def df_d_params(self):
result = []
tphkl = 2 * math.pi * matrix.col(self.hkl)
h,k,l = self.hkl
d_exp_huh_d_u_star = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
for scatterer in self.scatterers:
assert scatterer.scattering_type == "const"
w = scatterer.occupancy
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
ffp = 1 + scatterer.fp
fdp = scatterer.fdp
ff = ffp + 1j * fdp
d_site = matrix.col([0,0,0])
if (not scatterer.flags.use_u_aniso()):
d_u_iso = 0
d_u_star = None
else:
d_u_iso = None
d_u_star = matrix.col([0,0,0,0,0,0])
d_occ = 0
d_fp = 0
d_fdp = 0
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = r.transpose()
d_site += site_gtmx * (
w * dw * ff * e * 1j * tphkl)
if (not scatterer.flags.use_u_aniso()):
d_u_iso += w * dw * ff * e * mtps * self.d_star_sq
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d_u_star += u_star_gtmx * (
w * dw * ff * e * mtps * d_exp_huh_d_u_star)
d_occ += dw * ff * e
d_fp += w * dw * e
d_fdp += w * dw * e * 1j
result.append(gradients(
site=d_site,
u_iso=d_u_iso,
u_star=d_u_star,
occupancy=d_occ,
fp=d_fp,
fdp=d_fdp))
return result
def df_d_params(self):
result = []
tphkl = 2 * math.pi * matrix.col(self.hkl)
h,k,l = self.hkl
d_exp_huh_d_u_star = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
for scatterer in self.scatterers:
assert scatterer.scattering_type == "const"
w = scatterer.occupancy
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
ffp = 1 + scatterer.fp
fdp = scatterer.fdp
ff = ffp + 1j * fdp
d_site = matrix.col([0,0,0])
if (not scatterer.flags.use_u_aniso()):
d_u_iso = 0
d_u_star = None
else:
d_u_iso = None
d_u_star = matrix.col([0,0,0,0,0,0])
d_occ = 0
d_fp = 0
d_fdp = 0
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = r.transpose()
d_site += site_gtmx * (
w * dw * ff * e * 1j * tphkl)
if (not scatterer.flags.use_u_aniso()):
d_u_iso += w * dw * ff * e * mtps * self.d_star_sq
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d_u_star += u_star_gtmx * (
w * dw * ff * e * mtps * d_exp_huh_d_u_star)
d_occ += dw * ff * e
d_fp += w * dw * e
d_fdp += w * dw * e * 1j
result.append(gradients(
site=d_site,
u_iso=d_u_iso,
u_star=d_u_star,
occupancy=d_occ,
fp=d_fp,
fdp=d_fdp))
return result
def d_u(self):
result = flex.double(6, 0)
h,k,l = self.hkl
d_exp_huh_d_u = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
for op in self.ops:
op_u = (op*matrix.sym(sym_mat3=self.u)*op.transpose()).as_sym_mat3()
huh = (matrix.row(self.hkl) \
* matrix.sym(sym_mat3=op_u)).dot(matrix.col(self.hkl))
d_op_u = math.exp(mtps * huh) * mtps * d_exp_huh_d_u
gtmx = tensor_rank_2_gradient_transform_matrix(op)
d_u = gtmx.matrix_multiply(flex.double(d_op_u))
result += d_u
return result
def d_u(self):
result = flex.double(6, 0)
h, k, l = self.hkl
d_exp_huh_d_u = matrix.col(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
for op in self.ops:
op_u = (op * matrix.sym(sym_mat3=self.u) *
op.transpose()).as_sym_mat3()
huh = (matrix.row(self.hkl) \
* matrix.sym(sym_mat3=op_u)).dot(matrix.col(self.hkl))
d_op_u = math.exp(mtps * huh) * mtps * d_exp_huh_d_u
gtmx = tensor_rank_2_gradient_transform_matrix(op)
d_u = gtmx.matrix_multiply(flex.double(d_op_u))
result += d_u
return result
def d2_u(self):
result = flex.double(flex.grid(6,6), 0)
h,k,l = self.hkl
d_exp_huh_d_u = flex.double([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_uu = d_exp_huh_d_u.matrix_outer_product(d_exp_huh_d_u)
for op in self.ops:
op_u = (op*matrix.sym(sym_mat3=self.u)*op.transpose()).as_sym_mat3()
huh = (matrix.row(self.hkl) \
* matrix.sym(sym_mat3=op_u)).dot(matrix.col(self.hkl))
d2_op_u = math.exp(mtps * huh) * mtps**2 * d2_exp_huh_d_uu
gtmx = tensor_rank_2_gradient_transform_matrix(op)
d2_u = gtmx.matrix_multiply(d2_op_u).matrix_multiply(
gtmx.matrix_transpose())
result += d2_u
return result
def d2_u(self):
result = flex.double(flex.grid(6, 6), 0)
h, k, l = self.hkl
d_exp_huh_d_u = flex.double(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
d2_exp_huh_d_uu = d_exp_huh_d_u.matrix_outer_product(d_exp_huh_d_u)
for op in self.ops:
op_u = (op * matrix.sym(sym_mat3=self.u) *
