Docs and 2.4 roundup (help!)
Hi all, There's been a flurry of activity on the docs this week. * All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying. Here's my current draft of the changelog for 2.4. Did I forget anything? https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r... We're just about good to go. These things still need to be done: * Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented. In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts. I think that's about it. There are two additional technical tickets that should be addressed: https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds I can do the second, but I don't know what to do about the first. Thanks all, -Matt
I'm signed up for writing testing docs, but it's been so long since I've used the testing I will have to relearn how it works. If anyone else would like to take it, that would be great. I need to finish up the documentation of the new simulation time series stuff now that the old EnzoSimulation is gone. I'd like to get this in before we push this out the door. Britton On Wed, Jul 25, 2012 at 2:19 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field. While we're thinking about this, are there any other universal fields that depend on enzo-only fields? Cheers, Nathan On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-Matt _______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues. On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3. Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation. I can't speak to the other codes. Cheers, Nathan On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
In what context is the Entropy field supposed to apply? If you're talking galaxy clusters, then it's typically the number density of electrons that is in the definition, not the number density of _everything_. In multispecies runs you should be able to define it using Abar and Zbar fields, but keep in mind that typically in these cases we also have a possibly spatially varying gamma. I'd actually be -1 in retaining the field, since it seems that its definition could be very context-dependent. John On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343@gmail.com>wrote:
FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3.
Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation.
I can't speak to the other codes.
Cheers,
Nathan
On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote: maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields
that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget
anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
-- John ZuHone Postdoctoral Researcher NASA/Goddard Space Flight Center jzuhone@gmail.com john.zuhone@nasa.gov
John has an excellent point. However, I think having a built in Entropy definition is so useful, that I have a different conclusion -- instead I would be +1 on using the physical density instead of the number density (T/rho^(gamma-1)), since this is the standard thermodynamic definition for an ideal gas. Of course: (i) this is not the real entropy, (the real entropy is Nk times the log of our definition, plus a constant) , and (ii) individual research areas have their own estimate of this quantity, as John points out, but that can be added on a per-user basis. As always, feel free to ignore... Cheers, Greg On Jul 25, 2012, at 5:22 PM, John Zuhone wrote:
In what context is the Entropy field supposed to apply? If you're talking galaxy clusters, then it's typically the number density of electrons that is in the definition, not the number density of _everything_.
In multispecies runs you should be able to define it using Abar and Zbar fields, but keep in mind that typically in these cases we also have a possibly spatially varying gamma.
I'd actually be -1 in retaining the field, since it seems that its definition could be very context-dependent.
John
On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote: FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3.
Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation.
I can't speak to the other codes.
Cheers,
Nathan
On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
-- John ZuHone
Postdoctoral Researcher NASA/Goddard Space Flight Center
jzuhone@gmail.com john.zuhone@nasa.gov
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
---------------------------------- Greg Bryan Associate Professor of Astronomy Department of Astronomy, Columbia University 1325 Pupin Physics Laboratories, Mail Code 5246 550 West 120th Street New York, New York 10027 (USA) email: gbryan@astro.columbia.edu phone: +1(212)854-6837 fax : +1(212)854-8121
I'm +1 on Greg's suggestion of replacing the number density with just the density, but that still leaves us with the problem of gamma. If gamma is a field (as it sometimes is in FLASH, don't know about any other codes) then it should be incorporated somehow. Does anybody know which gamma would be part of the entropy definition? "gamc" (as defined from the sound speed) or "game" (as defined from the energy-pressure relation), which can be different? On Jul 25, 2012, at 6:40 PM, Greg Bryan wrote:
John has an excellent point. However, I think having a built in Entropy definition is so useful, that I have a different conclusion -- instead I would be +1 on using the physical density instead of the number density (T/rho^(gamma-1)), since this is the standard thermodynamic definition for an ideal gas. Of course: (i) this is not the real entropy, (the real entropy is Nk times the log of our definition, plus a constant) , and (ii) individual research areas have their own estimate of this quantity, as John points out, but that can be added on a per-user basis. As always, feel free to ignore...
Cheers, Greg
On Jul 25, 2012, at 5:22 PM, John Zuhone wrote:
In what context is the Entropy field supposed to apply? If you're talking galaxy clusters, then it's typically the number density of electrons that is in the definition, not the number density of _everything_.
