def test_fill():
atomset = cryspy.crystal.Atomset({cryspy.crystal.Atom("Fe1", "Fe", fs("p 1/2 1/2 1/2"))})
atomset = cryspy.utils.fill(atomset, [0.6, 0.6, 0.6])
assert len(atomset.menge) == 27
atomset = cryspy.crystal.Atomset({cryspy.crystal.Atom("Fe1", "Fe", fs("p 0 0 0"))})
atomset = cryspy.utils.fill(atomset, [0.1, 0.1, 0.1])
assert len(atomset.menge) == 8
def read_atomset_from_cif(infilepathname):
# So far only for cif-files generated by JANA2006, and even this
# without any warranty, and maybe not all parameters.
infile = open(infilepathname, "r")
status = "waiting_for_loop"
loop_header = []
menge = set([])
for line in infile:
words = line.split()
if len(words) >= 1:
if status == "reading_loop_header":
if words[0][0] == "_":
loop_header += [words[0]]
else:
print(loop_header)
status = "reading_loop_data"
if status == "reading_loop_data":
if len(words) == len(loop_header):
atom_name = None
atom_type = None
x = None
y = None
z = None
for i in range(len(loop_header)):
if loop_header[i] == "_atom_site_label":
atom_name = words[i]
if loop_header[i] == "_atom_site_type_symbol":
atom_type = words[i]
if loop_header[i] == "_atom_site_fract_x":
x = fs(words[i])
if loop_header[i] == "_atom_site_fract_y":
y = fs(words[i])
if loop_header[i] == "_atom_site_fract_z":
z = fs(words[i])
if isinstance(atom_name, str) \
and isinstance(atom_type, str) \
and isinstance(x, cryspy.numbers.Mixed) \
and isinstance(y, cryspy.numbers.Mixed) \
and isinstance(z, cryspy.numbers.Mixed):
print(atom_name, atom_type, x, y, z)
menge.add(
cryspy.crystal.Atom(
atom_name, atom_type,
cryspy.geo.Pos(
cryspy.numbers.Matrix([[x], [y], [z], [1]])
)
)
)
if words[0] == "loop_":
loop_header = []
status = "reading_loop_header"
if len(words) == 0:
if status == "reading_loop_data":
status = "waiting_for_loop"
infile.close()
return cryspy.crystal.Atomset(menge)
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_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_Karussell():
metric = cryspy.geo.Cellparameters(1, 1, 1, 90, 90, 90).to_Metric()
k = cryspy.utils.Karussell(metric, fs("d 1 0 0"), fs("d 0 1 0"))
d1 = k.direction(0)
assert float(metric.length(d1 - fs("d 1.0 0.0 0"))) < 1e-9
d2 = k.direction(np.pi / 2)
assert float(metric.length(d2 - fs("d 0 1 0"))) < 1e-9
metric = cryspy.geo.Cellparameters(1, 1, 1, 90, 90, 45).to_Metric()
k = cryspy.utils.Karussell(metric, fs("d 1 0 0"), fs("d 0 1 0"))
d1 = k.direction(0)
assert float(metric.length(d1 - fs("d 1.0 0.0 0"))) < 1e-9
d2 = k.direction(np.pi / 4)
assert float(metric.length(d2 - fs("d 0 1 0"))) < 1e-9
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_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_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 read_metric_from_cif(infilepathname):
# So far only for cif-files generated by JANA2006, and even this
# without any warranty, and maybe not all parameters.
infile = open(infilepathname, "r")
for line in infile:
words = line.split()
if len(words) >= 2:
if words[0] == "_cell_length_a":
a = fs(words[1])
if words[0] == "_cell_length_b":
b = fs(words[1])
if words[0] == "_cell_length_c":
c = fs(words[1])
if words[0] == "_cell_angle_alpha":
alpha = fs(words[1])
if words[0] == "_cell_angle_beta" :
beta = fs(words[1])
if words[0] == "_cell_angle_gamma":
gamma = fs(words[1])
infile.close()
return cryspy.geo.Cellparameters(
a, b, c, alpha, beta, gamma
).to_Metric()
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
import sys
sys.path.append('../../src/')
import cryspy
from cryspy.fromstr import fromstr as fs
metric = cryspy.geo.Cellparameters(10.4416, 10.4416, 6.3432, 90, 90, 120).to_Metric()
atomset = cryspy.crystal.Atomset( { \
cryspy.crystal.Atom("Ca1", "Ca", fs("p 0 0 0 ")), \
cryspy.crystal.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")), \
cryspy.crystal.Atom("Mn2", "Mn", fs("p 1/2 0 1/2 ")), \
cryspy.crystal.Atom("Mn3", "Mn", fs("p 0 0 1/2 ")), \
cryspy.crystal.Atom("O1", "O", fs("p 0.2226 0.2731 0.0814 ")), \
cryspy.crystal.Atom("O2", "O", fs("p 0.34219 0.5221 0.3410 "))
} )
Rm3 = cryspy.tables.spacegroup(148)
atomset = Rm3 ** atomset
atomset1 = fs("x, y, z+1") ** atomset
atomset2 = fs("x, y+1, z ") ** atomset
atomset3 = fs("x, y+1, z+1") ** atomset
atomset4 = fs("x+1, y, z ") ** atomset
atomset5 = fs("x+1, y, z+1") ** atomset
atomset6 = fs("x+1, y+1, z ") ** atomset
atomset7 = fs("x+1, y+1, z+1") ** atomset
menge = set([])
for atom in atomset.menge:
menge = menge.union({atom})
def test_formfactor():
assert 72.633286681565636 == tb.formfactor('Au', fs('0.13445'))
def test_Subset():
a1 = cr.Atom("Fe1", "Fe", fs("p 0 0 0"))
a2 = cr.Atom("Fe2", "Fe", fs("p 0 0 1/4"))
subset = cr.Subset("Sub", fs("p 0 0 1/8"), {a1, a2})
subset1 = cr.Subset("Sub1", fs("p 0 0 1/8"), {a1, a2})
subset2 = cr.Subset("Sub", fs("p 0 0 0"), {a1, a2})
subset3 = cr.Subset("Sub", fs("p 0 0 1/8"), {a1})
assert subset == subset1
assert (subset == subset2) == False
assert (subset == subset3) == False
assert str(subset) == "Subset"
subset4 = cr.Subset("Sub", fs("p 7/8 0 1/8"),
{cr.Atom("Fe1", "Fe", fs("p 7/8 0 0")),
cr.Atom("Fe2", "Fe", fs("p 7/8 0 1/4"))})
assert fs("x+7/8, y, z") ** subset == subset4
assert fs("{x-1/8, y, z}") ** subset == subset4
subset5 = cr.Subset("Sub", fs("p 1/2 0 1/8"),
{cr.Atom("Fe1", "Fe", fs("p 1/2 0 0")),
cr.Atom("Fe2", "Fe", fs("p 1/2 0 1/4"))})
assert subset + fs("d 1/2 0 0") == subset5
def test_fromstr():
string = "1/2"
assert isinstance(fs(string), nb.Mixed)
assert fs(string) == nb.Mixed(fr.Fraction(1, 2))
string = "1.2+/-0.1"
assert fs(string).value.n == nb.Mixed(uc.ufloat(1.2, 0.1)).value.n
assert fs(string).value.s == nb.Mixed(uc.ufloat(1.2, 0.1)).value.s
string = "1.2(1)"
assert fs(string).value.n == nb.Mixed(uc.ufloat(1.2, 0.1)).value.n
assert fs(string).value.s == nb.Mixed(uc.ufloat(1.2, 0.1)).value.s
string = "4"
assert fs(string) == nb.Mixed(fr.Fraction(4, 1))
string = "4.5"
assert fs(string) == nb.Mixed(4.5)
string = "1 2 3"