op.transpose()).as_sym_mat3()
huh = (matrix.row(self.hkl) \
* matrix.sym(sym_mat3=op_u)).dot(matrix.col(self.hkl))
d2_op_u = math.exp(mtps * huh) * mtps**2 * d2_exp_huh_d_uu
gtmx = tensor_rank_2_gradient_transform_matrix(op)
d2_u = gtmx.matrix_multiply(d2_op_u).matrix_multiply(
gtmx.matrix_transpose())
result += d2_u
return result
def d2f_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
tphkl_outer = tphkl.outer_product()
h,k,l = self.hkl
d_exp_huh_d_u_star = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.outer_product()
for scatterer in self.scatterers:
assert scatterer.scattering_type == "const"
w = scatterer.occupancy
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
ffp = 1 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(flex.grid(3,3), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3,1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3,6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3,1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(flex.grid(6,6), 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6,1), 0j)
d2_occ_fp = 0j
d2_occ_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = r.transpose()
d2_site_site += flex.complex_double(
site_gtmx *
(w * dw * ff * e * (-1) * tphkl_outer)
* site_gtmx.transpose())
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += flex.complex_double(site_gtmx * (
w * dw * ff * e * 1j * mtps * self.d_star_sq * tphkl))
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d2_site_u_star += flex.complex_double(
site_gtmx
* ((w * dw * ff * e * 1j * tphkl).outer_product(
mtps * d_exp_huh_d_u_star))
* u_star_gtmx.transpose())
d2_site_occ += flex.complex_double(site_gtmx * (
dw * ff * e * 1j * tphkl))
d2_site_fp += flex.complex_double(site_gtmx * (
w * dw * e * 1j * tphkl))
d2_site_fdp += flex.complex_double(site_gtmx * (
w * dw * e * (-1) * tphkl))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
d2_u_iso_occ += dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star += flex.complex_double(
u_star_gtmx
* (w * dw * ff * e * mtps**2 * d2_exp_huh_d_u_star_u_star)
* u_star_gtmx.transpose())
d2_u_star_occ += flex.complex_double(u_star_gtmx * (
dw * ff * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fp += flex.complex_double(u_star_gtmx * (
w * dw * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fdp += flex.complex_double(u_star_gtmx * (
w * dw * 1j * e * mtps * d_exp_huh_d_u_star))
d2_occ_fp += dw * e
d2_occ_fdp += dw * e * 1j
if (not scatterer.flags.use_u_aniso()):
i_occ, i_fp, i_fdp, np = 4, 5, 6, 7
else:
i_occ, i_fp, i_fdp, np = 9, 10, 11, 12
dp = flex.complex_double(flex.grid(np,np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site, 0,0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0,3)
paste(d2_site_u_iso.matrix_transpose(), 3,0)
else:
paste(d2_site_u_star, 0,3)
paste(d2_site_u_star.matrix_transpose(), 3,0)
paste(d2_site_occ, 0,i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ,0)
paste(d2_site_fp, 0,i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp,0)
paste(d2_site_fdp, 0,i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp,0)
if (not scatterer.flags.use_u_aniso()):
dp[3*7+3] = d2_u_iso_u_iso
dp[3*7+4] = d2_u_iso_occ
dp[4*7+3] = d2_u_iso_occ
dp[3*7+5] = d2_u_iso_fp
dp[5*7+3] = d2_u_iso_fp
dp[3*7+6] = d2_u_iso_fdp
dp[6*7+3] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star, 3,3)
paste(d2_u_star_occ, 3, 9)
paste(d2_u_star_occ.matrix_transpose(), 9, 3)
paste(d2_u_star_fp, 3, 10)
paste(d2_u_star_fp.matrix_transpose(), 10, 3)
paste(d2_u_star_fdp, 3, 11)
paste(d2_u_star_fdp.matrix_transpose(), 11, 3)
dp[i_occ*np+i_fp] = d2_occ_fp
dp[i_fp*np+i_occ] = d2_occ_fp
dp[i_occ*np+i_fdp] = d2_occ_fdp
dp[i_fdp*np+i_occ] = d2_occ_fdp
yield dp
def df_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
h, k, l = self.hkl
d_exp_huh_d_u_star = matrix.col(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
for i_scatterer, scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
wwo = scatterer.weight_without_occupancy()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = ffp + 1j * fdp
