<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN">
<html><body>
<p>Hi Matt,</p>
<p>Thanks. The problem is (which was going to be my next email, and the reason I was trying out 2.5), I can't seem to make plots in the 3.0 branch anymore since updating it. I don't recall which version it was when I could, but now I get the error at the end of the email when I try and make a slice/projection (it happens both with the PlotCollection method as well as SlicePlot). </p>
<p>-Mike</p>
<p> </p>
<p>In [5]: pc.add_slice("Density",2)<br />---------------------------------------------------------------------------<br />AssertionError Traceback (most recent call last)<br />/home/itp/butler/yt-x86_64/src/yt-hg/scripts/iyt in <module>()<br />----> 1 pc.add_slice("Density",2)<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py in add_slice(self, field, axis, coord, center, use_colorbar, figure, axes, fig_size, periodic, obj, field_parameters)<br /> 427 if obj is None:<br /> 428 if field_parameters is None: field_parameters = {}<br />--> 429 obj = self.pf.hierarchy.slice(axis, coord, field,<br /> 430 center=center, **field_parameters)<br /> 431 p = self._add_plot(PCSlicePlot(<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py in hierarchy(self)<br /> 223 raise RuntimeError("You should not instantiate StaticOutput.")<br /> 224 self._instantiated_hierarchy = self._hierarchy_class(<br />--> 225 self, data_style=self.data_style)<br /> 226 return self._instantiated_hierarchy<br /> 227 h = hierarchy # alias<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py in __init__(self, pf, data_style)<br /> 301 <br /> 302 self.float_type = np.float64<br />--> 303 super(RAMSESGeometryHandler, self).__init__(pf, data_style)<br /> 304 <br /> 305 def _initialize_oct_handler(self):<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py in __init__(self, pf, data_style)<br /> 66 <br /> 67 mylog.debug("Setting up domain geometry.")<br />---> 68 self._setup_geometry()<br /> 69 <br /> 70 mylog.debug("Initializing data grid data IO")<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/geometry/oct_geometry_handler.py in _setup_geometry(self)<br /> 48 def _setup_geometry(self):<br /> 49 mylog.debug("Initializing Octree Geometry Handler.")<br />---> 50 self._initialize_oct_handler()<br /> 51 <br /> 52 def get_smallest_dx(self):<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py in _initialize_oct_handler(self)<br /> 306 nv = len(self.fluid_field_list)<br /> 307 self.domains = [RAMSESDomainFile(self.parameter_file, i + 1, nv)<br />--> 308 for i in range(self.parameter_file['ncpu'])]<br /> 309 total_octs = sum(dom.local_oct_count #+ dom.ngridbound.sum()<br /> 310 for dom in self.domains)<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py in __init__(self, pf, domain_id, nvar)<br /> 70 self._read_amr_header()<br /> 71 self._read_particle_header()<br />---> 72 self._read_amr()<br /> 73 <br /> 74 _hydro_offset = None<br /><br />/home/itp/butler/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py in _read_amr(self)<br /> 248 assert(pos.shape[0] == ng)<br /> 249 n = self.oct_handler.add(cpu + 1, level - min_level, pos)<br />--> 250 assert(n == ng)<br /> 251 self.oct_handler.finalize()<br /> 252 <br /><br />AssertionError: <br /><br /><br /></p>
<p> </p>
<p>On Fri, 4 Oct 2013 09:11:36 -0400, Matthew Turk wrote:</p>
<blockquote type="cite" style="padding-left:5px; border-left:#1010ff 2px solid; margin-left:5px; width:100%"><!-- html ignored --><!-- head ignored --><!-- meta ignored -->
<p dir="ltr">Hi Mike,</p>
<p dir="ltr">The stable branch of yt probably doesn't work with RAMSES anymore... I think we even disabled it recently.</p>
<p dir="ltr">However, the 3.0 branch (listed as "bleeding edge" on the website) full supports Ramses and is considerably faster and more memory conservative. I'd suggest you give it a shot - at this point it's quite stable and production ready. The docs are still lagging but that's next up; for Ramses it should be mostly identical in usage. If you do run into any trouble, drop a line here?</p>
<p dir="ltr">Matt</p>
<div class="gmail_quote">On Oct 4, 2013 9:04 AM, "Butler,Michael J" <<a href="mailto:butler85@astro.ufl.edu">butler85@astro.ufl.edu</a>> wrote:<br />
<blockquote class="gmail_quote" style="margin: 0 0 0 .8ex; border-left: 1px #ccc solid; padding-left: 1ex;">Hi everyone,<br /><br /> I have been working with the stable branch of yt to look at RAMSES data and have run into a problem. When doing simple projections of e.g. Density with take_log=True, the projection becomes blocky (see attached image). This doesn't happen if I take out the take_log line. Here is what I am doing :<br /><br /> pf = load("output_00427/info_00427.<span style="text-decoration: underline;"></span>txt")<br /> pf.h<br /> pf.field_info['Density'].take_<span style="text-decoration: underline;"></span>log = True<br /> p=SlicePlot(pf,2,"Density")<br /><br /> Any ideas what is going on here?<br /><br /> Thanks,<br /><br /> Mike<br />_______________________________________________<br /> yt-users mailing list<br /><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br /><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br /><br /></blockquote>
</div>
</blockquote>
<p> </p>
<div> </div>
</body></html>