[yt-users] Derivative Error

Nathan Butcher butchernate at gmail.com
Thu Jun 14 10:59:17 PDT 2012


Okay, makes sense. Thank you.

Nathan

On Thu, Jun 14, 2012 at 1:57 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Nathan,
>
> On Thu, Jun 14, 2012 at 1:55 PM, Nathan Butcher <butchernate at gmail.com>
> wrote:
> > Hello,
> >
> > The images are the same as before. I will try to create a simpler test
> case
> > to check this field and see if it behaves properly. Thank you for all of
> the
> > help.
>
> Okay, I figured out what is going on.
>
> Without spatial validation, this sequence:
>
> new_field = na.zeros(data['PotentialField'].shape)
> new_field[1:-1] = data["PotentialField"][sl_right]/ds
> new_field[1:-1] -= data["PotentialField"][sl_left]/ds
>
> is operating on 1D, mostly unsorted arrays.  The points next to each
> other are probably not in x-order, so this doesn't do much.  When you
> do validate spatial, it oeprates on a grid-by-grid basis, and adjacent
> points are adjacent spatially.
>
> So this is okay, and the correct result is the one with the
> ValidateSpatial call.
>
> -Matt
>
> >
> > Nathan
> >
> >
> > On Thu, Jun 14, 2012 at 1:44 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Hi Nathan,
> >>
> >> How are you centering the slice?  This looks somewhat like a
> >> difference in the centering.  Can you try something like:
> >>
> >> pc = PlotCollection(pf, 'c')
> >> pc.add_slice("GravGradient", "x")
> >> pc.save()
> >>
> >> for both the old and new, and see if they look similar?
> >>
> >> -Matt
> >>
> >> On Thu, Jun 14, 2012 at 1:41 PM, Nathan Butcher <butchernate at gmail.com>
> >> wrote:
> >> > The colorbar scaling is similar, and the values have changed. It could
> >> > be a
> >> > large shift. It is hard for me to tell from the plot. I have attached
> >> > the
> >> > updated plot.
> >> >
> >> > Nathan
> >> >
> >> >
> >> > On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk at gmail.com>
> >> > wrote:
> >> >>
> >> >> On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <
> butchernate at gmail.com>
> >> >> wrote:
> >> >> > Hello Matt,
> >> >> >
> >> >> > Thanks, that seems to have done fixed the issue. I am seeing that
> the
> >> >> > graph
> >> >> > looks very different now compared to before. Would forgetting the
> >> >> > extra
> >> >> > zone
> >> >> > change the appearance of the overall plot beyond edge effects?
> >> >>
> >> >> It should shift the derivative considerably, but the only other
> >> >> differences should be at the edges.  Are the actual values different,
> >> >> or is the colorbar scaling differently now?
> >> >>
> >> >> >
> >> >> > Thank you,
> >> >> > Nathan Butcher
> >> >> >
> >> >> >
> >> >> > On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <
> matthewturk at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> Hi Nathan,
> >> >> >>
> >> >> >> Yup, I agree with your assessment -- there's an edge effect.  You
> >> >> >> need
> >> >> >> one more thing to get the derivative field working; you need to
> tell
> >> >> >> yt to give you an extra zone in each direction.  You can do that
> by
> >> >> >> changing your decorator for the derived field to:
> >> >> >>
> >> >> >> @derived_field(name = "GravGradientX", validators =
> >> >> >> [ValidateSpatial(1)])
> >> >> >>
> >> >> >> I don't believe you need any additional changes inside the source
> >> >> >> code.  Let us know if that fixes it!
> >> >> >>
> >> >> >> -Matt
> >> >> >>
> >> >> >> On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher
> >> >> >> <butchernate at gmail.com>
> >> >> >> wrote:
> >> >> >> > Hello,
> >> >> >> >
> >> >> >> > Using an Enzo dataset, I have written a function to find the
> >> >> >> > derivative
> >> >> >> > in
> >> >> >> > the x-direction of a field. When I try to plot the derivative, I
> >> >> >> > see
> >> >> >> > lines
> >> >> >> > that throughout the plot that I'm guessing are due to the edges
> of
> >> >> >> > cells.
> >> >> >> > The attached plot is a slice of the x-direction derivative of
> the
> >> >> >> > PotentialField viewed down the x-axis, but this error appears in
> >> >> >> > plots
> >> >> >> > for
> >> >> >> > density and pressure as well. I am new to using yt, and I am not
> >> >> >> > sure
> >> >> >> > what
> >> >> >> > is causing this.
> >> >> >> >
> >> >> >> > Thank you,
> >> >> >> > Nathan Butcher
> >> >> >> >
> >> >> >> > _______________________________________________
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> >> >> >> >
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