Interface model example

• Setup imports

  >>import xrr
  >>import compound

• Build some chemical components

  >>N2     = compound.Component(formula={'N':2})
  >>qtz    = compound.Component(formula={'Si':1,'O':2})
  >>fe2o3  = compound.Component(formula={'Fe':2,'O':3})
  >>al2o3  = compound.Component(formula={'Al':2,'O':3})

• Build some layers

  >>subs   = xrr.Layer(comp=[(qtz,1.),(fe2o3,0.000001)],density=2.65,thickness=1000.,roughness=10.)
  >>m1     = xrr.Layer(comp=[(qtz,1.),(fe2o3,0.0001)],density=2.45,thickness=30.,roughness=10.)
  >>m2     = xrr.Layer(comp=[(N2,1.)],density=0.001,thickness=1000.,roughness=0.)
  >>top    = xrr.Layer(comp=[(N2,1.)],density=0.001,thickness=1000.,roughness=0.)

• Parameters

  >>delta = 5.
  >>theta = num.arange(0.01, 1.0, 0.01)
  >>calc_params = {'energy':10000.,'wconv':0.01,'slen':20.,'bvert':0.01,
                   'aflag':1.,'fyidx':0,'fyenergy':7000.,'delz':delta,'pdepth':2.0}

• Create model

  >>model = xrr.Model(substrate=subs,layers=[m1,m2],top=top, theta=theta, params=calc_params)
  >>model.slabify(delta=delta)

• FY/R on init'd model

  >>model.calc_FY(fyel='Fe',fyenergy='Fe Ka')
  >>model.plot(ty='calc')

• various other potential plots

  >>model.plot(ty='density')
  >>model.plot(ty='comp')
  >>model.plot(ty='el')
  >>model.plot(ty='frac')
  >>model.slab.comp_mb()

• Change the element distribution

  Note distribution models are defined
  throughout the entire interface region!
  
  However, they do not apply to the component 
  distributions within the substrate or top layers
  (these are fixed)

  >>dist = {'type':'erf','cen':40.,'sig':20.,'CX':1.}
  >>model.slab.add_dpar('Fe2_O3',dist=dist,norm=1,init=True)
  >>
  >>dist = {'type':'gauss','cen':70.,'sig':10.,'CX':30.}
  >>model.slab.add_dpar('Fe2_O3',dist=dist)
  >>
  >>dist = {'type':'erf','cen':40.,'sig':20.,'CX':1.}
  >>model.slab.add_dpar('Si_O2',dist=dist,norm=1,init=True)
  >>
  >>model.slab.calc_dist()

• Recompute the FY

  >>model.calc_FY()
  >>model.plot(ty='calc',hold=True)
  >>model.plot(ty='density')
  >>model.plot(ty='comp')
  >>model.slab.comp_mb()

• Modify the distribution and recompute FY/R

  >>dist = {'cen':60.,'sig':40.,'CX':1.}
  >>model.slab.set_dpar('Fe2_O3',dist=dist,didx=0,norm=1)
  >>model.slab.calc_dist()
  >>model.calc_FY()
  >>model.plot(ty='calc',hold=True)
  >>model.plot(ty='density')
  >>model.plot(ty='comp')
  >>model.slab.comp_mb()