Пример #1
0
def run_test():
    dbf = Database()
    dbf.elements = frozenset(["A"])
    dbf.add_phase("TEST", {}, [1])
    dbf.add_phase_constituents("TEST", [["A"]])
    # add THETA parameters here
    dbf.add_parameter("THETA", "TEST", [["A"]], 0, 334.0)
    conds = {v.T: np.arange(1.0, 800.0, 1), v.P: 101325}
    res = calculate(dbf, ["A"], "TEST", T=conds[v.T], P=conds[v.P], model=EinsteinModel, output="testprop")
    # res_TE = calculate(dbf, ['A'], 'TEST', T=conds[v.T], P=conds[v.P],
    #                model=EinsteinModel, output='einstein_temperature')
    import matplotlib.pyplot as plt

    plt.scatter(res["T"], res["testprop"])
    plt.xlabel("Temperature (K)")
    plt.ylabel("Molar Heat Capacity (J/mol-K)")
    plt.savefig("einstein.png")
Пример #2
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def run_test():
    dbf = Database()
    dbf.elements = frozenset(['A'])
    dbf.add_phase('TEST', {}, [1])
    dbf.add_phase_constituents('TEST', [['A']])
    # add THETA parameters here
    dbf.add_parameter('THETA', 'TEST', [['A']], 0, 334.)
    conds = {v.T: np.arange(1.,800.,1), v.P: 101325}
    res = calculate(dbf, ['A'], 'TEST', T=conds[v.T], P=conds[v.P],
                    model=EinsteinModel, output='testprop')
    #res_TE = calculate(dbf, ['A'], 'TEST', T=conds[v.T], P=conds[v.P],
    #                model=EinsteinModel, output='einstein_temperature')
    import matplotlib.pyplot as plt
    plt.scatter(res['T'], res['testprop'])
    plt.xlabel('Temperature (K)')
    plt.ylabel('Molar Heat Capacity (J/mol-K)')
    plt.savefig('einstein.png')
    print(dbf.to_string(fmt='tdb'))
Пример #3
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def run_test():
    dbf = Database()
    dbf.elements = frozenset(['A'])
    dbf.add_phase('TEST', {}, [1])
    dbf.add_phase_constituents('TEST', [['A']])
    # add THETA parameters here
    dbf.add_parameter('THETA', 'TEST', [['A']], 0, 334.)
    conds = {v.T: np.arange(1., 800., 1), v.P: 101325}
    res = calculate(dbf, ['A'],
                    'TEST',
                    T=conds[v.T],
                    P=conds[v.P],
                    model=EinsteinModel,
                    output='testprop')
    #res_TE = calculate(dbf, ['A'], 'TEST', T=conds[v.T], P=conds[v.P],
    #                model=EinsteinModel, output='einstein_temperature')
    import matplotlib.pyplot as plt
    plt.scatter(res['T'], res['testprop'])
    plt.xlabel('Temperature (K)')
    plt.ylabel('Molar Heat Capacity (J/mol-K)')
    plt.savefig('einstein.png')
    print(dbf.to_string(fmt='tdb'))
Пример #4
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def initialize_database(phase_models,
                        ref_state,
                        dbf=None,
                        fallback_ref_state="SGTE91"):
    """Return a Database boostraped with elements, species, phases and unary lattice stabilities.

    Parameters
    ----------
    phase_models : Dict[str, Any]
        Dictionary of components and phases to fit.
    ref_state : str
        String of the reference data to use, e.g. 'SGTE91' or 'SR2016'
    dbf : Optional[Database]
        Initial pycalphad Database that can have parameters that would not be fit by ESPEI
    fallback_ref_state : str
        String of the reference data to use for SER data, defaults to 'SGTE91'

    Returns
    -------
    Database
        A new pycalphad Database object, or a modified one if it was given.

    """
    if dbf is None:
        dbf = Database()
    lattice_stabilities = getattr(espei.refdata, ref_state)
    ser_stability = getattr(espei.refdata, ref_state + "Stable")
    aliases = extract_aliases(phase_models)
    phases = sorted({ph.upper() for ph in phase_models["phases"].keys()})
    elements = {el.upper() for el in phase_models["components"]}
    dbf.elements.update(elements)
    dbf.species.update({v.Species(el, {el: 1}, 0) for el in elements})

