',
label_i='ES',
label_f='GS')
assert t1 == t2
assert hash(t1) == hash(t2)
t1_dec = DecayTransition(IonType.S, 1, 0, decay_rate=1e5)
t2_dec = DecayTransition(IonType.S,
1,
0,
decay_rate=1e5,
label_ion='Yb',
label_i='ES',
label_f='GS')
assert t1_dec == t2_dec
assert hash(t1_dec) == hash(t2_dec)
# different branching_ratios: not equal but same hash
t3 = DecayTransition(IonType.S, 1, 0, branching_ratio=0.1)
assert t3 != t1
assert t3 != t2
assert hash(t3) == hash(t1)
assert hash(t3) == hash(t2)
# compare Transitions with DecayTransitions, ignores values
t4 = Transition(IonType.S, 1, 0)
assert t1 == t4
assert t4 == t1
assert hash(t1) == hash(t4)
def setup_cte():
'''Load the cte data structure'''
class Cte(dict):
__getattr__= dict.__getitem__
__setattr__= dict.__setitem__
__delattr__= dict.__delitem__
cte = Cte({'version': 1,
'energy_transfer': OrderedDict({
'CR50': EneryTransferProcess([Transition(IonType.A, 5, 3),
Transition(IonType.A, 0, 2)],
mult=6, strength=887920884.0, name='CR50'),
'ETU53': EneryTransferProcess([Transition(IonType.A, 5, 6),
Transition(IonType.A, 3, 1)],
mult=6, strength=450220614.0, name='ETU53'),
'ETU55': EneryTransferProcess([Transition(IonType.A, 5, 6),
Transition(IonType.A, 5, 4)],
mult=6, strength=0.0, name='ETU55'),
'BackET': EneryTransferProcess([Transition(IonType.A, 3, 0),
Transition(IonType.S, 0, 1)],
mult=6, strength=4502.20614, name='BackET'),
'EM': EneryTransferProcess([Transition(IonType.S, 1, 0),
Transition(IonType.S, 0, 1)],
mult=6, strength=45022061400.0, name='EM'),
'ETU1': EneryTransferProcess([Transition(IonType.S, 1, 0),
Transition(IonType.A, 0, 2)],
mult=6, strength=10000.0, name='ETU1'),
'coop1': EneryTransferProcess([Transition(IonType.S, 1, 0),
Transition(IonType.S, 1, 0),
Transition(IonType.A, 0, 5)],
mult=6, strength=1000.0, name='coop1')
}),
'decay': {
'branching_A': {DecayTransition(IonType.A, 2, 1, branching_ratio=0.4),
DecayTransition(IonType.A, 3, 1, branching_ratio=0.3),
DecayTransition(IonType.A, 4, 3, branching_ratio=0.999),
DecayTransition(IonType.A, 5, 1, branching_ratio=0.15),
DecayTransition(IonType.A, 5, 2, branching_ratio=0.16),
DecayTransition(IonType.A, 5, 3, branching_ratio=0.04),
DecayTransition(IonType.A, 5, 4, branching_ratio=0.0),
DecayTransition(IonType.A, 6, 1, branching_ratio=0.43)},
'branching_S': {DecayTransition(IonType.S, 1, 0, branching_ratio=1.0)},
'decay_A': {DecayTransition(IonType.A, 1, 0, decay_rate=83.33333333333333),
DecayTransition(IonType.A, 2, 0, decay_rate=40000.0),
DecayTransition(IonType.A, 3, 0, decay_rate=500.0),
DecayTransition(IonType.A, 4, 0, decay_rate=500000.0),
DecayTransition(IonType.A, 5, 0, decay_rate=1315.7894736842104),
DecayTransition(IonType.A, 6, 0, decay_rate=14814.814814814814)},
'decay_S': {DecayTransition(IonType.S, 1, 0, decay_rate=400.0)}
},
'excitations': {
'NIR_1470': [Excitation(IonType.A, 5, 6, False, 9/5, 2e-4, 1e7, 1e-8)],
'NIR_800': [Excitation(IonType.A, 0, 3, False, 13/9, 0.0044, 1e7, 1e-8),
Excitation(IonType.A, 2, 5, False, 11/9, 0.002, 1e7, 1e-8)],
'NIR_980': [Excitation(IonType.S, 0, 1, False, 4/3, 0.0044, 1e7, 1e-8)],
