def test_sections_config(sections_data):
with pytest.raises(SettingsFileError) as excinfo:
with temp_config_filename(sections_data) as filename:
settings.load(filename)
assert excinfo.match(r"Those sections must be present")
assert excinfo.match(r"Sections that are needed but not present in the file")
assert excinfo.type == SettingsFileError
def test_not_all_states_decay():
data = data_abs_ok + '''sensitizer_decay:
# lifetimes in s
ES: 1e-3
activator_decay:
'''
with pytest.raises(SettingsValueError) as excinfo: # all states must have a decay rate
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"activator_decay")
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
data = data_abs_ok + '''sensitizer_decay:
activator_decay:
3F4: 12e-3
3H5: 25e-6
3H4: 2e-3
3F3: 2e-6
1G4: 760e-6
1D2: 67.5e-6
'''
with pytest.raises(SettingsValueError) as excinfo: # all states must have a decay rate
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"sensitizer_decay")
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_version_config():
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data_all_mandatory_ok.replace('version: 1',
'version: 2')) as filename:
settings.load(filename)
assert excinfo.match(r"cannot be larger than 1")
assert excinfo.type == SettingsValueError
def test_empty_states_config():
data = '''version: 1
lattice:
name: bNaYF4
N_uc: 8
# concentration
S_conc: 0.3
A_conc: 0.3
# unit cell
# distances in Angstrom
a: 5.9738
b: 5.9738
c: 3.5297
# angles in degree
alpha: 90
beta: 90
gamma: 120
# the number is also ok for the spacegroup
spacegroup: P-6
# info about sites
sites_pos: [[0, 0, 0], [2/3, 1/3, 1/2]]
sites_occ: [1, 1/2]
states: asd
excitations: asd
sensitizer_decay: asd
activator_decay: asd
'''
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r'Error validating section "states"')
assert excinfo.type == SettingsValueError
def test_excitations_config2():
data = data_states_ok + '''excitations:
Vis_473:'''
with pytest.raises(SettingsValueError) as excinfo: # emtpy excitation
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_pow_dep_config4(): # text instead numbers
data = data_ET_ok + '''power_dependence: [asd, 1e7, 8]'''
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_extra_sections_warning_config():
data = data_all_mandatory_ok+'''extra_unknown_section: dsa'''
with pytest.warns(SettingsExtraValueWarning) as warnings:
with temp_config_filename(data) as filename:
settings.load(filename)
assert len(warnings) == 2 # one warning
warning = warnings.pop(SettingsExtraValueWarning)
assert issubclass(warning.category, SettingsExtraValueWarning)
assert 'Some values or sections should not be present in the file' in str(warning.message)
def test_extra_value():
extra_data = '''version: 1
lattice:
name: bNaYF4
N_uc: 8
# concentration
S_conc: 0.3
A_conc: 0.3
# unit cell
# distances in Angstrom
a: 5.9738
b: 5.9738
c: 3.5297
# angles in degree
alpha: 90
beta: 90
gamma: 120
# the number is also ok for the spacegroup
spacegroup: P-6
# info about sites
sites_pos: [[0, 0, 0], [2/3, 1/3, 1/2]]
sites_occ: [1, 1/2]
extra_value: 3
states:
sensitizer_ion_label: Yb
sensitizer_states_labels: [GS, ES]
activator_ion_label: Tm
activator_states_labels: [3H6, 3F4, 3H5, 3H4, 3F3, 1G4, 1D2]
excitations:
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
pump_rate: 9.3e-4 # 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
sensitizer_branching_ratios:
activator_branching_ratios:
'''
with pytest.warns(SettingsExtraValueWarning) as warnings: # "extra_value" in lattice section
with temp_config_filename(extra_data) as filename:
settings.load(filename)
assert len(warnings) == 1 # one warning
warning = warnings.pop(SettingsExtraValueWarning)
assert issubclass(warning.category, SettingsExtraValueWarning)
assert 'Some values or sections should not be present in the file' in str(warning.message)
def test_conc_dep_config4(): # negative number
data = data_ET_ok + '''concentration_dependence:
concentrations: [[0, 1, 2], [-0.01, 0.1, 0.2, 0.3, 0.4, 0.5]]'''
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"cannot be smaller than 0")
assert excinfo.type == SettingsValueError
def test_pow_dep_config3(): # empty
data = data_ET_ok + '''power_dependence: []'''
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"Length of power_dependence")
assert excinfo.match(r"cannot be smaller than 3")
assert excinfo.type == SettingsValueError
def test_ET_coop_ok(): # ok
data = data_branch_ok + '''energy_transfer:
CR50:
process: Yb(ES) + Yb(ES) + Tm(3H6) -> Yb(GS) + Yb(GS) + Tm(1G4)
multipolarity: 6
strength: 1e3
'''
with temp_config_filename(data) as filename:
settings.load(filename)
def test_ET_config_missing_ETlabel():
data = data_branch_ok + '''energy_transfer:
process: Tm(1G4) + Tm(3H6) -> Tm(3H4) + Tm(3H5)
multipolarity: 6
'''
with pytest.raises(SettingsValueError) as excinfo: # label missing
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_optim_wrong_excitations(): # ok
data = data_ET_ok + '''optimization:
excitations: [Vis_473, wrong_label]'''
with pytest.raises(settings.LabelError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"in optimization: excitations")
assert excinfo.match(r"not found in excitations section above!")
