def exercise_gruber_1973_example():
start = ucgmx((4, 136, 76, -155, -31, 44))
assert start.is_similar_to(
uctbx.unit_cell(
(2, 11.66, 8.718, 139 + 40 / 60., 152 + 45 / 60., 19 + 24 / 60.)))
buerger = ucgmx((4, 16, 16, -16, -1, -3))
assert buerger.is_similar_to(
uctbx.unit_cell((2, 4, 4, 120, 93.5833, 100.807)))
niggli = ucgmx((4, 16, 16, 16, 3, 4))
assert niggli.is_similar_to(
uctbx.unit_cell((2, 4, 4, 60, 79.1931, 75.5225)))
red = reduction_base.gruber_parameterization(start)
assert not red.is_buerger_cell()
assert approx_equal(red.as_gruber_matrix(), (4, 136, 76, -155, -31, 44))
assert approx_equal(red.as_niggli_matrix(),
(4, 136, 76, -155 / 2., -31 / 2., 44 / 2.))
assert approx_equal(red.as_sym_mat3(),
(4, 136, 76, 44 / 2., -31 / 2., -155 / 2.))
assert red.as_unit_cell().is_similar_to(start)
red = reduction_base.gruber_parameterization(buerger)
assert red.is_buerger_cell()
assert not red.is_niggli_cell()
red = reduction_base.gruber_parameterization(niggli)
assert red.is_niggli_cell()
red = reduce(start)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (-1, 5, 9, 0, -1, -1, 0, 0, 1)
assert red.n_iterations() == 29
red = reduce(buerger)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (-1, 0, 0, 0, 1, 1, 0, 1, 0)
assert red.n_iterations() == 4
red = reduce(niggli)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert red.n_iterations() == 1
try:
red = krivy_gruber_1976.reduction(buerger, iteration_limit=1)
except krivy_gruber_1976.iteration_limit_exceeded:
pass
else:
raise Exception_expected
assert not start.is_buerger_cell()
assert not start.is_niggli_cell()
assert buerger.is_buerger_cell()
assert not buerger.is_niggli_cell()
assert niggli.is_buerger_cell()
assert niggli.is_niggli_cell()
red = start.niggli_reduction()
assert red.n_iterations() == 29
assert start.niggli_cell().is_similar_to(niggli)
def exercise_gruber_1973_example():
start = ucgmx((4,136,76,-155,-31,44))
assert start.is_similar_to(uctbx.unit_cell(
(2, 11.66, 8.718, 139+40/60., 152+45/60., 19+24/60.)))
buerger = ucgmx((4,16,16,-16,-1,-3))
assert buerger.is_similar_to(uctbx.unit_cell(
(2, 4, 4, 120, 93.5833, 100.807)))
niggli = ucgmx((4,16,16,16,3,4))
assert niggli.is_similar_to(uctbx.unit_cell(
(2, 4, 4, 60, 79.1931, 75.5225)))
red = reduction_base.gruber_parameterization(start)
assert not red.is_buerger_cell()
assert approx_equal(red.as_gruber_matrix(), (4,136,76,-155,-31,44))
assert approx_equal(red.as_niggli_matrix(), (4,136,76,-155/2.,-31/2.,44/2.))
assert approx_equal(red.as_sym_mat3(), (4,136,76,44/2.,-31/2.,-155/2.))
assert red.as_unit_cell().is_similar_to(start)
red = reduction_base.gruber_parameterization(buerger)
assert red.is_buerger_cell()
assert not red.is_niggli_cell()
red = reduction_base.gruber_parameterization(niggli)
assert red.is_niggli_cell()
red = reduce(start)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (-1, 5, 9, 0, -1, -1, 0, 0, 1)
assert red.n_iterations() == 29
red = reduce(buerger)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (-1, 0, 0, 0, 1, 1, 0, 1, 0)
assert red.n_iterations() == 4
red = reduce(niggli)
assert red.as_unit_cell().is_similar_to(niggli)
assert red.r_inv().elems == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert red.n_iterations() == 1
try:
red = krivy_gruber_1976.reduction(buerger, iteration_limit=1)
except krivy_gruber_1976.iteration_limit_exceeded:
pass
else:
raise Exception_expected
assert not start.is_buerger_cell()
assert not start.is_niggli_cell()
assert buerger.is_buerger_cell()
assert not buerger.is_niggli_cell()
assert niggli.is_buerger_cell()
assert niggli.is_niggli_cell()
red = start.niggli_reduction()
assert red.n_iterations() == 29
assert start.niggli_cell().is_similar_to(niggli)
def niggli_reduction(self, relative_epsilon=None, iteration_limit=None): from cctbx.uctbx import krivy_gruber_1976 return krivy_gruber_1976.reduction(self, relative_epsilon, iteration_limit)
def niggli_reduction(self, relative_epsilon=None, iteration_limit=None): from cctbx.uctbx import krivy_gruber_1976 return krivy_gruber_1976.reduction(self, relative_epsilon, iteration_limit)
def do_reduce(inp):
assert not inp.is_degenerate()
time_krivy_gruber_1976.start()
red = krivy_gruber_1976.reduction(inp, relative_epsilon=relative_epsilon)
time_krivy_gruber_1976.stop()
assert red.is_niggli_cell()
red_cell = red.as_unit_cell()
assert inp.change_basis(red.r_inv().elems).is_similar_to(red_cell)
if (relative_epsilon is None):
assert check_is_niggli_cell(red_cell).itva_is_niggli_cell()
time_gruber_1973.start()
gruber_reduction = gruber_1973.reduction(inp,
relative_epsilon=relative_epsilon)
time_gruber_1973.stop()
