File: test_formulas.py

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from __future__ import division
from copy import deepcopy
from pickle import loads, dumps

from periodictable import Ca, C, O, H, Fe, Ni, Si, D, Na, Cl, Co, Ti
from periodictable import formula, mix_by_weight, mix_by_volume

def test():
    ikaite = formula()
    # Note: this should be a tuple of tuples
    ikaite.structure = ((1, Ca), (1, C), (3, O), (6, ((2, H), (1, O))))

    # Test print
    assert str(ikaite) == "CaCO3(H2O)6"

    # Test constructors
    assert ikaite == formula([(1, Ca), (1, C), (3, O), (6, [(2, H), (1, O)])])
    assert ikaite == formula(ikaite)
    assert ikaite is not formula(ikaite)
    assert ikaite.structure is formula(ikaite).structure

    # Test parsers
    assert formula("Ca") == formula([(1, Ca)])
    assert formula("Ca") == formula(Ca)
    assert formula("CaCO3") == formula([(1, Ca), (1, C), (3, O)])
    assert ikaite == formula("CaCO3+6H2O")
    assert ikaite == formula("(CaCO3+6H2O)1")
    assert ikaite == formula("CaCO3 6H2O")
    assert ikaite == formula("CaCO3(H2O)6")
    assert ikaite == formula("(CaCO3(H2O)6)1")
    assert ikaite.hill == formula("CCaO3(H2O)6").hill
    assert str(ikaite.hill) == "CH12CaO9"
    assert formula([(0.75, Fe), (0.25, Ni)]) == formula("Fe0.75Ni0.25")

    # Test composition
    #print formula("CaCO3") + 6*formula("H2O")
    assert ikaite == formula("CaCO3") + 6*formula("H2O")
    f = formula('')
    assert not (3*f).structure
    f = formula('H2O')
    assert id((1*f).structure) == id(f.structure)

    # Check atom count
    assert formula("Fe2O4+3H2O").atoms == {Fe: 2, O: 7, H: 6}

    # Check charge
    assert formula("P{5+}O{2-}4").charge == -3
    try:
        formula("P{18-}")
        raise Exception("No exception raised for invalid charge")
    except ValueError:
        pass
    assert formula("Na{+}Cl{-}").charge == 0
    Na_frac = Na.ion[1].mass/(Na.ion[1].mass+Cl.ion[-1].mass)
    assert abs(formula("Na{+}Cl{-}").mass_fraction[Na.ion[1]] - Na_frac) < 1e-14

    # Check the mass calculator
    assert formula('H2O').mass == 2*H.mass+O.mass
    assert formula("Fe2O4+3H2O").mass == 2*Fe.mass+7*O.mass+6*H.mass
    assert (formula("Fe2O[18]4+3H2O").mass
            == 2*Fe.mass+4*O[18].mass+3*O.mass+6*H.mass)

    # Check natural density support
    assert (formula('D2O', natural_density=1).density
            == (2*D.mass + O.mass)/(2*H.mass + O.mass))
    D2O = formula('D2O', natural_density=1)
    D2Os = formula('D2O')
    D2Os.natural_density = 1
    assert abs(D2O.density - D2Os.density) < 1e-14
    assert abs(D2O.natural_density - 1) < 1e-14
    assert abs(D2Os.natural_density - 1) < 1e-14

    # Test isotopes; make sure this is last since it changes ikaite!
    assert ikaite != formula("CaCO[18]3+6H2O")
    assert formula("O[18]").mass == O[18].mass

    # Check x-ray and neutron sld
    rho, mu, inc = formula('Si', Si.density).neutron_sld(wavelength=4.5)
    rhoSi, muSi, incSi = Si.neutron.sld(wavelength=4.5)
    assert abs(rho - rhoSi) < 1e-14
    assert abs(mu - muSi) < 1e-14
    assert abs(inc - incSi) < 1e-14

    rho, mu = formula('Si', Si.density).xray_sld(wavelength=1.54)
    rhoSi, muSi = Si.xray.sld(wavelength=1.54)
    assert abs(rho - rhoSi) < 1e-14
    assert abs(mu - muSi) < 1e-14

    # Check that names work
    permalloy = formula('Ni8Fe2', 8.692, name='permalloy')
    assert str(permalloy) == 'permalloy'

    # Check that get/restore state works
    assert deepcopy(permalloy).__dict__ == permalloy.__dict__

    # Check that copy constructor works
    #print permalloy.__dict__
    #print formula(permalloy).__dict__
    assert formula(permalloy).__dict__ == permalloy.__dict__
    assert formula('Si', name='Silicon').__dict__ != formula('Si').__dict__