d_site = matrix.col([0, 0, 0])
if (not scatterer.flags.use_u_aniso()):
d_u_iso = 0
d_u_star = None
else:
d_u_iso = None
d_u_star = matrix.col([0, 0, 0, 0, 0, 0])
d_occ = 0j
d_fp = 0j
d_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r * matrix.sym(
sym_mat3=scatterer.u_star) * r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(
matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j * alpha)
site_gtmx = r.transpose()
d_site += site_gtmx * (w * dw * ff * e * 1j * tphkl)
if (not scatterer.flags.use_u_aniso()):
d_u_iso += w * dw * ff * e * mtps * self.d_star_sq
else:
u_star_gtmx = matrix.sqr(
tensor_rank_2_gradient_transform_matrix(r))
d_u_star += u_star_gtmx * (w * dw * ff * e * mtps *
d_exp_huh_d_u_star)
d_occ += wwo * dw * ff * e
d_fp += w * dw * e
d_fdp += w * dw * e * 1j
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_site = gsm * d_site
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_u_star = gsm * d_u_star
result = flex.complex_double(d_site)
if (not scatterer.flags.use_u_aniso()):
result.append(d_u_iso)
else:
result.extend(flex.complex_double(d_u_star))
result.extend(flex.complex_double([d_occ, d_fp, d_fdp]))
yield result
def d2f_d_params_diag(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h, k, l = self.hkl
d_exp_huh_d_u_star = flex.double(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
for i_scatterer, scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(3 * (3 + 1) // 2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
else:
d2_u_star_u_star = flex.complex_double(6 * (6 + 1) // 2, 0j)
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r * matrix.sym(
sym_mat3=scatterer.u_star) * r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(
matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j * alpha)
site_gtmx = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3, 3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps *
self.d_star_sq)**2
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
np = i_occ + 3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
#
dpd = flex.complex_double(flex.grid(np, 1), 0j)
def paste(d, i):
d.reshape(flex.grid(d.size(), 1))
dpd.matrix_paste_block_in_place(d, i, 0)
paste(d2_site_site.matrix_packed_u_diagonal(), 0)
if (not scatterer.flags.use_u_aniso()):
dpd[i_u] = d2_u_iso_u_iso
else:
paste(d2_u_star_u_star.matrix_packed_u_diagonal(), i_u)
yield dpd
def d2f_d_params(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h, k, l = self.hkl
d_exp_huh_d_u_star = flex.double(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
for i_scatterer, scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
wwo = scatterer.weight_without_occupancy()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(3 * (3 + 1) // 2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3, 1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3, 6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3, 1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3, 1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3, 1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(6 * (6 + 1) // 2, 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6, 1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6, 1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6, 1), 0j)
d2_occ_fp = 0j
d2_occ_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r * matrix.sym(
sym_mat3=scatterer.u_star) * r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(
matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j * alpha)
site_gtmx = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3, 3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += (w * dw * ff * e * 1j * mtps * self.d_star_sq) \
* site_gtmx.matrix_multiply(tphkl)
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_site_u_star += (w * dw * ff * e * 1j * mtps) \
* site_gtmx.matrix_multiply(
tphkl.matrix_outer_product(d_exp_huh_d_u_star)) \
.matrix_multiply(u_star_gtmx.matrix_transpose())
site_gtmx_tphkl = site_gtmx.matrix_multiply(tphkl)
d2_site_occ += (wwo * dw * ff * e * 1j) * site_gtmx_tphkl