'Vis_473': [Excitation(IonType.A, 0, 5, True, 13/9, 0.00093, 1e6, 1e-8)]},
'ions': {'activators': 113, 'sensitizers': 0, 'total': 113},
'lattice': {'A_conc': 0.3,
'N_uc': 20,
'S_conc': 0.3,
'a': 5.9738,
'alpha': 90.0,
'b': 5.9738,
'beta': 90.0,
'c': 3.5297,
'gamma': 120.0,
'd_max': 100.0,
'd_max_coop': 25.0,
'name': 'bNaYF4',
'sites_occ': [1.0, 0.5],
'sites_pos': [(0.0, 0.0, 0.0), (0.6666666666666666, 0.3333333333333333, 0.5)],
'spacegroup': 'P-6'},
'no_console': False,
'no_plot': False,
'concentration_dependence': {'concentrations': [(0.0, 0.1), (0.0, 0.3), (0.0, 0.5), (0.0, 1.0)],
'N_uc_list': [65, 40, 35, 25]},
'power_dependence': [10.0, 100.0, 1000.0, 10000.0, 100000.0, 1000000.0, 10000000.0],
'optimization': {'method': 'SLSQP',
'processes': [EneryTransferProcess([Transition(IonType.A, 5, 3), Transition(IonType.A, 0, 2)],
mult=6, strength=2893199540.0, name='CR50'),
DecayTransition(IonType.A, 3, 1, branching_ratio=0.3)],
'options': {'tol': 1e-3,
'N_points': 30,
'min_factor': 1e-2,
'max_factor': 2},
'excitations': ['Vis_473', 'NIR_980']
},
'simulation_params': {'N_steps': 1000,
'N_steps_pulse': 2,
'atol': 1e-15,
'rtol': 0.001},
'states': {'activator_ion_label': 'Tm',
'activator_states': 7,
'activator_states_labels': ['3H6', '3F4', '3H5', '3H4', '3F3', '1G4', '1D2'],
'sensitizer_ion_label': 'Yb',
'sensitizer_states': 2,
'sensitizer_states_labels': ['GS', 'ES'],
'energy_states': 791}
}
)
cte['config_file'] = '''
version: 1
lattice:
name: bNaYF4
N_uc: 20
S_conc: 0.3 # concentration
A_conc: 0.3
# unit cell
a: 5.9738 # distances in Angstrom
b: 5.9738
c: 3.5297
alpha: 90 # angles in degree
beta: 90
gamma: 120
spacegroup: P-6 # the number is also ok for the spacegroup
# info about sites
sites_pos: [[0, 0, 0], [2/3, 1/3, 1/2]]
sites_occ: [1, 1/2]
# optional
# maximum distance of interaction for normal ET and for cooperative
# if not present, both default to infinite
d_max: 100.0
# it's strongly advised to keep this number low,
# the number of coop interactions is very large (~num_atoms^3)
d_max_coop: 25.0
states:
# all fields here are mandatory,
# leave empty if necessary (i.e.: just "sensitizer_ion_label" on a line), but don't delete them
sensitizer_ion_label: Yb
sensitizer_states_labels: [GS, ES]
activator_ion_label: Tm
activator_states_labels: [3H6, 3F4, 3H5, 3H4, 3F3, 1G4, 1D2]
excitations:
# the excitation label can be any text
# at this point, only one active excitation is suported
# the t_pulse value is only mandatory for the dynamics, it's ignored in the steady state
Vis_473:
active: True
power_dens: 1e6 # power density W/cm^2
t_pulse: 1e-8 # pulse width, seconds
process: Tm(3H6) -> Tm(1G4) # both ion labels are required
degeneracy: 13/9 # initial_state_g/final_state_g
pump_rate: 9.3e-4 # cm2/J
NIR_1470:
active: False
power_dens: 1e7 # power density W/cm^2
t_pulse: 1e-8 # pulse width, seconds
process: Tm(1G4) -> Tm(1D2) # both ion labels are required
degeneracy: 9/5 # initial_state_g/final_state_g
pump_rate: 2e-4 # cm2/J
NIR_980:
active: False
power_dens: 1e7 # power density W/cm^2
t_pulse: 1e-8 # pulse width, seconds
process: Yb(GS)->Yb(ES)
degeneracy: 4/3
