Installation of KAPSEL binary †

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STEP 1: Download "KAPSEL" binary †

  • Visit KAPSEL-BBS and Login. Registration is required if you haven't yet completed it.
  • Follow "DOWNLOAD" -> "KAPSEL-2" -> "KAPSEL-2 binary executables" to download appropriate binary package for your system.
    • "kapsel2_linux.zip" (Linux on x86-64 machine)
    • "kapsel2_win.zip" (32-bit Windows Vista or XP) recommended!
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STEP 2: Run KAPSEL †

  • KAPSEL is a command line program which can be started as the following example.
  • Start test run using a sample input UDF "colloid_1.udf", with which one can simulate electrophoresis of a single charged particle in electrolyte solution.
  • for Linux
   > unzip kapsel2_linux.zip
   > ./kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf
  • for Windows
    • unzip "kapsel2_win.zip"
    • open command prompt
   > kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf
  • If you see the output as shown below, KAPSEL has been successfully installed.
   #using colloid_1.udf as input
   #using output.udf as output
   #using define.udf as definition
   #using restart.udf as restart
   #
   # Electrolyte eq. selected.
   #
   ...
  • If the program does not properly run or abnormally terminated, build KAPSEL from the source codes. (see this)
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STEP 3: Download and install GOURMET †

  • Linux version of GOURMET may not be installed properly. If this happens, install Windows version of KAPSEL and GOURMET (recommended). If you want to use KAPSEL on Linux, edit input UDF using GOURMET on Windows. Then copy it to Linux and run KAPSEL there (this is what we do).
  • GOURMET is a graphic platform developed by OCTA project. The complete OCTA package is not necessary, but GOURMET is needed to use KAPSEL.
  • Visit OCTA-BBS and Login. Registration is required if you haven't yet completed it.
  • For Linux
    • Follow "DOWNLOAD" -> "OCTA2007" -> "GOURMET 4.1.0 (on OCTA2007) for Windows and Linux".
    • download "gourmet_2007_linux.tar.gz"
   > tar zxvf gourmet_2007_linux.tar.gz
   > su
   > mkdir /usr/local/OCTA2007
   > mv GOURMET_2007 /usr/local/OCTA2007/.
   > setenv PF_FILES /usr/local/OCTA2007/GOURMET_2007
   > sh /usr/local/OCTA2007/GOURMET_2007/bin/gourmet.sh
  • For Windows
    • Follow "DOWNLOAD" -> "OCTA2007" -> "Platform GOURMET2007 in OCTA2007 (for Windows)".
    • download "GOURMET2007.exe" and click it.
    • "Start Menu" > "All Programs" > "OCTA2007" > "StartGourmet"
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STEP 4: Visualize the result †

  • The above test run takes about an hour. Save &ref(): File not found: "output.udf" at page "InstallB"; if you cannot wait until it terminates.
  • Animation on GOURMET
    • Save fileparticleshow.py and fileshow_field.py.
    • Start GOURMET
    • "File" -> "Open" -> Open "output.udf".
    • Move down to "Python" panel, and click "Load"
    • Open "particleshow.py" (particle only) or "show_field.py" (particle with flow field, very slow!!).
    • Click "Run"
    • A new window will open, and click the playback button ">" there.
      000.jpg
  • Gnuplot on GOURMET
    • Save fileplot.py.
    • Start GOURMET
    • "File" -> "Open" -> Open "output.udf".
    • Move down to "Python" panel, and click "Load"
    • Open "plot.py", and click "Run"
    • Move up "View" box, and check "Table"
    • Move down-left and select "Graph Sheet[]".
    • Move down to "Plot" panel, and type "plot "plot.dat" using 2:6 title 'vx0' with lines" in the command box.
    • Click "Plot", and you will see the time evoluation of Vx.
      velocity_x.jpg
  • Animation on AVS/Express (optional)
    • One can enjoy much advanced data-visualization with AVS/Express. A sample visualization network fileavs_charge.v is attached.