def norm_at(E, Qaxis, Ei):
"compute normalization(Q) array for the given energy transfer"
ki = conversion.e2k(Ei)
Ef = Ei - E
kf = conversion.e2k(Ef)
Qmin = np.abs(ki - kf)
Qmax = ki + kf
rt = np.zeros(Qaxis.shape)
in_range = (Qaxis < Qmax) * (Qaxis > Qmin)
rt[in_range] = (Qaxis * (2 * np.pi / ki / kf))[in_range]
return rt
def dgs_setEi(sample, Ei):
"""set incident energy for DGS experiment
A sample has kernels with parameters that may be affected by Ei.
For example, a powder SQE kernel has Qrange and Erange.
When this sample is put into a beam in a DGS instrument,
it is better to simulate only within the dynamical range determined
by Ei and instrument geometry.
Here we do some quick calculation to estimate the dynamical range
for the given Ei, without considering the instrument geometry.
The main purpose of this is to limit the simulation dynamical
range to speed up the simulation
Ei: float. unit: meV
"""
from mcni.utils import conversion
ki = conversion.e2k(Ei) # \AA^-1
Qrange = (0., 2*ki)
Erange = (-Ei, Ei*.99)
for excitation in sample.excitations:
if 'Qrange' in excitation.__dict__:
excitation.Qrange = ','.join(_to_str_tuple_with_unit(
_combine_range(Qrange, _to_float_tuple(excitation.Qrange, '1./angstrom')),
'1./angstrom'))
if 'Erange' in excitation.__dict__:
excitation.Erange = ','.join(_to_str_tuple_with_unit(
_combine_range(Erange, _to_float_tuple(excitation.Erange, 'meV')),
'meV'))
continue
return
def test():
class powdersqe:
type = "powderSQE"
SQEhist = "Al-iqe.h5"
Erange = "-50*meV,50*meV"
Qrange = "1/angstrom, 10/angstrom"
class mysample:
class lattice:
constants = 1., 1., 1., 90., 90., 90.
basis_vectors = [[1,0,0],[0,1,0],[0,0,1]]
chemical_formula="V"
class shape:
class sphere:
radius = 3
mysample.excitations = [powdersqe]
Ei = 30.; ki = C.e2k(Ei)
sample.dgs_setEi(mysample, Ei)
Qmin, Qmax = sample._to_float_tuple(mysample.excitations[0].Qrange, '1./angstrom')
assert np.isclose(Qmin, 1.)
assert np.isclose(Qmax, 2*ki)
Emin, Emax = sample._to_float_tuple(mysample.excitations[0].Erange, 'meV')
assert np.isclose(Emin, -Ei)
assert np.isclose(Emax, Ei*.99)
return
def Eresidual(xtalori, hkl, Etarget, angles, Ei):
"""compute residual of energy transfer
This method compute a series of psi angle and corresponding residual
(E - Etarget).
We only need to simulate crystal orientation where the residual
is close to zero.
"""
from mcni.utils import conversion as conv
ki = conv.e2k(Ei)
kiv = np.array([ki,0,0])
r = np.zeros((len(angles), 2))
for i, psi in enumerate(angles):
xtalori.psi = psi / 180. * np.pi
hkl2cartesian = xtalori.hkl2cartesian_mat()
# cart2hkl = xtalori.cartesian2hkl_mat()
Qcart = np.dot(hkl, hkl2cartesian)
# print hkl, np.dot(Qcart, cart2hkl)
# print Qcart
kfv = kiv - Qcart
kf = np.linalg.norm(kfv)
Ef = conv.k2e(kf)
E = Ei - Ef
r[i] = psi, E-Etarget
continue
return r
def convolveSQE(self, IQE, Ei, *args):
max_det_angle = 140. * np.pi / 180.
