Mailman 3 April 2011 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Clear memory?
by Elizabeth Tasker 01 Sep '11

01 Sep '11

Hi, Is there any way in yt to get a script to delete (or ignore) all the .yt and .harray files and clear its memory? I run into errors when I'm re-doing a plot or I've re-run the simulation and over-written the last data set I looked at with yt. I have to exit yt, delete the above files by hand and restart, which is a bit of a pain. Elizabeth

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new fields in output
by Elizabeth Tasker 17 Jul '11

17 Jul '11

Hi, I've added PotentialField to the data that gets outputted. I'd like to read this into yt, but how does this work when yt won't be expecting PotentialField to be one of the data sets? Elizabeth

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Reason
by Christine Simpson 08 Jun '11

08 Jun '11

Hi all, I'm not sure if this is the right list to send this to, but I think a bunch of knowledgeable people read this one, and hopefully one of you can help me. I'm trying to use Reason and I'm kind of confused about the ssh tunneling part. I start up yt serve on a remote machine (ranger) and I'm told to create a ssh tunnel by executing these commands: ~C -L55185:localhost:55185 My local machine doesn't recognize "~C" and I'm not sure what it is either. I tried creating an ssh tunnel with this: ssh tg803911(a)ranger.tacc.utexas.edu -L 55185:localhost:55185 I was then able to successfully open the gui in a browser with the url provided, but I am unable to load data (I can view the help though). In order to do the ssh tunnel properly do I need to install something on my local machine? Christine

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yt Logo Contest, and possibly a free mug!
by Sam Skillman 10 May '11

10 May '11

Hi all, yt is in need of an awesome new logo, which is why we are announcing the first ever new logo contest! So here's the deal: We'll accept entries for the next two weeks. Let's arbitrarily say Tuesday, May 10th, at 11:59:59 pm EST. If there is more than one entry, we will put it up for a community vote at that time. Oh, and the most important part -- the winner will get a coffee mug with their new logo front and center!!! Please email yt(a)enzotools.org with your image attached. Good luck, and happy logo-ing! Sam

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ray problem with cell volume
by Elizabeth Tasker 02 May '11

02 May '11

Hi, When using the ray feature in yt, we hit problems if we try to plot any variable that contains the cell volume. e.g. def _Momentum(field, data): return (data["Density"]*data["CellVolume"]*sqrt( data["x-velocity"]**2.0 + data["y-velocity"]**2.0 + data["z-velocity"]**2.0 )) ray = pf.h.ray([0.5, 0.5, 0.5], [1.0,1.0,1.0], "Momentum") pylab.plot(ray["RadiusCode"], ray["Momentum"], 'o') Gives: IndexError Traceback (most recent call last) /saw_sfs/work/chris/yt/scripts/iyt in <module>() ----> 1 2 3 4 5 /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key) 274 if key not in self.fields: 275 self.fields.append(key) --> 276 self.get_data(key) 277 return self.data[key] 278 /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 445 mylog.info("Getting field %s from %s", field, len(self._grids)) 446 if field not in self.hierarchy.field_list and not in_grids: --> 447 if field not in ("dts", "t") and self._generate_field(field): 448 continue # True means we already assigned it 449 self[field] = na.concatenate( /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in _generate_field(self, field) 423 return False 424 else: --> 425 self[field] = self.pf.field_info[field](self) 426 return True 427 else: # Can't find the field, try as it might /saw_sfs/work/chris/yt/yt/data_objects/field_info_container.pyc in __call__(self, data) 292 ii = self.check_available(data) 293 original_fields = data.keys() # Copy --> 294 dd = self._function(self, data) 295 dd *= self._convert_function(data) 296 for field_name in data.keys(): /saw_sfs/work/chris/yt/scripts/iyt in _Momentum(field, data) 14 15 def _Momentum(field, data): ---> 16 return (data["Density"]*data["CellVolume"]*sqrt( 17 data["x-velocity"]**2.0 18 + data["y-velocity"]**2.0 /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key) 274 if key not in self.fields: 275 self.fields.append(key) --> 276 self.get_data(key) 277 return self.data[key] 278 /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 445 mylog.info("Getting field %s from %s", field, len(self._grids)) 446 if field not in self.hierarchy.field_list and not in_grids: --> 447 if field not in ("dts", "t") and self._generate_field(field): 448 continue # True means we already assigned it 449 self[field] = na.concatenate( /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in _generate_field(self, field) 423 return False 424 else: --> 425 self[field] = self.pf.field_info[field](self) 426 return True 427 else: # Can't find the field, try as it might /saw_sfs/work/chris/yt/yt/data_objects/field_info_container.pyc in __call__(self, data) 292 ii = self.check_available(data) 293 original_fields = data.keys() # Copy --> 294 dd = self._function(self, data) 295 dd *= self._convert_function(data) 296 for field_name in data.keys(): /saw_sfs/work/chris/yt/yt/data_objects/universal_fields.pyc in _CellVolume(field, data) 392 393 def _CellVolume(field, data): --> 394 if data['dx'].size == 1: 395 try: 396 return data['dx']*data['dy']*data['dx']*\ /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key) 274 if key not in self.fields: 275 self.fields.append(key) --> 276 self.get_data(key) 277 return self.data[key] 278 /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 449 self[field] = na.concatenate( 450 [self._get_data_from_grid(grid, field) --> 451 for grid in self._grids]) 452 if not self.data.has_key(field): 453 continue /saw_sfs/work/chris/yt/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 558 if field == 'dts': return self._dts[grid.id][mask] 559 if field == 't': return self._ts[grid.id][mask] --> 560 return grid[field][mask] 561 562 @cache_mask IndexError: invalid index to scalar variable. Any ideas? Elizabeth