assert fromstr.typefromstr(string) == nb.Matrix
assert fs(string) == nb.Matrix([[1, 2, 3]])
string = "/ 1 2 \ \n \ 3 4 /"
assert fs(string) == \
nb.Matrix([nb.Row([nb.Mixed(1), nb.Mixed(2)]),
nb.Row([nb.Mixed(3), nb.Mixed(4)])])
string = "1 2 \n 3 4"
assert fs(string) == \
nb.Matrix([nb.Row([nb.Mixed(1), nb.Mixed(2)]),
nb.Row([nb.Mixed(3), nb.Mixed(4)])])
string = "x+y,y - x +1/3,2z"
g = fs(string)
assert g == geo.Symmetry(
fs("/ 1 1 0 0 \n"
" -1 1 0 1/3 \n"
" 0 0 2 0 \n"
" 0 0 0 1"))
string = "O->(0,0,0)\n" \
"then\n" \
"a' = a-b \n" \
"b' = b+a \n" \
"c' = 2c"
g = fs(string)
assert g == geo.Transformation(
fs(" 1 1 0 0 \n"
"-1 1 0 0 \n"
" 0 0 2 0 \n"
" 0 0 0 1").inv())
string = "O->(0,0,0) \n" \
"then\n" \
"a' = c \n" \
"b' = a \n" \
"c' = b"
g = fs(string)
assert g == geo.Transformation(
fs("0 1 0 0 \n"
"0 0 1 0 \n"
"1 0 0 0 \n"
"0 0 0 1").inv())
string = "O -> (1/2, 0, 0) \n" \
"then\n" \
"a' = a \n" \
"b' = b \n" \
"c' = c"
g = fs(string)
assert g == geo.Transformation(
fs("1 0 0 -1/2 \n"
"0 1 0 0 \n"
"0 0 1 0 \n"
"0 0 0 1"))
string1 = "O -> (1/2, 0, 0) \n" \
"then\n" \
"a' = a \n" \
"b' = b \n" \
"c' = c"
string2 = "O -> (0,0,0) \n" \
"then\n" \
"a' = b\n" \
"b' = a\n" \
"c' = c"
string = "O -> (1/2, 0, 0) \n" \
"then\n"\
"a' = b\n"\
"b' = a\n"\
"c' = c"
g1 = fs(string1)
g2 = fs(string2)
g = fs(string)
assert g == g2 * g1
string = "O -> (1/2, 0, 0) \n" \
"then\n" \
"a' = a + b\n" \
"b' = b\n" \
"c' = c"
print("--------")
g = fs(string)
print(g.value)
assert g**fs("p 1/2 0 0") == fs("p 0 0 0")
assert g**fs("p 1/2 1/3 0") == fs("p 0 1/3 0")
assert g**fs("p 0 0 0") == fs("p -1/2 1/2 0")
assert g * g.inv() == geo.Transformation(nb.Matrix.onematrix(4))
string = "p0 0 0"
p = fs(string)
assert p == geo.Pos(fs("0 \n 0 \n 0 \n 1"))
string = "P0 0 0"
p = fs(string)
assert p == geo.Pos(fs("0 \n 0 \n 0 \n 1"))
string = "r0 0 0"
p = fs(string)
assert p == geo.Pos(fs("0 \n 0 \n 0 \n 1"))
string = "R0 0 0"
p = fs(string)
assert p == geo.Pos(fs("0 \n 0 \n 0 \n 1"))
string = p.__str__()
assert string == "Pos / 0 \ \n" \
" | 0 |\n" \
" \ 0 / "
p1 = fs(string)
assert p == p1
string = "R1/2 1/2 1/2"
p = fs(string)
assert p == geo.Pos(fs("1/2 \n 1/2 \n 1/2 \n 1"))
q = fs("k1 2 3")
assert q == geo.Rec(fs("1 2 3 0"))
q = fs("K 1 2 3")
assert q == geo.Rec(fs("1 2 3 0"))
q = fs("q 1/2 1/2 0")
assert q == geo.Rec(fs("1/2 1/2 0 0"))
q = fs("Q0 0 0")
assert q == geo.Rec(fs("0 0 0 0"))
q = fs("Rec < 1 2 3 > ")
assert q == geo.Rec(fs("1 2 3 0"))
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 fill(atomset, extraextensions):
assert isinstance(atomset, cryspy.crystal.Atomset), \
"First argument of cryspy.utils.fill(...) must be of " \
"type cryspy.crystal.Atomset."
assert isinstance(extraextensions, list), \
"Second argument of cryspy.utils.fill(...) must be of " \
"type list."
assert len(extraextensions) == 3, \
"Second argument of cryspy.utils.fill(...) must be a " \
"list of three numbers."
for item in extraextensions:
assert isinstance(item, cryspy.numbers.Mixed) \
or isinstance(item, float) or isinstance(item, int), \
"Scond argument of cryspy.utils.fill(...) must be a " \
"list of three numbers."
atomset_new = \
((atomset + "lbd") + fs("d -1 -1 -1")) \
+ ((atomset + "lb") + fs("d -1 -1 0")) \
+ ((atomset + "lbu") + fs("d -1 -1 +1")) \
+ ((atomset + "ld") + fs("d -1 0 -1")) \
+ ((atomset + "l") + fs("d -1 0 0")) \
+ ((atomset + "lu") + fs("d -1 0 +1")) \
+ ((atomset + "lfd") + fs("d -1 +1 -1")) \
+ ((atomset + "lf") + fs("d -1 +1 0")) \
+ ((atomset + "lfu") + fs("d -1 +1 +1")) \
+ ((atomset + "bd") + fs("d 0 -1 -1")) \
+ ((atomset + "b") + fs("d 0 -1 0")) \
+ ((atomset + "bu") + fs("d 0 -1 +1")) \
+ ((atomset + "d") + fs("d 0 0 -1")) \
+ ((atomset + "") + fs("d 0 0 0")) \
+ ((atomset + "u") + fs("d 0 0 +1")) \
+ ((atomset + "fd") + fs("d 0 +1 -1")) \
+ ((atomset + "f") + fs("d 0 +1 0")) \
+ ((atomset + "fu") + fs("d 0 +1 +1")) \
+ ((atomset + "rbd") + fs("d +1 -1 -1")) \
+ ((atomset + "rb") + fs("d +1 -1 0")) \
+ ((atomset + "rbu") + fs("d +1 -1 +1")) \
+ ((atomset + "rd") + fs("d +1 0 -1")) \
+ ((atomset + "r") + fs("d +1 0 0")) \
+ ((atomset + "ru") + fs("d +1 0 +1")) \
+ ((atomset + "rfd") + fs("d +1 +1 -1")) \
+ ((atomset + "rf") + fs("d +1 +1 0")) \
+ ((atomset + "rfu") + fs("d +1 +1 +1")) \
menge = atomset_new.menge
menge_new = set([])
extra_x = extraextensions[0]
extra_y = extraextensions[1]
extra_z = extraextensions[2]
for atom in menge:
if (0 - extra_x <= float(atom.pos.x()) <= 1 + extra_x) \
and (0 - extra_y <= float(atom.pos.y()) <= 1 + extra_y) \
and (0 - extra_z <= float(atom.pos.z()) <= 1 + extra_z):
menge_new.add(atom)
return cryspy.crystal.Atomset(menge_new)
import sys
sys.path.append('../../src/')
import cryspy
from cryspy.fromstr import fromstr as fs
metric = cryspy.geo.Cellparameters(10.4416, 10.4416, 6.3432, 90, 90, 120).to_Metric()
atomset = cryspy.crystal.Atomset( { \
cryspy.crystal.Atom("Ca1", "Ca", fs("p 0 0 0 ")), \
cryspy.crystal.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")), \
cryspy.crystal.Atom("Mn2", "Mn", fs("p 1/2 0 1/2 ")), \
cryspy.crystal.Atom("Mn3", "Mn", fs("p 0 0 1/2 ")), \
cryspy.crystal.Atom("O1", "O", fs("p 0.2226 0.2731 0.0814 ")), \
cryspy.crystal.Atom("O2", "O", fs("p 0.34219 0.5221 0.3410 "))
} )
Rm3 = cryspy.tables.spacegroup(148)
atomset = Rm3 ** atomset
atomset1 = fs("x, y, z+1") ** atomset
atomset2 = fs("x, y+1, z ") ** atomset
atomset3 = fs("x, y+1, z+1") ** atomset
atomset4 = fs("x+1, y, z ") ** atomset
atomset5 = fs("x+1, y, z+1") ** atomset
atomset6 = fs("x+1, y+1, z ") ** atomset
atomset7 = fs("x+1, y+1, z+1") ** atomset
menge = set([])
for atom in atomset.menge:
menge = menge.union({atom})
def make_blender_script(atomset, metric, structurename, outfilename):
assert isinstance(atomset, crystal.Atomset), \
"atomset must be of type crystal.Atomset."
assert isinstance(metric, geo.Metric), \
"metric must be of type geo.Metric."
assert isinstance(outfilename, str), \
"outfilename must be of type str."
