def test_shift_reference_state_model_contribs_take_effect():
"""Shift reference state with contrib_mods set adds contributions to the pure elements."""
TDB = """
ELEMENT A GRAPHITE 12.011 1054.0 5.7423 !
ELEMENT B BCC_A2 55.847 4489.0 27.2797 !
TYPE_DEFINITION % SEQ * !
PHASE TEST % 1 1 !
CONSTITUENT TEST : A,B: !
"""
dbf = Database(TDB)
comps = ['A', 'B']
phase = 'TEST'
m = Model(dbf, comps, phase)
refstates = [ReferenceState('A', phase), ReferenceState('B', phase)]
m.shift_reference_state(refstates, dbf)
statevars = {
v.T: 298.15,
v.P: 101325,
v.SiteFraction(phase, 0, 'A'): 0.5,
v.SiteFraction(phase, 0, 'B'): 0.5,
}
# ideal mixing should be present for GMR
idmix_val = 2 * 0.5 * np.log(0.5) * v.R * 298.15
check_output(m, statevars, 'GMR', idmix_val)
# shifting the reference state, adding an excess contribution
# should see that addition in the output
m.shift_reference_state(refstates, dbf, contrib_mods={'xsmix': S(1000.0)})
# each pure element contribution is has xsmix changed from 0 to 1
# At x=0.5, the reference xsmix energy is added to by 0.5*1000.0, which is
# then subtracted out of the GM energy
check_output(m, statevars, 'GMR', idmix_val - 1000.0)
def test_non_zero_reference_mixing_enthalpy_for_va_interaction():
"""The referenced mixing enthalpy for a Model with a VA interaction parameter is non-zero."""
m = Model(VA_INTERACTION_DBF, ['AL', 'VA'], 'FCC_A1')
refstates = [ReferenceState('AL', 'FCC_A1')]
m.shift_reference_state(refstates, VA_INTERACTION_DBF)
statevars_pure = {
v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 1,
v.SiteFraction('FCC_A1', 0, 'VA'): 0,
v.SiteFraction('FCC_A1', 1, 'VA'): 1
}
check_output(m, statevars_pure, 'GMR', 0.0)
statevars_mix = {
v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 0.5,
v.SiteFraction('FCC_A1', 0, 'VA'): 0.5,
v.SiteFraction('FCC_A1', 1, 'VA'): 1
}
# 4000.0 * 0.5=2000 +500 # (Y0VA doesn't contribute), but the VA endmember does (not referenced)
check_output(m, statevars_mix, 'HMR', 2500.0)
statevars_mix = {
v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 0.5,
v.SiteFraction('FCC_A1', 0, 'VA'): 0.5,
v.SiteFraction('FCC_A1', 1, 'VA'): 1
}
# 4000.0 * 0.5 (Y0VA doesn't contribute)
check_output(m, statevars_mix, 'HM_MIX', 2000.0)
def test_shift_reference_state_model_contribs_take_effect():
"""Shift reference state with contrib_mods set adds contributions to the pure elements."""
TDB = """
ELEMENT A GRAPHITE 12.011 1054.0 5.7423 !
ELEMENT B BCC_A2 55.847 4489.0 27.2797 !
TYPE_DEFINITION % SEQ * !
PHASE TEST % 1 1 !
CONSTITUENT TEST : A,B: !
"""
dbf = Database(TDB)
comps = ['A', 'B']
phase = 'TEST'
m = Model(dbf, comps, phase)
refstates = [ReferenceState('A', phase), ReferenceState('B', phase)]
m.shift_reference_state(refstates, dbf)
statevars = {
v.T: 298.15, v.P: 101325,
v.SiteFraction(phase, 0, 'A'): 0.5, v.SiteFraction(phase, 0, 'B'): 0.5,
}
# ideal mixing should be present for GMR
idmix_val = 2*0.5*np.log(0.5)*v.R*298.15
check_output(m, statevars, 'GMR', idmix_val)
# shifting the reference state, adding an excess contribution
# should see that addition in the output
m.shift_reference_state(refstates, dbf, contrib_mods={'xsmix': S(1000.0)})
# each pure element contribution is has xsmix changed from 0 to 1
# At x=0.5, the reference xsmix energy is added to by 0.5*1000.0, which is
# then subtracted out of the GM energy
check_output(m, statevars, 'GMR', idmix_val-1000.0)
def test_reference_energy_of_unary_twostate_einstein_magnetic_is_zero():
"""The referenced energy for the pure elements in a unary Model with twostate and Einstein contributions referenced to that phase is zero."""
m = Model(FEMN_DBF, ['FE', 'VA'], 'LIQUID')
statevars = {v.T: 298.15, v.SiteFraction('LIQUID', 0, 'FE'): 1, v.SiteFraction('LIQUID', 1, 'VA'): 1}
refstates = [ReferenceState(v.Species('FE'), 'LIQUID')]
m.shift_reference_state(refstates, FEMN_DBF)
check_output(m, statevars, 'GMR', 0.0)
def test_reference_energy_for_different_phase():
"""The referenced energy a different phase should be correct."""
