Simple example of running ion_effects in elegant. 
J. Calvey, M. Borland (APS)

aps.lte
        Lattice file

* Setup files:
Basic.ele
        Use to create file with twiss parameters.
makeBunch.ele
        Used to make an initial bunch distribution.

* Ion simulation files
gasMix.sdds
        Simple pressure vs s file. Just have uniform pressure for
        several species.
ionProperties.sdds
        Cross sections for ion production.
ion1.ele
        Run ion simulation for 324 uniformly spaced bunches


=== 
Sequence

elegant Basic.ele
        Uses aps.lte
        Makes Basic.twi, Basic.mag, Basic.mom

elegant makeBunch.ele 
        Uses aps.lte, Basic.twi, Basic.mom
        Makes makeBunch.out

mpiexec -np <numberOfCores> Pelegant ion1.ele
        Replace <numberOfCores> with appropriate value for your system. Up to 64 recommended for this problem.
        Uses aps.lte, Basic.twi, gasMix.sdds, ionProperties.sdds, makeBunch.out
        Makes
        ion1.wp00 --- turn-by-turn parameter data for bunch 0 from WATCH element
        ion1.wp162 --- turn-by-turn parameter data for bunch 162 from WATCH element
        ion1.ebeam --- turn-by-turn, bunch-by-bunch data for electron beam from ion elements
        ion1.ionDens --- turn-by-turn, bunch-by-bunch data for ions from ion elements

sddsplot -column=Pass,Cy ion1.wp* -graph=line,vary 
         Shows growth in centroid position on two bunches
sddsplot -col=t,Cy -graph=sym,vary=subtype ion1.ebeam -order=spect -split=col=Bunch
         Shows growth in centroid position for all bunches
sddsplot -col=Pass,nMacroIons ion1.ionDens -graph=dot,vary
         Shows number of macro ions vs turn