outstr = "import bpy\n" \
"import bmesh\n" \
"\n"
# Delete the old structure, if exists:
outstr += "for ob in bpy.data.objects:\n"
outstr += " if ob.name.startswith('%s'):\n" % (structurename)
outstr += " ob.select = True\n"
outstr += "bpy.ops.object.delete()\n"
outstr += "for me in bpy.data.meshes:\n"
outstr += " if me.name.startswith('%s'):\n" % (structurename)
outstr += " bpy.data.meshes.remove(me)\n"
outstr += "for mat in bpy.data.materials:\n"
outstr += " if mat.name.startswith('%s'):\n" % (structurename)
outstr += " bpy.data.materials.remove(mat)\n"
# Delete all existing lamps:
outstr += "bpy.ops.object.select_all(action='DESELECT')\n"
outstr += "for object in bpy.data.objects:\n"
outstr += " if object.type == 'LAMP':\n"
outstr += " object.select = True\n"
outstr += "bpy.ops.object.delete()\n"
# Set background color:
outstr += "bpy.data.worlds['World'].horizon_color = %s\n" \
% (str(const.blender__background_color))
# Place some cool lamps:
outstr += "bpy.ops.object.lamp_add(type='POINT')\n"
outstr += "l = bpy.context.object\n"
outstr += "l.name = '%s.Lamp1'\n" % (structurename)
outstr += "l.location = %s\n" % (str(const.blender__location_of_lamp1))
outstr += "bpy.ops.object.lamp_add(type='HEMI')\n"
outstr += "l = bpy.context.object\n"
outstr += "l.name = '%s.LampHemi'\n" % (structurename)
outstr += "l.location = (-10, -10, 10)\n"
outstr += "l.data.energy = %10.4f\n" % (const.blender__diffuse_light)
# Plot the axes:
t = metric.schmidttransformation
pos = fs("p 1 0 0")
x = float((t**pos).x())
y = float((t**pos).y())
z = float((t**pos).z())
outstr += add_axis(structurename, 'XAxis', x, y, z)
pos = fs("p 0 1 0")
x = float((t**pos).x())
y = float((t**pos).y())
z = float((t**pos).z())
outstr += add_axis(structurename, 'YAxis', x, y, z)
pos = fs("p 0 0 1")
x = float((t**pos).x())
y = float((t**pos).y())
z = float((t**pos).z())
outstr += add_axis(structurename, 'ZAxis', x, y, z)
# Create empty mesh for the positions of the atoms
outstr += "bpy.ops.mesh.primitive_cube_add(location=(0,0,0))\n"
outstr += "bpy.ops.object.mode_set(mode='EDIT')\n"
outstr += "bpy.ops.mesh.delete(type='VERT')\n"
outstr += "bpy.ops.object.mode_set(mode='OBJECT')\n"
outstr += "posobject = bpy.context.object\n"
outstr += "posobject.name = '%s.Positions'\n" % (structurename)
# Inspect atomset for different kinds of object and sort them into different lists
typs = []
atomlist = []
momentumlist = []
bondlist = []
facelist = []
for item in atomset.menge:
if isinstance(item, crystal.Atom):
atomlist.append(item)
elif isinstance(item, crystal.Momentum):
momentumlist.append(item)
elif isinstance(item, crystal.Bond):
bondlist.append(item)
elif isinstance(item, crystal.Face):
facelist.append(item)
# Create a mesh for each atom-type, respectively
for atom in atomlist:
if atom.typ not in typs:
typs.append(atom.typ)
for typ in typs:
(spheresize, color) = tables.colorscheme_jmol(typ)
outstr += "bpy.ops.mesh.primitive_ico_sphere_add(location=(0,0,0), size=%f, subdivisions=%i)\n" \
% (spheresize, const.blender__atom_icosphere_subdivisions)
outstr += "ob = bpy.context.object\n"
outstr += "me = ob.data\n"
outstr += "me.name = '%s.mesh.%s'\n" % (structurename, typ)
outstr += "bpy.ops.object.delete()\n"
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n" \
% (structurename, typ)
outstr += "mat.diffuse_color = %s\n" % (color.__str__())
outstr += "me.materials.append(mat)\n"
# Create spheres for the atoms and add a vertex
# to the position-mesh, respectively
materialnumber = 0
atomnumber = 0
for atom in atomlist:
atomnumber += 1
materialnumber += 1
x = float((t**atom.pos).x())
y = float((t**atom.pos).y())
z = float((t**atom.pos).z())
outstr += "posobject.data.vertices.add(1)\n"
outstr += "posobject.data.vertices[-1].co = (%f, %f, %f)\n" % (x, y, z)
outstr += "ob = bpy.data.objects.new( \
'%s.Atom%03i(%s)', bpy.data.meshes['%s.mesh.%s'])\n" \
% (structurename, atomnumber, atom.name, structurename, atom.typ)
outstr += "ob.location = (%f, %f, %f)\n" % (x, y, z)
outstr += "bpy.ops.object.shade_smooth()\n"
outstr += "bpy.context.scene.objects.link(ob)\n"
# Create arrows for the momentums:
momentumindex = 0
for momentum in momentumlist:
momentumindex += 1
momentumname = "Momentum%03i" % (momentumindex)
if momentum.has_plotlength:
plotlength = momentum.plotlength
else:
plotlength = const.blender__std_momentum_plotlength
if momentum.has_color:
color = momentum.color
else:
color = const.blender__std_momentum_color
x0 = float((t**momentum.pos).x())
y0 = float((t**momentum.pos).y())
z0 = float((t**momentum.pos).z())
dx = float((t**momentum.direction).x())
dy = float((t**momentum.direction).y())
dz = float((t**momentum.direction).z())
length = np.sqrt(dx * dx + dy * dy + dz * dz)
x1 = x0 - dx * plotlength / length
y1 = y0 - dy * plotlength / length
z1 = z0 - dz * plotlength / length
x2 = x0 + dx * plotlength / length
y2 = y0 + dy * plotlength / length
z2 = z0 + dz * plotlength / length
outstr += add_momentum(structurename, momentumname, x1, y1, z1, x2, y2,
z2, color)
# Create Cylinders for the Bonds:
bondindex = 0
for bond in bondlist:
bondindex += 1
bondname = "Bond%03i" % (bondindex)
if bond.has_color:
color = bond.color
else:
color = const.blender__std_bond_color
if bond.has_thickness:
thickness = bond.thickness
else:
thickness = const.blender__std_bond_thickness
x1 = float((t**bond.start).x())
y1 = float((t**bond.start).y())
z1 = float((t**bond.start).z())
x2 = float((t**bond.target).x())
y2 = float((t**bond.target).y())
z2 = float((t**bond.target).z())
outstr += add_cylinder(structurename, bondname, x1, y1, z1, x2, y2, z2,
thickness,
const.blender__num_of_segments_of_bond)
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n"\
% (structurename, bondname)
outstr += "mat.diffuse_color = %s\n"\
% (str(color))
outstr += "mat.specular_color = (0, 0, 0)\n"
outstr += "ob1.data.materials.append(mat)\n"
# Create Faces:
faceindex = 0
for face in facelist:
faceindex += 1
facename = "Face%03i" % (faceindex)
if face.has_color:
color = face.color
else:
color = const.blender__std_face_color
verts = []
for corner in face.corners:
cartesian_corner = t**corner
x = float(cartesian_corner.x())
y = float(cartesian_corner.y())
z = float(cartesian_corner.z())
verts.append((x, y, z))
outstr += add_face(structurename, facename, verts)
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n" \
%(structurename, facename)
if face.has_opacity:
opacity = face.opacity
else:
opacity = const.blender__std_face_opacity
if opacity < 1:
outstr += "mat.use_transparency = True\n"
outstr += "mat.alpha = %10.4f\n" % (opacity)
outstr += "mat.diffuse_color = %s\n" % (str(color))
outstr += "mat.specular_color = (0, 0, 0)\n"
outstr += "ob1.data.materials.append(mat)\n"
# Make all atoms looking smooth:
outstr += "for ob in bpy.data.objects:\n"
outstr += " if ob.name.startswith('%s.Atom'):\n" % (structurename)
outstr += " ob.select = True\n"
outstr += " else:\n"
outstr += " ob.select = False\n"
outstr += "bpy.ops.object.shade_smooth()\n"
outfile = open(outfilename, "w")
outfile.write(outstr)
outfile.close()
def test_Momentum():
m = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
assert isinstance(m, cr.Momentum)
m.set_color((0, 0, 1))
m.set_color((fs("0.3"), 0.1, 1))
m.set_plotlength(1)
m.set_plotlength(0.5)
m.set_plotlength(fs("1/2"))
d = fs("d 0 0 1/2")
m1 = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
m2 = cr.Momentum("M", fs("p 1 2 3"), fs("d 0 0 1"))
m3 = cr.Momentum("M", fs("p 0 0 0"), fs("d 1 2 3"))
assert m == m1
assert hash(m) == hash(m1)
assert (m == m2) == False
assert (m == m3) == False
assert m + d == cr.Momentum("M", fs("p 0 0 1/2"), fs("d 0 0 1"))
