def exercise_fast_minimum_reduction():
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)))
assert mr.iteration_limit() == 100
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90, 8)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90, 8, 4)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 4
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((2, 3, 5, 80, 90, 100)))
assert approx_equal(mr.as_gruber_matrix(),
(4, 9, 25, -5.209445, 0, -2.083778))
assert approx_equal(mr.as_niggli_matrix(),
(4, 9, 25, -5.209445 / 2, 0, -2.083778 / 2))
assert approx_equal(mr.as_sym_mat3(),
(4, 9, 25, -2.083778 / 2, 0, -5.209445 / 2))
assert mr.as_unit_cell().is_similar_to(
uctbx.unit_cell((2, 3, 5, 100, 90, 100)))
assert approx_equal(mr.r_inv(), (-1, 0, 0, 0, -1, 0, 0, 0, 1))
assert mr.n_iterations() == 1
assert not mr.termination_due_to_significant_change_test()
assert mr.type() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((5, 3, 2, 50, 120, 130)),
8)
assert mr.n_iterations() == 8
assert not mr.termination_due_to_significant_change_test()
try:
uctbx.fast_minimum_reduction(uctbx.unit_cell((5, 3, 2, 50, 120, 130)),
2, 7)
except RuntimeError as e:
assert str(e) == "cctbx Error: Iteration limit exceeded."
else:
raise AssertionError('exception expected')
try:
u = uctbx.unit_cell((2, 3, 5, 70, 120, 50))
except Exception:
pass
else:
try:
uctbx.fast_minimum_reduction(u)
except RuntimeError as e:
if ("--Verbose" in sys.argv[1:]):
print("Expected:", e)
def exercise_fast_minimum_reduction():
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1,1,1,90,90,90)))
assert mr.iteration_limit() == 100
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1,1,1,90,90,90)), 90)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1,1,1,90,90,90)), 90,8)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1,1,1,90,90,90)), 90,8,4)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 4
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((2,3,5,80,90,100)))
assert approx_equal(mr.as_gruber_matrix(),(4,9,25,-5.209445,0,-2.083778))
assert approx_equal(mr.as_niggli_matrix(),(4,9,25,-5.209445/2,0,-2.083778/2))
assert approx_equal(mr.as_sym_mat3(),(4,9,25,-2.083778/2,0,-5.209445/2))
assert mr.as_unit_cell().is_similar_to(uctbx.unit_cell((2,3,5,100,90,100)))
assert approx_equal(mr.r_inv(), (-1,0,0,0,-1,0,0,0,1))
assert mr.n_iterations() == 1
assert not mr.termination_due_to_significant_change_test()
assert mr.type() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((5,3,2,50,120,130)), 8)
assert mr.n_iterations() == 8
assert not mr.termination_due_to_significant_change_test()
try:
uctbx.fast_minimum_reduction(uctbx.unit_cell((5,3,2,50,120,130)), 2, 7)
except RuntimeError, e:
assert str(e) == "cctbx Error: Iteration limit exceeded."
def reduced_cell(self): #convenience function to transform the orientation matrix to the reduced cell from cctbx.uctbx import fast_minimum_reduction from scitbx import matrix uc = self.unit_cell() R = fast_minimum_reduction(uc) rinverse = matrix.sqr( R.r_inv() ) return self.change_basis(rinverse.transpose().inverse().elems)
def reduced_cell(self):
#convenience function to transform the orientation matrix to the reduced cell
from cctbx.uctbx import fast_minimum_reduction
from scitbx import matrix
uc = self.unit_cell()
R = fast_minimum_reduction(uc)
rinverse = matrix.sqr(R.r_inv())
return self.change_basis(rinverse.transpose().inverse().elems)
def rwgk_niggli(UC,epsilon=None,cutoff=100.):
'''Reference:
R.W. Grosse-Kunstleve, N.K. Sauter and P.D. Adams.
Numerically stable algorithms for the computation of reduced unit cells.
