def prepare(conc, size, temp):
path = "."
unitcell = UnitCell.from_file("log.txt")
ecis = Ecis.from_dirc(".")
matrix = Matrix(conc, unitcell, ecis, size)
matrix.adjust_conc_fine(conc)
mc = MonteCarlo(matrix, temp)
return mc
def _test_montecalro(self):
""" montecalro """
path = os.path.join(self.PATH, "MonteCarlo", "FeH_BCCI")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
conc = 0.2
ecis = Ecis.from_dirc(path)
matrix = Matrix(conc, unitcell, ecis, 20)
mc = MonteCarlo(matrix, 5000)
pairs = mc.get_exchange_pairs([1, 3, 5])
assert pairs[0].sum() == pairs[1].sum()
assert (matrix.matrix[pairs[0]] == 0).all()
assert (matrix.matrix[pairs[1]] == 1).all()
mc.exe_flip(pairs)
mc.loop_test(1)
def test_SymmetryOperator(self):
""" SymmetryOperator """
path = os.path.join(self.PATH, "UnitCell")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
# opertate_symm
## 160412
clus = [[1/2, 1/2, 0]]
clus_dst = SymmetryOperator.operate_symm(clus, unitcell)
assert np.array(clus_dst).shape == (6, 1, 4)
clus = [[0, 1/2, 1/2], [3/4, 1/2, 1/4]]
clus_dst = SymmetryOperator.operate_symm(clus, unitcell)
assert np.array(clus_dst).shape == (48, 2, 4)
clus = [[0, 1/2, 1/2], [1/2, 1/2, 0]]
assert np.array(
SymmetryOperator.operate_symm(clus, unitcell)).shape == (12, 2, 4)
# centering
## 160412
clus = [[0, 1/2, 1/2], [1/2, 1/2, 0]]
out = [[[0.5, 0, -0.5]]]
assert (np.array(
SymmetryOperator.centerings(clus, unitcell)[6]) == out).all()
out = [[[-0.5, 0, 0.5]]]
assert (np.array(
SymmetryOperator.centerings(clus, unitcell)[8]) == out).all()
clus = [[3/4, 1/2, 1/4]]
assert not SymmetryOperator.centerings(clus, unitcell)[0][0]
# get_symmetrized_clusters
## 160412
clus = [[1/2, 1/2, 0], [-1/2, -1/2, 0]] # delta = [1, 0, 0]
out = [[[0, -1, -1, 0]], [[0, 1, 1, 0]]]
assert SymmetryOperator.get_equiv_clusters(
clus, unitcell)[6] == out
clus = [[1/2, 0, 1/2], [3/4, 1/2, 1/4]]
dst = SymmetryOperator.get_equiv_clusters(clus, unitcell)
assert set(dst.keys()) == set(range(9))
# centerings_idx
## 160307
clus = [unitcell.site2idx(site)
for site in [[0, 1/2, 1/2], [1/2, 1/2, 0]]]
out = {8: [np.array([[0, 0, 0, -2]])],
6: [np.array([[0, 0, 0, 2]])]}
assert (SymmetryOperator.centerings_idx(clus)[8][0] == out[8][0]).all()
assert (SymmetryOperator.centerings_idx(clus)[6][0] == out[6][0]).all()
def test_UnitCell(self):
""" UnitCell """
path = os.path.join(self.PATH, "UnitCell")
# from_file
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
# cell
## 160305
out = np.array(
[[1.414893, 1.414893, 1.414893],
[1.414893, -1.414893, -1.414893],
[-1.414893, 1.414893, -1.414893]])
assert (unitcell.atoms.cell == out).all()
# site
## 160305
out = np.array(
[[0.75, 0.50, 0.25],
[0.75, 0.25, 0.50],
[0.50, 0.25, 0.75],
[0.25, 0.75, 0.50],
[0.50, 0.75, 0.25],
[0.25, 0.50, 0.75],
[0.00, 0.50, 0.50],
[0.50, 1.00, 0.50],
[0.50, 0.50, 0.00]])
assert np.allclose(unitcell.atoms.get_scaled_positions(), out)
# out = ['symmorphic', '48']
# assert xtal.symm == out
out = [0, 0, 0, 0, 0, 0, 6, 6, 6]
assert (unitcell.symm['equivalent_atoms'] == out).all()
# site2idx
## 160305
site = np.array([-0.75, -0.5, -0.25])
assert (unitcell.site2idx(site) == [-1, -1, -1, 5])
site = [1/2, 0, 1/2]
assert (unitcell.site2idx(site) == [0, -1, 0, 7])
site = [1, 1/2, 1/2]
assert (unitcell.site2idx(site) == [1, 0, 0, 6])
site = np.array([-0.75, -0.5, 0.25])
try:
unitcell.site2idx(site)
assert False
except KeyError:
assert True
# site2pos
## 160306
site = np.array([3/4, 1/2, 1/4])
out = [1/2, 1/4, 0]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = np.array([3/4, 1/4, 1/2])
out = [1/4, 1/2, 0]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = np.array([1/2, 1/4, 3/4])
out = [0, 1/2, -1/4]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = np.array([1/4, 3/4, 1/2])
out = [1/4, 0, -1/2]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = np.array([1/2, 3/4, 1/4])
out = [1/2, 0, -1/4]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = np.array([1/4, 1/2, 3/4])
out = [0, 1/4, -1/2]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, out)
site = [1/2, 1/2, 0]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, [1/2, 0, 0])
site = [-1/2, -1/2, 0]
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, [-1/2, 0, 0])
site = np.array([1, 1/2, 1/2])
pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
assert np.allclose(pos, [1/2, 1/2, 0])
# get_ineq_group
## 160305
assert unitcell.get_ineq_group([-0.75, -0.5, -0.25]) == 0
assert unitcell.get_ineq_group([1, -0.5, -0.5]) == 6
assert unitcell.get_ineq_group([3/4, 1/2, 1/4]) == 0
try:
unitcell.get_ineq_group([0.0, 1.0, -0.5])
assert False
except KeyError:
assert True
def test_Matrix(self):
""" Matrix """
# __init__
# TO
## 160309
path = os.path.join(self.PATH, "Matrix", "AlCu_TO")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
ecis = Ecis.from_dirc(path)
conc = 0
matrix = Matrix(conc, unitcell, ecis, 2)
# FCC (HCP0*A1B0*TO)
matrix.matrix[:] = 1
assert np.allclose(matrix.get_energy(), -1.440741)
# FCC (HCP0*A0B1*TO)
matrix.matrix[:] = 0
assert np.allclose(matrix.get_energy(), -115.824971)
# L10 (HCP3*A1B1)
matrix.matrix[:] = 0
matrix.matrix[0, 0, 0, 0] = 1
matrix.matrix[1, 1, 1, 0] = 1
matrix.matrix[0, 1, 0, 0] = 1
matrix.matrix[1, 0, 1, 0] = 1
assert np.allclose(matrix.get_energy(), -211.482477833)
# L12 (HCP27*A1B3)
matrix.matrix[0, 0, 0, 0] = 0
matrix.matrix[1, 1, 1, 0] = 0
assert np.allclose(matrix.get_energy(), -173.72808675)
# L12 (HCP28*A3B1)
matrix.matrix[:] = 1
matrix.matrix[0, 1, 0, 0] = 0
matrix.matrix[1, 0, 1, 0] = 0
assert np.allclose(matrix.get_energy(), -172.812058)
# BCCI 2N
## 160311
path = os.path.join(self.PATH, "Matrix", "FeH_BCCI_2N")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
conc = 0.5
ecis = Ecis.from_dirc(path)
# BCCI (HCP0*A9B0*OP)
matrix = Matrix(conc, unitcell, ecis, 1,
order=[1, 1, 1, 1, 1, 1, 1, 1, 1])
assert np.allclose(matrix.get_energy(), -17.1659116)
# FeH6 (HCP99999*A6B3*OP)
matrix = Matrix(conc, unitcell, ecis, 2,
order=[1, 1, 1, 1, 1, 1, 0, 0, 0])
assert np.allclose(matrix.get_energy(), 0)
# FeH3 (HCP10*A3B6*OP)
matrix = Matrix(conc, unitcell, ecis, 3,
order=[0, 0, 0, 0, 0, 0, 1, 1, 1])
assert np.allclose(matrix.get_energy(), 0)
# FeH5 (HCP99998*5B4*OP)
matrix = Matrix(conc, unitcell, ecis, 4,
order=[1, 0, 1, 0, 1, 0, 1, 0, 1])
assert np.allclose(matrix.get_energy(), -.572197E+01)
# FeH6 (HCP99997*A6B3*OP)
matrix = Matrix(conc, unitcell, ecis, 5,
order=[1, 1, 1, 0, 0, 0, 1, 1, 1])
assert np.allclose(matrix.get_energy(), -.858296E+01)
# # BCCI
# ## 160309
path = os.path.join(self.PATH, "Matrix", "FeH_BCCI")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
conc = 0.5
ecis = Ecis.from_dirc(path)
# BCCI (HCP0*A9B0*OP)
matrix = Matrix(conc, unitcell, ecis, 1,
order=[1, 1, 1, 1, 1, 1, 1, 1, 1])
assert np.allclose(matrix.get_energy(), 0.132641E+01)
