1. NEEP 541 Using Kalypso Fall 2002 Jake Blanchard

2. Outline Using the Kalypso code Run file Model file Impact file Inelastic file Output file Winnow

3. Input files for Kalypso Spider prepares input files Kalypso runs simulation Winnow does post-processing (filtering)

4. spider Files are text files Target file defines initial atom locations and type (.trg) 0.00000 0.00000 0.00000 14 28.08550 0 Si Projectile file defines projectile (.prj) 1.000 18 39.94800 0 Ar First number is energy in keV flags

5. .run file 1 Checkbox parameter 001 Sample frequency parameter (timesteps) 5 Checkbox parameter 90.00 Polar angle of projectile incidence 0.00 Azimuthal angle of projectile incidence 01.0E-0016 Initial simulation timestep (s) 10 Frequency of updating neighbour list 1000.0 10.0 Termination times (fs): maximum, minimum 50 'Max. neighbours' parameter (allowed number of collision partners) [ke/ep > 20.0] User-defined output expression

6. More Spider Files.mdl file defines potential.imp file defines: impact parameter of the projectile in the XY plane (vary over many runs) height above the surface from which the projectile flight begins relative to the anchor atom in the target lattice (located by default at (0,0,0))..inl file defines parameters for electronic stopping

7. Output Files Kalypso outputs.snk files Winnow allows post-processing (filtering) of these files.snk files store position vector, momentum vector, time, mass, label for target row and impact parameter row This file will typically contain information for many runs

8. Winnow Approach First filter out data you don’t want …then compute desired result Averaging, histogram, and collating operators exist

9. Identifiers rx ry rz = position vx vy vz = velocity px py pz = momentum lx ly lz = angular momentum ti = time elapsed (t = 0 at the start of a simulated trajectory) ms = mass ke = kinetic energy phi, alt,phid,phi2, phi4, phi8, altd = angles phi = arctan(py/px) [azimuthal angle]

10. Sample Filters [rw > 0] [ke/ep >= 10.0] [pz > 0.0] & [rz > 0.0] & [ke/ep > 0.5]