def loadPattern(xyz, laz):
text = open(laz).read()
from mccomponents.sample.diffraction.parsers.laz import parse
peaks = parse(text).peaks
# load structure
from sampleassembly.crystal.ioutils import xyzfile2unitcell
structure = xyzfile2unitcell(xyz)
# diffraction pattern
return DiffractionPattern(structure, peaks)
def loadPattern(xyz, laz):
text = open(laz).read()
from mccomponents.sample.diffraction.parsers.laz import parse
peaks = parse(text).peaks
# load structure
from sampleassembly.crystal.ioutils import xyzfile2unitcell
structure = xyzfile2unitcell(xyz)
# diffraction pattern
return DiffractionPattern(structure, peaks)
def onXYZfile(self, xyzfile):
from sampleassembly.crystal.ioutils import xyzfile2unitcell
try:
self.element.unitcell = xyzfile2unitcell(xyzfile)
except:
import traceback
tb = traceback.format_exc()
marker = '*' * 60
msg = "Unable to parse xyz file %s. traceback:\n%s\n%s\n%s" % (
xyzfile, marker, tb, marker)
raise RuntimeError(msg)
return
def test1(self):
# load peaks
laz = os.path.join(aluminum_dir, 'powderdiffr', 'Al.laz')
text = open(laz).read()
from mccomponents.sample.diffraction.parsers.laz import parse
peaks = parse(text).peaks
# load structure
from sampleassembly.crystal.ioutils import xyzfile2unitcell
xyz = os.path.join(aluminum_dir, 'crystal', 'Al.xyz')
structure = xyzfile2unitcell(xyz)
# diffraction pattern
from mccomponents.sample.diffraction.powder import total_scattering_cross_section, DiffractionPattern
dp = DiffractionPattern(structure, peaks)
# compute
for Ei in [10, 100, 1000, 10000]:
print Ei, total_scattering_cross_section(Ei, dp)
return
def test1(self):
# load peaks
laz = os.path.join(aluminum_dir, 'powderdiffr', 'Al.laz')
text = open(laz).read()
from mccomponents.sample.diffraction.parsers.laz import parse
peaks = parse(text).peaks
# load structure
from sampleassembly.crystal.ioutils import xyzfile2unitcell
xyz = os.path.join(aluminum_dir, 'crystal', 'Al.xyz')
structure = xyzfile2unitcell(xyz)
# diffraction pattern
from mccomponents.sample.diffraction.powder import total_scattering_cross_section, DiffractionPattern
dp = DiffractionPattern(structure, peaks)
# compute
for Ei in [10, 100, 1000, 10000]:
print Ei, total_scattering_cross_section(Ei, dp)
return
def from_data_dir(
datadir=None,
disp=None,
N=int(1e6),
Q_bins=np.arange(0, 11, 0.1),
E_bins=np.arange(0, 50, 0.5),
doshist=None,
T=300.,
Ei=100.,
max_det_angle=135.,
include_multiphonon=True,
):
if disp is None:
from mccomponents.sample.phonon import periodicdispersion_fromidf
dispersion = periodicdispersion_fromidf(datadir)
from mccomponents.sample import scattererEngine
disp = scattererEngine(dispersion)
#
poscar = os.path.join(datadir, 'POSCAR')
from mcvine.phonon import from_phonopy
from_phonopy.make_crystal_xyz('structure.xyz', poscar)
from sampleassembly.crystal.ioutils import xyzfile2unitcell
uc = xyzfile2unitcell('structure.xyz')
# generate Q points
max_Q = Q_bins[-1]
Qmag_p3 = np.random.rand(N) * max_Q**3
Qmag = Qmag_p3**(1. / 3)
cos_theta = np.random.rand(N) * 2 - 1 # -1 -- 1
phi = np.random.rand(N) * 2 * np.pi
sin_theta = np.sqrt(1 - cos_theta * cos_theta)
sin_phi = np.sin(phi)
cos_phi = np.cos(phi)
Qx = Qmag * sin_theta * cos_phi
Qy = Qmag * sin_theta * sin_phi
Qz = Qmag * cos_theta
Qpoints = np.array([Qx, Qy, Qz]).T
# in reciprocal units
hkls = np.dot(Qpoints, uc.lattice.base.T) / (2 * np.pi)
#
omega, pols = _getEsAndPols(disp, Qpoints)
from phonopy.interface import vasp
atoms = vasp.read_vasp(poscar)
masses = atoms.get_masses()
average_mass = np.mean(masses)
from ._calc import calcIQE, apply_corrections
Qbb, Ebb, I = calcIQE(uc, omega, pols, Qpoints, Q_bins, E_bins)
# additional corrections
IQEhist = apply_corrections(I, Qbb, Ebb, N, average_mass, uc, doshist, T,
Ei, max_det_angle)
if include_multiphonon:
from ._calc import multiphononSQE
mphIQE = multiphononSQE(T=T,
doshist=doshist,
mass=average_mass,
Q_bins=Q_bins,
E_bins=E_bins)
symbols = [a.element for a in uc]
from ..atomic_scattering import AtomicScattering
total_xs = sum(AtomicScattering(s).sigma() for s in symbols)
return IQEhist, mphIQE * (total_xs / 4 / np.pi, 0)
return IQEhist