a = self.calc_res_a(Ei, *args)
E_new, Q, I_new = convolveSQE(a, IQE, Ei)
mask = np.zeros(I_new.shape, dtype=bool)
from mcni.utils import conversion
ki = conversion.e2k(Ei)
for iE in range(E_new.size):
E1 = E_new[iE]
if E1 > Ei:
mask[:, iE] = 1
continue
Ef1 = Ei - E1
kf1 = conversion.e2k(Ef1)
Qmin = abs(ki - kf1)
Qmax = np.sqrt(ki * ki + kf1 * kf1 -
2 * ki * kf1 * np.cos(max_det_angle))
mask[Q < Qmin, iE] = 1
mask[Q > Qmax, iE] = 1
I_new[mask] = np.nan
return E_new, Q, I_new
def hklE2rtz(hkl, E, xtalori, Ei, r):
"""convert from hkl to cylinderical coordinate sytem
"""
ki_scalar = conv.e2k(Ei)
ki = [ki_scalar, 0, 0]
Q = hkl2Q(hkl, xtalori)
kf = ki - Q
kf_dir = kf/np.linalg.norm(kf)
scale_factor = r/np.linalg.norm(kf_dir[:, :3])
position = kf_dir * scale_factor
np.allclose(np.linalg.norm(position[:, :3]), r)
theta = np.arctan2(position[:, 1], position[:, 0])
return r, theta, position[:, 2]
def sqe(
E, g, Qmax=None, Qmin=0, dQ=None,
T=300, M=50, N=5, starting_order=2, Emax=None,
):
"""compute sum of multiphonon SQE from dos
S = \sum_{i=2,N} S_i(Q,E)
Note: single phonon scattering is not included. only 2-phonons and up
E,g: input DOS data
energy axis is inferred from input DOS data
Q axis is defined by Qmax, Qmin, and dQ
T: temperature (Kelvin)
M: atomic mass
N: maximum number of order for multi-phonon scattering
starting_order: 2: start with 2 phonon scattering
"""
dos_sample = len(E)
e0 = E[0]
de = E[1] - E[0]
emax = E[-1]
# expand E
Emax = Emax or e0+de*3*dos_sample
E = np.arange(e0, Emax, de)
g = np.concatenate((g, np.zeros(len(E)-len(g))))
# normalize
int_g = np.sum(g) * de
g/=int_g
# Q axis
if Qmax is None:
from mcni.utils import conversion
Qmax = conversion.e2k(emax) * 3
if dQ is None:
dQ = (Qmax-Qmin)/200
Q = np.arange(Qmin, Qmax, dQ)
# beta
kelvin2mev = 0.0862
beta = 1./(T*kelvin2mev)
# compute S
S = None
for i, (Q,E,S1) in enumerate(iterSQESet(N, Q, dQ, E, de, M, g, beta)):
if i < starting_order - 1: continue
if S is None: S = S1; continue
S += S1
continue
# sum over 2..N
# S = S_set[starting_order-1:].sum(axis=0)
return Q, E, S
def computeKf(Ei, E, Q, log):
ki = Conv.e2k(Ei);
log.write( "* ki=%s\n" % (ki,) )
kiv = np.array([ki, 0, 0])
kfv = kiv - Q
log.write( "* vectors ki=%s, kf=%s\n" % (kiv, kfv) )
Ef = Ei - E
# ** Verify the momentum and energy transfers **
log.write( "These two numbers should be very close:\n")
log.write( " %s\n" % (Ei-Conv.k2e(np.linalg.norm(kfv)),) )
log.write( " %s\n" % (Ei-Ef,) )
assert np.isclose(Ef, Conv.k2e(np.linalg.norm(kfv)))
log.write( " Ei=%s, Ef=%s\n" % (Ei,Ef) )
return kfv, Ef
def rtzE2hkl(r, theta, z, E, xtalori, Ei):
"""convert from cylinderical coordinate sytem to hkl
"""
kf_dir = [r*np.cos(theta), r*np.sin(theta), z]
kf_dir = np.array(kf_dir).T # (N,3)
kf_dir /= np.linalg.norm(kf_dir, axis=-1)[:, np.newaxis] # (N,3)
Ef = Ei - E # (N,)
kf_scalar = (conv.SE2V*conv.V2K) * Ef**.5 # (N,)
del Ef
kf = kf_dir * kf_scalar[:, np.newaxis] # (N,3)
del kf_scalar
ki_scalar = conv.e2k(Ei)
ki = [ki_scalar, 0, 0]
Q = ki - kf; del ki, kf
return Q2hkl(Q, xtalori)
def compute_xE_curve(xaxis, hkl0, ex, mat, Ei):
"""given xaxis and ex, compute hkl = hkl0+ x*ex
and then compute energy transfer E
mat: convert hkl to Q
"""
ki = Conv.e2k(Ei)
kiv = np.array([ki, 0, 0])
hkl = hkl0 + xaxis[:, np.newaxis] * ex
Q = np.dot(hkl, mat) # NX3
kfv = kiv - Q # NX3
kf2 = np.sum(kfv**2, -1) # N
kf = np.sqrt(kf2) # N
# theta is the angle in the scattering plane (x-y)
theta = np.arctan2(kfv[:, 1], kfv[:, 0]) # N
# phi is the angle off the scattering plane. sin(phi) = z/r
phi = np.arcsin(kfv[:, 2] / kf)
Ef = kf2 * (Conv.K2V**2 * Conv.VS2E)
E = Ei - Ef
return E, theta, phi
def total_scattering_cross_section(Ei, dp):
"""compute the total scattering cross section
by powder diffraction
from the given known list of peaks.