pump_rate: 4.4e-3 # cm2/J
NIR_800: # ESA: list of processes, degeneracies and pump rates
active: False
power_dens: 1e7 # power density W/cm^2
t_pulse: 1e-8 # pulse width, seconds
process: [Tm(3H6)->Tm(3H4), Tm(3H5)->Tm(1G4)]
degeneracy: [13/9, 11/9]
pump_rate: [4.4e-3, 2e-3] # cm2/J
sensitizer_decay:
# lifetimes in s
ES: 2.5e-3
activator_decay:
# lifetimes in s
3F4: 12e-3
3H5: 25e-6
3H4: 2e-3
3F3: 2e-6
1G4: 760e-6
1D2: 67.5e-6
activator_branching_ratios:
# 3H5 and 3H4 to 3F4
3H5->3F4: 0.4
3H4->3F4: 0.3
# 3F3 to 3H4
3F3->3H4: 0.999
# 1G4 to 3F4, 3H5, 3H4 and 3F3
1G4->3F4: 0.15
1G4->3H5: 0.16
1G4->3H4: 0.04
1G4->3F3: 0.00
# 1D2 to 3F4
1D2->3F4: 0.43
energy_transfer:
CR50:
process: Tm(1G4) + Tm(3H6) -> Tm(3H4) + Tm(3H5)
multipolarity: 6
strength: 8.87920884e+08
ETU53:
process: Tm(1G4) + Tm(3H4) -> Tm(1D2) + Tm(3F4)
multipolarity: 6
strength: 4.50220614e+08
ETU55:
process: Tm(1G4) + Tm(1G4) -> Tm(1D2) + Tm(3F3)
multipolarity: 6
strength: 0 # 4.50220614e+7
ETU1:
process: Yb(ES) + Tm(3H6) -> Yb(GS) + Tm(3H5)
multipolarity: 6
strength: 1e4
BackET:
process: Tm(3H4) + Yb(GS) -> Tm(3H6) + Yb(ES)
multipolarity: 6
strength: 4502.20614
EM:
process: Yb(ES) + Yb(GS) -> Yb(GS) + Yb(ES)
multipolarity: 6
strength: 4.50220614e+10
coop1:
process: Yb(ES) + Yb(ES) + Tm(3H6) -> Yb(GS) + Yb(GS) + Tm(1G4)
multipolarity: 6
strength: 1000
optimization:
processes: [CR50, 3H4->3F4]
method: SLSQP
options:
tol: 1e-3
N_points: 30
min_factor: 1e-2
max_factor: 2
excitations: [Vis_473, NIR_980]
simulation_params: # default values for certain parameters in the ODE solver
rtol: 1e-3 # relative tolerance
atol: 1e-15 # absolute tolerance
N_steps_pulse: 2 # number of steps for the pulse (only for dynamics)
N_steps: 1000 # number of steps for relaxation (also for steady state)
power_dependence: [1e1, 1e7, 7]
concentration_dependence:
concentrations: [[0], [0.1, 0.3, 0.5, 1.0]]
N_uc_list: [65, 40, 35, 25]
'''
cte['no_console'] = False
cte['no_plot'] = False
return cte
@author: Pedro
"""
import pytest
import numpy as np
import warnings
from lmfit import Parameters
import simetuc.optimize as optimize
import simetuc.simulations as simulations
from simetuc.util import IonType, DecayTransition, EneryTransferProcess, Transition
from simetuc.util import temp_bin_filename, temp_config_filename
B_43 = DecayTransition(IonType.A, 3, 1, branching_ratio=0.3)
CR50 = EneryTransferProcess([Transition(IonType.A, 5, 3), Transition(IonType.A, 0, 2)],
mult=6, strength=2893199540.0, name='CR50')
def idfn_param(param):
'''Returns the name of the test according to the parameters'''
return 'method={}'.format(param)
def idfn_avg(param):
'''Returns the name of the test according to the parameters'''
return 'avg={}'.format(param)
def idfn_proc(param):
'''Returns the name of the test according to the parameters'''
return 'num={}'.format(len(param))
@pytest.mark.parametrize('method', ['COBYLA', 'L-BFGS-B', 'TNC',
'SLSQP', 'brute', 'leastsq'],
ids=idfn_param)
@pytest.mark.parametrize('function', ['optimize_dynamics', 'optimize_concentrations'])
@pytest.mark.parametrize('average', [True, False], ids=idfn_avg)
