def fit_crystal(uc, refl_list):
try:
uc_system, uc_params = uc.get_lattice_params()
start = uc_params
lower = [
0,
] * len(uc_params)
upper, sigma = _get_uc_upper_limits(uc_system)
except AttributeError:
raise DiffcalcException(
"UB matrix not initialised. Cannot run UB matrix fitting procedure."
)
try:
from org.apache.commons.math3.optim.nonlinear.scalar.noderiv import CMAESOptimizer
from org.apache.commons.math3.optim.nonlinear.scalar import GoalType
from org.apache.commons.math3.optim import MaxEval, InitialGuess, SimpleBounds
from org.apache.commons.math3.random import MersenneTwister
optimizer = CMAESOptimizer(30000, 0, True, 10, 0, MersenneTwister(),
True, None)
opt = optimizer.optimize(
(MaxEval(5000), get_crystal_target(refl_list,
uc_system), GoalType.MINIMIZE,
CMAESOptimizer.PopulationSize(15), CMAESOptimizer.Sigma(sigma),
InitialGuess(start), SimpleBounds(lower, upper)))
vals = opt.getPoint()
#res = opt.getValue()
except ImportError:
from scipy.optimize import minimize
ref_data = _get_refl_hkl(refl_list)
bounds = zip(lower, upper)
res = minimize(_func_crystal,
start,
args=(uc_system, ref_data),
method='SLSQP',
tol=1e-10,
options={
'disp': False,
'maxiter': 10000,
'eps': 1e-6,
'ftol': 1e-10
},
bounds=bounds)
vals = res.x
res_cr = CrystalUnderTest('trial', uc_system, 1, 1, 1, 90, 90, 90)
res_cr._set_cell_for_system(uc_system, *vals)
return res_cr
def _func_crystal(vals, uc_system, ref_data):
trial_cr = CrystalUnderTest('trial', uc_system, 1, 1, 1, 90, 90, 90)
try:
trial_cr._set_cell_for_system(uc_system, *vals)
except Exception:
return 1e6
res = 0
I = matrix('1 0 0; 0 1 0; 0 0 1')
for (hkl_vals, pos_vals, en) in ref_data:
wl = 12.3984 / en
[_, DELTA, NU, _, _, _] = create_you_matrices(*pos_vals.totuple())
q_pos = (NU * DELTA - I) * matrix([[0], [2 * pi / wl], [0]])
q_hkl = trial_cr.B * hkl_vals
res += (norm(q_pos) - norm(q_hkl))**2
return res
