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ElasticIsoRotDiff¶
Description¶
This fitting function models the elastic part of the dynamic structure factor for a particle undergoing continuous and isotropic rotational diffusion [1], IsoRotDiff.
where:
\(Height\) - Intensity scaling, a fit parameter
\(Q\) - Momentum transfer, an attribute (non-fitting)
\(Radius\) - Radius of rotation, a fit parameter
\(Centre\) - Centre of peak, a fit parameter
Because of the spherical symmetry of the problem, the structure factor is expressed in terms of the \(j_l(z)\) spherical Bessel functions.
Attributes (non-fitting parameters)¶
Name |
Type |
Default |
Description |
|---|---|---|---|
Q |
\(Q\) (double, default=0.3) Momentum transfer
Properties (fitting parameters)¶
Name |
Default |
Description |
|---|---|---|
Height |
1.0 |
Scaling factor to be applied to the resolution. |
Centre |
0.0 |
Shift along the x-axis to be applied to the resolution. |
Radius |
0.98 |
Radius of rotation (Angstroms) |
References¶
Usage¶
Example - Global fit to a synthetic elastic signal:
The signal is modeled by the convolution of a resolution function with the elastic component of a rotator. The resolution is modeled as a normal distribution. We insert a random noise in the rotator. Finally, we choose a linear background noise. The goal is to find out the radius of the rotator and the overal intensity of the signal with a fit to the following model:
\(S(Q,E) = R(Q,E) \otimes ElasticIsoRotDiff(Q,E) + (a+bE)\)
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. Normal distribution along the energy axis, same for all Q-values
2. FWHM = 0.005 meV
3. Dynamic range = [-0.1, 0.1] meV with spacing 0.0004 meV
"""
FWHM=0.005
sigma = FWHM/(2*np.sqrt(2*np.log(2)))
dE=0.0004 # spacing in the dynamic range
dataX = np.arange(-0.1,0.1,dE) # dynamic range
Emin=min(dataX)
Emax=max(dataX)
nE=len(dataX)
dataY = 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)
# Workspace containing resolution for each Q, the same in this case
resolution=CreateWorkspace(np.tile(dataX,nQ), np.tile(dataY,nQ), NSpec=nQ, UnitX="deltaE",
VerticalAxisUnit="MomentumTransfer", VerticalAxisValues=Qs)
"""Generate a synthetic elastic signal for a particle undergoing isotropic rotational diffusion.
1. Radius of rotation = 2.5 Angstroms
2. Up to 10% of noise in the rotator signal
3. Linear background noise, up to 1% of the intensity
"""
R=2.5 # Nominal radius, a value to find in the fit
qdataY=np.empty(0)
H=2-np.random.random() # global intensity, a value to find in the fit
for Q in Qs:
centre=dE*np.random.random() # some shift along the energy axis
dataY = np.exp(-0.5*((dataX-centre)/sigma)**2) # resolution shifted by "centre"
noise = dataY*np.random.random(nE)*0.1 # noise is up to 10% of the elastic 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% of H
j0 = sjn(0,Q*R)[0]
qdataY=np.append(qdataY, H*j0**2*(dataY+noise) + background)
# Create data workspace
data=CreateWorkspace(np.tile(dataX,nQ), qdataY, NSpec=nQ, UnitX="deltaE",
VerticalAxisUnit="MomentumTransfer", VerticalAxisValues=Qs)
"""Now we fit our model to the data workspace. Our model is:
S(Q,E) = Convolution(resolution, ElasticIsoRotDiff) + LinearBackground
We do a global fit (all spectra) to find out the radius R and height H
"""
# Our initial guess are Height=1.0 and Radius=0.98. Here's a template of the
# model for each spectrum:
single_model_template="""(composite=Convolution,FixResolution=true,NumDeriv=true;
name=TabulatedFunction,Workspace=resolution,WorkspaceIndex=_WI_,Scaling=1,Shift=0,XScaling=1;
name=ElasticIsoRotDiff,Q=_Q_,Height=1,Centre=0,Radius=0.98);
name=LinearBackground,A0=0,A1=0"""
# Now create the string representation model for all spectra:
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)) # insert workspace index
global_model += "(composite=CompositeFunction,NumDeriv=true,$domains=i;{0});\n".format(single_model)
wi+=1
# Introduce ties: Height and Radius same for all spectra
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))]) ]
global_model += "ties=("+','.join(ties)+')' # introduce ties in the global model
# 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 of the fit are three workspaces, but we are interested in workspace
with name glofit_data_Parameters, containing optimized values for Radius and Height
"""
output_workspace = "glofit_"+data.name()
Fit(Function=global_model, Output=output_workspace, CreateOutput=True, MaxIterations=500, **domain_model)
# Extract Height and Radius from workspace glofit_data_Parameters.
# Check optimal values are close to nominal ones
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"] # Extract value of optimized Radius
nparms+=1
elif row["Name"]=="f0.f0.f1.Height":
Height=row["Value"] # Extract value of optimized Height
nparms+=1
if nparms==2:
break
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")
Output:
Optimal Height within 10% of nominal value
Optimal Radius within 5% of nominal value
Categories: FitFunctions | QuasiElastic
Source¶
C++ header: ElasticIsoRotDiff.h
C++ source: ElasticIsoRotDiff.cpp