assert fs("x+1/2,y,z") ** m == cr.Momentum("M", fs("p 1/2 0 0"), fs("d 0 0 1"))
assert fs("{x+3/2,y,z}") ** m == cr.Momentum("M", fs("p 1/2 0 0"), fs("d 0 0 1"))
m1 = cr.Momentum("M", fs("p 0 0 1/2"), fs("d 0 0 1"))
assert (m1 + "test").name == "Mtest"
def test_Bond():
b = cr.Bond("B", fs("p 0 0 0"), fs("p 0 0 1/2"))
assert isinstance(b, cr.Bond)
b.set_color((0, 0, 1))
b.set_color((fs("0.3"), 0.1, 1))
b.set_thickness(1)
assert b.thickness == 1
b.set_thickness(0.5)
assert b.thickness == 0.5
b.set_thickness(fs("1/2"))
assert b.thickness == fs("1/2")
d = fs("d 0 0 1/2")
b1 = cr.Bond("Bblabla", fs("p 0 0 0"), fs("p 0 0 1/2"))
b2 = cr.Bond("B", fs("p 1 2 3"), fs("p 0 0 1/2"))
b3 = cr.Bond("B", fs("p 0 0 0"), fs("p 1 2 3"))
b4 = cr.Bond("B", fs("p 0 0 1/2"), fs("p 0 0 0"))
assert hash(b) == hash(b4)
assert (b == b4) == False
assert b == b1
assert (b == b2) == False
assert (hash(b) == hash(b3)) == False
assert (b == b3) == False
assert b + d == cr.Bond("B", fs("p 0 0 1/2"), fs("p 0 0 1"))
assert fs("x+1/2,y,z") ** b == cr.Bond("B", fs("p 1/2 0 0"), fs("p 1/2 0 1/2"))
assert fs("{x+3/2,y,z}") ** b == cr.Bond("B", fs("p 1/2 0 0"), fs("p 1/2 0 1/2"))
b = cr.Bond("B", fs("p 0 0 0"), fs("p 0 0 1/2"))
assert (b + "test").name == "Btest"
def test_Face():
f = cr.Face("F", [fs("p 0 0 0"), fs("p 1 0 0"), fs("p 0 1 0")])
assert isinstance(f, cr.Face)
f.set_color((0, 0, 1))
f.set_color((fs("0.3"), 0.1, 1))
d = fs("d 0 0 1/2")
f1 = cr.Face("F", [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 == 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"
def make_blender_script(atomset, metric, structurename, outfilename):
assert isinstance(atomset, crystal.Atomset), \
"atomset must be of type crystal.Atomset."
assert isinstance(metric, geo.Metric), \
"metric must be of type geo.Metric."
assert isinstance(outfilename, str), \
"outfilename must be of type str."
outstr = "import bpy\n" \
"import bmesh\n" \
"\n"
atomset = atomset.unpack_subsets()
# Delete the old structure, if exists:
outstr += "for ob in bpy.data.objects:\n"
outstr += " if ob.name.startswith('%s'):\n" % (structurename)
outstr += " ob.select = True\n"
outstr += "bpy.ops.object.delete()\n"
outstr += "for me in bpy.data.meshes:\n"
outstr += " if me.name.startswith('%s'):\n" % (structurename)
outstr += " bpy.data.meshes.remove(me)\n"
outstr += "for mat in bpy.data.materials:\n"
outstr += " if mat.name.startswith('%s'):\n" % (structurename)
outstr += " bpy.data.materials.remove(mat)\n"
# Delete all existing lamps:
outstr += "bpy.ops.object.select_all(action='DESELECT')\n"
outstr += "for object in bpy.data.objects:\n"
outstr += " if object.type == 'LAMP':\n"
outstr += " object.select = True\n"
outstr += "bpy.ops.object.delete()\n"
# Set background color:
outstr += "bpy.data.worlds['World'].horizon_color = %s\n" \
% (str(const.blender__background_color))
# Place some cool lamps:
outstr += "bpy.ops.object.lamp_add(type='POINT')\n"
outstr += "l = bpy.context.object\n"
outstr += "l.name = '%s.Lamp1'\n" % (structurename)
outstr += "l.location = %s\n" % (str(const.blender__location_of_lamp1))
outstr += "bpy.ops.object.lamp_add(type='HEMI')\n"
outstr += "l = bpy.context.object\n"
outstr += "l.name = '%s.LampHemi'\n" % (structurename)
outstr += "l.location = (-10, -10, 10)\n"
outstr += "l.data.energy = %10.4f\n" % (const.blender__diffuse_light)
# Plot the axes:
t = metric.schmidttransformation
pos = fs("p 1 0 0")
x = float((t ** pos).x())
y = float((t ** pos).y())
z = float((t ** pos).z())
outstr += add_axis(structurename, 'XAxis', x, y, z)
pos = fs("p 0 1 0")
x = float((t ** pos).x())
y = float((t ** pos).y())
z = float((t ** pos).z())
outstr += add_axis(structurename, 'YAxis', x, y, z)
pos = fs("p 0 0 1")
x = float((t ** pos).x())
y = float((t ** pos).y())
z = float((t ** pos).z())
outstr += add_axis(structurename, 'ZAxis', x, y, z)
# Create empty mesh for the positions of the atoms
outstr += "bpy.ops.mesh.primitive_cube_add(location=(0,0,0))\n"
outstr += "bpy.ops.object.mode_set(mode='EDIT')\n"
outstr += "bpy.ops.mesh.delete(type='VERT')\n"
outstr += "bpy.ops.object.mode_set(mode='OBJECT')\n"
outstr += "posobject = bpy.context.object\n"
outstr += "posobject.name = '%s.Positions'\n" % (structurename)
# Inspect atomset for different kinds of object and sort them into different lists
typs = []
atomlist = []
momentumlist = []
bondlist = []
facelist = []
for item in atomset.menge:
if isinstance(item, crystal.Atom):
atomlist.append(item)
elif isinstance(item, crystal.Momentum):
momentumlist.append(item)
elif isinstance(item, crystal.Bond):
bondlist.append(item)
elif isinstance(item, crystal.Face):
facelist.append(item)
# Create a mesh for each atom-type, respectively
for atom in atomlist:
if atom.typ not in typs:
typs.append(atom.typ)
for typ in typs:
(spheresize, color) = tables.colorscheme_jmol(typ)
outstr += "bpy.ops.mesh.primitive_ico_sphere_add(location=(0,0,0), size=%f, subdivisions=%i)\n" \
% (spheresize, const.blender__atom_icosphere_subdivisions)
outstr += "ob = bpy.context.object\n"
outstr += "me = ob.data\n"
outstr += "me.name = '%s.mesh.%s'\n" % (structurename, typ)
outstr += "bpy.ops.object.delete()\n"
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n" \
% (structurename, typ)
outstr += "mat.diffuse_color = %s\n" % (color.__str__())
outstr += "me.materials.append(mat)\n"
# Create spheres for the atoms and add a vertex
# to the position-mesh, respectively
materialnumber = 0
atomnumber = 0
for atom in atomlist:
atomnumber += 1
materialnumber += 1
x = float((t ** atom.pos).x())
y = float((t ** atom.pos).y())
z = float((t ** atom.pos).z())
outstr += "posobject.data.vertices.add(1)\n"
outstr += "posobject.data.vertices[-1].co = (%f, %f, %f)\n" % (x, y, z)
outstr += "ob = bpy.data.objects.new( \
'%s.Atom%03i(%s)', bpy.data.meshes['%s.mesh.%s'])\n" \
% (structurename, atomnumber, atom.name, structurename, atom.typ)
outstr += "ob.location = (%f, %f, %f)\n" % (x, y, z)
outstr += "bpy.ops.object.shade_smooth()\n"
outstr += "bpy.context.scene.objects.link(ob)\n"
# Create arrows for the momentums:
momentumindex = 0
for momentum in momentumlist:
momentumindex += 1
momentumname = "Momentum%03i" % (momentumindex)
if momentum.has_plotlength:
plotlength = momentum.plotlength
else:
plotlength = const.blender__std_momentum_plotlength
if momentum.has_color:
color = momentum.color
else:
color = const.blender__std_momentum_color
x0 = float((t ** momentum.pos).x())
y0 = float((t ** momentum.pos).y())
z0 = float((t ** momentum.pos).z())
dx = float((t ** momentum.direction).x())
dy = float((t ** momentum.direction).y())
dz = float((t ** momentum.direction).z())
length = np.sqrt(dx * dx + dy * dy + dz * dz)
x1 = x0 - dx * plotlength / length
y1 = y0 - dy * plotlength / length
z1 = z0 - dz * plotlength / length
x2 = x0 + dx * plotlength / length
y2 = y0 + dy * plotlength / length
z2 = z0 + dz * plotlength / length
outstr += add_momentum(structurename, momentumname,
x1, y1, z1, x2, y2, z2, color)
# Create Cylinders for the Bonds:
bondindex = 0
for bond in bondlist:
bondindex += 1
bondname = "Bond%03i" % (bondindex)
if bond.has_color:
color = bond.color
else:
color = const.blender__std_bond_color
if bond.has_thickness:
thickness = bond.thickness
else:
thickness = const.blender__std_bond_thickness
x1 = float((t ** bond.start).x())
y1 = float((t ** bond.start).y())
z1 = float((t ** bond.start).z())
x2 = float((t ** bond.target).x())
y2 = float((t ** bond.target).y())
z2 = float((t ** bond.target).z())
outstr += add_cylinder(structurename, bondname,
x1, y1, z1, x2, y2, z2,
thickness, const.blender__num_of_segments_of_bond)