assert gruber_reduction.is_buerger_cell()
buerger_cell = gruber_reduction.as_unit_cell()
assert inp.change_basis(
gruber_reduction.r_inv().elems).is_similar_to(buerger_cell)
time_krivy_gruber_1976_minimum.start()
min_reduction = krivy_gruber_1976.minimum_reduction(inp)
time_krivy_gruber_1976_minimum.stop()
assert min_reduction.type() in (1, 2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(
min_reduction.r_inv().elems).is_similar_to(min_cell)
time_gruber_1973_minimum.start()
min_reduction = gruber_1973.minimum_reduction(inp)
time_gruber_1973_minimum.stop()
assert min_reduction.type() in (1, 2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(
min_reduction.r_inv().elems).is_similar_to(min_cell)
time_gruber_1973_fast_minimum.start()
min_reduction = gruber_1973.fast_minimum_reduction(inp)
time_gruber_1973_fast_minimum.stop()
assert min_reduction.type() in (1, 2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(
min_reduction.r_inv().elems).is_similar_to(min_cell)
time_uctbx_fast_minimum.start()
min_reduction = uctbx.fast_minimum_reduction(inp)
time_uctbx_fast_minimum.stop()
assert min_reduction.type() in (1, 2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(min_reduction.r_inv()).is_similar_to(min_cell)
global fast_minimum_reduction_max_n_iterations
fast_minimum_reduction_max_n_iterations = max(
fast_minimum_reduction_max_n_iterations, min_reduction.n_iterations())
if (track_infinite):
if (eq_always_false):
red0 = reduction_with_tracking_and_eq_always_false(inp)
else:
red0 = reduction_with_tracking(inp)
if (red0.iteration_limit_exceeded):
n = 20
print(inp)
print("red0.action_log:", red0.action_log[-n:])
print("red0.type_log:", red0.type_log[-n:])
print("red0.meets_primary_conditions_log:", \
red0.meets_primary_conditions_log[-n:])
print("red0.meets_main_conditions_log:", \
red0.meets_main_conditions_log[-n:])
print("red0.is_niggli_cell_log:", red0.is_niggli_cell_log[-n:])
if (1):
for cell in red0.cell_log[-n:]:
print(cell)
print()
sys.stdout.flush()
return red
def do_reduce(inp):
assert not inp.is_degenerate()
time_krivy_gruber_1976.start()
red = krivy_gruber_1976.reduction(
inp, relative_epsilon=relative_epsilon)
time_krivy_gruber_1976.stop()
assert red.is_niggli_cell()
red_cell = red.as_unit_cell()
assert inp.change_basis(red.r_inv().elems).is_similar_to(red_cell)
if (relative_epsilon is None):
assert check_is_niggli_cell(red_cell).itva_is_niggli_cell()
time_gruber_1973.start()
gruber_reduction = gruber_1973.reduction(
inp, relative_epsilon=relative_epsilon)
time_gruber_1973.stop()
assert gruber_reduction.is_buerger_cell()
buerger_cell = gruber_reduction.as_unit_cell()
assert inp.change_basis(gruber_reduction.r_inv().elems).is_similar_to(
buerger_cell)
time_krivy_gruber_1976_minimum.start()
min_reduction = krivy_gruber_1976.minimum_reduction(inp)
time_krivy_gruber_1976_minimum.stop()
assert min_reduction.type() in (1,2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(min_reduction.r_inv().elems).is_similar_to(min_cell)
time_gruber_1973_minimum.start()
min_reduction = gruber_1973.minimum_reduction(inp)
time_gruber_1973_minimum.stop()
assert min_reduction.type() in (1,2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(min_reduction.r_inv().elems).is_similar_to(min_cell)
time_gruber_1973_fast_minimum.start()
min_reduction = gruber_1973.fast_minimum_reduction(inp)
time_gruber_1973_fast_minimum.stop()
assert min_reduction.type() in (1,2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(min_reduction.r_inv().elems).is_similar_to(min_cell)
time_uctbx_fast_minimum.start()
min_reduction = uctbx.fast_minimum_reduction(inp)
time_uctbx_fast_minimum.stop()
assert min_reduction.type() in (1,2)
min_cell = min_reduction.as_unit_cell()
assert approx_equal(min_cell.parameters()[:3], red_cell.parameters()[:3])
assert inp.change_basis(min_reduction.r_inv()).is_similar_to(min_cell)
global fast_minimum_reduction_max_n_iterations
fast_minimum_reduction_max_n_iterations = max(
fast_minimum_reduction_max_n_iterations, min_reduction.n_iterations())
if (track_infinite):
if (eq_always_false):
red0 = reduction_with_tracking_and_eq_always_false(inp)
else:
red0 = reduction_with_tracking(inp)
if (red0.iteration_limit_exceeded):
n = 20
print inp
print "red0.action_log:", red0.action_log[-n:]
print "red0.type_log:", red0.type_log[-n:]
print "red0.meets_primary_conditions_log:", \
red0.meets_primary_conditions_log[-n:]
print "red0.meets_main_conditions_log:", \
red0.meets_main_conditions_log[-n:]
print "red0.is_niggli_cell_log:", red0.is_niggli_cell_log[-n:]
if (1):
for cell in red0.cell_log[-n:]:
print cell
print
sys.stdout.flush()
return red