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documentation:tutorial [2013/04/03 22:21]
127.0.0.1 external edit
documentation:tutorial [2015/09/09 09:43] (current)
macke
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   - set "qz max" to 0.6. If the edit field is disabled click the checkbox "use dataset x-range for simulation"​   - set "qz max" to 0.6. If the edit field is disabled click the checkbox "use dataset x-range for simulation"​
   - number of points should be set to 300. If the edit field is disabled go to the tab datasets and disable the checkbox "use measurement x-range for simulation"​   - number of points should be set to 300. If the edit field is disabled go to the tab datasets and disable the checkbox "use measurement x-range for simulation"​
-  - The "​x-Axis"​ should be set to the momentum transfer qz and theta. Both is Ok.+  - The "​x-Axis"​ should be set to the momentum transfer qz and theta. Both are Ok.
  
   * simulation parameters   * simulation parameters
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 Change Mode to monochromatic and press button "​Reflectivity"​. A curve in the color red should be calculated and displayed. Change Mode to monochromatic and press button "​Reflectivity"​. A curve in the color red should be calculated and displayed.
  
-Play around with the values in the layers tables and see how the curve changes. An easy method to do this is by clicking on a table entry one time and then use the scrollbar below the table to change that value. This is a very usefull ​tool for manual fitting.+Play around with the values in the layers tables and see how the curve changes. An easy method to do this is by clicking on a table entry one time and then use the scrollbar below the table to change that value. This is a very useful ​tool for manual fitting.
  
  
 ==== Retrieving the refractive index ==== ==== Retrieving the refractive index ====
  
-As for now the simulation uses not the real refractive indices. Off-resonance scattering factors are tabulated for each element. With these factors the refractive index can be calculated. The program dbEditor and the X-ray database website provided in the links section on this webpage is capable to build compatible tables. In both cases the chemical formulas of each compound (of each layer) and the density are required. The "​vaccuum"​-layer needs a .db file too but should be filled with zeros for all energies. ​+As for now the simulation uses not the real refractive indices. Off-resonance scattering factors are tabulated for each element. With these factors the refractive index can be calculated. The X-ray database website provided in the links section on this webpage is capable to build compatible tables. In both cases the chemical formulas of each compound (of each layer) and the density are required. The "​vaccuum"​-layer needs a .db file too but should be filled with zeros for all energies. ​
  
-The created tables ​is processing ReMagX ​automatically. To do this the files should have the same names as in the column db with file name extension .db. These files can be found in the tutorial zip-file too. They should be in the same folder as the .all file Tut1.all. +The created tables ​are processes ​automatically ​by ReMagX. To do this the files should have the same names as in the column db with file name extension .db. These files can be found in the tutorial zip-file too. They should be in the same folder as the .all file Tut1.all. 
-The refractive indices are loaded by right clicking on the layer table and then clicking on "Get delta/beta from database"​ +The refractive indices ​for the selected energy ​are loaded by right clicking on the layer table and then clicking on "Get delta/beta from database"​The columns delta and beta are changed automatically to the correct values of the incident beam energy of 1000eV.
-The columns delta and beta are changed automatically to the correct values of the incident beam energy of 1000eV.+
  
 The table should look like: The table should look like:
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 ==== Prepare measurement data  ==== ==== Prepare measurement data  ====
  
-So far we have done some simulation of reflectivity curves. To fit some measurements one has prepare the measurements to load into ReMagX. ReMagX needs the data in text format ​spearately in columns. The decimal point must be "​."​. +So far we have done some simulation of reflectivity curves. To fit some measurements one has prepare the measurements to load into ReMagX. ReMagX needs the data in a column ​text format. The decimal point must be "​."​. 
-For standard reflectivity (const-energy) scans one has to provide two columns: the momentum transfer qz and the reflected intensity R0.+For standard reflectivity (const-energy) scans one has to provide two columns: the momentum transfer qz (in units 1/A) and the reflected intensity R0.
  
 ==== Load Datasets ==== ==== Load Datasets ====
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   - Type, File, and Datapoints cannot be changed.   - Type, File, and Datapoints cannot be changed.
  