In multispecies runs you should be able to define it using Abar and Zbar fields, but keep in mind that typically in these cases we also have a possibly spatially varying gamma.
I'd actually be -1 in retaining the field, since it seems that its definition could be very context-dependent.
John
On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote: FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3.
Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation.
I can't speak to the other codes.
Cheers,
Nathan
On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
-- John ZuHone
Postdoctoral Researcher NASA/Goddard Space Flight Center
jzuhone@gmail.com john.zuhone@nasa.gov
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
---------------------------------- Greg Bryan Associate Professor of Astronomy Department of Astronomy, Columbia University 1325 Pupin Physics Laboratories, Mail Code 5246 550 West 120th Street New York, New York 10027 (USA)
email: gbryan@astro.columbia.edu phone: +1(212)854-6837 fax : +1(212)854-8121
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
John -- Sorry, I'm not sure. I would guess "game" since it seems more fundamental. Greg On Jul 27, 2012, at 1:26 PM, John ZuHone <jzuhone@gmail.com> wrote:
I'm +1 on Greg's suggestion of replacing the number density with just the density, but that still leaves us with the problem of gamma. If gamma is a field (as it sometimes is in FLASH, don't know about any other codes) then it should be incorporated somehow.
Does anybody know which gamma would be part of the entropy definition? "gamc" (as defined from the sound speed) or "game" (as defined from the energy-pressure relation), which can be different?
On Jul 25, 2012, at 6:40 PM, Greg Bryan wrote:
John has an excellent point. However, I think having a built in Entropy definition is so useful, that I have a different conclusion -- instead I would be +1 on using the physical density instead of the number density (T/rho^(gamma-1)), since this is the standard thermodynamic definition for an ideal gas. Of course: (i) this is not the real entropy, (the real entropy is Nk times the log of our definition, plus a constant) , and (ii) individual research areas have their own estimate of this quantity, as John points out, but that can be added on a per-user basis. As always, feel free to ignore...
Cheers, Greg
On Jul 25, 2012, at 5:22 PM, John Zuhone wrote:
In what context is the Entropy field supposed to apply? If you're talking galaxy clusters, then it's typically the number density of electrons that is in the definition, not the number density of _everything_.
In multispecies runs you should be able to define it using Abar and Zbar fields, but keep in mind that typically in these cases we also have a possibly spatially varying gamma.
I'd actually be -1 in retaining the field, since it seems that its definition could be very context-dependent.
John
On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote: FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3.
Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation.
I can't speak to the other codes.
Cheers,
Nathan
On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f... https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
-- John ZuHone
Postdoctoral Researcher NASA/Goddard Space Flight Center
jzuhone@gmail.com john.zuhone@nasa.gov
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
---------------------------------- Greg Bryan Associate Professor of Astronomy Department of Astronomy, Columbia University 1325 Pupin Physics Laboratories, Mail Code 5246 550 West 120th Street New York, New York 10027 (USA)
email: gbryan@astro.columbia.edu phone: +1(212)854-6837 fax : +1(212)854-8121
_______________________________________________ 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
Hi all, John has issued a Pull Request on this topic: https://bitbucket.org/yt_analysis/yt/pull-request/228/redefining-the-entropy... Does this seem to address the use cases for Entropy? -Matt On Sun, Jul 29, 2012 at 12:06 AM, Greg Bryan <gbryan@astro.columbia.edu> wrote:
John -- Sorry, I'm not sure. I would guess "game" since it seems more fundamental.
Greg
On Jul 27, 2012, at 1:26 PM, John ZuHone <jzuhone@gmail.com> wrote:
I'm +1 on Greg's suggestion of replacing the number density with just the density, but that still leaves us with the problem of gamma. If gamma is a field (as it sometimes is in FLASH, don't know about any other codes) then it should be incorporated somehow.
Does anybody know which gamma would be part of the entropy definition? "gamc" (as defined from the sound speed) or "game" (as defined from the energy-pressure relation), which can be different?