This cross section is per unit cell.
According to Squires, cross section by one Debye Scherrer cone is
\sigma_{\tau} = 1/v_0 \lambda^3/(4sin(\theta/2)) \sum_{all \tau\prime of same length} |F_N(\tau\prime)|^2
The total cross section is the sum of all such cones
(number of cones is limited by Ei)
Limitation:
* the diffraction peaks list usually could be limited
if they are loaded from a file such as laz.
Probably better be computed directly from the structure.
When the peaks list is limited, the calculation
would be wrong when Ei gets larger
(should see more diff peaks but they are not counted).
* only consider the ideal powder diffraction without
vibrations.
"""
from mcni.utils import conversion as conv
import numpy as np
k = conv.e2k(Ei)
l = np.pi * 2 / k
ucvol = dp.structure.lattice.getVolume()
# loop over peaks, for each peak that contributes
# add its contribution
sigma = 0
for peak in dp.peaks:
q = peak.q
if q > 2*k: continue
sinthetaover2 = q/2/k
F_squared = peak.F_squared
mul = peak.multiplicity
sigma += l**3 / ucvol / 4 / sinthetaover2 * F_squared * mul
continue
return sigma
def compute_hE_curve(hmin, hmax, dh, k, l, mat, Ei):
"""given k, l values, compute h, E
mat: convert hkl to Q
"""
ki = Conv.e2k(Ei)
kiv = np.array([ki, 0, 0])
h = np.arange(hmin, hmax, dh) # N
hkl = np.vstack((h, np.repeat(k, h.size), np.repeat(l, h.size))).T # NX3
Q = np.dot(hkl, mat) # NX3
kfv = kiv - Q # NX3
kf2 = np.sum(kfv**2, -1) # N
kf = np.sqrt(kf2) # N
# theta is the angle in the scattering plane (x-y)
theta = np.arctan2(kfv[:, 1], kfv[:, 0]) # N
# phi is the angle off the scattering plane. sin(phi) = z/r
phi = np.arcsin(kfv[:, 2], kf)
Ef = kf2 * (Conv.K2V**2 * Conv.VS2E)
E = Ei - Ef
return h, E, theta, phi
def total_scattering_cross_section(Ei, dp):
"""compute the total scattering cross section
by powder diffraction
from the given known list of peaks.
This cross section is per unit cell.
According to Squires, cross section by one Debye Scherrer cone is
\sigma_{\tau} = 1/v_0 \lambda^3/(4sin(\theta/2)) \sum_{all \tau\prime of same length} |F_N(\tau\prime)|^2
The total cross section is the sum of all such cones
(number of cones is limited by Ei)
Limitation:
* the diffraction peaks list usually could be limited
if they are loaded from a file such as laz.
Probably better be computed directly from the structure.
When the peaks list is limited, the calculation
would be wrong when Ei gets larger
(should see more diff peaks but they are not counted).
* only consider the ideal powder diffraction without
vibrations.
"""
from mcni.utils import conversion as conv
import numpy as np
k = conv.e2k(Ei)
l = np.pi * 2 / k
ucvol = dp.structure.lattice.getVolume()
# loop over peaks, for each peak that contributes
# add its contribution
sigma = 0
for peak in dp.peaks:
q = peak.q
if q > 2 * k: continue
sinthetaover2 = q / 2 / k
F_squared = peak.F_squared
mul = peak.multiplicity
sigma += l**3 / ucvol / 4 / sinthetaover2 * F_squared * mul
continue
return sigma
def test1(self):
'kernel orientation'
# source
from mcni.components.MonochromaticSource import MonochromaticSource
import mcni, numpy as np
Ei = 100
from mcni.utils import conversion as Conv
ki = Conv.e2k(Ei)
vi = Conv.e2v(Ei)
Qdir = np.array([np.sqrt(3)/2, 0, -1./2])
Q = Qdir * 2
kf = np.array([0,0,ki]) - Q
Ef = Conv.k2e(np.linalg.norm(kf))
E = Ei-Ef
dv = Qdir * Conv.k2v(Q)
vf = np.array([0,0,vi]) - dv
# print ki, Q, kf
# print Ei, Ef, E
neutron = mcni.neutron(r=(0,0,-1), v=(0,0,vi), prob=1)
source = MonochromaticSource('s', neutron, dx=0.001, dy=0.001, dE=0)
# sample
from mccomponents.sample import samplecomponent
scatterer = samplecomponent('sa', 'cyl/sampleassembly.xml' )
# incident
N = 1000
neutrons = mcni.neutron_buffer(N)
neutrons = source.process(neutrons)
# print neutrons
# scatter
scatterer.process(neutrons)
# print neutrons
self.assertEqual(len(neutrons), N)
for neutron in neutrons:
np.allclose(neutron.state.velocity, vf)
self.assert_(neutron.probability > 0)
continue
return
def compute(sample_yml,
Ei,
dynamics,
psi_scan,
instrument,
pixel,
tofwidths,
beamdivs,
samplethickness,
plot=False):
# XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# should P be the T0 chopper?
L_PM = mcvine.units.parse(
instrument.L_m2fc
) / mcvine.units.meter # P chopper to M chopper distance
L_PS = mcvine.units.parse(
instrument.L_m2s) / mcvine.units.meter # P chopper to sample
L_MS = L_PS - L_PM
#
R = mcvine.units.parse(instrument.detsys_radius) / mcvine.units.meter #
hkl0 = dynamics.hkl0
hkl_dir = dynamics.hkl_dir # projection
psimin = psi_scan.min
psimax = psi_scan.max
dpsi = psi_scan.step
# dynamics calculations
E = dynamics.E
dq = dynamics.dq
hkl = hkl0 + dq * hkl_dir
from mcni.utils import conversion as Conv
vi = Conv.e2v(Ei)
ti = L_PM / vi * 1e6 # microsecond
Ef = Ei - E
vf = Conv.e2v(Ef)
# find the psi angle
from mcvine.workflow.singlextal.io import loadXtalOriFromSampleYml
xtalori = loadXtalOriFromSampleYml(sample_yml)
from mcvine.workflow.singlextal.solve_psi import solve
results = solve(xtalori,
Ei,
hkl,
E,
psimin,
psimax,
Nsegments=NSEGMENTS_SOLVE_PSI)
from mcvine.workflow.singlextal.coords_transform import hkl2Q
for r in results:
xtalori.psi = r * np.pi / 180
print("psi=%s, Q=%s" % (r, hkl2Q(hkl, xtalori)))
print("hkl2Q=%r\n(Q = hkl dot hkl2Q)" %
(xtalori.hkl2cartesian_mat(), ))
# these are the psi angles that the particular point of interest will be measured
# print results
assert len(results)
# XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# only select the first one. this is OK for most cases but there are cases where more than
# one psi angles satisfy the condition
psi = results[0]
xtalori.psi = psi * np.pi / 180
Q = hkl2Q(hkl, xtalori)
hkl2Q_mat = xtalori.hkl2cartesian_mat()
# print Q
# print hkl2Q_mat
#
Q_len = np.linalg.norm(Q)
# print Q_len
ki = Conv.e2k(Ei)
# print ki
kiv = np.array([ki, 0, 0])
kfv = kiv - Q
# print kfv
#
# ** Verify the momentum and energy transfers **
# print Ei-Conv.k2e(np.linalg.norm(kfv))
# print Ei-Ef
assert np.isclose(Ei - Ef, E)
# ** Compute detector pixel position **
z = kfv[2] / (kfv[0]**2 + kfv[1]**2)**.5 * R
L_SD = (z**2 + R**2)**.5
# print z, L_SD
# ### Constants
eV = 1.60218e-19
meV = eV * 1e-3
mus = 1.e-6
hbar = 1.0545718e-34
AA = 1e-10
m = 1.6750e-24 * 1e-3 #kg
from numpy import sin, cos
# dE calcuation starts here
# ## Differentials
pE_pt = -m * (vi**3 / L_PM + vf**3 / L_SD * L_MS / L_PM)
# convert to eV/microsecond
pE_pt /= meV / mus
# print pE_pt
pE_ptMD = m * vf**3 / L_SD
pE_ptMD /= meV / mus
# print pE_ptMD
pE_pLPM = m / L_PM * (vi**2 + vf**3 / vi * L_MS / L_SD)
pE_pLPM /= meV
