def gethkls_xfab(self,dsmax,spg):
"""
Generate hkl list
Argument dsmax is the d* limit (eg 1/d)
Argument spg is the space group name, e.g. 'R3-c'
"""
stl_max = dsmax/2.
from xfab import tools,sg
raw_peaks = tools.genhkl_all(self.lattice_parameters,
0 , stl_max,
sgname=spg,
output_stl=True)
peaks = []
for i in range(len(raw_peaks)):
peaks.append([raw_peaks[i,3]*2,(raw_peaks[i,0],raw_peaks[i,1],raw_peaks[i,2])])
self.peaks = peaks
return peaks
def gen_miller(param, phase):
"""
Generate set of miller indices.
Changed from old tools.genhkl to new tools.genhkl_all
"""
sintlmin = n.sin(param['theta_min'] * n.pi / 180) / param['wavelength']
sintlmax = n.sin(param['theta_max'] * n.pi / 180) / param['wavelength']
hkl = tools.genhkl_all(
param['unit_cell_phase_%i' % phase],
sintlmin,
sintlmax,
sgname=param['sgname_phase_%i' % phase],
cell_choice=param['cell_choice_phase_%i' % phase],
)
return hkl
def initializeHKL(PARfile, sg):
# Read files for information from both .log and .gve
(unitcell, lattice, distance, omat, tilts, wavelength, wedge, centers,
pixsize) = readparfile(PARfile)
pixx = 2048
pixy = pixx
## Calculate largest possible ring portion on detector
## units in mm from edge of detector
xdist_a = (pixx - centers[0]) * pixsize[0]
xdist_b = (centers[0]) * pixsize[0]
ydist_a = (pixy - centers[1]) * pixsize[1]
ydist_b = (centers[1]) * pixsize[1]
ring_rad = np.zeros((4))
ring_rad[0] = math.sqrt(xdist_a**2 + ydist_a**2)
ring_rad[1] = math.sqrt(xdist_a**2 + ydist_b**2)
ring_rad[2] = math.sqrt(xdist_b**2 + ydist_a**2)
ring_rad[3] = math.sqrt(xdist_b**2 + ydist_b**2)
max_rad = np.max(ring_rad)
max2th = math.atan(max_rad / distance)
## Calculates min and max sin2th on detector
sintlmin = 0
sintlmax = np.sin((max2th) / 2) / wavelength
sintlmax = sintlmax * 1.05 # over estimates a bit
# Lattice information for unit cell
hkls = tools.genhkl_all(unitcell,
sintlmin,
sintlmax,
sgno=int(sg),
output_stl=True)
sinth = np.zeros((hkls.shape[0]))
for i in range(0, hkls.shape[0]):
sinth[i] = hkls[i, 3] * wavelength
sinth_unique = np.unique(sinth)
return (sinth_unique)
def gen_miller(param, phase):
"""
Generate set of miller indices.
Henning Osholm Sorensen, Risoe DTU
Changed from old tools.genhkl to new tools.genhkl_all
Jette Oddershede, DTU Physics, March 2013
"""
sintlmin = n.sin(param['theta_min'] * n.pi / 180) / param['wavelength']
sintlmax = n.sin(param['theta_max'] * n.pi / 180) / param['wavelength']
hkl = tools.genhkl_all(
param['unit_cell_phase_%i' % phase],
sintlmin,
sintlmax,
sgname=param['sgname_phase_%i' % phase],
cell_choice=param['cell_choice_phase_%i' % phase],
)
return hkl
def gen_Miller_ds(param, phasenum):
"""
Generate a list of peaks for a given crystal structure
Parameter:
- param
- phasenum: phase number
In the param dictionnary
- param['theta_min']
- param['theta_max']
- param['wavelength']
- param['unit_cell_phase_%i' % phasenum] as [a,b,c,alpha,beta,gamma']
- param['sgname_phase_%i' % phasenum]: space group number
- param['cell_choice_phase_%i' % phasenum]
Returns
- an array of hkl with hkl[i]=[h, k, l, ds] with ds = 1/d
Inspired from code in polyxsim.reflections, with the addition of ds in return value
Created: 12/2019, S. Merkel, Univ. Lille, France
"""
sintlmin = numpy.sin(numpy.radians(
param['theta_min'])) / param['wavelength']
sintlmax = numpy.sin(numpy.radians(
param['theta_max'])) / param['wavelength']
hkl = tools.genhkl_all(param['unit_cell_phase_%i' % phasenum], \
sintlmin, \
sintlmax, \
sgname=param['sgname_phase_%i' % phasenum], \
cell_choice=param['cell_choice_phase_%i' % phasenum], \
output_stl=True)
# Calculating ds, with is 2*sin(theta)/lambda
hkl[:, 3] = hkl[:, 3] * 2
# print hkl
# exit()
return hkl