def test_direct_summation():
# correct values
p = pdb.input(source_info='string', lines=test_pdb)
x = p.xray_structure_simple()
for s in x.scatterers():
s.set_use_u(False, False)
fc = x.structure_factors(anomalous_flag=False,
d_min=2.0,
algorithm='direct').f_calc()
fcd = fc.data()
indices = fc.indices()
# test values
xyz = x.sites_frac()
h = flex.vec3_double(len(indices))
fm = matrix.sqr(
p.crystal_symmetry().unit_cell().fractionalization_matrix())
om = matrix.sqr(
p.crystal_symmetry().unit_cell().orthogonalization_matrix())
for i in range(len(indices)):
h[i] = fm * indices[i]
sr = x.scattering_type_registry()
st = x.scattering_types()
sg = p.crystal_symmetry().space_group()
r = flex.double()
t = flex.vec3_double(len(sg))
for i in range(len(sg)):
r_i = om * matrix.sqr(sg[i].r().as_double())
for a in r_i:
r.append(a)
t[i] = om * matrix.col(sg[i].t().as_double())
bls = flex.double(len(xyz), 0.0)
amplitudes = direct_summation()
amplitudes.add(st, xyz, bls, h, r, t, sr, False)
amplitudes = amplitudes.get_sum()
cpu_i = flex.norm(fcd)
gpu_i = flex.norm(amplitudes)
mean = 0.0
for i in range(len(cpu_i)):
e = math.fabs(cpu_i[i] - gpu_i[i]) / cpu_i[i]
mean += e
mean = mean / (len(cpu_i))
assert (mean < 1.0e-3)
def test_direct_summation():
# correct values
p = pdb.input(source_info='string',lines=test_pdb)
x = p.xray_structure_simple()
for s in x.scatterers():
s.set_use_u(False,False)
fc = x.structure_factors(anomalous_flag=False,d_min=2.0,
algorithm='direct').f_calc()
fcd = fc.data()
indices = fc.indices()
# test values
xyz = x.sites_frac()
h = flex.vec3_double(len(indices))
fm = matrix.sqr(p.crystal_symmetry().unit_cell().fractionalization_matrix())
om = matrix.sqr(p.crystal_symmetry().unit_cell().orthogonalization_matrix())
for i in xrange(len(indices)):
h[i] = fm * indices[i]
sr = x.scattering_type_registry()
st = x.scattering_types()
sg = p.crystal_symmetry().space_group()
r = flex.double()
t = flex.vec3_double(len(sg))
for i in xrange(len(sg)):
r_i = om * matrix.sqr(sg[i].r().as_double())
for a in r_i:
r.append(a)
t[i] = om * matrix.col(sg[i].t().as_double())
bls = flex.double(len(xyz),0.0)
amplitudes = direct_summation()
amplitudes.add(st,xyz,bls,h,r,t,sr,False)
amplitudes = amplitudes.get_sum()
cpu_i = flex.norm(fcd)
gpu_i = flex.norm(amplitudes)
mean = 0.0
for i in xrange(len(cpu_i)):
e = math.fabs(cpu_i[i] - gpu_i[i])/cpu_i[i]
mean += e
mean = mean/(len(cpu_i))
assert(mean < 1.0e-3)
def test_saxs(): p = pdb.input(source_info='string',lines=test_pdb) x = p.xray_structure_simple() xyz = x.sites_cart() blsf = flex.double(len(xyz),0.0) sr = x.scattering_type_registry() st = x.scattering_types() q = flex.double(range(101))/200.0 t_w = flex.double(len(t_x),1.0) l = flex.double() l.extend(t_x) l.extend(t_y) l.extend(t_z) intensities = direct_summation() intensities.prepare_saxs(st,xyz,blsf,q,t_w,l,sr,False) intensities.run_saxs_kernel() intensities.sum_over_lattice() intensities = intensities.get_sum() assert(approx_equal(intensities[10].real,3584.9828125,out=None))
def test_saxs():
p = pdb.input(source_info='string', lines=test_pdb)
x = p.xray_structure_simple()
xyz = x.sites_cart()
blsf = flex.double(len(xyz), 0.0)
sr = x.scattering_type_registry()
st = x.scattering_types()
q = flex.double(range(101)) / 200.0
t_w = flex.double(len(t_x), 1.0)
l = flex.double()
l.extend(t_x)
l.extend(t_y)
l.extend(t_z)
intensities = direct_summation()
intensities.prepare_saxs(st, xyz, blsf, q, t_w, l, sr, False)
intensities.run_saxs_kernel()
intensities.sum_over_lattice()
intensities = intensities.get_sum()
assert (approx_equal(intensities[10].real, 3584.9828125, out=None))