# print pE_pLPM
pE_pLMS = -m / L_SD * (vf**3 / vi)
pE_pLMS /= meV
# print pE_pLMS
pE_pLSD = -m * vf * vf / L_SD
pE_pLSD /= meV
# print pE_pLSD
# we don't need pE_pLSD, instead we need pE_pR and pE_pz. R and z are cylinder radius and z coordinate
pE_pR = pE_pLSD * (R / L_SD)
pE_pz = pE_pLSD * (z / L_SD)
# print pE_pR, pE_pz
# XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# ## ** Paramters: Estimate of standard deviations
# tau_P = 10 # microsecond
# tau_M = 8 # microsecond
tau_P = tofwidths.P
tau_M = tofwidths.M
#
# tau_D = 10 # microsecond
tau_D = mcvine.units.parse(
pixel.radius) / mcvine.units.meter * 2 / vf * 1e6 # microsecond
# ## Calculations
pE_p_vec = [pE_pt, pE_ptMD, pE_pLPM, pE_pLMS, pE_pR, pE_pz]
pE_p_vec = np.array(pE_p_vec)
J_E = pE_p_vec / E
# print J_E
sigma_t = (tau_P**2 + tau_M**2)**.5
sigma_tMD = (tau_M**2 + tau_D**2)**.5
# XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
div = (beamdivs.theta**2 + beamdivs.phi**2)**.5 # a crude approx
sigma_LPM = L_PM * div * div
# mainly due to sample size
sigma_LMS = samplethickness
# mainly due to det tube diameter
sigma_R = mcvine.units.parse(pixel.radius) / mcvine.units.meter * 2
# pixel size
sigma_z = mcvine.units.parse(pixel.height) / mcvine.units.meter
sigma = np.array(
[sigma_t, sigma_tMD, sigma_LPM, sigma_LMS, sigma_R, sigma_z])
# print sigma
sigma2 = sigma * sigma
# print sigma2
sigma2 = np.diag(sigma2)
# print J_E
# print np.dot(sigma2, J_E)
cov = np.dot(J_E, np.dot(sigma2, J_E))
# print cov, np.sqrt(cov)
sigma_E = E * np.sqrt(cov)
# print sigma_E
# Not sure if this is right:
#
# * ** Note: this may be more like FWHM than sigma_E because of the approx I made **
# * ** FWHM is 2.355 sigma **
# ## Include Q
# print "ti=",ti
tf = L_SD / vf * 1e6
# print "tf=",tf
thetai = 0
phii = 0
# print "R=", R
# print "Q=", Q
eeta = np.arctan2(kfv[1], kfv[0])
# print "eeta=", eeta
pQx_pt = -m / hbar * (L_PM / ti / ti / mus / mus * cos(thetai) * cos(phii)
+ R / tf / tf / mus / mus * L_MS / L_PM * cos(eeta))
pQx_pt /= 1. / AA / mus
# print pQx_pt
pQx_ptMD = m / hbar * R / tf / tf * cos(eeta) / mus / mus
pQx_ptMD /= 1. / AA / mus
# print pQx_ptMD
pQx_pLPM = m / hbar * (cos(thetai) * cos(phii) / ti + ti / tf / tf * R *
L_MS / L_PM / L_PM * cos(eeta)) / mus
pQx_pLPM /= 1. / AA
# print pQx_pLPM
pQx_pLMS = -m / hbar * R / tf / tf * ti / L_PM * cos(eeta) / mus
pQx_pLMS /= 1. / AA
# print pQx_pLMS
pQx_pR = -m / hbar / tf * cos(eeta) / mus
pQx_pR /= 1. / AA