m = Model(ALFE_DBF, ['AL', 'FE', 'VA'], 'AL2FE')
# formation reference states
refstates = [ReferenceState('AL', 'FCC_A1'), ReferenceState('FE', 'BCC_A2')]
m.shift_reference_state(refstates, ALFE_DBF)
statevars = {v.T: 300, v.SiteFraction('AL2FE', 0, 'AL'): 1, v.SiteFraction('AL2FE', 1, 'FE'): 1}
check_output(m, statevars, 'GMR', -28732.525) # Checked in Thermo-Calc
def test_reference_energy_of_unary_twostate_einstein_magnetic_is_zero():
"""The referenced energy for the pure elements in a unary Model with twostate and Einstein contributions referenced to that phase is zero."""
m = Model(FEMN_DBF, ['FE', 'VA'], 'LIQUID')
statevars = {
v.T: 298.15,
v.SiteFraction('LIQUID', 0, 'FE'): 1,
v.SiteFraction('LIQUID', 1, 'VA'): 1
}
refstates = [ReferenceState(v.Species('FE'), 'LIQUID')]
m.shift_reference_state(refstates, FEMN_DBF)
check_output(m, statevars, 'GMR', 0.0)
def test_magnetic_reference_energy_is_zero():
"""The referenced energy binary magnetic Model is zero."""
m = Model(CRFE_DBF, ['CR', 'FE', 'VA'], 'BCC_A2')
refstates = [ReferenceState('CR', 'BCC_A2'), ReferenceState('FE', 'BCC_A2')]
m.shift_reference_state(refstates, CRFE_DBF)
statevars_FE = {v.T: 300,
v.SiteFraction('BCC_A2', 0, 'CR'): 0, v.SiteFraction('BCC_A2', 0, 'FE'): 1,
v.SiteFraction('BCC_A2', 1, 'VA'): 1}
check_output(m, statevars_FE, 'GMR', 0.0)
statevars_CR = {v.T: 300,
v.SiteFraction('BCC_A2', 0, 'CR'): 1, v.SiteFraction('BCC_A2', 0, 'FE'): 0,
v.SiteFraction('BCC_A2', 1, 'VA'): 1}
check_output(m, statevars_CR, 'GMR', 0.0)
def test_reference_energy_for_different_phase():
"""The referenced energy a different phase should be correct."""
m = Model(ALFE_DBF, ['AL', 'FE', 'VA'], 'AL2FE')
# formation reference states
refstates = [
ReferenceState('AL', 'FCC_A1'),
ReferenceState('FE', 'BCC_A2')
]
m.shift_reference_state(refstates, ALFE_DBF)
statevars = {
v.T: 300,
v.SiteFraction('AL2FE', 0, 'AL'): 1,
v.SiteFraction('AL2FE', 1, 'FE'): 1
}
check_output(m, statevars, 'GMR', -28732.525) # Checked in Thermo-Calc
def test_non_zero_reference_mixing_enthalpy_for_va_interaction():
"""The referenced mixing enthalpy for a Model with a VA interaction parameter is non-zero."""
m = Model(VA_INTERACTION_DBF, ['AL', 'VA'], 'FCC_A1')
refstates = [ReferenceState('AL', 'FCC_A1')]
m.shift_reference_state(refstates, VA_INTERACTION_DBF)
statevars_pure = {v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 1, v.SiteFraction('FCC_A1', 0, 'VA'): 0,
v.SiteFraction('FCC_A1', 1, 'VA'): 1}
check_output(m, statevars_pure, 'GMR', 0.0)
statevars_mix = {v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 0.5, v.SiteFraction('FCC_A1', 0, 'VA'): 0.5,
v.SiteFraction('FCC_A1', 1, 'VA'): 1}
# 4000.0 * 0.5=2000 +500 # (Y0VA doesn't contribute), but the VA endmember does (not referenced)
check_output(m, statevars_mix, 'HMR', 2500.0)
statevars_mix = {v.T: 300,
v.SiteFraction('FCC_A1', 0, 'AL'): 0.5, v.SiteFraction('FCC_A1', 0, 'VA'): 0.5,
v.SiteFraction('FCC_A1', 1, 'VA'): 1}
# 4000.0 * 0.5 (Y0VA doesn't contribute)
check_output(m, statevars_mix, 'HM_MIX', 2000.0)
def test_magnetic_reference_energy_is_zero():
"""The referenced energy binary magnetic Model is zero."""
m = Model(CRFE_DBF, ['CR', 'FE', 'VA'], 'BCC_A2')
refstates = [
ReferenceState('CR', 'BCC_A2'),
ReferenceState('FE', 'BCC_A2')
]
m.shift_reference_state(refstates, CRFE_DBF)
statevars_FE = {
v.T: 300,
v.SiteFraction('BCC_A2', 0, 'CR'): 0,
v.SiteFraction('BCC_A2', 0, 'FE'): 1,
v.SiteFraction('BCC_A2', 1, 'VA'): 1
}
check_output(m, statevars_FE, 'GMR', 0.0)
statevars_CR = {
v.T: 300,
v.SiteFraction('BCC_A2', 0, 'CR'): 1,
v.SiteFraction('BCC_A2', 0, 'FE'): 0,
v.SiteFraction('BCC_A2', 1, 'VA'): 1
}
check_output(m, statevars_CR, 'GMR', 0.0)
def get_thermochemical_data(dbf,
comps,
phases,
datasets,
weight_dict=None,
symbols_to_fit=None):
"""
Parameters
----------
dbf : pycalphad.Database
Database to consider
comps : list
List of active component names
phases : list
List of phases to consider
datasets : espei.utils.PickleableTinyDB
Datasets that contain single phase data
weight_dict : dict
Dictionary of weights for each data type, e.g. {'HM': 200, 'SM': 2}
symbols_to_fit : list
Parameters to fit. Used to build the models and PhaseRecords.