d2_site_fp += (w * dw * e * 1j) * site_gtmx_tphkl
d2_site_fdp += (w * dw * e * (-1)) * site_gtmx_tphkl
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps *
self.d_star_sq)**2
d2_u_iso_occ += wwo * dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
u_star_gtmx_d_exp_huh_d_u_star = u_star_gtmx.matrix_multiply(
d_exp_huh_d_u_star)
d2_u_star_occ += (wwo * dw * ff * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fp += (w * dw * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fdp += (w * dw * 1j * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_occ_fp += wwo * dw * e
d2_occ_fdp += wwo * dw * e * 1j
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
i_fp, i_fdp, np = i_occ + 1, i_occ + 2, i_occ + 3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = gsm.matrix_multiply(d2_site_u_iso)
else:
d2_site_u_star = gsm.matrix_multiply(d2_site_u_star)
d2_site_occ = gsm.matrix_multiply(d2_site_occ)
d2_site_fp = gsm.matrix_multiply(d2_site_fp)
d2_site_fdp = gsm.matrix_multiply(d2_site_fdp)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_site_u_star = d2_site_u_star.matrix_multiply(
gsm.matrix_transpose())
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
d2_u_star_occ = gsm.matrix_multiply(d2_u_star_occ)
d2_u_star_fp = gsm.matrix_multiply(d2_u_star_fp)
d2_u_star_fdp = gsm.matrix_multiply(d2_u_star_fdp)
dp = flex.complex_double(flex.grid(np, np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site.matrix_packed_u_as_symmetric(), 0, 0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0, i_u)
paste(d2_site_u_iso.matrix_transpose(), i_u, 0)
else:
paste(d2_site_u_star, 0, i_u)
paste(d2_site_u_star.matrix_transpose(), i_u, 0)
paste(d2_site_occ, 0, i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ, 0)
paste(d2_site_fp, 0, i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp, 0)
paste(d2_site_fdp, 0, i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp, 0)
if (not scatterer.flags.use_u_aniso()):
dp[i_u * np + i_u] = d2_u_iso_u_iso
dp[i_u * np + i_occ] = d2_u_iso_occ
dp[i_occ * np + i_u] = d2_u_iso_occ
dp[i_u * np + i_fp] = d2_u_iso_fp
dp[i_fp * np + i_u] = d2_u_iso_fp
dp[i_u * np + i_fdp] = d2_u_iso_fdp
dp[i_fdp * np + i_u] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star.matrix_packed_u_as_symmetric(), i_u,
i_u)
paste(d2_u_star_occ, i_u, i_occ)
paste(d2_u_star_occ.matrix_transpose(), i_occ, i_u)
paste(d2_u_star_fp, i_u, i_fp)
paste(d2_u_star_fp.matrix_transpose(), i_fp, i_u)
paste(d2_u_star_fdp, i_u, i_fdp)
paste(d2_u_star_fdp.matrix_transpose(), i_fdp, i_u)
dp[i_occ * np + i_fp] = d2_occ_fp
dp[i_fp * np + i_occ] = d2_occ_fp
dp[i_occ * np + i_fdp] = d2_occ_fdp
dp[i_fdp * np + i_occ] = d2_occ_fdp
yield dp
def d2f_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
tphkl_outer = tphkl.outer_product()
h,k,l = self.hkl
d_exp_huh_d_u_star = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.outer_product()
for scatterer in self.scatterers:
assert scatterer.scattering_type == "const"
w = scatterer.occupancy
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
ffp = 1 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(flex.grid(3,3), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3,1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3,6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3,1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(flex.grid(6,6), 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6,1), 0j)
d2_occ_fp = 0j
d2_occ_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = r.transpose()
d2_site_site += flex.complex_double(
site_gtmx *
(w * dw * ff * e * (-1) * tphkl_outer)
* site_gtmx.transpose())
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += flex.complex_double(site_gtmx * (
w * dw * ff * e * 1j * mtps * self.d_star_sq * tphkl))
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d2_site_u_star += flex.complex_double(
site_gtmx
* ((w * dw * ff * e * 1j * tphkl).outer_product(
mtps * d_exp_huh_d_u_star))
* u_star_gtmx.transpose())
d2_site_occ += flex.complex_double(site_gtmx * (
dw * ff * e * 1j * tphkl))
d2_site_fp += flex.complex_double(site_gtmx * (