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FLASH and spherical coords
by Massimo Gaspari 30 Apr '11

30 Apr '11

Hi all, I am using FLASH3.3, testing the (3D) spherical coordinate system. Is it possible with YT to make a slice with this kind of coords (r,theta,phi)? If so, how can I do that? Could you provide a template? Thank you in advance, Massimo Gaspari

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Re: [yt-users] yt-users Digest, Vol 38, Issue 38
by Wolfram Schmidt 29 Apr '11

29 Apr '11

Hi Matt, thanks a lot for your reply! Of course, I am aware that you cannot account for every special situation in the design of yt right from the beginning, so sometimes we have to resort to provisional solutions. I followed the procedure you suggested on the machine behind the firewall (I think there was a confusion of A and B - never mind;-). After removing and re-creating the yt-hg subdirectory and changing into this directory, the execution of ~/yt/bin/hg unbundle ~/yt/yt-20110428.hg yielded the error message: abort: There is no Mercurial repository here (.hg not found)! Now, one thing is for sure: yt-20110428.hg is right where it is supposed to be: ls -l ~/yt/yt-20110428.hg -rw-r--r-- 1 lu78tar3 pr47bi 25682789 2011-04-29 19:18 /home/hlrb2/pr47bi/lu78tar3/yt/yt-20110428.hg So that's curious... Wolfram

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h5py from install script on kraken
by Britton Smith 28 Apr '11

28 Apr '11

Hi everyone, I just tried a new install of yt on kraken form the install script. It failed on installing h5py 1.3 with the following error: ****************************************** Configure: Autodetecting HDF5 settings... Custom HDF5 dir: /lustre/scratch/britton/local-dev Custom API level: None /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /lustre/scratch/britton/local-dev/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate': H5Zdeflate.c:(.text+0x134): undefined reference to `compress2' H5Zdeflate.c:(.text+0x1ee): undefined reference to `inflateInit_' H5Zdeflate.c:(.text+0x209): undefined reference to `inflate' H5Zdeflate.c:(.text+0x270): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x3de): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x410): undefined reference to `inflateEnd' /usr/bin/ld: link errors found, deleting executable `detect/vers' collect2: ld returned 1 exit status Failed to compile HDF5 test program. Please check to make sure: * You have a C compiler installed * A development version of Python is installed (including header files) * A development version of HDF5 is installed (including header files) * If HDF5 is not in a default location, supply the argument --hdf5=<path> ****************************************** error: command 'cc' failed with exit status 1 I checked that the kraken yt install from the yt module is using h5py 1.2, which I believe suffers from the h5py bug that was mentioned not too long ago. I double checked that I had gnu compiler module loaded, so I don't think that's it. Does anyone have any ideas? Britton

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FixedResolutionBuffer problem
by Stephen Skory 28 Apr '11

28 Apr '11

Hi all, I am attempting to follow the examples of how to make a fixed resolution buffer, and I have run into a problem. If I follow the first example on this page <http://yt.enzotools.org/doc/analyzing/generating_processed_data.html>: sl = pf.h.proj(0, 0.6) frb = FixedResolutionBuffer(sl, (0.3, 0.5, 0.6, 0.8), (512, 512)) my_image = frb["Density"] I get this error <http://paste.enzotools.org/show/1603/> which makes it look like it's trying to use the second term of .proj() '0.6' as a data field. So, if I change things to: sl = pf.h.proj(0, 'Density') I get this error <http://paste.enzotools.org/show/1604/> complaining about 'px'. Am I doing something wrong, or is this a bug? I am using 4216:5c6f932b9f34. Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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