def test_structurefactor():
asyunit = cr.Atomset({
cr.Atom("Ca1", "Ca", fs("p 0 0 0")),
cr.Atom("Mn1", "Mn", fs("p 1/2 0 0")),
cr.Atom("Mn2", "Mn", fs("p 1/2 0 0")),
cr.Atom("Mn3", "Mn", fs("p 0 0 1/2")),
cr.Atom("O1", "O", fs("p 0.223 0.274 0.081")),
cr.Atom("O2", "O", fs("p 0.342 0.522 0.341"))
})
sg = tables.spacegroup(148)
cell = sg**asyunit
cellparameters = geo.Cellparameters(10.46, 10.46, 6.35, 90, 90, 120)
metric = cellparameters.to_Metric()
q = fs("q 3 0 0")
wavelength = 0.71073
F = cr.structurefactor(cell, metric, q, wavelength)
# assert test_numbers_Mixed.approx(-6.540191224, F.real)
# assert test_numbers_Mixed.approx(0.0, F.imag)
cell = cr.Atomset({
cr.Atom("Au1", "Au", fs("p 0 0 0 ")),
cr.Atom("Cu1", "Cu", fs("p 0 1/2 1/2")),
cr.Atom("Cu2", "Cu", fs("p 1/2 0 1/2")),
cr.Atom("Cu3", "Cu", fs("p 1/2 1/2 0 "))
})
cellparameters = geo.Cellparameters(3.71, 3.71, 3.71, 90, 90, 90)
metric = cellparameters.to_Metric()
q = fs("q 1 0 0")
sintl = 0.5 * metric.length(q)
def test_Face():
f = cr.Face("F", [fs("p 0 0 0"), fs("p 1.0 0 0"), fs("p 0 1.0 0")])
f_ = cr.Face("F", [fs("p 0 1.0 0"), fs("p 0 0 0"), fs("p 1.0 0 0")])
f__ = cr.Face("F", [fs("p 0 1.0 0"), fs("p 1.0 0 0"), fs("p 0 0 0")])
assert f == f_
assert hash(f) == hash(f_)
assert f == f__
assert hash(f) == hash(f__)
f = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
f_ = cr.Face("F", [fs("p 0 1 0"), fs("p 0 0 0"), fs("p 1 0 0")])
assert isinstance(f, cr.Face)
f.set_color((0, 0, 1))
f.set_color((fs("0.3"), 0.1, 1))
f.set_opacity(0.5)
d = fs("d 0 0 1/2")
f1 = cr.Face("Fblabla", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
f2 = cr.Face("F", [fs("p 0 0 0"), fs("p 0.7 0 0"), fs("p 0 1 0")])
f3 = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 2 0")])
assert f == f1
assert f == f_
assert hash(f) == hash(f_)
assert (f == f2) == False
assert (f == f3) == False
assert f + d == cr.Face("F", [fs("p 0 0 1/2"), fs("p 1 0 1/2"), fs("p 0 1 1/2")])
assert fs("x+1/2,y,z") ** f == cr.Face("F", [fs("p 1/2 0 0"), fs("p 3/2 0 0"), fs("p 1/2 1 0")])
assert fs("{x+3/2,y,z}") ** f == cr.Face("F", [fs("p 1/2 0 0"), fs("p 1/2 0 0"), fs("p 1/2 0 0")])
f = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
assert (f + "test").name == "Ftest"
three = fs("{-y,x-y,z}")
sg = geo.Spacegroup(
geo.canonical,
[fs("{x,y,z}"), three, three*three]
)
p1 = fs("p 0.1740 0.8260 0.5871")
p2 = fs("-y,x-y,z")**p1
p3 = fs("-y,x-y,z")**p2
a1 = cr.Atom("Fe1", "Fe", p1)
a2 = cr.Atom("Fe2", "Fe", p2)
a3 = cr.Atom("Fe3", "Fe", p3)
atomset = cr.Atomset({a1, a2, a3})
atomset = sg**atomset
print(atomset)
assert len(atomset.menge) == 3
f = cr.Face("F", [p1, p2, p3])
atomset = cr.Atomset({f})
assert len(atomset.menge) == 1
atomset = sg ** atomset
assert len(atomset.menge) == 1
def test_print_cif():
atomset = \
cr.Atomset({cr.Atom("Dy1", "Dy", fs("p 0.982(0) 0.082(0) 1/4 ")),
cr.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")),
cr.Atom("O1", "O", fs("p 0.108(2) 0.471(2) 1/4 ")),
cr.Atom("O2", "O", fs("p 0.707(1) 0.328(1) 0.052(1) "))})
sg = geo.Spacegroup(geo.canonical, [fs("{x,y,z}"), fs("{-x,-y,-z}")])
liste = ["Dy1", "Mn1", "O1", "O2"]
atomset_all = (sg**atomset) % geo.canonical
assert cryspy_niceprint.print_cif_without_symmetries(
liste, atomset_all) == "hallo"
def test_print_atomtable():
atomset = \