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
def test_optim_wrong_proc_2():
'''Wrong ET optimization process'''
data = data_ET_ok + '''optimization:
processes: [ETU53, ETU_does_no_exist]
'''
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
def test_ET_ok(): # ok
data = data_branch_ok + '''energy_transfer:
CR50:
process: Tm(1G4) + Tm(3H6) -> Tm(3H4) + Tm(3H5)
multipolarity: 6
strength: 1e3
strength_avg: 1e1
'''
with temp_config_filename(data) as filename:
settings.load(filename)
def test_conc_dep_config3(): # ok, but empty
data = data_ET_ok + '''concentration_dependence:
concentrations: []'''
with pytest.raises(SettingsValueError) as excinfo:
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"Length of concentrations")
assert excinfo.match(r"cannot be smaller than 2")
assert excinfo.type == SettingsValueError
def test_states_empty_list(): # empty list for S states
data = data_lattice_ok + '''states:
sensitizer_ion_label: Yb
sensitizer_states_labels: [GS, ES]
activator_ion_label: Tm
activator_states_labels: []'''
with pytest.raises(SettingsValueError) as excinfo: # empty S labels list
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r'Length of activator_states_labels \(0\) cannot be smaller than 1.')
assert excinfo.type == SettingsValueError
def test_states_no_states_labels():
data = data_lattice_ok + '''states:
sensitizer_states_labels: [GS, ES]
activator_ion_label: Tm
activator_states_labels: [3H6, 3F4, 3H5, 3H4, 3F3, 1G4, 1D2]'''
with pytest.raises(SettingsValueError) as excinfo: # missing key
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r'Error validating section "states"')
assert excinfo.match(r'"sensitizer_ion_label" not in dictionary')
assert excinfo.type == SettingsValueError
def test_ET_config_missing_strength():
data = data_branch_ok + '''energy_transfer:
CR50:
process: Tm(1G4) + Tm(3H6) -> Tm(3H4) + Tm(3H5)
multipolarity: 6
'''
with pytest.raises(SettingsValueError) as excinfo: # strength missing
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match('"strength" not in dictionary')
assert excinfo.type == SettingsValueError
def test_ET_config_wrong_initial_final_ion_label():
data = data_branch_ok + '''energy_transfer:
CR50:
process: Tm(1G4) + Tm(3H6) -> Yb(3H4) + Tm(3H5)
multipolarity: 6
strength: 8.87920884e+08
'''
with pytest.raises(settings.LabelError) as excinfo: # initial ion label should be the same
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"is not a valid state label")
assert excinfo.type == settings.LabelError
def test_abs_config8(): # ok, ESA on different ions
data = data_states_ok + '''excitations:
NIR_800:
active: True
power_dens: 1e7 # power density W/cm^2
t_pulse: 1e-8 # pulse width, seconds
process: [Tm(3H6)->Tm(3H4), Yb(GS)->Yb(ES)]
degeneracy: [13/9, 11/9]
pump_rate: [4.4e-3, 2e-3] # cm2/J
'''
with temp_config_filename(data) as filename:
settings.load(filename)
def test_ET_config_wrong_multipolarity():
data = data_branch_ok + '''energy_transfer:
CR50:
process: Tm(1G4) + Tm(3H6) -> Tm(3H4) + Tm(3H5)
multipolarity: fds
strength: 8.87920884e+08
'''
with pytest.raises(SettingsValueError) as excinfo: # wrong multipolarity
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_states_no_list():
data = data_lattice_ok + '''states:
sensitizer_ion_label: Yb
sensitizer_states_labels:
activator_ion_label: Tm
activator_states_labels: [3H6, 3F4, 3H5, 3H4, 3F3, 1G4, 1D2]'''
with pytest.raises(SettingsValueError) as excinfo: # empty S labels
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"sensitizer_states_labels")
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_abs_config_ok(): # good test
data = data_states_ok + '''excitations:
NIR_980:
active: True
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
'''
with temp_config_filename(data) as filename:
settings.load(filename)
def test_states_fractions(): # fractions in the state labels
data = data_lattice_ok + '''states:
sensitizer_ion_label: Yb
sensitizer_states_labels: [2F7/2, 2F5/2]
activator_ion_label: Tm
activator_states_labels: [3H6, 3F4, 3H5, 3H4, 3F3, 1G4, 1D2]'''
with pytest.raises(SettingsValueError) as excinfo: # it should fail in the excitations section
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r'Setting "excitations"')
assert excinfo.match(r'does not have the right type')
assert excinfo.type == SettingsValueError
def test_excitations_config7():
data = data_states_ok + '''excitations:
Vis_473:
active: True
t_pulse: 1e-8 # pulse width, seconds
process: Tm(3H6) -> Tm(1G4) # both ion labels are required
degeneracy: 13/9
pump_rate: 9.3e-4 # cm2/J
'''
with pytest.raises(SettingsValueError) as excinfo: # missing power_dens
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match('power_dens')
assert excinfo.type == SettingsValueError
def test_excitations_config5():
data = data_states_ok + '''excitations:
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
pump_rate: 9.3e-4 # cm2/J
'''
with pytest.raises(SettingsValueError) as excinfo: # label missing
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match(r"does not have the right type")
assert excinfo.type == SettingsValueError
def test_branch_config_ok(): # all ok
data = data_decay_ok + '''sensitizer_branching_ratios:
ES->GS: 1.0
activator_branching_ratios:
3H5->3F4: 0.4
3H4->3F4: 0.3
3F3->3H4: 0.999
1G4->3F4: 0.15
1G4->3H5: 0.16
1G4->3H4: 0.04
1G4->3F3: 0.00
1D2->3F4: 0.43
'''
with temp_config_filename(data) as filename:
settings.load(filename)
def test_abs_config7():
data = data_states_ok + '''excitations:
NIR_800:
active: True
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
'''
with pytest.raises(SettingsValueError) as excinfo: # pump rate must be positive
with temp_config_filename(data) as filename:
settings.load(filename)
assert excinfo.match("cannot be smaller than 0.")
assert excinfo.type == SettingsValueError
