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--- documentation:fittey [2012/08/02 00:09] – macke
+++ documentation:fittey [2013/11/28 11:44] – macke
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+====== Documentation for FitTEY ======
+The program FitTEY is a toolbox to fit the total electron yield (TEY) or calculated spectra to off-resonant tables (optical constants delta, beta or scattering factors f1, f2) and to do Kramers-Kronig calculations in one step.
+Furthermore it can create new optical constants for compounds.
+==== Fit ====
+Usage:
+FitTEY is a console application.
+<code>
+FitTEY.exe fit mode file1 file2 element model cutmin cutmax fitmin1 fitmax1 fitmin2 fitmax2 a b c shift
+</code>
+== fit [string] ==
+This is the command and should be exactly this string
+== mode [string] ==
+"db" or "ff" or "cF" dependent what you want to fit
+  * mode="ff": atomic conductivity to atomic scattering factor
+  * mode="F" : atomic conductivity tensor to atomic scattering tensor
+  * mode="db": conductivity to refractive index
+== file1 [string] ==
+file containing the measured or calculated data dependent on the mode variable.
+  * mode="ff": filename with data to merge with columns [energy 0 conductivity]
+  * mode="F" : filename with columns [energy conductivity tensor(18 entries)]
+  * mode="db": filename with data to merge with columns [energy 0 conductivity]
+Look in the file formats section of this documentation for more information
+== file2 [string] ==
+File containing the off-resonant data dependent on the mode variable
+  * mode="ff": filename with columns [energy f1 f2]
+  * mode="db": filename with columns [energy delta beta]
+  * mode="F" : filename with columns [energy f1 f2]
+Look in the file formats section of this documentation for more information
+== element [string] ==
+Chemical element or Chemical formula dependent on the mode variable
+  * mode="ff": chemical element e.g. Ni
+  * mode="F" : chemical element e.g. Ni
+  * mode="db": chemical formula e.g. LaNiO3
+== model [string] ==
+the model describes the different fitting models
+^ model      ^ mode       ^ formula          ^ fit parameters ^ fixed parameters ^ Comments ^
+| A    | db     | beta(E) = t(E) / E * a + b + c * E      | a b c | |
+| B    | db     | beta(E) = t(E) / E * a + b + c * E      | a b   | c |
+| C    | db     | beta(E) = t(E) / E * a + b + c * E      | a     | b c |
+| N    | db     | beta(E) = t(E) / E * a + b + c * E      |       | a b c |
+| D    | db     | beta(E) = (t(E)*a*sin( c*pi/180. ) / (1. - t*a) / b) / ((5.067769e-4 * E * 2.) | a b | c |
+| E    | db     | beta(E) = (t(E)*a*sin( c*pi/180. ) / (1. - t*a) / b) / ((5.067769e-4 * E * 2.) | a | b c |
+| F    | db     | beta(E) = t(E) / E * (a + c * e) + b    | a b c |
+| A    | ff     | f2(E) = t(E) * E * a + b + c * e        | a b c |
+| B    | ff     | f2(E) = t(E) * E * a + b + c * e        | a b   | c |
+| C    | ff     | f2(E) = t(E) * E * a + b + c * e        | a     | b c |
+| F    | ff     | f2(E) = t(E) * E * (a + c * e) + b      | a b c |
+| G    | db/ff  | beta(E)/ff(E) = t(E) * a + b + c * E      | a b c | | not officially supported|
+| H    | db/ff  | beta(E)/ff(E) = t(E) * a + b + c * E      | a b   | c | not officially supported|
+| I    | db/ff  | beta(E)/ff(E) = t(E) * a + b + c * E      | a     | b c | not officially supported|
+| J    | db/ff  | beta(E)/ff(E) = t(E) * a + b + c * E      |       | a b c | not officially supported|
+| K    | ff     | ff(E) = t(E)*E*E * a + b + c * E       | a b c |  | not officially supported|
+In all models the parameters a acts like a scaling factor for the TEY data.
+The variables t is the TEY signal and the parameter e is the energy in eV.
+Model D and E take the self-absorption into account. (Reiko Nakajima "Electron-yield saturation effects in L-edge x-ray magnetic circular dichroism spectra of Fe, Co and Ni" PRB Volume 59, Number 9 (1999) ) by the formulas
+<m> mu lambda_e = {t sin(theta) } / {1 - t} </m>  with <m> mu = 2 k_0 beta </m>  \\
+Parameter a is a scaling factor for the TEY signal.
+Parameter b is the escape length  <m>lambda_e</m> of the electrons in Angstrom.
+Paramter c corresponds to the Variable <m>theta</m> and is the angle (in degrees) of the incoming beam (perpendicular incoming ray is c=90).
+Variable k0 is the wavenumber of the incoming ray.
+== cutmin [number], cutmax [number] ==
+Energy range in eV for the measurement which should be merged with the off-resonance data.
+== fitmin1 [number], fitmax1 [number] ==
+Energy range used for fit before resonance
+== fitmin2 [number], fitmax2 [number] ==
+Energy range used for fit after resonance
+== a [number] ==
+Initial value for fit parameter a. Depends on the used model. In most cases a good initial value is a = 1.
+== b [number] ==
+Initial value for fit parameter b Depends on the used model. Good initial starting could be b = 0.
+== c [number] ==
+Initial value for fit parameter c. Depends on the used model. Good initial starting could be c = 0.
+== shift [number] ==
+Energy shift of the measurement. If unsure set it to zero.
+=== output merged.?? ===
+The output of the program is a file called merged.db or merged.ff with the fitted and merged TEY-data. It is dependent on the mode variable
+  * mode="ff": filename with columns [energy f1 f2]
+  * mode="db": filename with columns [energy delta beta]
+  * mode="F" : filename with columns [energy conductivity tensor(18 entries)]
+==== Create ====
+To create the off resonant values of the refractive index for a compound you can use following command
+<code>
+FitTEY.exe create chemical_formula density shift
+</code>
+== density [number] ==
+density of the compound in units of g/cm^3
+== shift [number] ==
+Energy shift of the off resonant values. If unsure set it to zero.
+==== Convert ====
+This command converts the fitted refractive index to atomic scattering factors
+<code>
+FitTEY.exe convert file1 chemical_formula density element cutmin cutmax shift
+</code>
+== file1 ==
+fitted .db file with resonances
+== element ==
+Element to extract from the file
+== cutmin, cutmax ==
+Lowest and highest energy values for the resonance you want to merge.
+== shift [number] ==
+Energy shift of the off resonant values. If unsure set it to zero.