cr.Atomset({cr.Atom("Dy1", "Dy", fs("p 0.982(0) 0.082(0) 1/4 ")),
cr.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")),
cr.Atom("O1", "O", fs("p 0.108(2) 0.471(2) 1/4 ")),
cr.Atom("O2", "O", fs("p 0.707(1) 0.328(1) 0.052(1) "))})
liste = ["Dy1", "Mn1", "O1", "O2"]
assert cryspy.niceprint.atomtable(liste, atomset) == \
" name type x y z \n" \
" ---- ---- --- --- ---\n" \
" Dy1 Dy 0.982(0) 0.082(0) 1/4\n" \
" Mn1 Mn 1/2 0 0\n" \
" O1 O 0.1080(20) 0.4710(20) 1/4\n" \
" O2 O 0.7070(10) 0.3280(10) 0.0520(10)"
def test_print_cif():
atomset = \
cr.Atomset({cr.Atom("Dy1", "Dy", fs("p 0.982(0) 0.082(0) 1/4 ")),
cr.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")),
cr.Atom("O1", "O", fs("p 0.108(2) 0.471(2) 1/4 ")),
cr.Atom("O2", "O", fs("p 0.707(1) 0.328(1) 0.052(1) "))})
sg = geo.Spacegroup(geo.canonical, [fs("{x,y,z}"), fs("{-x,-y,-z}")])
liste = ["Dy1", "Dy1_1", "Mn1", "O1", "O1_1", "O2", "O2_1"]
atomset_all = (sg**atomset) % geo.canonical
metric = geo.Cellparameters(5.0, 5.0, 5.0, 90, 90, 90).to_Metric()
print(
cryspy.niceprint.print_cif_without_symmetries(liste, atomset_all,
metric))
assert cryspy.niceprint.print_cif_without_symmetries(liste, atomset_all, metric) == \
"data_global _chemical_name 'noname' \n" \
"_cell_length_a 5.0\n" \
"_cell_length_b 5.0\n" \
"_cell_length_c 5.0\n" \
"_cell_angle_alpha 90\n" \
"_cell_angle_beta 90\n" \
"_cell_angle_gamma 90\n" \
"_symmetry_space_group_name_H-M 'P 1'\n" \
"loop_ \n" \
" _atom_site_label \n" \
" _atom_site_type_symbol \n" \
" _atom_site_fract_x \n" \
" _atom_site_fract_y \n" \
" _atom_site_fract_z \n" \
" Dy1_1 Dy 0.982000 0.082000 0.250000\n" \
" Dy1_1_1 Dy 0.018000 0.918000 0.750000\n" \
" Mn1_1 Mn 0.500000 0.000000 0.000000\n" \
" O1_1 O 0.108000 0.471000 0.250000\n" \
" O1_1_1 O 0.892000 0.529000 0.750000\n" \
" O2_1 O 0.707000 0.328000 0.052000\n" \
" O2_1_1 O 0.293000 0.672000 0.948000\n"
def test_Atomset():
atom1 = cr.Atom("Cs1", "Cs", fs("p 0 0 0"))
atom2 = cr.Atom("Cs2", "Cs", fs("p 1/4 1/4 0"))
momentum = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
bond = cr.Bond("B", fs("p 0 0 0"), fs("p 1/2 1/2 1/2"))
face = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
atomset = cr.Atomset({atom1, atom2, momentum, bond, face})
print(atomset)
assert atomset.__str__() == \
"Atomset \n" \
"------- \n" \
" Atom Cs1 Cs Pos / 0 \ \n" \
" | 0 |\n" \
" \ 0 / \n" \
" \n" \
" Atom Cs2 Cs Pos / 1/4 \ \n" \
" | 1/4 |\n" \
" \ 0 / \n" \
" \n" \
" Momentum\n" \
" Bond\n" \
" Face"
transformation = fs("O->(0,0,1/4) \n"
"then\n"
"a' = a+b \n"
"b' = b \n"
"c' = c")
atomset1 = transformation**atomset
atomset2 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 -1/4")), \
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4")), \
cr.Momentum("M", fs("p 0 0 -1/4"), fs("d 0 0 1")), \
cr.Bond("B", fs("p 0 0 -1/4"), fs("p 1/2 0 1/4")), \
cr.Face("F", [fs("p 0 0 -1/4"), fs("p 1 -1 -1/4"), fs("p 0 1 -1/4")])})
assert (transformation**bond) == cr.Bond("B", fs("p 0 0 -1/4"),
fs("p 1/2 0 1/4"))
assert (transformation**face) == cr.Face(
"F", [fs("p 0 0 -1/4"),
fs("p 1 -1 -1/4"),
fs("p 0 1 -1/4")])
assert atomset1 == atomset2
spacegroup = geo.Spacegroup(
geo.canonical, [fs("{x, y, z}"), fs("{-x, -y, -z}")])
atomset1 = spacegroup**atomset
atomset2 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 0")), \