    H2O = formula('H2O', natural_density=1)
    D2O = formula('D2O', natural_density=1)
    fm = mix_by_weight(H2O, 3, D2O, 2)
    fv = mix_by_volume(H2O, 3, D2O, 2)
    # quantity of H+D should stay in 2:1 ratio with O
    assert abs(fv.atoms[H]+fv.atoms[D] - 2*fv.atoms[O]) < 1e-14
    assert abs(fm.atoms[H]+fm.atoms[D] - 2*fm.atoms[O]) < 1e-14
    # H:D ratio should match H2O:D2O ratio when mixing by volume, but should
    # be skewed toward the lighter H when mixing by mass.
    assert abs(fv.atoms[H]/fv.atoms[D] - 1.5) < 1e-14
    assert abs(fm.atoms[H]/fm.atoms[D] - 1.5*D2O.density/H2O.density) < 1e-14
    # Mass densities should average according to H2O:D2O ratio when
    # mixing by volume but be skewed toward toward the more plentiful
    # H2O when mixing by mass
    H2O_fraction = 0.6
    assert abs(fv.density - (H2O.density*H2O_fraction + D2O.density*(1-H2O_fraction))) < 1e-14
    H2O_fraction = (3/H2O.density) / (3/H2O.density + 2/D2O.density)
    assert abs(fm.density - (H2O.density*H2O_fraction + D2O.density*(1-H2O_fraction))) < 1e-14

    # Make sure we are independent of unit cell size
    H2O = formula('3.2H2O', natural_density=1)
    D2O = formula('4.1D2O', natural_density=1)
    fm = mix_by_weight(H2O, 3, D2O, 2)
    fv = mix_by_volume(H2O, 3, D2O, 2)
    # quantity of H+D should stay in 2:1 ratio with O
    assert abs(fv.atoms[H]+fv.atoms[D] - 2*fv.atoms[O]) < 1e-14
    assert abs(fm.atoms[H]+fm.atoms[D] - 2*fm.atoms[O]) < 1e-14
    # H:D ratio should match H2O:D2O ratio when mixing by volume, but should
    # be skewed toward the lighter H when mixing by mass.
    assert abs(fv.atoms[H]/fv.atoms[D] - 1.5) < 1e-14
    assert abs(fm.atoms[H]/fm.atoms[D] - 1.5*D2O.density/H2O.density) < 1e-14
    # Mass densities should average according to H2O:D2O ratio when
    # mixing by volume but be skewed toward toward the more plentiful
    # H2O when mixing by mass
    H2O_fraction = 0.6
    assert abs(fv.density - (H2O.density*H2O_fraction + D2O.density*(1-H2O_fraction))) < 1e-14
    H2O_fraction = (3/H2O.density) / (3/H2O.density + 2/D2O.density)
    assert abs(fm.density - (H2O.density*H2O_fraction + D2O.density*(1-H2O_fraction))) < 1e-14

    # Pickle test
    assert loads(dumps(fm)) == fm
    ion = Fe[56].ion[2]
    assert id(loads(dumps(ion))) == id(ion)

    # zero quantities tests in mixtures
    f = mix_by_weight(H2O, 0, D2O, 2)
    assert f == D2O
    f = mix_by_weight(H2O, 2, D2O, 0)
    assert f == H2O
    f = mix_by_weight(H2O, 0, D2O, 0)
    assert f == formula()
    f = mix_by_volume(H2O, 0, D2O, 2)
    assert f == D2O
    f = mix_by_volume(H2O, 2, D2O, 0)
    assert f == H2O
    f = mix_by_volume(H2O, 0, D2O, 0)
    assert f == formula()

    # mix by weight with unknown component density
    # can't do mix by volume without component densities
    glass = mix_by_weight('SiO2', 75, 'Na2O', 15, 'CaO', 10, density=2.52)

    # layers and mixtures
    check_formula(formula('1mm Fe // 1mm Ni'), formula('50%vol Fe // Ni'))
    check_formula(formula('50%vol Co // Ti'), formula('2mL Co // 2mL Ti'))
    check_formula(formula('50%wt Co // Ti'), formula('2g Co // 2g Ti'))
    check_formula(formula('2mL Co // 2mL Ti'), formula(((1.5922466356368357, Co), (1, Ti))))
    check_formula(formula('2g Co // 2g Ti'), formula(((1, Co), (1.231186412350889, Ti))))
    check_formula(formula('5g NaCl // 50mL H2O@1'), formula('5g NaCl // 50g H2O'))
    check_formula(formula('5g NaCl // 50mL H2O@1'),
                  formula(((1, Na), (1, Cl), (32.4407, ((2, H), (1, O))))), tol=1e-5)
    assert abs(formula('1mm Fe // 1mm Ni').thickness - 0.002) < 0.002*1e014
    assert abs(formula('2g Co // 2g Ti').total_mass - 4) < 4*1e-14
    check_mass(formula('2mL Co // 2mL Ti'), mass=2*(Co.density+Ti.density))
    check_mass(formula("50 g (49 mL H2O@1 // 1 g NaCl) // 20 mL D2O@1n"),
               mass=50 + 20*D2O.density)
    check_mass(formula("50 mL (45 mL H2O@1 // 5 g NaCl)@1.0707 // 20 mL D2O@1n"),
               mass=50*1.0707 + 20*D2O.density)

    # fasta
    check_formula(formula('aa:A'), formula('C3H4H[1]NO'))

def check_mass(f1, mass, tol=1e-14):
    """Check that the total mass of f1 is as expected."""
    assert abs(f1.total_mass - mass) < mass*tol

def check_formula(f1, f2, tol=1e-14):
    """Check that the number of atoms in f1 and f2 are about equal."""
    f2_atoms = f2.atoms
    for atom, count in f1.atoms.items():
        if atom not in f2_atoms or abs(f2_atoms[atom] - count) > tol*count:
            raise RuntimeError("Formulas differ: %s and %s"%(f1, f2))

if __name__ == "__main__":
    test()