[petsc-users] how to get full trajectory from TS into petsc binary

[Barry Smith]

  Ed,

   I have added a branch barry/feature-ts-monitor-binary  that supports -ts_monitor binary:timesteps that will store in simple binary format each of the time steps associated with each solution. This in conjugation with -ts_monitor_solution binary:solutions will give you two files you can read in. But note that timesteps is a simple binary file of double precision numbers you should read in directly in python, you cannot use PetscBinaryIO.py which is what you will use to read in the solutions file.

  Barry

Currently PETSc has a binary file format where we can save Vec, Mat, IS, each is marked with a type id for PetscBinaryIO.py to detect, we do not have type ids for simple double precision numbers or arrays of numbers. This is why I have no way of saving the time steps in a way that PetscBinaryIO.py could read them in currently. I don't know how far we want to go in "spiffing up" the PETSc binary format to do more elaborate things since, presumably, other more power IO tools exist that would be used for "real" problems?


> On Feb 29, 2016, at 3:24 PM, Ed Bueler <elbueler at alaska.edu> wrote:
> 
> Dear PETSc --
> 
> I have a short C ode code that uses TS to solve  y' = g(t,y)  where y(t) is a 2-dim'l vector.  My code defaults to -ts_type rk so it does adaptive time-stepping; thus using -ts_monitor shows times at stdout:
> 
> $ ./ode -ts_monitor
> solving from t0 = 0.000 with initial time step dt = 0.10000 ...
> 0 TS dt 0.1 time 0.
> 1 TS dt 0.170141 time 0.1
> 2 TS dt 0.169917 time 0.270141
> 3 TS dt 0.171145 time 0.440058
> 4 TS dt 0.173931 time 0.611203
> 5 TS dt 0.178719 time 0.785134
> 6 TS dt 0.0361473 time 0.963853
> 7 TS dt 0.188252 time 1.
> error at tf = 1.000 :  |y-y_exact|_inf = 0.000144484
> 
> I want to output the trajectory in PETSc binary and plot it in python using bin/PetscBinaryIO.py.  Clearly I need the times shown above to do that.
> 
> Note "-ts_monitor_solution binary:XX" gives me a binary file with only y values in it, but not the corresponding times.
> 
> My question is, how to get those times in either the same binary file (preferred) or separate binary files?  I have tried
> 
> $ ./ode -ts_monitor binary:foo.dat    # invalid
> $ ./ode -ts_monitor_solution binary:bar.dat   # no t in file
> $ ./ode -ts_monitor_solution binary:baz.dat -ts_save_trajectory   # no t in file
> 
> without success.  (I am not sure what the boolean option -ts_save_trajectory does, by the way.)
> 
> Thanks!
> 
> Ed
> 
> PS Sorry if this is a "RTFM" question, but so far I can't find the documentation.
> 
> 
> -- 
> Ed Bueler
> Dept of Math and Stat and Geophysical Institute
> University of Alaska Fairbanks
> Fairbanks, AK 99775-6660
> 301C Chapman and 410D Elvey
> 907 474-7693 and 907 474-7199  (fax 907 474-5394)