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n"\
% (structurename, bondname)
outstr += "mat.diffuse_color = %s\n"\
% (str(color))
outstr += "mat.specular_color = (0, 0, 0)\n"
outstr += "ob1.data.materials.append(mat)\n"
# Create Faces:
faceindex = 0
for face in facelist:
faceindex += 1
facename = "Face%03i" % (faceindex)
if face.has_color:
color = face.color
else:
color = const.blender__std_face_color
verts = []
for corner in face.corners:
cartesian_corner = t**corner
x = float(cartesian_corner.x())
y = float(cartesian_corner.y())
z = float(cartesian_corner.z())
verts.append((x, y, z))
outstr += add_face(structurename, facename, verts)
outstr += "mat = bpy.data.materials.new('%s.material.%s')\n" \
%(structurename, facename)
if face.has_opacity:
opacity = face.opacity
else:
opacity = const.blender__std_face_opacity
if opacity < 1:
outstr += "mat.use_transparency = True\n"
outstr += "mat.alpha = %10.4f\n"%(opacity)
outstr += "mat.diffuse_color = %s\n" % (str(color))
outstr += "mat.specular_color = (0, 0, 0)\n"
outstr += "ob1.data.materials.append(mat)\n"
# Make all atoms looking smooth:
outstr += "for ob in bpy.data.objects:\n"
outstr += " if ob.name.startswith('%s.Atom'):\n" % (structurename)
outstr += " ob.select = True\n"
outstr += " else:\n"
outstr += " ob.select = False\n"
outstr += "bpy.ops.object.shade_smooth()\n"
outfile = open(outfilename, "w")
outfile.write(outstr)
outfile.close()
def test_Metric():
M = nb.Matrix([[1, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])
metric = geo.Metric(M)
t = metric.schmidttransformation
assert t ** geo.canonical_e0 == geo.Dif(nb.Matrix([[1], [0], [0], [0]]))
assert t ** geo.canonical_e1 == geo.Dif(nb.Matrix([[0], [1], [0], [0]]))
assert t ** geo.canonical_e2 == geo.Dif(nb.Matrix([[0], [0], [1], [0]]))
metric = geo.Cellparameters(1, 1, 1, 90, 90, 45).to_Metric()
t = metric.schmidttransformation
assert t ** geo.canonical_e0 == geo.Dif(nb.Matrix([[1], [0], [0], [0]]))
e1 = t ** geo.canonical_e1
assert abs(e1.x() - 0.70710678).value < 0.000001
assert abs(e1.y() - 0.70710678).value < 0.000001
assert abs(e1.z() - 0).value < 0.000001
e2 = t ** geo.canonical_e2
assert abs(e2.x() - 0).value < 0.000001
assert abs(e2.y() - 0).value < 0.000001
assert abs(e2.z() - 1).value < 0.000001
t = metric.schmidttransformation.inv()
M = nb.Matrix([[9, 0, 0, 0],
[0, 4, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])
metric = geo.Metric(M)
assert metric.__str__() == "Metric / 9 0 0 0 \ \n" \
" | 0 4 0 0 |\n" \
" | 0 0 1 0 |\n" \
" \ 0 0 0 1 / "
o = geo.Pos(nb.Matrix([[0], [0], [0], [1]]))
p1 = geo.Pos(nb.Matrix([[1], [0], [0], [1]]))
p2 = geo.Pos(nb.Matrix([[0], [1], [0], [1]]))
q1 = geo.Rec(nb.Matrix([[1, 0, 0, 0]]))
q2 = geo.Rec(nb.Matrix([[0, 1, 0, 0]]))
q3 = geo.Rec(nb.Matrix([[1, 1, 0, 0]]))
assert metric.dot(p1 - o, p1 - o).__str__() == "9"
assert metric.dot(p1 - o, p2 - o).__str__() == "0"
assert metric.dot(q1, q1).__str__() == "1/9"
assert metric.dot(q2, q2).__str__() == "1/4"
assert metric.dot(q3, q3).__str__() == "13/36"
assert metric.length(p1 - o) == 3
assert np.abs(float(metric.angle(p1 - o, p2 - o)) - 1.5707963) < 0.0001
assert metric.dangle(p1 - o, p2 - o) == 90
assert metric.length(q1).__str__() == "1/3"
assert np.abs(float(metric.angle(q1, q2)) - 1.5707963) < 0.0001
assert metric.dangle(q1, q2) == 90
assert metric.angle(p1 - o, p1 - o).__str__() == "0.0"
assert metric.dangle(p1 - o, p1 - o).__str__() == "0"
assert metric.angle(q1, q1).__str__() == "0.0"
assert metric.dangle(q1, q1).__str__() == "0"
metric = geo.Cellparameters(4.15, 4.15, 28.64, 90, 90, 120).to_Metric()
M = nb.Matrix([[9, 0, 0, 0],
[0, 4, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])
metric = geo.Metric(M)
cell = metric.to_Cellparameters()
assert cell.__str__() == \
geo.Cellparameters(3, 2, 1, 90, 90, 90).__str__()
t = geo.Transformation(nb.Matrix([[0, 1, 0, 0],
[1, 0, 0, 0],
[0, 0, 1, 0.5],
[0, 0, 0, 1]]))
assert t ** metric == geo.Metric(nb.Matrix([[4, 0, 0, 0],
[0, 9, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]]))
metric = geo.Cellparameters(fs("8.534(5)"), fs("8.556(5)"), fs("7.015(5)"),
fs("101.53(8)"), fs("114.97(8)"),
fs("103.38(8)")).to_Metric()
assert np.abs(metric.cellvolume().value.n - 425.24239) < 0.0001
metric = geo.Cellparameters(fs("1.0(1)"), 1, 1, 90, 90, 90).to_Metric()
print(metric.cellvolume())
assert np.abs(metric.cellvolume().value.n - 1) < 0.00000001
assert np.abs(metric.cellvolume().value.s - 0.1) < 0.00000001
a = fs("1.0(1)")
metric = geo.Cellparameters(a, a, a, 90, 90, 90).to_Metric()
m00 = metric.value.liste[0].liste[0]
m11 = metric.value.liste[1].liste[1]
assert (m00 - m11).value.n == 0.0
assert (m00 - m11).value.s == 0.0
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_Atom():
atom1 = cr.Atom("Cs1", "Cs", fs("p 0 0 0"))
assert atom1.has_color == False
assert atom1.__str__() == \
"Atom Cs1 Cs Pos / 0 \ \n" \
" | 0 |\n" \
" \ 0 / "
assert (atom1 + "hallo").name == atom1.name + "hallo"
atom2 = cr.Atom("Cs2", "Cs", fs("p 0 0 0"))
assert atom2 == atom1
assert {atom2} == {atom1}
atom3 = cr.Atom("Cs3", "Cs", fs("p0.1 0 0"))
assert atom3 != atom1
atom4 = cr.Atom("Cs1", "Fe", fs("p 0 0 0"))
assert atom4 != atom1
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 1/2 1/2"))
transformation = fs("O->(0,0,0) \n"
"then\n"
"a' = a \n"
"b' = 2b \n"
"c' = c")
atom_trans = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 1/2"))
assert (transformation**atom).__str__() == atom_trans.__str__()
sym = fs("-x+1/2,-y+1/2, z")
atom_sym = cr.Atom("Cl1", "Cl", fs("p0 0 1/2"))
assert (sym**atom).__str__() == atom_sym.__str__()
coset = fs("{x, -y, z+1}")
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 1/2"))
atom1 = coset**atom
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 3/4 1/2"))
assert atom1.__str__() == atom2.__str__()
transgen = geo.Transgen(fs("d 1 0 0"), fs("d 0 1 0"), fs("d 0 0 2"))
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 5/4 -1/2"))
atom1 = atom % transgen
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 3/2"))
assert atom1 == atom2
d = fs("d 1/2 0 0")
atom1 = cr.Atom("Cl1", "Cl", fs("p 0 0 0"))
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 0 0"))
atom3 = atom1 + d
assert atom2 == atom3
import cryspy
from cryspy.fromstr import fromstr as fs
# Nach [Alonso2000a table 2]
metric = cryspy.geo.Cellparameters(fs("5.29314(5)"), fs("5.8384(1)"), fs("7.4025(1)"), 90, 90, 90).to_Metric()
atomset = cryspy.crystal.Atomset({
cryspy.crystal.Atom("Tb1", "Tb", fs("p 0.9831(4) 0.0824(3) 1/4 ")),
cryspy.crystal.Atom("Mn1", "Mn", fs("p 1/2 0 0 ")),
cryspy.crystal.Atom("O1", "O", fs("p 0.1038(5) 0.4667(4) 1/4 ")),
cryspy.crystal.Atom("O2", "O", fs("p 0.7039(4) 0.3262(3) 0.0510(2)"))
})
# Raumgruppe Pbnm (durch Transformation aus Pnma):
sg = fs("a' = c\n"
"b' = a\n"
"c' = b") \
** \
cryspy.tables.spacegroup(62)
atomset = sg ** atomset
atomset = cryspy.utils.fill(atomset, [0.5, 0.05, 0.05])
"""
face1 = cryspy.crystal.Face("Face1", [atomset.get_atom("O2_6").pos, atomset.get_atom("O2_3").pos, atomset.get_atom("O1_2").pos])
face2 = cryspy.crystal.Face("Face2", [atomset.get_atom("O2_2r").pos, atomset.get_atom("O2_3").pos, atomset.get_atom("O1_2").pos])
face3 = cryspy.crystal.Face("Face3", [atomset.get_atom("O2_2r").pos, atomset.get_atom("O2_7r").pos, atomset.get_atom("O1_2").pos])
face4 = cryspy.crystal.Face("Face4", [atomset.get_atom("O2_6").pos, atomset.get_atom("O2_7r").pos, atomset.get_atom("O1_2").pos])
def fill(atomset, extraextensions):
assert isinstance(atomset, cryspy.crystal.Atomset), \
"First argument of cryspy.utils.fill(...) must be of " \
"type cryspy.crystal.Atomset."
