+1 on datasets, although I would like to see the unit object(s) at the field level.

On Thu, Mar 29, 2012 at 4:04 PM, Cameron Hummels <chummels@astro.columbia.edu> wrote:
+1 on datasets.

On 3/29/12 6:58 PM, Nathan Goldbaum wrote:
+1.  I'd also be up to help out with the sprint.  Doing a virtual sprint using a google hangout might help mitigate some of the distance problems.

While we're brining up Enzo-isms that we should get rid of, I think it might be a good idea to make a conceptual shift in the basic python UI.  Instead referring to the interface between the user and the data as a parameter file, I think instead we should be talking about datasets.  One would instantiate a dataset just like we do now with parameter files:

ds = load(filename)

A dataset would also have some universal attributes which would present themselves to the user as a dict, e.g. ds.units, ds.parameters, ds.basic_info (like current_time, timestep, filename, and simulation code), and ds.hierarchy (not sure how that would interfere with the geometry refactor).

This may be a paintibg the bike shed discussion, but I think this shift will help new users understand how to access their data.  Thoughts?

On Mar 29, 2012, at 3:40 PM, Matthew Turk<matthewturk@gmail.com>  wrote:

Hi Nathan and Casey,

I agree with what both of you have said.  The Orion/Nyx units should
be made to be consistent, but more importantly I think we should
continue breaking away from Enzo-isms in the code.

As it stands, all of the universal fields call underlying Enzo-named
aliases -- Density, ThermalEnergy, etc etc.  I hope we can have a 3.0
out within a calendar year, hopefully by the end of this year.  (I've
been pushing on the geometry refactor, although recently other efforts
have been paying off which has decreased my output there.)  I am much,
much less doubtful than Casey is that we cannot do this; in fact, I'm
completely in favor of this and I think it would be relatively
straightforward to implement.

In the existing system we have a mechanism for aliasing fields.  What
we can do is provide an additional translation system where we
enumerate the fields that are available for items in UniversalFields,
and then construct aliases to those.  This would mean changing what is
aliased in existing non-Enzo frontends, and adding aliases in Enzo.
The style of name Casey proposes is what I woudl also agree with:
underscores, lower cases, and erring on the side of verbosity.  The
fields off hand that we would need to do this for (in their current

x-velocity =>  velocity_x (same for y, z)
Density =>  density
TotalEnergy =>  ?
GasEnergy =>  thermal_energy_specific (and thermal_energy_density)
Temperature =>  temperature

and so on.

Once we have these aliases in place, an overall cleanup of
UniversalFields should take place.  One place we should clean up is
ensuring that there are no conditionals; rather than conditionals
inside the functions, we should place those conditionals inside the
parameter file types.  So for instance, if you have a field that is
calculated differently depending on the parameter HydroMethod (in Enzo
for instance) you simply set a validator on the field requiring the
parameter be set to a particular value, and then only the field which
satisfies that validator will be called when requested.

So we've gotten rid of a bunch of enzo-isms in the parameter files;
after fields, what else can we address?  And, I'd be up for sprinting
on this (which should take just a few hours) basically any time next
week or after.  I'd also be up for talking more about geometry
refactoring, if anyone is interested, but it's not quite to the point
that I think I am satisfied enough with the architecture to request
input / contributions.  Sometimes (especially with big architectural
things like this) I think it's a shame we do all of our work
virtually, as I think a lot of this would be easier to bang out in
person for a couple hours.


On Wed, Mar 28, 2012 at 6:14 PM, Casey W. Stark<caseywstark@gmail.com>  wrote:
Hi Nathan.

I'm also worried about this and I agree that fields with the same name
should all be consistent. I would support some sort of cleanup of frontend
fields, and I can get the Nyx fields in line and help with Enzo.

I doubt we can do this, but I would prefer changing the field names as part
of the removing enzo-isms and geometry handling refactoring pushes. For
instance, the field in Orion could be thermal_energy_density and the field
in Enzo could be specific_thermal_energy. I also noticed this issue when I
was using "Density" in Enzo (proper density in cgs) and "density" in Nyx
(comoving density in cgs).


On Wed, Mar 28, 2012 at 1:47 PM, Nathan Goldbaum<goldbaum@ucolick.org>
Hi all,

On IRC today we noticed that Orion defines its ThermalEnergy field per
unit volume but Enzo and FLASH define ThermalEnergy per unit mass.  Is this
a problem?  Since yt defaults to the Enzo field names, should we try to make
sure that all fields are defined using the same units as in Enzo?  Is there
a convention for how different codes should define derived fields that are
aliased to Enzo fields?

One problem for this particular example is that the Pressure field is
defined in terms of ThermalEnergy in universal_fields.py so the units of
ThermalEnergy become important if a user merely wants the gas pressure in
the simulation.

One possible solution for this issue would be the units overhaul we're
planning. If all fields are associated with a unit object, we can simply
query the units to ensure that units are taken care of correctly and
code-to-code comparisons aren't sensitive to the units chosen for fields in
the frontend.

Personally, I think it would be best if we could make sure that all of the
fields aliased to Enzo fields have the same units.

Nathan Goldbaum
Graduate Student
Astronomy&  Astrophysics, UCSC

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