• The added line is THIS COLOR.
  • The deleted line is THIS COLOR.
* How to simulate [#f5c9dfdb]

** To perform normal simulation [#le4c697d]

- Obtain an appropriate sample UDF file for your purpose from our examples.

- Start GOURMET and open the UDF file. Modify it for your own purpose and save it as "input.udf".

- Run KAPSEL as follows. (remove "./" if you use Windows command prompt)
- Run KAPSEL as follows.

    > ./kapsel -Iinput.udf -Ooutput.udf -Ddefine_2.10.udf -Rrestart.udf
    > ../kapsel -Iinput.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf

-- "''-I''" option defines the name of UDF file which contains details of simulation (type of simulation, initial conditions, physical and simulation parameters, etc...).
-- "''-O''" option defines the name of UDF file which contains the results (time-dependent positions and velocities of all the particles, etc...) of the simulation.
-- "''-D''" option defines the name of UDF file which contains definitions of KAPSEL data dormat. This is common for any simulations.
-- "''-D''" option defines the name of UDF file which contains definitions of KAPSEL data format. This is common for any simulations, but the versions of input.udf and define.udf must be the same.
-- "''-R''" option defines the name of UDF file which contains values of all dynamical variables at the end of the simulation See "Re-start run" below.
-- Field data (fluid velocities, ionic densitied, etc...) is saved in a subdirectory specified in "input.udf" if "output.AVS" = "on". This requires huge disk space (GB order). No field data is saved if "output.AVS" = "off".

- Start GOURMET and open "output.udf". 
-- Instantaneous  positions and velocities of all the particles can be seen as variables in "Particles[]". Use slide bar at the bottom of GOURMET viewer window to see variables at different time steps.
-- Load "plot.py" to plot time evolutions of the variables. ([[See STEP4>InstallB]])
-- Load "particleshow.py" to visualize motions of particles. ([[See STEP4>InstallB]])
//-- Load "plot.py" to plot time evolutions of the variables. ([[See STEP4>InstallB]])
//-- Load "particleshow.py" to visualize motions of particles. ([[See STEP4>InstallB]])

** Visualize the simulation result [#de6c8fcf]

- The sample input.udf takes less than a minute to run.

- Animation on GOURMET
-- Save &ref(particleshow.py);.
-- Start GOURMET
-- "File" -> "Open" -> Open "output.udf".
-- Move down to "Python" panel, and click "Load"
-- Open "particleshow.py".
-- 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 2:7 title 'vy0' 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)


** To re-start previous simulation  [#u7810c9a]

- One can re-start simulations from the end of the previous run.

- Start GOURMET, and open "restart.udf"

- Set "resume.Calculation" = "CONTINUE"

- Increase "output.Num_step", and save it as "input2.udf"

- Run KAPSEL as follows.  (remove "./" if you use Windows command prompt)
- Run KAPSEL as follows. 

    > ./kapsel -Iinput2.udf -Ooutput2.udf -Ddefine_2.10.udf -Rrestart2.udf
    > ../kapsel -Iinput2.udf -Ooutput2.udf -Ddefine.udf -Rrestart2.udf

** To analyze simulation data [#hcc313c6]

- The history of simulation run (instantaneous positions and velocities of particles) is stored in "output.udf". One can access to this file by one of the following methods.

-- Python program. Read the manual below.
--- English: &ref(pythoninterface_eng.pdf); 
--- Japanese: &ref(PythonInterface_jpn.pdf);
--- &ref(sk.py); is a sample python script to calculate the static structure factor S(k) from the temporal particle positions stored in "output.udf". Read and edit the script for your purpose. 
 - For Windows
   "Start Menu" > "All Programs" > "OCTA2007" > "StartGourmetTerm"
   "Start Menu" > "All Programs" > "OCTA2010" > "StartGourmetTerm"
   > python sk.py  (sample only, can be abnormally terminated)

-- Fortran or C program with libplatform (library to access UDF). Read the manual below.
--- English: &ref(Install/libplatform_eng.pdf);
--- Japanese: &ref(Install/libplatform_jpn.pdf);

- KAPSEL outputs some important data to stderr. It usually appears in command line, but one can redirect stderr to a file on csh and tcsh
 > ./kapsel  -Iinput2.udf -Ooutput2.udf -Ddefine_2.10.udf -Rrestart2.udf >& out1
 > ../kapsel  -Iinput.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf >& out1
or on sh, bash, and Windows command prompt
 # ./kapsel  -Iinput2.udf -Ooutput2.udf -Ddefine_2.10.udf -Rrestart2.udf  2> out1
 # ../kapsel  -Iinput.udf -Ooutput.udf -Ddefine.udf -Rrestart.udf  2> out1