assert isinstance(extraextensions, list), \
"Second argument of cryspy.utils.fill(...) must be of " \
"type list."
assert len(extraextensions) == 3, \
"Second argument of cryspy.utils.fill(...) must be a " \
"list of three numbers."
for item in extraextensions:
assert isinstance(item, cryspy.numbers.Mixed) \
or isinstance(item, float) or isinstance(item, int), \
"Scond argument of cryspy.utils.fill(...) must be a " \
"list of three numbers."
atomset_new = \
((atomset + "lbd") + fs("d -1 -1 -1")) \
+ ((atomset + "lb") + fs("d -1 -1 0")) \
+ ((atomset + "lbu") + fs("d -1 -1 +1")) \
+ ((atomset + "ld") + fs("d -1 0 -1")) \
+ ((atomset + "l") + fs("d -1 0 0")) \
+ ((atomset + "lu") + fs("d -1 0 +1")) \
+ ((atomset + "lfd") + fs("d -1 +1 -1")) \
+ ((atomset + "lf") + fs("d -1 +1 0")) \
+ ((atomset + "lfu") + fs("d -1 +1 +1")) \
+ ((atomset + "bd") + fs("d 0 -1 -1")) \
+ ((atomset + "b") + fs("d 0 -1 0")) \
+ ((atomset + "bu") + fs("d 0 -1 +1")) \
+ ((atomset + "d") + fs("d 0 0 -1")) \
+ ((atomset + "") + fs("d 0 0 0")) \
+ ((atomset + "u") + fs("d 0 0 +1")) \
+ ((atomset + "fd") + fs("d 0 +1 -1")) \
+ ((atomset + "f") + fs("d 0 +1 0")) \
+ ((atomset + "fu") + fs("d 0 +1 +1")) \
+ ((atomset + "rbd") + fs("d +1 -1 -1")) \
+ ((atomset + "rb") + fs("d +1 -1 0")) \
+ ((atomset + "rbu") + fs("d +1 -1 +1")) \
+ ((atomset + "rd") + fs("d +1 0 -1")) \
+ ((atomset + "r") + fs("d +1 0 0")) \
+ ((atomset + "ru") + fs("d +1 0 +1")) \
+ ((atomset + "rfd") + fs("d +1 +1 -1")) \
+ ((atomset + "rf") + fs("d +1 +1 0")) \
+ ((atomset + "rfu") + fs("d +1 +1 +1")) \
menge = atomset_new.menge
menge_new = set([])
extra_x = extraextensions[0]
extra_y = extraextensions[1]
extra_z = extraextensions[2]
for atom in menge:
if (0 - extra_x <= float(atom.pos.x()) <= 1 + extra_x) \
and (0 - extra_y <= float(atom.pos.y()) <= 1 + extra_y) \
and (0 - extra_z <= float(atom.pos.z()) <= 1 + extra_z):
menge_new.add(atom)
return cryspy.crystal.Atomset(menge_new)
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_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_Momentum():
m = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
assert isinstance(m, cr.Momentum)
m.set_color((0, 0, 1))
m.set_color((fs("0.3"), 0.1, 1))
m.set_plotlength(1)
m.set_plotlength(0.5)
m.set_plotlength(fs("1/2"))
d = fs("d 0 0 1/2")
m1 = cr.Momentum("M", fs("p 0 0 0"), fs("d 0 0 1"))
m2 = cr.Momentum("M", fs("p 1 2 3"), fs("d 0 0 1"))
m3 = cr.Momentum("M", fs("p 0 0 0"), fs("d 1 2 3"))
assert m == m1
assert (m == m2) == False
assert (m == m3) == False
assert m + d == cr.Momentum("M", fs("p 0 0 1/2"), fs("d 0 0 1"))
assert fs("x+1/2,y,z")**m == cr.Momentum("M", fs("p 1/2 0 0"),
fs("d 0 0 1"))
assert fs("{x+3/2,y,z}")**m == cr.Momentum("M", fs("p 1/2 0 0"),
fs("d 0 0 1"))
m1 = cr.Momentum("M", fs("p 0 0 1/2"), fs("d 0 0 1"))
assert (m1 + "test").name == "Mtest"
def test_formfactor():
assert 72.633286681565636 == tb.formfactor('Au', fs('0.13445'))
def test_Bond():
b = cr.Bond("B", fs("p 0 0 0"), fs("p 0 0 1/2"))
assert isinstance(b, cr.Bond)
b.set_color((0, 0, 1))
b.set_color((fs("0.3"), 0.1, 1))
b.set_thickness(1)
b.set_thickness(0.5)
b.set_thickness(fs("1/2"))
d = fs("d 0 0 1/2")
b1 = cr.Bond("B", fs("p 0 0 0"), fs("p 0 0 1/2"))
b2 = cr.Bond("B", fs("p 1 2 3"), fs("p 0 0 1/2"))
b3 = cr.Bond("B", fs("p 0 0 0"), fs("p 1 2 3"))
assert b == b1
assert (b == b2) == False
assert (b == b3) == False
assert b + d == cr.Bond("B", fs("p 0 0 1/2"), fs("p 0 0 1"))
assert fs("x+1/2,y,z")**b == cr.Bond("B", fs("p 1/2 0 0"),
fs("p 1/2 0 1/2"))
assert fs("{x+3/2,y,z}")**b == cr.Bond("B", fs("p 1/2 0 0"),
fs("p 1/2 0 1/2"))
b = cr.Bond("B", fs("p 0 0 0"), fs("p 0 0 1/2"))
assert (b + "test").name == "Btest"
def spacegroup(number):
if number == 10:
return geo.Spacegroup(
geo.canonical,
[fs("{x,y,z}"),
fs("{-x,y,-z}"),
fs("{-x,-y,-z}"),
fs("{x,-y,z}")])
if number == 13:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,y,-z+1/2}"),
fs("{-x,-y,-z}"),
fs("{x,-y,z+1/2}")
])
if number == 15:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,y,-z+1/2}"),
fs("{-x,-y,-z}"),
fs("{x,-y,z+1/2}"),
fs("{x+1/2,y+1/2,z}"),
fs("{-x+1/2,y+1/2,-z+1/2}"),
fs("{-x+1/2,-y+1/2,-z}"),
fs("{x+1/2,-y+1/2,z+1/2}")
])
if number == 33:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,-y,z+1/2}"),
fs("{x+1/2,-y+1/2,z}"),
fs("{-x+1/2,y+1/2,z+1/2}")
])
if number == 46:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,-y,z}"),
fs("{x+1/2,-y,z}"),
fs("{-x+1/2,y,z}"),
fs("{x+1/2,y+1/2,z+1/2}"),
fs("{-x+1/2,-y+1/2,z+1/2}"),
fs("{x,-y+1/2,z+1/2}"),
fs("{-x,y+1/2,z+1/2}")
