def exercise_fast_terms():
space_group = sgtbx.space_group_info("P 21 21 21").group()
miller_indices_f_obs = flex.miller_index(((3,4,5),(4,5,6)))
f = translation_search.fast_terms(
gridding=(20,20,36),
anomalous_flag=False,
miller_indices_p1_f_calc=flex.miller_index(((1,2,3),)),
p1_f_calc=flex.complex_double((12,)))
assert f.summation(
space_group=space_group,
miller_indices_f_obs=miller_indices_f_obs,
m=flex.double((1,2)),
f_part=None,
squared_flag=False).fft().accu_real_copy().all() == (20,20,36)
def exercise_fast_terms():
space_group = sgtbx.space_group_info("P 21 21 21").group()
miller_indices_f_obs = flex.miller_index(((3, 4, 5), (4, 5, 6)))
f = translation_search.fast_terms(
gridding=(20, 20, 36),
anomalous_flag=False,
miller_indices_p1_f_calc=flex.miller_index(((1, 2, 3), )),
p1_f_calc=flex.complex_double((12, )))
assert f.summation(space_group=space_group,
miller_indices_f_obs=miller_indices_f_obs,
m=flex.double((1, 2)),
f_part=None,
squared_flag=False).fft().accu_real_copy().all() == (20,
20,
36)
def run_fast_terms(structure_fixed, structure_p1,
f_obs, f_calc_fixed, f_calc_p1,
symmetry_flags, gridding, grid_tags,
n_sample_grid_points=10,
test_origin=False,
verbose=0):
if (f_calc_fixed is None):
f_part = flex.complex_double()
else:
f_part = f_calc_fixed.data()
m = flex.double()
for i in xrange(f_obs.indices().size()):
m.append(random.random())
assert f_obs.anomalous_flag() == f_calc_p1.anomalous_flag()
fast_terms = translation_search.fast_terms(
gridding=gridding,
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_p1_f_calc=f_calc_p1.indices(),
p1_f_calc=f_calc_p1.data())
for squared_flag in (False, True):
map = fast_terms.summation(
space_group=f_obs.space_group(),
miller_indices_f_obs=f_obs.indices(),
m=m,
f_part=f_part,
squared_flag=squared_flag).fft().accu_real_copy()
assert map.all() == gridding
map_stats = maptbx.statistics(map)
if (0 or verbose):
map_stats.show_summary()
grid_tags.build(f_obs.space_group_info().type(), symmetry_flags)
assert grid_tags.n_grid_misses() == 0
assert grid_tags.verify(map)
for i_sample in xrange(n_sample_grid_points):
run_away_counter = 0
while 1:
run_away_counter += 1
assert run_away_counter < 1000
if (i_sample == 0 and test_origin):
grid_point = [0,0,0]
else:
grid_point = [random.randrange(g) for g in gridding]
grid_site = [float(x)/g for x,g in zip(grid_point,gridding)]
structure_shifted = structure_fixed.deep_copy_scatterers()
assert structure_shifted.special_position_indices().size() == 0
structure_shifted.add_scatterers(
scatterers=structure_p1.apply_shift(grid_site).scatterers())
if (structure_shifted.special_position_indices().size() == 0):
break
if (test_origin):
assert i_sample != 0
i_grid = flex.norm(f_obs.structure_factors_from_scatterers(
xray_structure=structure_shifted, algorithm="direct").f_calc().data())
if (squared_flag): p = 4
else: p = 2
map_value = map[grid_point] * f_obs.space_group().n_ltr()**p
if (not squared_flag):
sum_m_i_grid = flex.sum(m * i_grid)
else:
sum_m_i_grid = flex.sum(m * flex.pow2(i_grid))
assert "%.6g" % sum_m_i_grid == "%.6g" % map_value, (
sum_m_i_grid, map_value)