settings.load(filename)
assert excinfo.match(r"Wrong labels in optimization: processes")
assert excinfo.type == settings.LabelError
def test_optim_wrong_B_proc_label():
'''Wrong branching ration optimization process'''
data = data_ET_ok + '''optimization:
processes: [3H145->3F4]
'''
with pytest.raises(settings.LabelError) as excinfo: # wrong ET process label
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"Wrong labels in optimization: processes")
assert excinfo.type == settings.LabelError
@pytest.mark.parametrize('data_proc', [(data_ET_ok, '3H5->3F4', Transition(IonType.A, 2, 1)),
(data_ET_ok_full_S, '3ES->1ES', Transition(IonType.S, 3, 1))])
def test_optim_ok_proc(data_proc): # ok
data = data_proc[0] + '''optimization:
processes: [ETU53, {}]
'''.format(data_proc[1])
with temp_config_filename(data) as filename:
cte = settings.load(filename)
ETU53 = EneryTransferProcess([Transition(IonType.A, 5, 6), Transition(IonType.A, 3, 1)],
mult=6, strength=2.5e8, name='ETU53')
assert cte.optimization['processes'] == [ETU53, data_proc[2]]
def test_optim_method(): # ok
data = data_ET_ok + '''optimization:
method: COBYLA'''
def _parse_ET(parsed_settings: Settings) -> Dict:
'''Parse the energy transfer processes'''
dict_states = parsed_settings.states
sensitizer_ion_label = dict_states['sensitizer_ion_label']
activator_ion_label = dict_states['activator_ion_label']
list_ion_label = [sensitizer_ion_label, activator_ion_label]
sensitizer_labels = dict_states['sensitizer_states_labels']
activator_labels = dict_states['activator_states_labels']
tuple_state_labels = (sensitizer_labels, activator_labels)
# ET PROCESSES.
ET_dict = {} # type: Dict
for num, (name, et_subdict) in enumerate(
parsed_settings['energy_transfer'].items()):
process = et_subdict['process']
mult = et_subdict['multipolarity']
strength = et_subdict['strength']
strength_avg = et_subdict.get('strength_avg', None)
# get the ions and states labels involved
list_init_final = _get_ion_and_state_labels(process)
list_ions_num = [
_get_ion_index(list_ion_label, ion)
for ion, label in list_init_final
]
list_indices = [
_get_state_index(tuple_state_labels[ion_num],
label,
section='ET process',
process=process,
num=num)
for ion_num, (ion_label,
label) in zip(list_ions_num, list_init_final)
]
# list with all information about this ET process
# tuples with ion and states labels and numbers
list_ion_states = [(ion_label, state_label, ion_num, state_num)
for (ion_label, state_label), ion_num, state_num in
zip(list_init_final, list_ions_num, list_indices)]
# fold the list of ion, state labels in two
# so that each tuple has two tuples with the states belonging to the same transition
folded_lst = list(
zip(list_ion_states[:len(list_ion_states) // 2],
list_ion_states[len(list_ion_states) // 2:]))
# store the data
trans_lst = [
Transition(IonType(tuple_i[2]),
tuple_i[3],
tuple_f[3],
label_ion=tuple_i[0],
label_i=tuple_i[1],
label_f=tuple_f[1]) for tuple_i, tuple_f in folded_lst
]
# print(trans_lst)
ET_dict[name] = EneryTransferProcess(trans_lst,
mult=mult,
strength=strength,
strength_avg=strength_avg,
name=name)
return ET_dict