def test1(self):
from mccomponents.sample.sansmodel import sansspheremodel_kernel
scale=1.0e-6
radius=60.0 #A
contrast=1.0 #A-2
background=0 #cm-1
absorption_cross_section = 0
scattering_cross_section = 1
Qmin = 0
Qmax = 10
k = sansspheremodel_kernel(
scale, radius, contrast, background,
absorption_cross_section, scattering_cross_section,
Qmin, Qmax)
from mccomponents.sample import scattererEngine
kengine = scattererEngine( k )
print dir(kengine)
n = mcni.neutron( r = (0,0,0), v = (0,0,3000) )
kengine.scatter( n )
print n
return
def test2(self):
from mccomponents.sample.phonon import periodicdispersion_fromidf
dispersion = periodicdispersion_fromidf(datapath)
from mccomponents.sample import scattererEngine
disp = scattererEngine(dispersion)
from mccomponents.sample.phonon.bindings import default
binding = default()
b = 2.001014429
N = 20
Qs = [
[b / 2, b / 2, 0],
[0, 0, 0],
[b, 0, 0],
[b / 2, b / 2, b / 2],
[0, 0, 0],
]
xs = [[] for i in range(3)]
ys = [[] for i in range(3)]
segment = 0
for start, end in zip(Qs[:-1], Qs[1:]):
start = numpy.array(start)
end = numpy.array(end)
diff = end - start
step = diff / N
qs = [start + step * i for i in range(N + 1)]
for br in range(3):
es = [disp.energy(br, binding.Q(q)) for q in qs]
xs[br] += list(numpy.arange(0, 1. + 1e-10, 1. / N) + segment)
ys[br] += es
segment += 1
for br in range(3):
x = xs[br]
y = ys[br]
pylab.plot(x, y)
pylab.show()
return
def test2(self):
from mccomponents.sample.phonon import periodicdispersion_fromidf
dispersion = periodicdispersion_fromidf( datapath )
from mccomponents.sample import scattererEngine
disp = scattererEngine( dispersion )
from mccomponents.sample.phonon.bindings import default
binding = default()
b = 2.001014429
N = 20
Qs = [
[b/2,b/2,0],
[0,0,0],
[b,0,0],
[b/2,b/2,b/2],
[0,0,0],
]
xs=[[] for i in range(3)]; ys=[[] for i in range(3)]
segment = 0
for start, end in zip(Qs[:-1], Qs[1:]):
start = numpy.array(start)
end = numpy.array(end)
diff = end-start
step = diff/N
qs = [ start + step*i for i in range(N+1) ]
for br in range(3):
es = [ disp.energy(br, binding.Q(q)) for q in qs ]
xs[br] += list(numpy.arange(0, 1.+1e-10, 1./N)+segment)
ys[br] += es
segment += 1
for br in range(3):
x = xs[br]
y = ys[br]
pylab.plot(x,y)
pylab.show()
return
def test1(self):
from mccomponents.sample.phonon import dispersion_fromidf
dispersion = dispersion_fromidf(datapath)
from mccomponents.sample import scattererEngine
disp = scattererEngine(dispersion)
a = 3.52 # Ni lattice parameter
from math import pi
ra = 2 * pi / a # reciprocal lattice parameter
N = 10
qs = [(0, 0, ra * i / N) for i in range(N)]
from mccomponents.sample.phonon.bindings import default
binding = default()
es = [disp.energy(0, binding.Q(q)) for q in qs]
print qs, es
return
def test1(self):
from mccomponents.sample.sansmodel import sansspheremodel_kernel
scale = 1.0e-6
radius = 60.0 #A
contrast = 1.0 #A-2
background = 0 #cm-1
absorption_cross_section = 0
scattering_cross_section = 1
Qmin = 0
Qmax = 10
k = sansspheremodel_kernel(scale, radius, contrast, background,
absorption_cross_section,
scattering_cross_section, Qmin, Qmax)
from mccomponents.sample import scattererEngine
kengine = scattererEngine(k)
print dir(kengine)
n = mcni.neutron(r=(0, 0, 0), v=(0, 0, 3000))
kengine.scatter(n)
print n
return
def test2(self):
from mccomponents.sample.phonon import periodicdispersion_fromidf
dispersion = periodicdispersion_fromidf(datapath)
from mccomponents.sample import scattererEngine
disp = scattererEngine(dispersion)
a = 3.52 # Ni lattice parameter
from math import pi
ra = 2 * pi / a # reciprocal lattice parameter
N = 10
qs = [(0, 0, ra * i / N) for i in range(N)]
from mccomponents.sample.phonon.bindings import default
binding = default()
es = [disp.energy(0, binding.Q(q)) for q in qs]
print qs, es
q = qx, qy, qz = 1.2, 0.3, 0.22
Q = binding.Q(q)
self.assertAlmostEqual(
disp.energy(0, binding.Q(qx + 2 * ra, qy + 8 * ra, qz - 6 * ra)),
disp.energy(0, Q), 3)
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
def disp_from_datadir(datadir):
from mccomponents.sample.phonon import periodicdispersion_fromidf
dispersion = periodicdispersion_fromidf(datadir)
from mccomponents.sample import scattererEngine
return scattererEngine(dispersion)