cr.Atom("Cs2", "Cs", fs("p 1/4 1/4 0")), \
cr.Atom("Cs2_1", "Cs", fs("p 3/4 3/4 0")), \
momentum, \
bond, \
cr.Face("F", [fs("p 0 0 0"), fs("p 0 0 0"), fs("p 0 0 0")])})
assert atomset1 == atomset2
assert atomset1.atomnames == atomset2.atomnames
atomset1 = spacegroup**(atomset + "_1")
atomset2 = cr.Atomset({cr.Atom("Cs1_1", "Cs", fs("p 0 0 0")), \
cr.Atom("Cs2_1", "Cs", fs("p 1/4 1/4 0")), \
cr.Atom("Cs2_2", "Cs", fs("p 3/4 3/4 0")), \
momentum, \
bond, \
cr.Face("F", [fs("p 0 0 0"), fs("p 0 0 0"), fs("p 0 0 0")])})
assert atomset1 == atomset2
assert atomset1.atomnames == atomset2.atomnames
atomset = cr.Atomset({
cr.Atom("Cs1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4"))
})
atomset1 = atomset % geo.canonical
atomset2 = cr.Atomset({
cr.Atom("Cs1", "Cs", fs("p 0 0 3/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 3/4"))
})
assert atomset1 == atomset2
atomset1 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 0"))})
atomset2 = cr.Atomset({cr.Atom("Cu1", "Cu", fs("p 1/2 1/2 1/2"))})
atomset3 = atomset1 + atomset2
atomset4 = cr.Atomset({
cr.Atom("Cs1", "Cs", fs("p 0 0 0")),
cr.Atom("Cu1", "Cu", fs("p 1/2 1/2 1/2"))
})
assert atomset3 == atomset4
d = fs("d 1/2 0 0")
atomset5 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 1/2 0 0"))})
atomset6 = atomset1 + d
atomset7 = d + atomset1
assert atomset5 == atomset6
assert atomset5 == atomset7
atomset = cr.Atomset({
cr.Atom("Cs1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4"))
})
assert atomset.nextname("Cs1") == "Cs1_1"
assert atomset.nextname("Cs3") == "Cs3"
atomset = cr.Atomset({
cr.Atom("Cs_1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Ar_1", "Cs", fs("p 1/4 0 -1/4")),
cr.Atom("Ar_2", "Ar", fs("p 0 1/2 0"))
})
assert atomset.nextname("Cs_1") == "Cs_2"
assert atomset.nextname("Ar_2") == "Ar_3"
assert atomset.nextname("Ar_1") == "Ar_3"
def test_Atomset():
atom1 = cr.Atom("Cs1", "Cs", fs("p 0.0000 0 0"))
atom1a = cr.Atom("Cs1", "Cs", fs("p 0.00000001 0 0"))
atom2 = cr.Atom("Cs2", "Cs", fs("p 1/4 1/4 0"))
momentum = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
bond = cr.Bond("B", fs("p 0 0 0"), fs("p 1/2 1/2 1/2"))
face = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
assert hash(atom1) == hash(atom1a)
assert len({atom1, atom1a}) == 1
atomset = cr.Atomset({atom1, atom1a, atom2, momentum, bond, face})
assert atomset.__str__() == \
"Atomset \n" \
"------- \n" \
" Atom Cs1 Cs Pos / 1e-08 \ \n" \
" | 0 |\n" \
" \ 0 / \n" \
" \n" \
" Atom Cs2 Cs Pos / 1/4 \ \n" \
" | 1/4 |\n" \
" \ 0 / \n" \
" \n" \
" Momentum\n" \
" Bond\n" \
" Face"
transformation = fs("O->(0,0,1/4) \n"
"then\n"
"a' = a+b \n"
"b' = b \n"
"c' = c")
atomset1 = transformation**atomset
print(atomset1)
atomset2 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0.00000001 -0.00000001 -1/4")), \
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4")), \
cr.Momentum("M", fs("p 0 0 -1/4"), fs("d 0 0 1")), \
cr.Bond("B", fs("p 0 0 -1/4"), fs("p 1/2 0 1/4")), \
cr.Face("F", [fs("p 0 0 -1/4"), fs("p 1 -1 -1/4"), fs("p 0 1 -1/4")])})
assert (transformation ** bond) == cr.Bond("B", fs("p 0 0 -1/4"), fs("p 1/2 0 1/4"))
assert (transformation ** face) == cr.Face("F", [fs("p 0 0 -1/4"), fs("p 1 -1 -1/4"), fs("p 0 1 -1/4")])
assert atomset1 == atomset2
atom1 = cr.Atom("Cs1", "Cs", fs("p 0 0 0"))
