NumberDensity in clumps and on FLASH data
Hi all, Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email: "Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset." The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data. I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas? -Matt
Matt, Getting on a plane soon but when I hit the ground in Chicago I'll have a look at it. I think I know what to do. John John ZuHone Laboratory for High-Energy Astrophysics NASA/Goddard Space Flight Center 8800 Greenbelt Rd., Code 662 Greenbelt, MD 20771 (w) 301-286-2531 (m) 773-758-0172 jzuhone@gmail.com john.zuhone@nasa.gov On Oct 25, 2012, at 7:09 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi all,
Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data.
I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas?
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
Hi Matt, There's actually an issue related to this that we closed before the 2.4 release: https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... Basically, we would need to pare the FLASH data dumps, search for the appropriate runtime parameters that control the EOS settings (as described in section 15 of the FLASH docs: http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug/node22.html), and from that back out what mean molecular weight is. I think it would be possible for Mark to define his own NumberDensity field in his .yt/my_plugins file as a stopgap solution. -Nathan On Oct 25, 2012, at 4:09 PM, Matthew Turk wrote:
Hi all,
Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data.
I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas?
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
Hi everyone, It looks to me like this issue was never resolved - for instance when I attempt to save the clump hierarchy (which I can now find thanks to Kacper!), it complains about not finding NumberDensity (traceback here: http://pastebin.com/NSuaj8XH ). I got it to work using a potentially non-optimal solution, namely adding the following lines to the end of yt/frontends/flash/fields.py -- http://pastebin.com/jYWcZCDj I can imagine this failing if the dataset uses the Helmholtz EoS or maybe with multispecies, but maybe it would work (I don't have any datasets handy which use these). Thank you, John On Thu, Oct 25, 2012 at 4:18 PM, Nathan Goldbaum <nathan12343@gmail.com>wrote:
Hi Matt,
There's actually an issue related to this that we closed before the 2.4 release: https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
Basically, we would need to pare the FLASH data dumps, search for the appropriate runtime parameters that control the EOS settings (as described in section 15 of the FLASH docs: http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug/node22.html), and from that back out what mean molecular weight is.
I think it would be possible for Mark to define his own NumberDensity field in his .yt/my_plugins file as a stopgap solution.
-Nathan
On Oct 25, 2012, at 4:09 PM, Matthew Turk wrote:
Hi all,
Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data.
I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas?
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
Hey John, This is a longstanding issue with the FLASH frontend, see e.g. this e-mail from last year: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-October/00257... I think your patch is a good starting point and it's probably worth issuing a pull request about this to at least start a discussion. -Nathan On Tue, Jul 9, 2013 at 6:48 PM, John Forbes <jforbes@ucolick.org> wrote:
Hi everyone,
It looks to me like this issue was never resolved - for instance when I attempt to save the clump hierarchy (which I can now find thanks to Kacper!), it complains about not finding NumberDensity (traceback here: http://pastebin.com/NSuaj8XH ). I got it to work using a potentially non-optimal solution, namely adding the following lines to the end of yt/frontends/flash/fields.py -- http://pastebin.com/jYWcZCDj
I can imagine this failing if the dataset uses the Helmholtz EoS or maybe with multispecies, but maybe it would work (I don't have any datasets handy which use these).
Thank you, John
On Thu, Oct 25, 2012 at 4:18 PM, Nathan Goldbaum <nathan12343@gmail.com>wrote:
Hi Matt,
There's actually an issue related to this that we closed before the 2.4 release: https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
Basically, we would need to pare the FLASH data dumps, search for the appropriate runtime parameters that control the EOS settings (as described in section 15 of the FLASH docs: http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug/node22.html), and from that back out what mean molecular weight is.
I think it would be possible for Mark to define his own NumberDensity field in his .yt/my_plugins file as a stopgap solution.
-Nathan
On Oct 25, 2012, at 4:09 PM, Matthew Turk wrote:
Hi all,
Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data.
I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas?
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
Oops, didn't see that you were replying to the old thread I linked to. On Tue, Jul 9, 2013 at 7:43 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hey John,
This is a longstanding issue with the FLASH frontend, see e.g. this e-mail from last year: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-October/00257...
I think your patch is a good starting point and it's probably worth issuing a pull request about this to at least start a discussion.
-Nathan
On Tue, Jul 9, 2013 at 6:48 PM, John Forbes <jforbes@ucolick.org> wrote:
Hi everyone,
It looks to me like this issue was never resolved - for instance when I attempt to save the clump hierarchy (which I can now find thanks to Kacper!), it complains about not finding NumberDensity (traceback here: http://pastebin.com/NSuaj8XH ). I got it to work using a potentially non-optimal solution, namely adding the following lines to the end of yt/frontends/flash/fields.py -- http://pastebin.com/jYWcZCDj
I can imagine this failing if the dataset uses the Helmholtz EoS or maybe with multispecies, but maybe it would work (I don't have any datasets handy which use these).
Thank you, John
On Thu, Oct 25, 2012 at 4:18 PM, Nathan Goldbaum <nathan12343@gmail.com>wrote:
Hi Matt,
There's actually an issue related to this that we closed before the 2.4 release: https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
Basically, we would need to pare the FLASH data dumps, search for the appropriate runtime parameters that control the EOS settings (as described in section 15 of the FLASH docs: http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug/node22.html), and from that back out what mean molecular weight is.
I think it would be possible for Mark to define his own NumberDensity field in his .yt/my_plugins file as a stopgap solution.
-Nathan
On Oct 25, 2012, at 4:09 PM, Matthew Turk wrote:
Hi all,
Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data.
I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas?
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
participants (5)
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John Forbes -
John ZuHone -
Matthew Turk -
Nathan Goldbaum -
Nathan Goldbaum