-Double click on the dataset again to activate the changes for this measurement. You should see in the tab for example +Double click on the dataset again to activate the changes for this measurement. You should see in the tab for example "​Const. Energy Settings"​ that the energy jumped from 1000eV to 900eV.
-"​Const. Energy Settings"​ that the energy jumped from 1000eV to 900eV.+
  
 Load the new optical constants for this energy as we did before. Now you can start the reflectivity simulation by clicking on "​Reflectivity"​. Load the new optical constants for this energy as we did before. Now you can start the reflectivity simulation by clicking on "​Reflectivity"​.
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 ==== Prepare for fitting ==== ==== Prepare for fitting ====
  
-The first step should be a manual coarse fitting of the curve as the fitting algorithms are not as good as humans to  +The first step should be a manual coarse fitting of the curve as the fitting algorithms are not as good as humans to determine the structure of curve. Especially the thicknesses should be set to more reliable ​number.
-determine the structure of curve. Especially the thicknesses should be set to more reliable ​numbers.+
  
-Very close to the initial values a much better fit of the thickness fringes can be achieved by setting layer 1 to 150A and both roughnesses to 3 Angstrom.+Very close to the initial values a much better fit of the thickness fringes can be achieved by setting layer 1 to a thickness of 150A and both roughnesses to 3 Angstrom.
  
 ==== Fitting a reflectivity curve ==== ==== Fitting a reflectivity curve ====
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 So right click on the thickness cell and click on fit. Do the same for the roughness of the substrate and of the film. The cells should be marked red. Additionally we want to fit the scaling factor of the measurement. Go to the tab "​Additional Fit Parameters"​ check "​measurement multiplicator"​. So right click on the thickness cell and click on fit. Do the same for the roughness of the substrate and of the film. The cells should be marked red. Additionally we want to fit the scaling factor of the measurement. Go to the tab "​Additional Fit Parameters"​ check "​measurement multiplicator"​.
  
-In the "​Parameters"​ tab you should see four rows with the names "​thickness 1", "sigma 1", "sigma 0", and "meas. mult.".  +In the "​Parameters"​ tab you should see four rows with the names "​thickness 1", "sigma 1", "sigma 0", and "meas. mult." ​followed by three columns: The initial ​value for the fit parameteras ​well as the boundarys. They are set to reasonable numbers but can be changed of course.
-In the following ​three columns ​the initial ​parameter ​for the fit is written as well as the boundarys ​for this fit. They are set to reasonable numbers but can be changed of course.+
  
-As the last parameters ​the qz-window in which the error function is calculated (chi-square) ​should be set. This can be done in the tab "​Fitting window"​. Normally you cannot trust the lowest and the highest angles of the measurement. Therefore the qz-range is set to 0.03 - 0.45 1/A.+The last paremter we should set is the qz-window in which the error function is calculated (chi-square). This can be done in the tab "​Fitting window"​. Normally you cannot trust the lowest and the highest angles of the measurement. Therefore the qz-range is set to 0.03 - 0.45 1/A.
  
-In the tab "​DataSet" ​clock on dataset with the name "​LCO_900eV.dat"​ and click the Fit button next to it. This tells ReMagX which curves you want to fit. +In the tab "​DataSet" ​click on dataset with the name "​LCO_900eV.dat"​ and click the Fit button next to it. This tells ReMagX which curves you want to fit. 
  
 The current state you can find in Tut3.all The current state you can find in Tut3.all
  
 In the last step the fit can be started in the tab "​Start/​Stop"​. It takes less than a second to converge. So the stop button can be pressed right after start was pressed. Our manual fit was already good. So the fit changed the thickness to around 148 Angstrom. ​ In the last step the fit can be started in the tab "​Start/​Stop"​. It takes less than a second to converge. So the stop button can be pressed right after start was pressed. Our manual fit was already good. So the fit changed the thickness to around 148 Angstrom. ​
-The result is plotted during ​fit.+The result is plotted during ​the fitting procedure.
  
  
documentation/tutorial.txt · Last modified: 2015/09/09 09:43 by macke