atom2 = cr.Atom("Cs2", "Cs", fs("p 1/4 1/4 0"))
momentum = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
bond = cr.Bond("B", fs("p 0 0 0"), fs("p 1/2 1/2 1/2"))
face = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
atomset = cr.Atomset({atom1, atom2, momentum, bond, face})
spacegroup = geo.Spacegroup(geo.canonical, [fs("{x, y, z}"),
fs("{-x, -y, -z}")])
atomset1 = spacegroup ** atomset
atomset2 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 0")), \
cr.Atom("Cs2", "Cs", fs("p 1/4 1/4 0")), \
cr.Atom("Cs2_1", "Cs", fs("p 3/4 3/4 0")), \
momentum, \
bond, \
cr.Face("F", [fs("p 0 0 0"), fs("p 0 0 0"), fs("p 0 0 0")])})
assert atomset1 == atomset2
assert atomset1.names == atomset2.names
atomset1 = spacegroup ** (atomset + "_1")
atomset2 = cr.Atomset({cr.Atom("Cs1_1", "Cs", fs("p 0 0 0")), \
cr.Atom("Cs2_1", "Cs", fs("p 1/4 1/4 0")), \
cr.Atom("Cs2_2", "Cs", fs("p 3/4 3/4 0")), \
momentum, \
bond, \
cr.Face("F", [fs("p 0 0 0"), fs("p 0 0 0"), fs("p 0 0 0")])})
assert atomset1 == atomset2
assert atomset1.names == atomset2.names
atomset = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4"))})
atomset1 = atomset % geo.canonical
atomset2 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 3/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 3/4"))})
assert atomset1 == atomset2
atomset1 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 0"))})
atomset2 = cr.Atomset({cr.Atom("Cu1", "Cu", fs("p 1/2 1/2 1/2"))})
atomset3 = atomset1 + atomset2
atomset4 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 0")),
cr.Atom("Cu1", "Cu", fs("p 1/2 1/2 1/2"))})
assert atomset3 == atomset4
d = fs("d 1/2 0 0")
atomset5 = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 1/2 0 0"))})
atomset6 = atomset1 + d
atomset7 = d + atomset1
assert atomset5 == atomset6
assert atomset5 == atomset7
atomset = cr.Atomset({cr.Atom("Cs1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Cs2", "Cs", fs("p 1/4 0 -1/4"))})
assert atomset.nextname("Cs1") == "Cs1_1"
assert atomset.nextname("Cs3") == "Cs3"
atomset = cr.Atomset({cr.Atom("Cs_1", "Cs", fs("p 0 0 -1/4")),
cr.Atom("Ar_1", "Cs", fs("p 1/4 0 -1/4")),
cr.Atom("Ar_2", "Ar", fs("p 0 1/2 0"))})
assert atomset.nextname("Cs_1") == "Cs_2"
assert atomset.nextname("Ar_2") == "Ar_3"
assert atomset.nextname("Ar_1") == "Ar_3"
atomset = cr.Atomset({cr.Subset("S_1", fs("p 0 0 0"), {
cr.Atom("Fe1", "Fe", fs("p -0.1 0 0")),
cr.Atom("Fe2", "Fe", fs("p 0.1 0 0"))
}
)
})
sg = geo.Spacegroup(geo.canonical, [fs("{x, y, z}"), fs("{x, -y+1/2, z}")])
assert sg.is_really_a_spacegroup()
atomset1 = cr.Atomset({cr.Subset("S_1", fs("p 0 0 0"), {
cr.Atom("Fe1", "Fe", fs("p -0.1 0 0")),
cr.Atom("Fe2", "Fe", fs("p 0.1 0 0"))
}
),
cr.Subset("S_2", fs("p 0 1/2 0"), {
cr.Atom("Fe1", "Fe", fs("p -0.1 1/2 0")),
cr.Atom("Fe2", "Fe", fs("p 0.1 1/2 0"))
}
)
})
assert sg ** atomset == atomset1
atomset_unpacked = cr.Atomset({
cr.Atom("S_1:Fe1", "Fe", fs("p -0.1 0 0")),
cr.Atom("S_1:Fe2", "Fe", fs("p 0.1 0 0")),
cr.Atom("S_2:Fe1", "Fe", fs("p -0.1 1/2 0")),
cr.Atom("S_2:Fe2", "Fe", fs("p 0.1 1/2 0"))
})
for subset in (sg ** atomset).menge:
print(subset.name)
assert (sg ** atomset).unpack_subsets() == atomset_unpacked
assert (sg ** atomset).names \
== atomset1.names
assert ((sg ** atomset).unpack_subsets()).names \
== atomset_unpacked.names