w * dw * e * 1j * tphkl))
d2_site_fdp += flex.complex_double(site_gtmx * (
w * dw * e * (-1) * tphkl))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
d2_u_iso_occ += dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star += flex.complex_double(
u_star_gtmx
* (w * dw * ff * e * mtps**2 * d2_exp_huh_d_u_star_u_star)
* u_star_gtmx.transpose())
d2_u_star_occ += flex.complex_double(u_star_gtmx * (
dw * ff * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fp += flex.complex_double(u_star_gtmx * (
w * dw * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fdp += flex.complex_double(u_star_gtmx * (
w * dw * 1j * e * mtps * d_exp_huh_d_u_star))
d2_occ_fp += dw * e
d2_occ_fdp += dw * e * 1j
if (not scatterer.flags.use_u_aniso()):
i_occ, i_fp, i_fdp, np = 4, 5, 6, 7
else:
i_occ, i_fp, i_fdp, np = 9, 10, 11, 12
dp = flex.complex_double(flex.grid(np,np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site, 0,0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0,3)
paste(d2_site_u_iso.matrix_transpose(), 3,0)
else:
paste(d2_site_u_star, 0,3)
paste(d2_site_u_star.matrix_transpose(), 3,0)
paste(d2_site_occ, 0,i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ,0)
paste(d2_site_fp, 0,i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp,0)
paste(d2_site_fdp, 0,i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp,0)
if (not scatterer.flags.use_u_aniso()):
dp[3*7+3] = d2_u_iso_u_iso
dp[3*7+4] = d2_u_iso_occ
dp[4*7+3] = d2_u_iso_occ
dp[3*7+5] = d2_u_iso_fp
dp[5*7+3] = d2_u_iso_fp
dp[3*7+6] = d2_u_iso_fdp
dp[6*7+3] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star, 3,3)
paste(d2_u_star_occ, 3, 9)
paste(d2_u_star_occ.matrix_transpose(), 9, 3)
paste(d2_u_star_fp, 3, 10)
paste(d2_u_star_fp.matrix_transpose(), 10, 3)
paste(d2_u_star_fdp, 3, 11)
paste(d2_u_star_fdp.matrix_transpose(), 11, 3)
dp[i_occ*np+i_fp] = d2_occ_fp
dp[i_fp*np+i_occ] = d2_occ_fp
dp[i_occ*np+i_fdp] = d2_occ_fdp
dp[i_fdp*np+i_occ] = d2_occ_fdp
yield dp
def df_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
h,k,l = self.hkl
d_exp_huh_d_u_star = matrix.col([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
for i_scatterer,scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
wwo = scatterer.weight_without_occupancy()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = ffp + 1j * fdp
d_site = matrix.col([0,0,0])
if (not scatterer.flags.use_u_aniso()):
d_u_iso = 0
d_u_star = None
else:
d_u_iso = None
d_u_star = matrix.col([0,0,0,0,0,0])
d_occ = 0j
d_fp = 0j
d_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = r.transpose()
d_site += site_gtmx * (
w * dw * ff * e * 1j * tphkl)
if (not scatterer.flags.use_u_aniso()):
d_u_iso += w * dw * ff * e * mtps * self.d_star_sq
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d_u_star += u_star_gtmx * (
w * dw * ff * e * mtps * d_exp_huh_d_u_star)
d_occ += wwo * dw * ff * e
d_fp += w * dw * e
d_fdp += w * dw * e * 1j
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_site = gsm * d_site
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_u_star = gsm * d_u_star
result = flex.complex_double(d_site)
if (not scatterer.flags.use_u_aniso()):
result.append(d_u_iso)
else:
result.extend(flex.complex_double(d_u_star))
result.extend(flex.complex_double([d_occ, d_fp, d_fdp]))
yield result
def d2f_d_params_diag(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h,k,l = self.hkl
d_exp_huh_d_u_star = flex.double([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
for i_scatterer,scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(3*(3+1)//2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
else:
d2_u_star_u_star = flex.complex_double(6*(6+1)//2, 0j)
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3,3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
np = i_occ+3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
#
dpd = flex.complex_double(flex.grid(np,1), 0j)
def paste(d, i):
d.reshape(flex.grid(d.size(),1))
dpd.matrix_paste_block_in_place(d, i,0)
paste(d2_site_site.matrix_packed_u_diagonal(), 0)
if (not scatterer.flags.use_u_aniso()):