On Jul 25, 2012, at 6:40 PM, Greg Bryan wrote:
John has an excellent point. However, I think having a built in Entropy definition is so useful, that I have a different conclusion -- instead I would be +1 on using the physical density instead of the number density (T/rho^(gamma-1)), since this is the standard thermodynamic definition for an ideal gas. Of course: (i) this is not the real entropy, (the real entropy is Nk times the log of our definition, plus a constant) , and (ii) individual research areas have their own estimate of this quantity, as John points out, but that can be added on a per-user basis. As always, feel free to ignore...
Cheers, Greg
On Jul 25, 2012, at 5:22 PM, John Zuhone wrote:
In what context is the Entropy field supposed to apply? If you're talking galaxy clusters, then it's typically the number density of electrons that is in the definition, not the number density of _everything_.
In multispecies runs you should be able to define it using Abar and Zbar fields, but keep in mind that typically in these cases we also have a possibly spatially varying gamma.
I'd actually be -1 in retaining the field, since it seems that its definition could be very context-dependent.
John
On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo. I'm not sure if there is an equivalent parameter in FLASH 2 and 3.
Of course in multispecies runs eos_singleSpeciesA is not defined so you would need to build the number density field as in the enzo frontend. FLASH allows for an arbitrary species specification - I'm not sure how that is represented in the data dumps since I've never run a true multispecies simulation.
I can't speak to the other codes.
Cheers,
Nathan
On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
New build: http://yt-project.org/docs/2.4/ The cookbook in particular is coming along: http://yt-project.org/docs/2.4/cookbook/index.html
Thanks for taking on the making_plots.rst, Nathan. Britton, don't worry about the testing stuff, we can push it off for now. As for NumberDensity, is there a mu value we could use? Otherwise, we can build it from the species fields as we do for Enzo. I'm also in support of searching out problematic fields; I think the particle fields in particular may have a handful of issues.
On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document?
I can take care of that one.
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
This will require defining a NumberSpecies field, currently only defined in the enzo frontend. Really, NumberDensity should be a univseral field but I guess its definition will be highly code-dependent with respect to how different codes handle multispecies simulations. Each of the maintainers for the different codes will have to update their frontend to include the NumberDensity field.
While we're thinking about this, are there any other universal fields that depend on enzo-only fields?
Cheers,
Nathan
On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
Hi all,
There's been a flurry of activity on the docs this week.
* All the cookbook recipes have been moved into the docs and the cookbook shut down. We now have 45 cookbook recipes, and they're integrated much better into the docs. * Most of the docs have been rewritten to remove PlotCollection * The data index is now part of the website repo. It's up, but the files are still copying.
Here's my current draft of the changelog for 2.4. Did I forget anything?
https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.r...
We're just about good to go. These things still need to be done:
* Rewrite the remaining docs that use PlotCollection. Specifically, orientation/making_plots.rst needs to be completely redone. Can someone volunteer to rewrite this document? * Volume rendering docs need to be rewritten en masse, as they are quite out of date and don't reflect best practices or new functionality (ticket #382). * Do we want to put answer testing docs in for this release, or should we push that off to a point release at a slightly later date? * Write docs about the Hub, which I will do. * Check to make sure that everything that SHOULD be documented in the API docs IS documented.
In the past we've also talked about slides demonstrating new functionality, as well as the possibility of doing screencasts. I'm going to throw together some HTML slides, but if anybody wants to do a screencast that would be outstanding. We actually have gotten *many* views in the past of screencasts.
I think that's about it. There are two additional technical tickets that should be addressed:
https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-f...
https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
I can do the second, but I don't know what to do about the first.
Thanks all,
-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
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
-- John ZuHone
Postdoctoral Researcher NASA/Goddard Space Flight Center
jzuhone@gmail.com john.zuhone@nasa.gov
_______________________________________________ yt-dev mailing list yt-dev@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
---------------------------------- Greg Bryan Associate Professor of Astronomy Department of Astronomy, Columbia University 1325 Pupin Physics Laboratories, Mail Code 5246 550 West 120th Street New York, New York 10027 (USA)
email: gbryan@astro.columbia.edu phone: +1(212)854-6837 fax : +1(212)854-8121
_______________________________________________ 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 (6)
-
Britton Smith -
Greg Bryan -
John Zuhone -
John ZuHone
-
Matthew Turk -
Nathan Goldbaum