# print pQx_pR
pQx_peeta = m / hbar * R / tf * sin(eeta) / mus
pQx_peeta /= 1. / AA
# print pQx_peeta
pQx_pthetai = -m / hbar * L_PM / ti * sin(thetai) * cos(phii) / mus
pQx_pthetai /= 1. / AA
# print pQx_pthetai
pQx_pphii = -m / hbar * L_PM / ti * cos(thetai) * sin(phii) / mus
pQx_pphii /= 1. / AA
# print pQx_pphii
pQx_p_vec = [
pQx_pt, pQx_ptMD, pQx_pLPM, pQx_pLMS, pQx_pR, 0, pQx_peeta,
pQx_pthetai, pQx_pphii
]
pQx_p_vec = np.array(pQx_p_vec)
J_Qx = pQx_p_vec / Q_len
# **Qy**
pQy_pt = -m / hbar * (L_PM / ti / ti * sin(thetai) * cos(phii) +
R / tf / tf * L_MS / L_PM * sin(eeta)) / mus / mus
pQy_pt /= 1. / AA / mus
# print pQy_pt
pQy_ptMD = m / hbar * R / tf / tf * sin(eeta) / mus / mus
pQy_ptMD /= 1. / AA / mus
# print pQy_ptMD
pQy_pLPM = m / hbar * (sin(thetai) * cos(phii) / ti + ti / tf / tf * R *
L_MS / L_PM / L_PM * sin(eeta)) / mus
pQy_pLPM /= 1. / AA
# print pQy_pLPM
pQy_pLMS = -m / hbar * R / tf / tf * ti / L_PM * sin(eeta) / mus
pQy_pLMS /= 1. / AA
# print pQy_pLMS
pQy_pR = -m / hbar / tf * sin(eeta) / mus
pQy_pR /= 1. / AA
# print pQy_pR
pQy_peeta = -m / hbar * R / tf * cos(eeta) / mus
pQy_peeta /= 1. / AA
# print pQy_peeta
pQy_pthetai = m / hbar * L_PM / ti * cos(thetai) * cos(phii) / mus
pQy_pthetai /= 1. / AA
# print pQy_pthetai
pQy_pphii = -m / hbar * L_PM / ti * sin(thetai) * sin(phii) / mus
pQy_pphii /= 1. / AA
# print pQy_pphii
pQy_p_vec = [
pQy_pt, pQy_ptMD, pQy_pLPM, pQy_pLMS, pQy_pR, 0, pQy_peeta,
pQy_pthetai, pQy_pphii
]
pQy_p_vec = np.array(pQy_p_vec)
J_Qy = pQy_p_vec / Q_len
# ** Qz **
pQz_pt = -m / hbar * (L_PM / ti / ti * sin(phii) +
z / tf / tf * L_MS / L_PM) / mus / mus
pQz_pt /= 1. / AA / mus
# print pQz_pt
pQz_ptMD = m / hbar * z / tf / tf / mus / mus
pQz_ptMD /= 1. / AA / mus
# print pQz_ptMD
pQz_pLPM = m / hbar * (sin(phii) / ti +
ti / tf / tf * z * L_MS / L_PM / L_PM) / mus
pQz_pLPM /= 1. / AA
# print pQz_pLPM
pQz_pLMS = -m / hbar * z / tf / tf * ti / L_PM / mus
pQz_pLMS /= 1. / AA
# print pQz_pLMS
pQz_pz = -m / hbar / tf / mus
pQz_pz /= 1. / AA
# print pQz_pz
pQz_pphii = m / hbar * L_PM / ti * cos(phii) / mus
pQz_pphii /= 1. / AA
# print pQz_pphii
pQz_p_vec = [
pQz_pt, pQz_ptMD, pQz_pLPM, pQz_pLMS, 0, pQz_pz, 0, 0, pQz_pphii
]
pQz_p_vec = np.array(pQz_p_vec)
J_Qz = pQz_p_vec / Q_len
# ** Here we need to extend the J vector for E to include the additional variables eeta, thetai, and phii **
pE_p_vec = [pE_pt, pE_ptMD, pE_pLPM, pE_pLMS, pE_pR, pE_pz, 0, 0, 0]
pE_p_vec = np.array(pE_p_vec)
J_E = pE_p_vec / E
J = np.array((J_Qx, J_Qy, J_Qz, J_E))
