InelasticIsoRotDiff¶

import numpy as np
try:
    from scipy.special import spherical_jn
    def sjn(n, z): return spherical_jn(range(n+1), z)
except ImportError:
    from scipy.special import sph_jn
    def sjn(n, z): return sph_jn(n, z)[0]
"""Generate resolution function with the following properties:
1. Gaussian in Energy
2. Dynamic range = [-0.1, 0.1] meV with spacing 0.0004 meV
3. FWHM = 0.005 meV
"""
dE=0.0004; FWHM=0.005; sigma = FWHM/(2*np.sqrt(2*np.log(2)))
dataX = np.arange(-0.1,0.1,dE); Emin=min(dataX); Emax=max(dataX); nE=len(dataX)
rdataY = np.exp(-0.5*(dataX/sigma)**2)  # the resolution function
Qs = np.array([0.3, 0.5, 0.7, 0.9, 1.1, 1.3, 1.5, 1.9])  # Q-values
nQ = len(Qs)
resolution=CreateWorkspace(np.tile(dataX,nQ), np.tile(rdataY,nQ), NSpec=nQ, UnitX="deltaE",
    VerticalAxisUnit="MomentumTransfer", VerticalAxisValues=Qs)

"""Generate a synthetic inelastic signal for a particle undergoing isotropic rotational diffusion.
1. Radius of rotation = 2.5 Angstroms
2. Relaxation time = 187 ps
3. Up to 10% of noise in the quasi-elastic signal
4. Linear background noise, up to 1% of the quasi-elastic intensity
"""
R=2.5;  tau=187.0;  hbar=0.658211626  # hbar units are ps*meV
N=25  # number of harmonics in the inelastic signal
qdataY=np.empty(0)  # will hold all Q-values (all spectra)
H=2-np.random.random() # global intensity
for Q in Qs:
    centre=dE*np.random.random()  # some shift along the energy axis
    dataY=np.zeros(nE)  # holds the inelastic signal for this Q-value
    js=sjn(N,Q*R)  # spherical bessel functions from L=0 to L=N
    for L in range(1,N+1):
        HWHM = L*(L+1)*hbar/tau; aL=(2*L+1)*js[L]**2
        dataY += H*aL/np.pi * HWHM/(HWHM**2+(dataX-centre)**2)  # add component
    dataY = dE*np.convolve(rdataY, dataY, mode="same")  # convolve with resolution
    noise = dataY*np.random.random(nE)*0.1 # noise is up to 10% of the inelastic signal
    background = np.random.random()+np.random.random()*dataX # linear background
    background = (0.01*H*max(dataY)) * (background/max(np.abs(background))) # up to 1%
    qdataY=np.append(qdataY, dataY+background)
data=CreateWorkspace(np.tile(dataX,nQ), qdataY, NSpec=nQ, UnitX="deltaE",
    VerticalAxisUnit="MomentumTransfer", VerticalAxisValues=Qs)

"""Our fitting model is:
    S(Q,E) = Convolution(resolution, InelasticIsoRotDiff) + LinearBackground
We do a global fit (all spectra) to the synthetic data workspace to find out
the global intensity H, the radius R, and the relaxation time tau.
"""
# This is the template fitting model for each spectrum (each Q-value):
single_model_template="""(composite=Convolution,FixResolution=true,NumDeriv=true;
name=TabulatedFunction,Workspace=resolution,WorkspaceIndex=_WI_,Scaling=1,Shift=0,XScaling=1;
name=InelasticIsoRotDiff,N=25,Q=_Q_,Height=1,Radius=0.98,Tau=10,Centre=0,
constraints=(0<Height,0.1<Radius,0.1<Tau));
name=LinearBackground,A0=0,A1=0"""

# Now create the string representation of the global model (all spectra, all Q-values):
global_model="composite=MultiDomainFunction,NumDeriv=true;"
wi=0
for Q in Qs:
    single_model = single_model_template.replace("_Q_", str(Q))  # insert Q-value
    single_model = single_model.replace("_WI_", str(wi))  # workspace index
    global_model += "(composite=CompositeFunction,NumDeriv=true,$domains=i;{0});\n".format(single_model)
    wi+=1
# The Height, Radius, and Tau are the same for all spectra, thus tie them:
ties=['='.join(["f{0}.f0.f1.Radius".format(wi) for wi in reversed(range(nQ))]),
    '='.join(["f{0}.f0.f1.Height".format(wi) for wi in reversed(range(nQ))]),
    '='.join(["f{0}.f0.f1.Tau".format(wi) for wi in reversed(range(nQ))]) ]
global_model += "ties=("+','.join(ties)+')'  # insert ties in the global model string
# Now relate each domain(i.e. spectrum) to each single model
domain_model=dict()
for wi in range(nQ):
    if wi == 0:
        domain_model.update({"InputWorkspace": data.name(), "WorkspaceIndex": str(wi),
            "StartX": str(Emin), "EndX": str(Emax)})
    else:
        domain_model.update({"InputWorkspace_"+str(wi): data.name(), "WorkspaceIndex_"+str(wi): str(wi),
            "StartX_"+str(wi): str(Emin), "EndX_"+str(wi): str(Emax)})

# Invoke the Fit algorithm using global_model and domain_model:
output_workspace = "glofit_"+data.name()
Fit(Function=global_model, Output=output_workspace, CreateOutput=True, MaxIterations=500, **domain_model)
# Extract Height, Radius, and Tau from workspace glofit_data_Parameters, the output of Fit:
nparms=0
parameter_ws = mtd[output_workspace+"_Parameters"]
for irow in range(parameter_ws.rowCount()):
    row = parameter_ws.row(irow)
    if row["Name"]=="f0.f0.f1.Radius":
        Radius=row["Value"]
        nparms+=1
    elif row["Name"]=="f0.f0.f1.Height":
        Height=row["Value"]
        nparms+=1
    elif row["Name"]=="f0.f0.f1.Tau":
        Tau=row["Value"]
        nparms+=1
    if nparms==3:
        break  # We got the three parameters we are interested in
# Check nominal and optimal values are within error ranges:
if abs(H-Height)/H < 0.1:
    print("Optimal Height within 10% of nominal value")
if abs(R-Radius)/R < 0.05:
    print("Optimal Radius within 5% of nominal value")
if abs(tau-Tau)/tau < 0.1:
    print("Optimal Tau within 10% of nominal value")