dpd[i_u] = d2_u_iso_u_iso
else:
paste(d2_u_star_u_star.matrix_packed_u_diagonal(), i_u)
yield dpd
def d2f_d_params(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h,k,l = self.hkl
d_exp_huh_d_u_star = flex.double([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
for i_scatterer,scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
wwo = scatterer.weight_without_occupancy()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(3*(3+1)//2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3,1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3,6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3,1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(6*(6+1)//2, 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6,1), 0j)
d2_occ_fp = 0j
d2_occ_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r*matrix.sym(sym_mat3=scatterer.u_star)*r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j*alpha)
site_gtmx = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3,3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += (w * dw * ff * e * 1j * mtps * self.d_star_sq) \
* site_gtmx.matrix_multiply(tphkl)
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_site_u_star += (w * dw * ff * e * 1j * mtps) \
* site_gtmx.matrix_multiply(
tphkl.matrix_outer_product(d_exp_huh_d_u_star)) \
.matrix_multiply(u_star_gtmx.matrix_transpose())
site_gtmx_tphkl = site_gtmx.matrix_multiply(tphkl)
d2_site_occ += (wwo * dw * ff * e * 1j) * site_gtmx_tphkl
d2_site_fp += (w * dw * e * 1j) * site_gtmx_tphkl
d2_site_fdp += (w * dw * e * (-1)) * site_gtmx_tphkl
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
d2_u_iso_occ += wwo * dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
u_star_gtmx_d_exp_huh_d_u_star = u_star_gtmx.matrix_multiply(
d_exp_huh_d_u_star)
d2_u_star_occ += (wwo * dw * ff * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fp += (w * dw * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fdp += (w * dw * 1j * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_occ_fp += wwo * dw * e
d2_occ_fdp += wwo * dw * e * 1j
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
i_fp, i_fdp, np = i_occ+1, i_occ+2, i_occ+3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = gsm.matrix_multiply(d2_site_u_iso)
else:
d2_site_u_star = gsm.matrix_multiply(d2_site_u_star)
d2_site_occ = gsm.matrix_multiply(d2_site_occ)
d2_site_fp = gsm.matrix_multiply(d2_site_fp)
d2_site_fdp = gsm.matrix_multiply(d2_site_fdp)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_site_u_star = d2_site_u_star.matrix_multiply(
gsm.matrix_transpose())
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
d2_u_star_occ = gsm.matrix_multiply(d2_u_star_occ)
d2_u_star_fp = gsm.matrix_multiply(d2_u_star_fp)
d2_u_star_fdp = gsm.matrix_multiply(d2_u_star_fdp)
dp = flex.complex_double(flex.grid(np,np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site.matrix_packed_u_as_symmetric(), 0,0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0,i_u)
paste(d2_site_u_iso.matrix_transpose(), i_u,0)
else:
paste(d2_site_u_star, 0,i_u)
paste(d2_site_u_star.matrix_transpose(), i_u,0)
paste(d2_site_occ, 0,i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ,0)
paste(d2_site_fp, 0,i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp,0)
paste(d2_site_fdp, 0,i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp,0)
if (not scatterer.flags.use_u_aniso()):
dp[i_u*np+i_u] = d2_u_iso_u_iso
dp[i_u*np+i_occ] = d2_u_iso_occ
dp[i_occ*np+i_u] = d2_u_iso_occ
dp[i_u*np+i_fp] = d2_u_iso_fp
dp[i_fp*np+i_u] = d2_u_iso_fp
dp[i_u*np+i_fdp] = d2_u_iso_fdp
dp[i_fdp*np+i_u] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star.matrix_packed_u_as_symmetric(), i_u, i_u)
paste(d2_u_star_occ, i_u, i_occ)
paste(d2_u_star_occ.matrix_transpose(), i_occ, i_u)
paste(d2_u_star_fp, i_u, i_fp)
paste(d2_u_star_fp.matrix_transpose(), i_fp, i_u)
paste(d2_u_star_fdp, i_u, i_fdp)
paste(d2_u_star_fdp.matrix_transpose(), i_fdp, i_u)
dp[i_occ*np+i_fp] = d2_occ_fp
dp[i_fp*np+i_occ] = d2_occ_fp
dp[i_occ*np+i_fdp] = d2_occ_fdp
dp[i_fdp*np+i_occ] = d2_occ_fdp
yield dp