Returns
-------
list
List of data dictionaries to iterate over
"""
# phase by phase, then property by property, then by model exclusions
if weight_dict is None:
weight_dict = {}
if symbols_to_fit is not None:
symbols_to_fit = sorted(symbols_to_fit)
else:
symbols_to_fit = database_symbols_to_fit(dbf)
# estimated from NIST TRC uncertainties
property_std_deviation = {
'HM': 500.0 / weight_dict.get('HM', 1.0), # J/mol
'SM': 0.2 / weight_dict.get('SM', 1.0), # J/K-mol
'CPM': 0.2 / weight_dict.get('CPM', 1.0), # J/K-mol
}
properties = [
'HM_FORM', 'SM_FORM', 'CPM_FORM', 'HM_MIX', 'SM_MIX', 'CPM_MIX'
]
ref_states = []
for el in get_pure_elements(dbf, comps):
ref_state = ReferenceState(el, dbf.refstates[el]['phase'])
ref_states.append(ref_state)
all_data_dicts = []
for phase_name in phases:
for prop in properties:
desired_data = get_prop_data(
comps,
phase_name,
prop,
datasets,
additional_query=(where('solver').exists()))
if len(desired_data) == 0:
continue
unique_exclusions = set([
tuple(sorted(d.get('excluded_model_contributions', [])))
for d in desired_data
])
for exclusion in unique_exclusions:
data_dict = {
'phase_name': phase_name,
'prop': prop,
# needs the following keys to be added:
# species, calculate_dict, phase_records, model, output, weights
}
# get all the data with these model exclusions
if exclusion == tuple([]):
exc_search = (
~where('excluded_model_contributions').exists()) & (
where('solver').exists())
else:
exc_search = (where('excluded_model_contributions').test(
lambda x: tuple(sorted(x)) == exclusion)) & (
where('solver').exists())
curr_data = get_prop_data(comps,
phase_name,
prop,
datasets,
additional_query=exc_search)
calculate_dict = get_prop_samples(dbf, comps, phase_name,
curr_data)
mod = Model(dbf, comps, phase_name, parameters=symbols_to_fit)
if prop.endswith('_FORM'):
output = ''.join(prop.split('_')[:-1]) + 'R'
mod.shift_reference_state(
ref_states,
dbf,
contrib_mods={e: sympy.S.Zero
for e in exclusion})
else:
output = prop
for contrib in exclusion:
mod.models[contrib] = sympy.S.Zero
mod.reference_model.models[contrib] = sympy.S.Zero
species = sorted(unpack_components(dbf, comps), key=str)
data_dict['species'] = species
model = {phase_name: mod}
statevar_dict = {
getattr(v, c, None): vals
for c, vals in calculate_dict.items()
if isinstance(getattr(v, c, None), v.StateVariable)
}
statevar_dict = OrderedDict(
sorted(statevar_dict.items(), key=lambda x: str(x[0])))
str_statevar_dict = OrderedDict(
(str(k), vals) for k, vals in statevar_dict.items())
phase_records = build_phase_records(
dbf,
species, [phase_name],
statevar_dict,
model,
output=output,
parameters={s: 0
for s in symbols_to_fit},
build_gradients=False,
build_hessians=False)
data_dict['str_statevar_dict'] = str_statevar_dict
data_dict['phase_records'] = phase_records
data_dict['calculate_dict'] = calculate_dict
data_dict['model'] = model
data_dict['output'] = output
data_dict['weights'] = np.array(
property_std_deviation[prop.split('_')[0]]) / np.array(
calculate_dict.pop('weights'))
all_data_dicts.append(data_dict)
return all_data_dicts
def test_underspecified_refstate_raises():
"""A Model cannot be shifted to a new reference state unless references for all pure elements are specified."""
m = Model(FEMN_DBF, ['FE', 'MN', 'VA'], 'LIQUID')
refstates = [ReferenceState(v.Species('FE'), 'LIQUID')]
with pytest.raises(DofError):
m.shift_reference_state(refstates, FEMN_DBF)
def test_underspecified_refstate_raises():
"""A Model cannot be shifted to a new reference state unless references for all pure elements are specified."""
m = Model(FEMN_DBF, ['FE', 'MN', 'VA'], 'LIQUID')
refstates = [ReferenceState(v.Species('FE'), 'LIQUID')]
m.shift_reference_state(refstates, FEMN_DBF)