## -*- config -*-
###########################################################################
## This configuration file is for Demeter version 0.9.21.
##
##                     Demeter is copyright (c) 2007-2016 Bruce Ravel
##                                   http://bruceravel.github.io/home
##
##                   Ifeffit is copyright (c) 1992-2016 Matt Newville
##                                https://github.com/newville/ifeffit
##
##	  The latest version of Demeter can always be found at
##               http://bruceravel.github.io/demeter/
##
## -------------------------------------------------------------------
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##     University of Chicago, University of Washington, or the authors
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###########################################################################


## This file contains the bkg configuration group for Demeter


######################################################################
section=bkg
section_description
  These parameters determine how background removal and normalization
  is done by Demeter.

variable=e0
type=list
options=derivative zero fraction atomic peak
default=derivative  
units=eV
description
  This determines how the default value of E0 is determined.  The
  derivative method is the Ifeffit default and is related to finding
  the first maximum of the first derivative of mu(E).  The zero method
  finds the zero-crossing of the second derivative which is closest to
  the E0 value found by Ifeffit.  The half method will find by
  interpolation the energy value at a fraction the step height (see
  the e0_fraction parameter).  The atomic method asigns the tabulated
  value to E0.  This works by first determining E0 using the
  derivative method to determine the atomic species of the absorber.
  Then the E0 value is reset to the tabulated value.  Finally the peak
  method works by first finding E0 using the derivative method, then finding
  first peak after that value of E0.


variable=e0_fraction
type=real
default=0.5
description
  This variable is used when the e0 preference is set to "fraction".
  In that case the edge energy is found by default as the point that
  is some fraction of the edge step.  By default this is 0.5, i.e. the
  edge energy is set to the position of the half edge step.  Setting
  this to a different value puts the edge position at a different spot
  on the edge.  If you set this 0 or a negative number, 0.5 will be
  used.  If you set this to a number larger than 1, 1 will be used.

variable=kw
type=positive integer
default=2
maxint=3
description
  The default value for the k-weighting used to fit the background
  spline.

variable=rbkg
type=real
default=1.0
units=Angstroms
description
  The default value for the Rbkg parameter.  This is the parameter
  that defines the cutoff between the Fourier components associated
  with the data from those associated with the background function.
  The Fourier components below this value are optimized to determine
  the spline.  In the absence of a background removal standard, these
  components are simply minimized.  With a background removal
  standard, these components are optimized to be like those of the
  standard.  A good rule of thumb for this parameter is that it should
  be about 1/2 the distance to the first shell peak.  Since peak
  position varies from data set to data set, 1.0 is reasonable,
  general-purpose default.

variable=dk
type=real
default=0
units=inverse Angstroms
description
  The width of the Fourier window sill used for the Forward transform
  during background removal.

variable=pre1
type=real
default=-150
units=eV (relative to e0 or to the beginning of the data)
description
  The beginning value for regressing the pre-edge line used in
  normalization in units of eV.  This is normally a negative number
  and is relative to e0, i.e. something like -150 rather than
  something like 8829.  Pre2 should be closer to the edge energy than
  pre1.  A zero value means to use the *second* point in the imported
  data.  A positive number is interpreted as being that many volts
  above the first data point.  If you use a positive number, you run a
  risk of placing this parameter past the edge, leading to a reduction
  in the edge-step and an error in the determination of S02 and/or
  coordination number in the data.  A number between -1 and 1 will be
  interpreted as keV.

variable=pre2
type=real
default=-30
units=eV (relative to e0 or to the beginning of the data)
description
  The ending value for regressing the pre-edge line used in
  normalization in units of eV.  This should be a negative number and
  is relative to e0, i.e. something like -30 rather than something
  like 8949.  Pre2 should be closer to the edge energy than pre1.  A
  positive number is interpreted as being that many volts above the
  first data point.  If you use a positive number, you run a risk
  of placing this parameter past the edge.  The pre-edge line should
  start at least a few tens of eV below e0, or else the pre-edge line
  will be influenced by the onset of the edge, leading to a reduction
  in the edge-step and an error in the determination of S02 and/or
  coordination number in the data.  A number between -1 and 1 will be
  interpreted as keV.

variable=nor1
type=real
default=150
units=eV (relative to e0)
description
  The beginning value for regressing the post-edge line used to
  determine the edge step, in units of eV.  This should be a positive
  number and is relative to e0, i.e. something like 100 rather than
  something like 9079.  Nor1 should be closer to zero than nor2.  A
  number between -5 and 5 will be interpreted as keV.  Note that all
  the data between nor1 and nor2 is used in the post-edge line
  regression.  If this range is wide compared to an oscillation in the
  data, then the regression will be insensitive to the placement of
  nor1 relative to the oscillations in the data.