    # Add SER reference data for this element
    for element in dbf.elements:
        if element in dbf.refstates:
            continue  # Do not clobber user reference states
        el_ser_data = _get_ser_data(element,
                                    ref_state,
                                    fallback_ref_state=fallback_ref_state)
        # Try to look up the alias that we are using in this fitting
        el_ser_data["phase"] = aliases.get(el_ser_data["phase"],
                                           el_ser_data["phase"])
        # Don't warn if the element is a species with no atoms because per-atom
        # formation energies are not possible (e.g. VA (VACUUM) or /- (ELECTRON_GAS))
        if el_ser_data["phase"] not in phases and v.Species(
                element).number_of_atoms != 0:
            # We have the Gibbs energy expression that we need in the reference
            # data, but this phase is not a candidate in the phase models. The
            # phase won't be added to the database, so looking up the phases's
            # energy won't work.
            _log.warning(
                "The reference phase for %s, %s, is not in the supplied phase models "
                "and won't be added to the Database phases. Fitting formation "
                "energies will not be possible.", element,
                el_ser_data["phase"])
        dbf.refstates[element] = el_ser_data

    # Add the phases
    for phase_name, phase_data in phase_models['phases'].items():
        if phase_name not in dbf.phases.keys():  # Do not clobber user phases
            # TODO: Need to support model hints for: magnetic, order-disorder, etc.
            site_ratios = phase_data['sublattice_site_ratios']
            subl_model = phase_data['sublattice_model']
            # Only generate the sublattice model for active components
            subl_model = [
                sorted(set(subl).intersection(dbf.elements))
                for subl in subl_model
            ]
            if all(len(subl) > 0 for subl in subl_model):
                dbf.add_phase(phase_name, dict(), site_ratios)
                dbf.add_phase_constituents(phase_name, subl_model)

    # Add the GHSER functions to the Database
    for element in dbf.elements:
        # Use setdefault here to not clobber user-provided functions
        if element == "VA":
            dbf.symbols.setdefault("GHSERVA", 0)
        else:
            # note that `c.upper()*2)[:2]` returns "AL" for "Al" and "BB" for "B"
            # Using this ensures that GHSER functions will be unique, e.g.
            # GHSERC would be an abbreviation for GHSERCA.
            sym_name = "GHSER" + (element.upper() * 2)[:2]
            dbf.symbols.setdefault(sym_name, ser_stability[element])
    return dbf
Пример #5
0
def generate_parameters(phase_models, datasets, ref_state, excess_model):
    """Generate parameters from given phase models and datasets

    Parameters
    ----------
    phase_models : dict
        Dictionary of components and phases to fit.
    datasets : PickleableTinyDB
        database of single- and multi-phase to fit.
    ref_state : str
        String of the reference data to use, e.g. 'SGTE91' or 'SR2016'
    excess_model : str
        String of the type of excess model to fit to, e.g. 'linear'

    Returns
    -------
    pycalphad.Database

    """
    logging.info('Generating parameters.')
    dbf = Database()
    dbf.elements = set(phase_models['components'])
    for el in dbf.elements:
        if Species is not None:  # TODO: drop this on release of pycalphad 0.7
            dbf.species.add(Species(el, {el: 1}, 0))
    # Write reference state to Database
    refdata = getattr(espei.refdata, ref_state)
    stabledata = getattr(espei.refdata, ref_state + 'Stable')
    for key, element in refdata.items():
        if isinstance(element, sympy.Piecewise):
            newargs = element.args + ((0, True), )
            refdata[key] = sympy.Piecewise(*newargs)
    for key, element in stabledata.items():
        if isinstance(element, sympy.Piecewise):
            newargs = element.args + ((0, True), )
            stabledata[key] = sympy.Piecewise(*newargs)
    comp_refs = {
        c.upper(): stabledata[c.upper()]
        for c in dbf.elements if c.upper() != 'VA'
    }
    comp_refs['VA'] = 0
    # note that the `c.upper()*2)[:2]` returns 'AL' for c.upper()=='AL' and 'VV' for c.upper()=='V'
    dbf.symbols.update(
        {'GHSER' + (c.upper() * 2)[:2]: data
         for c, data in comp_refs.items()})
    for phase_name, phase_obj in sorted(phase_models['phases'].items(),
                                        key=operator.itemgetter(0)):
        # Perform parameter selection and single-phase fitting based on input
        # TODO: Need to pass particular models to include: magnetic, order-disorder, etc.
        symmetry = phase_obj.get('equivalent_sublattices', None)
        aliases = phase_obj.get('aliases', None)
        # TODO: More advanced phase data searching
        site_ratios = phase_obj['sublattice_site_ratios']
        subl_model = phase_obj['sublattice_model']
        dbf.add_phase(phase_name, dict(), site_ratios)
        dbf.add_phase_constituents(phase_name, subl_model)
        dbf.add_structure_entry(phase_name, phase_name)
        phase_fit(dbf,
                  phase_name,
                  symmetry,
                  subl_model,
                  site_ratios,
                  datasets,
                  refdata,
                  aliases=aliases)
    logging.info('Finished generating parameters.')
    return dbf