# ## ** Parameters
sigma_eeta = mcvine.units.parse(pixel.radius) / mcvine.units.parse(
instrument.detsys_radius)
# sigma_thetai = 0.01
sigma_thetai = beamdivs.theta
# sigma_phii = 0.01
sigma_phii = beamdivs.phi
sigma = np.array([
sigma_t, sigma_tMD, sigma_LPM, sigma_LMS, sigma_R, sigma_z, sigma_eeta,
sigma_thetai, sigma_phii
])
sigma2 = sigma**2
sigma2 = np.diag(sigma2)
# print J.shape, sigma2.shape
cov = np.dot(J, np.dot(sigma2, J.T))
# print cov
M = np.linalg.inv(cov)
# print M
# ## Ellipsoid
# hkl = hkl0+hkl_dir*x
# dh,dk,dl = dx2dhkl*dx
dx2dhkl = np.array(hkl_dir)
# dQ = dx * dx2dhkl dot hkl2Q
# so dx2dQ = dx2dhkl * hkl2Q
# dQ = dx * dx2dQ
dx2dQ = np.dot(dx2dhkl, hkl2Q_mat)
# print dx2dQ
# [dQx,dQy,dQz,dE] = [dx dE] dot dxdE2dQdE
L = dxdE2dQdE = np.array([list(dx2dQ) + [0], [0., 0., 0., 1]])
# np.dot([1,1], dxdE2dQdE)
# $ [dX1,\; dX2,\; dX3,\; dX4]\; M\; [dX1,\; dX2,\; dX3,\; dX4 ]^T = 2ln(2)$
#
# $ dX_i = \frac{dQ_i}{|Q|}$ for i = 1,2,3
#
# $ dX_4 = \frac{dE}{E}$
#
# Let
# $ U = diag\big( \frac{1}{|Q|},\; \frac{1}{|Q|},\; \frac{1}{|Q|},\; 1/E \big) $
#
# $ [dx,\; dE]\; L U MU^TL^T [dx,\; dE ]^T = 2ln(2)$
#
# Let $N=L U MU^TL^T $
# print Q_len, E
U = np.diag([1. / Q_len, 1. / Q_len, 1. / Q_len, 1. / E])
N = LUMUTLT = np.dot(L, np.dot(U, np.dot(M, np.dot(U.T, L.T))))
# print N
# print 2*np.log(2)
r = np.linalg.eig(N)
mR = r[1]
lambdas = r[0]
# print np.dot(mR, mR.T)
# print np.dot(np.dot(mR.T, N), mR)
# Make 4-D inverse covariance matrix:
InvCov4D = UMUT = np.dot(U, np.dot(M, U.T))
hklE2QE = scipy.linalg.block_diag(hkl2Q_mat, 1.)
InvCov4D = np.dot(np.dot(hklE2QE, InvCov4D), hklE2QE.T)
# print np.dot(cov, M) # should be Eye
# $ u = [dx,\;dE]$
#
# $ u N u^T = 2ln(2)$ .... (1)
#
# Find eigen values ($\lambda_1$, $\lambda_2$) and eigne vectors ($e_1$, $e_2$, column vectors) of N,
# and let
#
# $ R = [e_1,\;e_2] $
#
# Then
#
# $ N' = R^T N R = diag([\lambda_1, \lambda_2]) $
#
# or
#
# $ N = R N' R^T $
#
# With $N'$ we can rewrite (1) as
#
# $ u'N'{u'}^T = 2ln2 = \lambda_1 {u'}_1^2 + \lambda_2 {u'}_2^2 $
#
# where
#
# $ u' = u . R $
# ${u'}_1 = \sqrt{2ln2/\lambda_1}*cos(\theta)$
#
# ${u'}_2 = \sqrt{2ln2/\lambda_2}*sin(\theta)$
# In[ ]:
RR = 2 * np.log(2)
theta = np.arange(0, 360, 1.) * np.pi / 180
u1p = np.sqrt(RR / lambdas[0]) * np.cos(theta)
u2p = np.sqrt(RR / lambdas[1]) * np.sin(theta)
up = np.array([u1p, u2p]).T
# print up.shape
u = np.dot(up, mR.T)
if plot:
from matplotlib import pyplot as plt
plt.plot(u[:, 0], u[:, 1], '.')
