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Running EMsoft

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jjc999 edited this page Jul 11, 2016 · 23 revisions

##Test to make sure EMsoft works independent of OpenXY

  • Create the xtal material file
    • Enter the following into the Terminal to launch the xtal file generator:
      EMmkxtal
    • Follow the prompts and input all of the crystal structure information
    • Save the file as 'material.xtal' (i.e. Al.xtal. Follow this pattern for every file).
      • You can see the list of usable material names here in the MainGUI of OpenXY.

Select_Material

  • NOTE: See the 'Supplemental Programs' documentation to learn how to use the New Material GUI if your material name is not already in OpenXY.
  • Create the '.nml' files by using a template. To create a template, open up the terminal, change directories to your EMdata folder (cd /direct/path/EMdata) and create the corresponding template by typing one of the following bolded and italicized commands:
    Monte Carlo file: EMMCOpenCL -t
    Master file: EMEBSDmaster -t
    EMEBSD file: EMEBSD -t

template

  • Right click on the file and select 'Get Info'. Rename each file so it contains the material name and is saved as a '.nml' file. For example, change 'EMMCOpenCL.template' to 'EMMCOpenCL_material.nml'. Hit enter and select 'Use.nml' in the pop-up window. Also in the 'Get Info' window, half way down click on 'Open With' and select XCode.

Get_Info_Copy

Use_nml

  • Create the euler angle file (defines orientation)
    • Create a text document in XCode and name it 'material_euler.txt'. Follow this template, subbing in the needed angles. Save it in the EMdata folder.

Euler Angles

  • Edit the '.nml' files to match your file names and settings
    • Important - the naming system for each file is very important. First, make sure that each '.nml' file is named correctly, meaning that is follows the pattern explained above (EMMCOpenCL_material.nml, EMEBSDmaster_material.nml ,EMEBSD_material.nml).
    • Change the file and output names on the corresponding lines in each file (the line above each of the below mentioned lines explains which name is needed):
      • EMMCOpenCL (lines 5, 38)
      • EMEBSDmaster (lines 7, 9)
      • EMEBSD (lines 21, 25, 27, 29)
    • Also edit the needed microscope settings.
  • Run the Monte Carlo code (takes about 1 hour 15 minutes for 1e9 electrons on Macbook Pro)
    • In the terminal type: cd /some/absolute/path/EMdata
    • To run the code, type: EMMCOpenCL EMMCOpenCL_material.nml

EMMCOpenCL

  • Run the code to produce a master pattern (takes about 4 minutes on MacbookPro)
    • In the same directory as above, type: EMEBSDmaster EMEBSDmaster_material.nml
  • Run the code to produce simulated pattern (Takes a couple of seconds)
    • Still in the same directory as above, type: EMEBSD EMEBSD_material.nml
  • Note: Inside the EMsoft folder, there is a subfolder named 'manuals'. Click on that to get to the documentation for all of the EMsoft programs.

##Use EMsoft with OpenXY

  • Create the Monte Carlo Simulation and Master Pattern before using OpenXY.
  • How to enable EMsoft (create and use dynamic simulations) while using OpenXY
    * Run MainGUI, click on the material drop down menu on the right side and select your material from the list.

Select_Material

  • Also in MainGUI, click on the Settings drop down menu
  • Click on Advanced Settings, and in the top drop down menu called 'Reference Image Type', select 'Simulated-Dyanmic'. At the bottom of the menu, click 'Save & Close'.

OpenXY

  • OpenXY is now ready to use dynamically simulated images. See the OpenXY documentation in this wiki to learn how to continue the cross correlation analysis.
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