])
if number == 62:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x+1/2,-y,z+1/2}"),
fs("{-x,y+1/2,-z}"),
fs("{x+1/2,-y+1/2,-z+1/2}"),
fs("{-x,-y,-z}"),
fs("{x+1/2,y,-z+1/2}"),
fs("{x,-y+1/2,z}"),
fs("{-x+1/2,y+1/2,z+1/2}")
])
if number == 63:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,-y,z+1/2}"),
fs("{-x,y,-z+1/2}"),
fs("{x,-y,-z}"),
fs("{-x,-y,-z}"),
fs("{x,y,-z+1/2}"),
fs("{x,-y,z+1/2}"),
fs("{-x,y,z}"),
fs("{x+1/2,y+1/2,z}"),
fs("{-x+1/2,-y+1/2,z+1/2}"),
fs("{-x+1/2,y+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,-z}"),
fs("{-x+1/2,-y+1/2,-z}"),
fs("{x+1/2,y+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,z+1/2}"),
fs("{-x+1/2,y+1/2,z}")
])
if number == 64:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x,-y+1/2,z+1/2}"),
fs("{-x,y+1/2,-z+1/2}"),
fs("{x,-y,-z}"),
fs("{-x,-y,-z}"),
fs("{x,y+1/2,-z+1/2}"),
fs("{x,-y+1/2,z+1/2}"),
fs("{-x,y,z}"),
fs("{x+1/2,y+1/2,z}"),
fs("{-x+1/2,-y,z+1/2}"),
fs("{-x+1/2,y,-z+1/2}"),
fs("{x+1/2,-y+1/2,-z}"),
fs("{-x+1/2,-y+1/2,-z}"),
fs("{x+1/2,y,-z+1/2}"),
fs("{x+1/2,-y,z+1/2}"),
fs("{-x+1/2,y+1/2,z}")
])
if number == 73:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x+1/2,-y,z+1/2}"),
fs("{-x,y+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,-z}"),
fs("{-x,-y,-z}"),
fs("{x+1/2,y,-z+1/2}"),
fs("{x,-y+1/2,z+1/2}"),
fs("{-x+1/2,y+1/2,z}"),
fs("{x+1/2,y+1/2,z+1/2}"),
fs("{-x,-y+1/2,z}"),
fs("{-x+1/2,y,-z}"),
fs("{x,-y,-z+1/2}"),
fs("{-x+1/2,-y+1/2,-z+1/2}"),
fs("{x,y+1/2,-z}"),
fs("{x+1/2,-y,z}"),
fs("{-x,y,z+1/2}")
])
if number == 142:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x+1/2,-y+1/2,z+1/2}"),
fs("{-y,x+1/2,z+1/4}"),
fs("{y+1/2,-x,z+3/4}"),
fs("{-x+1/2,y,-z+1/4}"),
fs("{x,-y+1/2,-z+3/4}"),
fs("{y+1/2,x+1/2,-z}"),
fs("{-y,-x,-z+1/2}"),
fs("{-x,-y+1/2,-z+1/4}"),
fs("{x+1/2,y,-z+3/4}"),
fs("{y,-x,-z}"),
fs("{-y+1/2,x+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,z}"),
fs("{-x,y,z+1/2}"),
fs("{-y+1/2,-x,z+1/4}"),
fs("{y,x+1/2,z+3/4}"),
fs("{x+1/2,y+1/2,z+1/2}"),
fs("{-x,-y,z}"),
fs("{-y+1/2,x,z+3/4}"),
fs("{y,-x+1/2,z+1/4}"),
fs("{-x,y+1/2,-z+3/4}"),
fs("{x+1/2,-y,-z+1/4}"),
fs("{y,x,-z+1/2}"),
fs("{-y+1/2,-x+1/2,-z}"),
fs("{-x+1/2,-y,-z+3/4}"),
fs("{x,y+1/2,-z+1/4}"),
fs("{y+1/2,-x+1/2,-z+1/2}"),
fs("{-y,x,-z}"),
fs("{x,-y,z+1/2}"),
fs("{-x+1/2,y+1/2,z}"),
fs("{-y,-x+1/2,z+3/4}"),
fs("{y+1/2,x,z+1/4}")
])
if number == 148:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-y,x-y,z}"),
fs("{-x+y,-x,z}"),
fs("{-x,-y,-z}"),
fs("{y,-x+y,-z}"),
fs("{x-y,x,-z}"),
fs("{x+2/3,y+1/3,z+1/3}"),
fs("{-y+2/3,x-y+1/3,z+1/3}"),
fs("{-x+y+2/3,-x+1/3,z+1/3}"),
fs("{-x+2/3,-y+1/3,-z+1/3}"),
fs("{y+2/3,-x+y+1/3,-z+1/3}"),
fs("{x-y+2/3,x+1/3,-z+1/3}"),
fs("{x+1/3,y+2/3,z+2/3}"),
fs("{-y+1/3,x-y+2/3,z+2/3}"),
fs("{-x+y+1/3,-x+2/3,z+2/3}"),
fs("{-x+1/3,-y+2/3,-z+2/3}"),
fs("{y+1/3,-x+y+2/3,-z+2/3}"),
fs("{x-y+1/3,x+2/3,-z+2/3}")
])
if number == 166:
return geo.Spacegroup(geo.canonical, [
fs("{x ,y ,z }"),
fs("{-y , x-y, z}"),
fs("{-x+y,-x ,z }"),
fs("{y ,x ,-z}"),
fs("{x-y ,-y ,-z}"),
fs("{-x ,-x+y,-z}"),
fs("{-x,-y,-z}"),
fs("{y ,-x+y,-z}"),
fs("{x-y ,x ,-z}"),
fs("{-y,-x,z }"),
fs("{-x+y,y ,z }"),
fs("{x ,x-y ,z }"),
fs("{x +2/3,y +1/3,z +1/3}"),
fs("{-y +2/3, x-y +1/3, z +1/3}"),
fs("{-x+y +2/3,-x +1/3,z +1/3}"),
fs("{y +2/3,x +1/3,-z +1/3}"),
fs("{x-y +2/3,-y +1/3,-z +1/3}"),
fs("{-x +2/3,-x+y +1/3,-z +1/3}"),
fs("{-x +2/3,-y +1/3,-z +1/3}"),
fs("{y +2/3,-x+y +1/3,-z +1/3}"),
fs("{x-y +2/3,x +1/3,-z +1/3}"),
fs("{-y +2/3,-x +1/3,z +1/3}"),
fs("{-x+y +2/3,y +1/3,z +1/3}"),
fs("{x +2/3,x-y +1/3,z +1/3}"),
fs("{x +1/3,y +2/3,z +2/3}"),
fs("{-y +1/3, x-y +2/3, z +2/3}"),
fs("{-x+y +1/3,-x +2/3,z +2/3}"),
fs("{y +1/3,x +2/3,-z +2/3}"),
fs("{x-y +1/3,-y +2/3,-z +2/3}"),
fs("{-x +1/3,-x+y +2/3,-z +2/3}"),
fs("{-x +1/3,-y +2/3,-z +2/3}"),
fs("{y +1/3,-x+y +2/3,-z +2/3}"),
fs("{x-y +1/3,x +2/3,-z +2/3}"),
fs("{-y +1/3,-x +2/3,z +2/3}"),
fs("{-x+y +1/3,y +2/3,z +2/3}"),
fs("{x +1/3,x-y +2/3,z +2/3}")
])
if number == 186:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-y,x-y,z}"),
fs("{-x+y,-x,z}"),
fs("{-x,-y,z+1/2}"),
fs("{y,-x+y,z+1/2}"),
fs("{x-y,x,z+1/2}"),
fs("{-y,-x,z}"),
fs("{-x+y,y,z}"),
fs("{x,x-y,z}"),
fs("{y,x,z+1/2}"),
fs("{x-y,-y,z+1/2}"),
fs("{-x,-x+y,z+1/2}")
])
if number == 194:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-y,x-y,z}"),
fs("{-x+y,-x,z}"),
fs("{-x,-y,z+1/2}"),
fs("{y,-x+y,z+1/2}"),
fs("{x-y,x,z+1/2}"),
fs("{y,x,-z}"),
fs("{x-y,-y,-z}"),
fs("{-x,-x+y,-z}"),
fs("{-y,-x,-z+1/2}"),
fs("{-x+y,y,-z+1/2}"),
fs("{x,x-y,-z+1/2}"),
fs("{-x,-y,-z}"),
