Backup of InstallB(No. 22) - KAPSEL-3 HP

Installation of KAPSEL binary †

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

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

Or you can download the same files from here.

&ref(): File not found: "kapsel2.1_linux64.zip" at page "InstallB"; (Linux on x86-64 machine)
&ref(): File not found: "kapsel2.1_win32.zip" at page "InstallB"; (32-bit Windows)

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 kapsel2.1_linux64.zip
   > ./kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine_2.10.udf -Rrestart.udf

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

   > 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_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)

STEP 3: Download and install GOURMET †

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

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: GourmetOperation_eng.pdf gourmetprimer_eng.pdf
- Japanese: GourmetOperation_jpn.pdf GourmetPrimer_jpn.pdf

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 particleshow.py and 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.

Gnuplot on GOURMET
- Save plot.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.

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