variable=nor2
type=real
default=-100
units=eV (relative to e0 or to the end of the data)
description
  The ending value for regressing the post-edge line used to determine
  the edge step in units of eV.  When positive, this is relative to
  e0, i.e. something like 400 rather than something like 9379.  A
  value of 0 means to use the last data point.  A negative value will
  be subtracted from the end of the data set and that value will be
  used as the ending value of the regression.  A number between -5 and
  5 will be interpreted as keV.  If nor2 ends up being smaller than
  nor1, they will be swapped.  Note that all the data between nor1 and
  nor2 is used in the post-edge line regression.  If this range is
  wide compared to an oscillation in the data, then the regression
  will be insensitive to the placement of nor1 relative to the
  oscillations in the data.

variable=spl1
type=real
default=0.0
units=inverse Angstroms
description
  The beginning value in k-space for the region over which the
  background spline is fit in units of inverse Angstroms.  0.0 or 0.5
  are good choices.  However if the white line is strong, it is useful
  to set this to something to its right.  Note that this will be the
  first non-zero value in the chi(k) data.

variable=spl2
type=real
default=0
units=inverse Angstroms
description
  The ending value in k-space for the region over which the background
  spline is fit in units of inverse Angstroms.  A value of 0 means to
  use the last data point.  A negative value will be subtracted from
  the end of the data set and used as the ending value of the
  regression.  If you give a negative number and the value ends up
  being below spl1, the end of the data set will be used instead.

##bkg_spl1e	  =>  0,	       # number
##bkg_spl2e	  =>  0,	       # number


variable=kwindow
type=list
default=hanning
options=hanning kaiser-bessel welch parzen sine
description
  The default window type to use for the Fourier transform during the
  background removal.


##bkg_slope	  => 0,		       # number
##bkg_int		  => 0,		       # number
##bkg_step		  => 0,		       # number
##bkg_fitted_step	  => 0,		       # number
##bkg_fixstep	  => 0,		       # boolean
##bkg_nc0		  => 0,		       # number
##bkg_nc1		  => 0,		       # number
##bkg_nc2		  => 0,		       # number

variable=flatten
type=boolean
onvalue=1
default=true
description
  This variable determines whether Demeter flattens a groups'
  normalized mu(E) spectra defore displaying normalized mu(E) plots.
  Flattening means to adjust the slope of the data after E0 such that
  the data oscillates about 1.  This is acomplished by fitting a
  quadratic polynomial to the pre-edge subtracted spectra before
  normalization.  Then norm(E) = [pre(E) + (step-poly(E))*theta(E)] /
  step, where
  . step     the value of the edge_step
  . pre(E)   pre-edge subtracted data
  . poly(E)  the fitted polynomial
  . theta(E) a step function centered at E0
  .
  Setting this variable true means that flattened data will be
  displayed, setting it to false means to display the normalized data
  as it comes out of ifeffit's spline() function.

variable=nnorm
type=list
default=3
options=1 2 3
description
  This sets the default normalization order.  3 means to use a cubic
  polynomial for the post-edge regression.  2 means to use a line.
  1 means to use the average of the signal between nor1 and nor2.

##bkg_stan		  => 'None',
##bkg_stan_lab	  => '0: None',

variable=nclamp
type=positive integer
default=5
description
  The number of data points used by the background removal algorithm
  to evaluate the clamping restraint.  A clamp is a numerical device
  used either at the beginning or the end of the data range over which
  the background spline is fit to coerce the spline not to deviate
  from the data.  Occassionally, the spline found by the Autobk
  algorithm will diverge from the data at one end of the range or the
  other.  A clamp is essentially a penalty applied to the fitting
  metric when this happens.  Only the first (last) nclamp data points
  are used to evaluate this penalty when a beginning (end) of data set
  clamp is applied.

variable=clamp1
type=positive integer
default=0
description
  The default strength for the low-energy spline clamp used in the
  background removal.  A spline clamp is a penalty applied to the
  fitting metric used in the background optimization.  This restraint
  penalizes the spline when it deviates from the data.  The strength
  of the clamp determines the size of the penalty.

variable=clamp2
type=positive integer
default=24
description
  The default strength for the high-energy spline clamp used in the
  background removal.  A spline clamp is a penalty applied to the
  fitting metric used in the background optimization.  This restraint
  penalizes the spline when it deviates from the data.  The strength
  of the clamp determines the size of the penalty.

##bkg_tie_e0	  => 0,		       # boolean
##bkg_former_e0	  => 0,		       # number
##bkg_cl		  => 0,		       # boolean
##bkg_z		  => 'H',	       # element