Acta Cryst. A60, 1-6 (2004)
'''
if isinstance(UC,unit_cell):
#return UC.niggli_cell(epsilon)
return fast_minimum_reduction(UC).as_unit_cell()
elif isinstance(UC,crystal_orientation.crystal_orientation):
uc = UC.unit_cell()
unit_cell_too_small(uc,cutoff=cutoff)
#R = uc.niggli_reduction(epsilon)
R = fast_minimum_reduction(uc)
#minimum reduction gets r_inv as a tuple instead of scitbx.matrix
rinverse = matrix.sqr( R.r_inv() )
#NIG = R.as_unit_cell().parameters()
#MIN = fast_minimum_reduction(uc).as_unit_cell().parameters()
return UC.change_basis(rinverse.transpose().inverse().elems)
def __init__(self, n_iterations=None):
if (n_iterations is not None):
self.n_iterations = n_iterations
else:
if ("--hardest" in sys.argv[1:]):
self.n_iterations = 1000000
elif ("--harder" in sys.argv[1:]):
self.n_iterations = 100000
elif ("--hard" in sys.argv[1:]):
self.n_iterations = 10000
else:
self.n_iterations = 100
self.n_stable = [0,0]
self.n_unstable = 0
i_iteration = 0
rnd = random.random
while 1:
lengths = [rnd(), rnd(), rnd()]
for alpha in xrange(10,180,10):
for beta in xrange(10,180,10):
for gamma in xrange(10,180,10):
try:
u = uctbx.unit_cell((2,3,5,alpha,beta,gamma))
except Exception:
pass
else:
is_degenerate = u.is_degenerate(1.e-10, 1.e-5)
try:
uctbx.fast_minimum_reduction(u)
self.n_stable[int(is_degenerate)] += 1
except RuntimeError, e:
assert is_degenerate
self.n_unstable += 1
i_iteration += 1
if (i_iteration == self.n_iterations):
return
def __init__(self, n_iterations=None):
if (n_iterations is not None):
self.n_iterations = n_iterations
else:
if ("--hardest" in sys.argv[1:]):
self.n_iterations = 1000000
elif ("--harder" in sys.argv[1:]):
self.n_iterations = 100000
elif ("--hard" in sys.argv[1:]):
self.n_iterations = 10000
else:
self.n_iterations = 100
self.n_stable = [0, 0]
self.n_unstable = 0
i_iteration = 0
rnd = random.random
while 1:
lengths = [rnd(), rnd(), rnd()]
for alpha in range(10, 180, 10):
for beta in range(10, 180, 10):
for gamma in range(10, 180, 10):
try:
u = uctbx.unit_cell((2, 3, 5, alpha, beta, gamma))
except Exception:
pass
else:
is_degenerate = u.is_degenerate(1.e-10, 1.e-5)
try:
uctbx.fast_minimum_reduction(u)
self.n_stable[int(is_degenerate)] += 1
except RuntimeError as e:
assert is_degenerate
self.n_unstable += 1
i_iteration += 1
if (i_iteration == self.n_iterations):
return
def exercise_fast_minimum_reduction():
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)))
assert mr.iteration_limit() == 100
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 16
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90, 8)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((1, 1, 1, 90, 90, 90)),
90, 8, 4)
assert mr.iteration_limit() == 90
assert mr.multiplier_significant_change_test() == 8
assert mr.min_n_no_significant_change() == 4
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((2, 3, 5, 80, 90, 100)))
assert approx_equal(mr.as_gruber_matrix(),
(4, 9, 25, -5.209445, 0, -2.083778))
assert approx_equal(mr.as_niggli_matrix(),
(4, 9, 25, -5.209445 / 2, 0, -2.083778 / 2))
assert approx_equal(mr.as_sym_mat3(),
(4, 9, 25, -2.083778 / 2, 0, -5.209445 / 2))
assert mr.as_unit_cell().is_similar_to(
uctbx.unit_cell((2, 3, 5, 100, 90, 100)))
assert approx_equal(mr.r_inv(), (-1, 0, 0, 0, -1, 0, 0, 0, 1))
assert mr.n_iterations() == 1
assert not mr.termination_due_to_significant_change_test()
assert mr.type() == 2
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((5, 3, 2, 50, 120, 130)),
8)
assert mr.n_iterations() == 8
assert not mr.termination_due_to_significant_change_test()
try:
uctbx.fast_minimum_reduction(uctbx.unit_cell((5, 3, 2, 50, 120, 130)),
2, 7)
except RuntimeError, e:
assert str(e) == "cctbx Error: Iteration limit exceeded."
mr = uctbx.fast_minimum_reduction(uctbx.unit_cell((5,3,2,50,120,130)), 8)
assert mr.n_iterations() == 8
assert not mr.termination_due_to_significant_change_test()
try:
uctbx.fast_minimum_reduction(uctbx.unit_cell((5,3,2,50,120,130)), 2, 7)
except RuntimeError, e:
assert str(e) == "cctbx Error: Iteration limit exceeded."
else:
raise AssertionError, 'exception expected'
try:
u = uctbx.unit_cell((2,3,5,70,120,50))
except Exception:
pass
else:
try:
uctbx.fast_minimum_reduction(u)
except RuntimeError, e:
if ("--Verbose" in sys.argv[1:]):
print "Expected:", e
class exercise_is_degenerate(object):
def __init__(self, n_iterations=None):
if (n_iterations is not None):
self.n_iterations = n_iterations
else:
if ("--hardest" in sys.argv[1:]):
self.n_iterations = 1000000
elif ("--harder" in sys.argv[1:]):
self.n_iterations = 100000
elif ("--hard" in sys.argv[1:]):
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
assert mr.n_iterations() == 8
assert not mr.termination_due_to_significant_change_test()
try:
uctbx.fast_minimum_reduction(uctbx.unit_cell((5, 3, 2, 50, 120, 130)),
2, 7)
except RuntimeError, e:
assert str(e) == "cctbx Error: Iteration limit exceeded."
else:
raise AssertionError, 'exception expected'
try:
u = uctbx.unit_cell((2, 3, 5, 70, 120, 50))
except Exception:
pass
else:
try:
uctbx.fast_minimum_reduction(u)
except RuntimeError, e:
if ("--Verbose" in sys.argv[1:]):
print "Expected:", e
class exercise_is_degenerate(object):
def __init__(self, n_iterations=None):
if (n_iterations is not None):
self.n_iterations = n_iterations
else:
if ("--hardest" in sys.argv[1:]):
self.n_iterations = 1000000
elif ("--harder" in sys.argv[1:]):
self.n_iterations = 100000
elif ("--hard" in sys.argv[1:]):