How to simulate †

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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_2.10.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)
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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_2.10.udf -Rrestart2.udf
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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: &ref(): File not found: "pythoninterface_eng.pdf" at page "Tutorial";
    • Japanese: &ref(): File not found: "PythonInterface_jpn.pdf" at page "Tutorial";
    • &ref(): File not found: "sk.py" at page "Tutorial"; 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: &ref(): File not found: "libplatform_eng.pdf" at page "Install";
    • Japanese: &ref(): File not found: "libplatform_jpn.pdf" at page "Install";
  • 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
    or on sh, bash, and Windows command prompt 
    # ./kapsel  -Iinput2.udf -Ooutput2.udf -Ddefine_2.10.udf -Rrestart2.udf  2> out1