- 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)