* Installation of KAPSEL binary [#h03d9749] ** 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 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) &color(red){recommended!}; ** 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 > 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>Install]]) ** STEP 3: Download and install GOURMET [#hdf41283] - 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. - 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/java --- Edit goumet.sh file and change the command "java" to "/usr/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); -- 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 until it terminates. - 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 -- "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)