************************************
A postcript file discussing the collision operator is available.
************************************
An input file with lots of comments is here .
************************************
A sample Load Leveler script for running on seaborg.nersc.gov is available. Replace runname with your run name, put in the appropriate email address, choose the number of nodes correctly, and submit in the directory with the executable and the runname.in file with the command "llqs runname.llq".
************************************
A short discussion of how to choose an appropriate number of processors on seaborg is also available.
************************************
Some notes about the allowable values of nesub, nesuper and ngauss may be found here . .
************************************
To plot fields do:
gnuplot
set data style lines
plot 'runname.fields' u 1:4
(This means to use columns 1 and 4 for x and y axes.)
column 1 is theta
column 2 is theta_0
column 3 is k_theta
column 4 is Re(Phi)
column 5 is Im(Phi)
column 6 is Re(A_par)
column 7 is Im(A_par)
column 8 is Re(delta B_par)
column 9 is Im(delta B_par)
column 10 is shifted theta (only for nonlinear runs with theta connections)
There is a blank line in the *.fields file separating different k_theta, theta_0 modes, which gnuplot interprets as starting a new curve.
You can get a normalized plot of the eigenfunctions by choosing
write_eigenfunc = .true.
in the gs2_diagnostics_knobs namelist. The output file is runname.eigenfunc. The columns are the same as in runname.fields.
************************************
The quantity phtot that is printed in the output is proportional to a sum of |phi|^2 integrated over the eigenfunction.
************************************
For optimal speed of linear runs on the NERSC T3E, do:
mpprun -n NCPUS ../gs2 runname
where NCPUS = (# of species)*(# of k's). You can run with even more NCPUS than this (though this will start to require more communication) by increasing it by an integer which is a factor of negrid (the next dimension which is parallelized). You can use the command
ps -fMPa
to see how many PE's are presently being used interactively (in the eighth
column of output). The total number available during the day is 132.
on the Origin-2000 hecate.princeton.edu:
mpirun -np NCPUS ../gs2 runname
On the Origin-2000's at acl.lanl.gov:
bsub -I -n 10 -R "span[ptile=10]" mpirun ../gs2 runname
where the -R "span[ptile=10]" command insures that all 10 processors are in the same machine (to avoid hippi communication).
************************************************************
GWH, WD