• The added line is THIS COLOR.
  • The deleted line is THIS COLOR.
* Step-by-step instructions to build KAPSEL [#m21c6f6d]
* Installation of KAPSEL binary [#h03d9749]

** STEP 0: Linux or Windows? [#aee6273c]
Here we assume that OCTA(GOURMET)-2007 is used, but the latest version of them should work fine.

- To build KAPSEL on Linux, goto STEP 1.
** STEP 1: Download "KAPSEL" binary [#ja8071fa]

- To build KAPSEL on Windows,  install "[[Cygwin:http://cygwin.com]]" first, then goto STEP 1. Be sure to include "gcc" and "make" packages.
- You can download the same files from here.

- KAPSEL can be build also on Mac OS-X. (not officially supported)
-- &ref(kapsel2.1_linux64.zip); (Linux on x86-64 machine) 
-- &ref(kapsel2.1_win32.zip); (32-bit Windows)

** STEP 1: Download and install "Gourmet" [#hdf41283]
- "Gourmet" is a graphic platform developed by OCTA project. The entire OCTA package is not necessarily. Only Gourmet is required to use KAPSEL.
//- 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.

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

- Follow "DOWNLOAD" -> "OCTA2007" -> "Platform GOURMET2007 in OCTA2007 (for Windows)"  or "GOURMET 4.1.0 (on OCTA2007) for Windows and Linux" to download "Gourmet" package.

- Follow the instruction there to install "Gourmet". 

** STEP 2: Build "libplatform" [#tbb7046c]
** STEP 2: Run KAPSEL [#l8a9ee25]

- "libplatform" is an I/O library developed by OCTA project. One needs this library to access to UDF-formatted files.
- KAPSEL is a command line program which can be started as the following example.

- Instruction for Linux:
- 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.

    > su
    > cd /usr/local/OCTA2007/GOURMET_2007
    > tar xvfpz gourmet*_src.tar.gz
    > cd src
    > make
    > make install
- for Linux

- Instruction for Windows: 
-- Logon Windows with an administrator authorization
-- Open Cygwin window
    > unzip kapsel2.1_linux64.zip
    > ./kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine_2.10.udf -Rrestart.udf

    $ ln -s /cygdrive/c/OCTA2007/ /usr/local/.
    $ cd /usr/local/OCTA2007/GOURMET_2007
    $ unzip GOURMET_2007_SRC.zip
    $ cd src
    $ make
    $ make install
- for Windows
-- unzip "kapsel2.1_win32.zip"
-- open command prompt

    > kapsel -Icolloid_1.udf -Ooutput.udf -Ddefine_2.10.udf -Rrestart.udf

** STEP 3: Download "KAPSEL" [#ja8071fa]
- If you see the output as shown below, KAPSEL has been successfully installed.

- 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.

- Follow "DOWNLOAD" -> "KAPSEL-2" -> "KAPSEL-2" to download "kapsel.tar.gz".

** STEP 4: Build "KAPSEL" [#yd1b04b3]

    > tar xvfpz kapsel.tar.gz
    > make

** STEP 5: Test "KAPSEL" [#l8a9ee25]

    > ./kapsel -Isample1.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf
    #using sample1.udf as input
    #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 you see the output as shown in the above panel, KAPSEL has been successfully built.

* Optional information for Intel compiler [#hc2750d1]
- If the program does not properly run or abnormally terminated, build KAPSEL from the source codes. ([[see this>Install]])

** STEP 2a: Build "libplatform" with icc on Linux [#t9627f89]
** STEP 3: Download and install GOURMET [#hdf41283]

- for icc 7.1:
- GOURMET is a graphic platform developed by OCTA project. The complete OCTA package is not necessary, but GOURMET is needed to use KAPSEL.

    > su
    > cd /usr/local/OCTA2007/GOURMET_2007/src
    > make clean
    > make WITHFC=no CC=icc CXX=icc
    > make install
- Visit [[OCTA-BBS:http://octa001.muse.aist.go.jp/phpBB3/]] and Login. Registration is required if you haven't yet completed it.

- for icc8.0:
- 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
    > cd /usr/local/OCTA2007/GOURMET_2007/src
    > make clean
    > make WITHFC=no CC=icc CXX="icpc -U GNU "
    > make install
    > 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 icc8.1 or later:
-- Linux version of GOURMET may not work properly on 64-bit Linux. 

    > su
    > cd /usr/local/OCTA2007/GOURMET_2007/src
    > make clean
    > make WITHFC=no CC=icc CXX="icpc -lcxaguard"
    > make install
     java.lang.UnsatisfiedLinkError: 
     /usr/local/OCTA2007/GOURMET_2007/lib/linux/libshaker.so: 
     wrong ELF class: ELFCLASS32

- numerous warnings may appear but can be ignored them.
:: 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

** STEP 4a: Build "KAPSEL" with icc on Linux [#zb3a949c]
- For Windows
-- Follow "DOWNLOAD" -> "OCTA2007" -> "Platform GOURMET2007 in OCTA2007 (for Windows)".
-- download "GOURMET2007.exe" and click it.
-- "Start Menu" > "All Programs" > "OCTA2007" > "StartGourmet"

- for icc
- 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);

    > make clean
    > make ENV=ICC
** STEP 4: Visualize the result [#de6c8fcf]

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

    > make clean
    > make ENV=ICC_MKL_OMP
- 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%)

- numerous warnings may appear but can be ignored them.
- Gnuplot on GOURMET
-- Save &ref(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.
#ref(velocity_x.jpg,,40%)

- 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)