# FeH6 (HCP99999*A6B3*OP)
matrix = Matrix(conc, unitcell, ecis, 2,
order=[1, 1, 1, 1, 1, 1, 0, 0, 0])
assert np.allclose(matrix.get_energy(), -.243349E+02)
# FeH3 (HCP10*A3B6*OP)
matrix = Matrix(conc, unitcell, ecis, 3,
order=[0, 0, 0, 0, 0, 0, 1, 1, 1])
assert np.allclose(matrix.get_energy(), -.848994E+02)
# FeH5 (HCP99998*A5B4*OP)
matrix = Matrix(conc, unitcell, ecis, 4,
order=[1, 0, 1, 0, 1, 0, 1, 0, 1])
assert np.allclose(matrix.get_energy(), -.565030E+02)
# FeH6 (HCP99997*A6B3*OP)
matrix = Matrix(conc, unitcell, ecis, 5,
order=[1, 1, 1, 0, 0, 0, 1, 1, 1])
assert np.allclose(matrix.get_energy(), -.100641E+03)
# get_de
matrix = Matrix(conc, unitcell, ecis, 5)
# [0, 0, 0, 0] のみの de
de = matrix.get_delta_energy([[[[True]]]])
# 全てのサイト
de_matrix = matrix.get_delta_energy(
matrix.matrix[:, :, :, :] != 0.5).reshape(5, 5, 5, 9)
before = matrix.get_energy()
matrix.matrix[0, 0, 0, 0] = 1 - matrix.matrix[0, 0, 0, 0]
after = matrix.get_energy()
assert np.allclose(de, (after - before)*(matrix.matrix.size))
assert np.allclose(de_matrix[0, 0, 0, 0],
(after - before)*(matrix.matrix.size))
# adjust_conc_fine
## 160329
matrix = Matrix(conc, unitcell, ecis, 4)
matrix.adjust_conc_fine(conc)
assert matrix.conc == 0.5
def test_Ecis(self):
""" Ecis """
path = os.path.join(self.PATH, "Ecis")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
# parse_ecitxt
## 160305
ecis = Ecis.parse_ecitxt(os.path.join(path, "eci.txt"))
out = {0: 0.680236051, 1: -673.192307, 2: -208.572905, 3: 1752.08986,
4: 306.073297, 5: 147.11169, 6: 129.361349, 7: 233.347231,
8: 237.242402, 9: -4.14835143, 10: -44.2051374, 11: -1652.97108,
12: -286.755208, 13: -668.664112, 14: -714.67382, 16: 1227.364,
17: -707.7569, 19: -8.39681819, 20: -20.1496428, 22: 26.7883166,
24: -118.547219, 26: -6.21356756, 27: 1404.19369, 28: 1180.73395,
29: 95.1228157, 31: 100.481087, 35: -1089.71922, 36: 150.635303,
38: -845.97957, 44: -312.645058, 45: -134.730871, 47: -244.485361,
48: -117.505334, 49: 444.617266, 52: 294.931568, 53: -274.314461,
54: 407.711243}
assert ecis == out
# parse_logtxt
## 160305
clus = Ecis.parse_logtxt(os.path.join(path, "log.txt"))
assert len(clus) == 54
out = np.array([[0.75, 0.5, 0.25], [0.5, 0.25, -0.25]])
assert (clus[3] == out).all()
# get_clusters_from_logtxt
## 160306
clus = Ecis.get_clusters_from_logtxt(os.path.join(path, "log.txt"))
assert len(clus) == 54
for i in range(len(clus)):
for idx in clus[i]:
equiv = unitcell.symm['equivalent_atoms'][idx]
assert len(clus[i][idx]) == len(clus[i][equiv])
# get_diff_clusters
## 160306
out = Ecis.get_diff_clusters(os.path.join(path, "eci.txt"),
os.path.join(path, "log.txt"),
os.path.join(path, "logN6.txt"),
msg=False)
test = ("16 13 11 0 44 3 17 24 7 29 2 4 19 34 45 36 9 21 1 54 \n"
"26 5 6 49 15 48 8 10 53 52 27 12 28 47 20 38 31 \n")
assert out.split() == test.split()
# form_dirc
## 160308
ecis = Ecis.from_dirc(path)
# Al-Cu_TO_P
## 160330
"""
BRAV=F の構造だとうまくいかない
log.txt の構造表記の部分は P, F で変化しないが、
cluster を記述する後半の部分が変わるので、そこで齟齬が生じる
"""
path = os.path.join(self.PATH, "Ecis", "Al-Cu_TO_P")
# path = os.path.join(self.PATH, "Ecis", "Al-Cu_TO_F")
unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
ecis = Ecis.parse_ecitxt(os.path.join(path, "eci.txt"))
clus = Ecis.parse_logtxt(os.path.join(path, "log.txt"))
# print(clus)
clus = Ecis.get_clusters_from_logtxt(os.path.join(path, "log.txt"))
