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How to simulate †

To perform normal simulation †

• 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)

   > ./kapsel -Iinput.udf -Ooutput.udf -Ddefine_2.00.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.
• "-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)
  • Load "particleshow.py" to visualize motions of particles. (See STEP4)

To re-start previous simulation †

• 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)

   > ./kapsel -Iinput2.udf -Ooutput2.udf -Ddefine_2.00.udf -Rrestart2.udf

To analyze simulation data †

• 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: pythoninterface_eng.pdf
  • Japanese: PythonInterface_jpn.pdf
  • 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"
      > python sk.py  (sample only, can be abnormally terminated)

• Fortran or C program with libplatform (library to access UDF). Read the manual below.
  • English: libplatform_eng.pdf
  • Japanese: 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_2.00.udf -Rrestart2.udf >& out1

  or on sh, bash, and Windows command prompt

  # ./kapsel  -Iinput2.udf -Ooutput2.udf -Ddefine_2.00.udf -Rrestart2.udf  2> out1