# plt.xlim(-.35, .1)
# plt.ylim(-5., 5.)
plt.show()
# u: 2D ellipsoid coordinates
# mR: 2D eigen vectors
# lambdas: and 2D eigen values of the scaled inverse covariance
# QxQyQzE_cov: 4D covariance matrix for Qx,Qy,Qz,E in instrument coordinate system
# hklE_inv_cov: inverse 4D covariance matrix for hklE
return dict(u=u,
mR=mR,
lambdas=lambdas,
QxQyQzE_cov=cov,
hklE_inv_cov=InvCov4D)
def updateSQEConvolution(self, uploaded_contents, uploaded_filename,
qgrid_dim, Nqsamples, temperature, Ei, *args):
if uploaded_contents is None: return
binfile = binfile_from_uploaded(uploaded_contents, uploaded_filename)
if binfile.endswith('.zip'):
zipfile = binfile
# compute sqe
Eaxis = np.linspace(-0. * Ei, .9 * Ei, 120)
from mcni.utils import conversion
Qmax = conversion.e2k(Ei) * 2
Qaxis = np.linspace(0, Qmax, 100)
from phonon import SQE_from_FCzip
print temperature
sqe = SQE_from_FCzip(Qaxis,
Eaxis,
zipfile,
Ei,
max_det_angle=140.,
T=temperature,
qgrid_dim=qgrid_dim,
Nqpoints=Nqsamples)
os.unlink(zipfile)
elif binfile.endswith('.h5'):
import histogram.hdf as hh
sqe = hh.load(binfile)
# plot sqe
z = sqe.I.T
zmedian = np.median(z[z > 0])
import plotly.graph_objs as go
fig = go.Figure(data=[
go.Heatmap(z=z,
x=sqe.Q,
y=sqe.E,
zmin=0.,
zmax=zmedian * 5,
colorscale='Viridis')
],
layout={
'title': 'Original',
})
# convolve
E_new, Q, I_new = self.convolveSQE(sqe, Ei, *args)
z = I_new.T
zmedian = np.median(z[z > 0])
fig2 = go.Figure(data=[
go.Heatmap(z=z,
x=Q,
y=E_new,
zmin=0.,
zmax=zmedian * 5,
colorscale='Viridis')
],
layout={
'title': 'Convolved',
})
graph_style = {'height': '25em', 'width': '30em'}
inline = {"display": "inline-flex"}
return html.Div([
html.Div([dcc.Graph(figure=fig, style=graph_style)], style=inline),
html.Div([dcc.Graph(figure=fig2, style=graph_style)],
style=inline),
],
style={"display": "inline-flex"})
def apply_corrections(I, Qbb, Ebb, N, mass, uc, doshist, T, Ei, max_det_angle):
"""apply remaining corrections to IQE. this needs to be combined with calcIQE"""
from mcni.utils import conversion
from multiphonon.forward.phonon import kelvin2mev
from multiphonon.forward import phonon
import histogram as H
Q = (Qbb[1:] + Qbb[:-1]) / 2
# correction 1
ki = conversion.e2k(Ei)
E = (Ebb[1:] + Ebb[:-1]) / 2
Ef = Ei - E
kf = conversion.e2k(Ef)
v0 = uc.lattice.volume
beta = 1. / (T * kelvin2mev)
thermal_factor = 1. / 2 * (1. / np.tanh(E / 2 * beta) + 1)
correction_E = thermal_factor * (2 * np.pi)**3 / v0 / (2 * ki * kf)
correction_Q = 1. / Q
# the additional 1/4pi comes from powder average. See notes
correction = 1. / 4 / np.pi * np.outer(correction_Q, correction_E)
I *= correction
# # Correction 2 - DW
dos_e = doshist.E if hasattr(doshist, 'E') else doshist.energy
dos_dE = dos_e[1] - dos_e[0]
dos_g = doshist.I / np.sum(doshist.I) / dos_dE
DW2 = phonon.DWExp(Q,
M=mass,
E=dos_e,
g=dos_g,
beta=beta,
dE=dos_e[1] - dos_e[0])
I *= np.exp(-DW2)[:, np.newaxis]
IQEhist = H.histogram('IQE',
(H.axis('Q', boundaries=Qbb, unit='1./angstrom'),
H.axis('E', boundaries=Ebb, unit='meV')),
data=I)
## Normalize
# first normalize by "event" count and make it density
dQ = Q[1] - Q[0]
dE = E[1] - E[0]
IQEhist.I /= dQ * dE
# Simulate "Vanadium" data
def norm_at(E, Qaxis, Ei):
"compute normalization(Q) array for the given energy transfer"
ki = conversion.e2k(Ei)
Ef = Ei - E
kf = conversion.e2k(Ef)
Qmin = np.abs(ki - kf)
Qmax = ki + kf
rt = np.zeros(Qaxis.shape)
in_range = (Qaxis < Qmax) * (Qaxis > Qmin)
rt[in_range] = (Qaxis * (2 * np.pi / ki / kf))[in_range]
return rt
norm_hist = IQEhist.copy()
norm_hist.I[:] = 0
for E_ in norm_hist.E:
norm_hist[(), E_].I[:] = norm_at(E_, Q, Ei)
# normalize
IQEhist = IQEhist / norm_hist
#
## Dynamical range
DR_Qmin = ki - kf
DR_Qmax = ((ki * ki + kf * kf -
2 * ki * kf * np.cos(max_det_angle * np.pi / 180)))**.5
I = IQEhist.I
for iE, (E1, Qmin1, Qmax1) in enumerate(zip(E, DR_Qmin, DR_Qmax)):
I[Q < Qmin1, iE] = np.nan
I[Q > Qmax1, iE] = np.nan
return IQEhist