• The added line is THIS COLOR.
  • The deleted line is THIS COLOR.
* Installation of KAPSEL binary [#h03d9749]

Here we assume that OCTA(GOURMET)-2007 is used, but the latest version of them should work fine.

** STEP 1: Download "KAPSEL" binary [#ja8071fa]

- Visit [[KAPSEL-BBS:http://www.cheme.kyoto-u.ac.jp/1koza/kapsel/phpBB3/]] and Login. Registration is required if you haven't yet complete it.
- You can download the same files from here.

- Follow "DOWNLOAD" -> "KAPSEL-2" -> "KAPSEL-2 binary executables" to download appropriate binary executables for your system.
-- "kapsel2_linux.tar.gz" (Linux on x86-64 machine) 
-- "kapsel2_win.zip" (32-bit Windows Vista or XP)  &color(red){recommended!};
-- &ref(kapsel2.1_linux64.zip); (Linux on x86-64 machine) 
-- &ref(kapsel2.1_win32.zip); (32-bit Windows)

** STEP 2: Test run [#l8a9ee25]
//- Visit [[KAPSEL-BBS:http://www-tph.cheme.kyoto-u.ac.jp/kapsel/phpBB3/]] and Login. Registration is required if you haven't yet completed it.

//- Follow "DOWNLOAD" -> "KAPSEL-2" -> "KAPSEL-2.10" to download appropriate binary package for your system.
//-- "kapsel2.1_linux64.zip" (Linux on x86-64 machine) 
//-- "kapsel2.1_win32.zip" (32-bit Windows)



** STEP 2: Run KAPSEL [#l8a9ee25]

- 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

    > tar zxvf kapsel2_linux.tar.gz
    > ./kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf
    > unzip kapsel2.1_linux64.zip
    > ./kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine_2.10.udf -Rrestart.udf

- for Windows
-- unzip "kapsel2_win.zip"
-- unzip "kapsel2.1_win32.zip"
-- open command prompt

    > kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf
    > kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine_2.10.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 define_2.10.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>Install]])

** STEP 3: Download and install "Gourmet" [#hdf41283]
** STEP 3: Download and install GOURMET [#hdf41283]

- &color(red){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 (optional).};
- GOURMET is a graphic platform developed by OCTA project. The complete OCTA package is not necessary, but GOURMET is needed to use KAPSEL.

- "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:http://octa001.muse.aist.go.jp/phpBB3/]] and Login. Registration is required if you haven't yet completed it.

- Visit [[OCTA-BBS:http://octa001.muse.aist.go.jp/phpBB3/]] and Login. Registration is required if you haven't yet complete 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

-- Linux version of GOURMET may not work properly on 64-bit Linux. 

     java.lang.UnsatisfiedLinkError: 
     /usr/local/OCTA2007/GOURMET_2007/lib/linux/libshaker.so: 
     wrong ELF class: ELFCLASS32

:: If this happens, do the following, where $version$ is the update version of your JVM installed.|
--- Install 32bit JVM (not RPM) in (for example) /usr/local/OCTA2007/java
--- Edit goumet.sh file and change the command "java" to "/usr/local/OCTA2007/java/jre1.6.0_$version$/bin/java -d32

- For Windows
-- Follow "DOWNLOAD" -> "OCTA2007" -> "Platform GOURMET2007 in OCTA2007 (for Windows)".
-- download "GOURMET2007.exe" and click it.
-- "Start Menu" > "All Programs" > "OCTA2007" > "StartGourmet"

- See manuals for more detailed information on Gourmet
-- English: &ref(gourmetoperation_eng.pdf); &ref(gourmetprimer_eng.pdf);
- See manuals for more detailed information on GOURMET
-- English: &ref(GourmetOperation_eng.pdf); &ref(gourmetprimer_eng.pdf);
-- Japanese: &ref(GourmetOperation_jpn.pdf); &ref(GourmetPrimer_jpn.pdf);

** STEP 4: Visualize the result [#de6c8fcf]

- The above test run takes about an hour. Save &ref(output.udf); if you cannot wait till it.
- The above test run takes about an hour. Save &ref(output.udf); if you cannot wait until it terminates.

- Gnuplot on Gourmet
- Animation on GOURMET
-- Save &ref(particleshow.py); and &ref(show_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.
#ref(000.jpg,,80%)

- Gnuplot on GOURMET
-- Save &ref(plot.py);.
-- Start "Gourmet"
-- 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.
#ref(velocity_x.jpg,,40%)

- Animation on Gourmet
-- Save &ref(particleshow.py); and &ref(show_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.
#ref(000.jpg,,80%)

- Animation on AVS/Express (optional)
-- One can enjoy much advanced data-visualization with AVS/Express. A sample visualization network &ref(avs_charge.v); is attached.
#youtube(Zuj8T6PunC8)