fs("{y,-x+y,-z}"),
fs("{x-y,x,-z}"),
fs("{x,y,-z+1/2}"),
fs("{-y,x-y,-z+1/2}"),
fs("{-x+y,-x,-z+1/2}"),
fs("{-y,-x,z}"),
fs("{-x+y,y,z}"),
fs("{x,x-y,z}"),
fs("{y,x,z+1/2}"),
fs("{x-y,-y,z+1/2}"),
fs("{-x,-x+y,z+1/2}")
])
if number == 198:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x+1/2,-y,z+1/2}"),
fs("{-x,y+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,-z}"),
fs("{z,x,y}"),
fs("{z+1/2,-x+1/2,-y}"),
fs("{-z+1/2,-x,y+1/2}"),
fs("{-z,x+1/2,-y+1/2}"),
fs("{y,z,x}"),
fs("{-y,z+1/2,-x+1/2}"),
fs("{y+1/2,-z+1/2,-x}"),
fs("{-y+1/2,-z,x+1/2}")
])
if number == 212:
return geo.Spacegroup(geo.canonical, [
fs("{x,y,z}"),
fs("{-x+1/2,-y,z+1/2}"),
fs("{-x,y+1/2,-z+1/2}"),
fs("{x+1/2,-y+1/2,-z}"),
fs("{z,x,y}"),
fs("{z+1/2,-x+1/2,-y}"),
fs("{-z+1/2,-x,y+1/2}"),
fs("{-z,x+1/2,-y+1/2}"),
fs("{y,z,x}"),
fs("{-y,z+1/2,-x+1/2}"),
fs("{y+1/2,-z+1/2,-x}"),
fs("{-y+1/2,-z,x+1/2}"),
fs("{y+1/4,x+3/4,-z+3/4}"),
fs("{-y+1/4,-x+1/4,-z+1/4}"),
fs("{ y+3/4,-x+3/4, z+1/4}"),
fs("{-y+3/4, x+1/4, z+3/4}"),
fs("{x+1/4,z+3/4,-y+3/4}"),
fs("{-x+3/4, z+1/4, y+3/4}"),
fs("{-x+1/4,-z+1/4,-y+1/4}"),
fs("{ x+3/4,-z+3/4, y+1/4}"),
fs("{z+1/4,y+3/4,-x+3/4}"),
fs("{ z+3/4,-y+3/4, x+1/4}"),
fs("{-z+3/4, y+1/4, x+3/4}"),
fs("{-z+1/4,-y+1/4,-x+1/4}")
])
if number == 227:
sg = geo.Spacegroup(geo.canonical, [
fs("{ x, y, z }"),
fs("{ -x, -y+1/2, z+1/2}"),
fs("{-x+1/2, y+1/2,-z }"),
fs("{ x+1/2,-y, -z+1/2}"),
fs("{ z, x, y }"),
fs("{ z+1/2,-x, -y+1/2}"),
fs("{-z, -x+1/2, y+1/2}"),
fs("{-z+1/2, x+1/2,-y }"),
fs("{ y, z, x }"),
fs("{ -y+1/2, z+1/2,-x }"),
fs("{ y+1/2,-z, -x+1/2}"),
fs("{-y, -z+1/2, x+1/2}"),
fs("{ y+3/4, x+1/4,-z+3/4}"),
fs("{-y+1/4, -x+1/4,-z+1/4}"),
fs("{ y+1/4,-x+3/4, z+3/4}"),
fs("{-y+3/4, x+3/4, z+1/4}"),
fs("{ x+3/4, z+1/4,-y+3/4}"),
fs("{-x+3/4, z+3/4, y+1/4}"),
fs("{-x+1/4,-z+1/4,-y+1/4}"),
fs("{ x+1/4,-z+3/4, y+3/4}"),
fs("{ z+3/4, y+1/4,-x+3/4}"),
fs("{ z+1/4, -y+3/4, x+3/4}"),
fs("{-z+3/4, y+3/4, x+1/4}"),
fs("{-z+1/4,-y+1/4,-x+1/4}"),
fs("{-x+1/4,-y+1/4,-z+1/4}"),
fs("{ x+1/4, y+3/4,-z+3/4}"),
fs("{ x+3/4,-y+3/4, z+1/4}"),
fs("{-x+3/4, y+1/4, z+3/4}"),
fs("{-z+1/4,-x+1/4,-y+1/4}"),
fs("{-z+3/4, x+1/4, y+3/4}"),
fs("{ z+1/4, x+3/4,-y+3/4}"),
fs("{ z+3/4,-x+3/4, y+1/4}"),
fs("{-y+1/4,-z+1/4,-x+1/4}"),
fs("{ y+3/4, -z+3/4, x+1/4}"),
fs("{-y+3/4, z+1/4, x+3/4}"),
fs("{ y+1/4, z+3/4,-x+3/4}"),
fs("{-y+1/2,-x, z+1/2}"),
fs("{ y, x, z }"),
fs("{-y, x+1/2,-z+1/2}"),
fs("{ y+1/2,-x+1/2,-z }"),
fs("{-x+1/2,-z, y+1/2}"),
fs("{ x+1/2, -z+1/2,-y }"),
fs("{ x, z, y }"),
fs("{-x, z+1/2,-y+1/2}"),
fs("{-z+1/2,-y, x+1/2}"),
fs("{-z, y+1/2,-x+1/2}"),
fs("{ z+1/2,-y+1/2,-x }"),
fs("{ z, y, x }")
])
sg = geo.Spacegroup(
geo.canonical, sg.liste_cosets +
[fs("{x,y+1/2,z+1/2}") * coset for coset in sg.liste_cosets] +
[fs("{x+1/2,y,z+1/2}") * coset for coset in sg.liste_cosets] +
[fs("{x+1/2,y+1/2,z}") * coset for coset in sg.liste_cosets])
return sg
def test_Atom():
atom1 = cr.Atom("Cs1", "Cs", fs("p 0 0 0"))
assert atom1.has_color == False
assert atom1.__str__() == \
"Atom Cs1 Cs Pos / 0 \ \n" \
" | 0 |\n" \
" \ 0 / "
assert (atom1 + "hallo").name == atom1.name + "hallo"
atom2 = cr.Atom("Cs2", "Cs", fs("p 0 0 0"))
assert atom2 == atom1
assert hash(atom2) == hash(atom1)
assert {atom2} == {atom1}
atom3 = cr.Atom("Cs3", "Cs", fs("p0.1 0 0"))
assert atom3 != atom1
atom4 = cr.Atom("Cs1", "Fe", fs("p 0 0 0"))
assert atom4 != atom1
atom5 = cr.Atom("Cs1", "Cs", fs("p 0.1234 0 0"))
atom6 = cr.Atom("Cs2", "Cs", fs("p 0.1234000000001 0 0"))
assert hash(atom5) == hash(atom6)
assert atom5 == atom6
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 1/2 1/2"))
transformation = fs("O->(0,0,0) \n"
"then\n"
"a' = a \n"
"b' = 2b \n"
"c' = c")
atom_trans = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 1/2"))
assert (transformation ** atom).__str__() == atom_trans.__str__()
sym = fs("-x+1/2,-y+1/2, z")
atom_sym = cr.Atom("Cl1", "Cl", fs("p0 0 1/2"))
assert (sym ** atom).__str__() == atom_sym.__str__()
coset = fs("{x, -y, z+1}")
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 1/2"))
atom1 = coset ** atom
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 3/4 1/2"))
assert atom1.__str__() == atom2.__str__()
transgen = geo.Transgen(fs("d 1 0 0"),
fs("d 0 1 0"),
fs("d 0 0 2"))
atom = cr.Atom("Cl1", "Cl", fs("p 1/2 5/4 -1/2"))
atom1 = atom % transgen
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 1/4 3/2"))
assert atom1 == atom2
d = fs("d 1/2 0 0")
atom1 = cr.Atom("Cl1", "Cl", fs("p 0 0 0"))
atom2 = cr.Atom("Cl1", "Cl", fs("p 1/2 0 0"))
atom3 = atom1 + d
assert atom2 == atom3
