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Kuo-Chuan Pan

1 Nov 2016 1 Nov '16

6:09 p.m.

Dear all, I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon). Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()? Many thanks, Kuo-Chuan

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Nathan Goldbaum

1 Nov 1 Nov

6:20 p.m.

Hi Kuo-Chuan, Can you show us how you've defined your derived field? Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right? -Nathan On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...

Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Kuo-Chuan Pan

6:25 p.m.

Dear Nathan, Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt. The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants. Many thanks, Kuo-Chuan 11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Nathan Goldbaum

6:52 p.m.

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification. Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend: https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units. Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though: from yt.units import kb from yt.units.dimensions import energy, temperature # load your dataset ds = yt.load(...) ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}') def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon") And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB". Please feel free to open issues or pull requests about any of the things I raised above. -Nathan On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan wrote:

...

Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/ PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...
Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Kuo-Chuan Pan

7:40 p.m.

Dear Nathan, Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’. The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that? Many thanks, Kuo-Chuan

...

On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...
On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Nathan Goldbaum

7:50 p.m.

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan wrote:

...

Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly. If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script? We have paste.yt-project.org set up for this purpose. -Nathan

...

The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9d d0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer= file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...
Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Kuo-Chuan Pan

8 p.m.

Dear Nathan, Thank you very much for your help. I was using ds.add_field() I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/ Many thanks, Kuo-Chuan

...

On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org http://paste.yt-project.org/ set up for this purpose.

-Nathan

The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...
On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Nathan Goldbaum

8:03 p.m.

At the top of your script, you have: from yt.units import kb but later you have: return kB*entrdens It should be: return kb*entrdens On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan wrote:

...

Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org set up for this purpose.

-Nathan

...
The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a 8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at= yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...
Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Kuo-Chuan Pan

8:13 p.m.

Dear Nathan, Thanks very much for your help. That was a stupid mistake and the error message is different with the previous one I said. If I changed to kb, the error message is: P014 yt : [ERROR ] 2016-11-01 16:11:53,531 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. File "volume_rendering.py", line 164, in <module> plot_a_vr(fn,cycle,rotate=False) File "volume_rendering.py", line 101, in plot_a_vr tfh.set_bounds() File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/visualization/volume_rendering/transfer_function_helper.py", line 66, in set_bounds bounds = self.ds.h.all_data().quantities['Extrema'](self.field, non_zero=True) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 510, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 67, in __call__ sto.result = self.process_chunk(ds, *args, **kwargs) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 518, in process_chunk fd = data[field] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1245, in _generate_fields raise YTFieldUnitParseError(fi) P015 yt : [ERROR ] 2016-11-01 16:11:53,572 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. -------------------------------------------------------------------------- Many thanks, Kuo-Chuan

...

On Nov 1, 2016, at 4:03 PM, Nathan Goldbaum wrote:

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/ http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org http://paste.yt-project.org/ set up for this purpose.

-Nathan

The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...
On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Nathan Goldbaum

8:16 p.m.

Which yt version is this? Can you reproduce it on yt 3.3.2? Does the following simple test script work? from yt.units import kb from yt.units.dimensions import energy, temperature # load your dataset ds = yt.load(...) ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}') def _entrdens(field,data): """ create a new derived field to show both entropy and density """ return data['ones'] ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon") ad = ds.all_data() print ad['Entropy'] On Tue, Nov 1, 2016 at 3:13 PM, Kuo-Chuan Pan wrote:

...

Dear Nathan,

Thanks very much for your help. That was a stupid mistake and the error message is different with the previous one I said. If I changed to kb, the error message is:

P014 yt : [ERROR ] 2016-11-01 16:11:53,531 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. File "volume_rendering.py", line 164, in <module> plot_a_vr(fn,cycle,rotate=False) File "volume_rendering.py", line 101, in plot_a_vr tfh.set_bounds() File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ visualization/volume_rendering/transfer_function_helper.py", line 66, in set_bounds bounds = self.ds.h.all_data().quantities['Extrema'](self.field, non_zero=True) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/derived_quantities.py", line 510, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/derived_quantities.py", line 67, in __call__ sto.result = self.process_chunk(ds, *args, **kwargs) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/derived_quantities.py", line 518, in process_chunk fd = data[field] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1245, in _generate_fields raise YTFieldUnitParseError(fi) P015 yt : [ERROR ] 2016-11-01 16:11:53,572 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. --------------------------------------------------------------------------

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 4:03 PM, Nathan Goldbaum wrote:

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org set up for this purpose.

-Nathan

...
The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a 8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt& fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...
Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Kuo-Chuan Pan

8:25 p.m.

Dear Nathan, It gives a different error message. http://paste.yt-project.org/show/6909/ I am using yt 3.3.2 installed from Anaconda on a Mac. Many thanks, Kuo-Chuan yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,280 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: current_time = 0.298820349993 yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: domain_dimensions = [80 80 80] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_left_edge = [ -1.00000000e+09 -1.00000000e+09 -1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_right_edge = [ 1.00000000e+09 1.00000000e+09 1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,304 Parameters: cosmological_simulation = 0.0 Traceback (most recent call last): File "test.py", line 15, in <module> print ad['Entropy'] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1243, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'Entropy')' returned data with units 'dimensionless' but was defined with units 'kB'.

...

On Nov 1, 2016, at 4:16 PM, Nathan Goldbaum wrote:

Which yt version is this? Can you reproduce it on yt 3.3.2?

Does the following simple test script work?

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ return data['ones'] ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

ad = ds.all_data()

print ad['Entropy']

On Tue, Nov 1, 2016 at 3:13 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. That was a stupid mistake and the error message is different with the previous one I said. If I changed to kb, the error message is:

P014 yt : [ERROR ] 2016-11-01 16:11:53,531 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. File "volume_rendering.py", line 164, in <module> plot_a_vr(fn,cycle,rotate=False) File "volume_rendering.py", line 101, in plot_a_vr tfh.set_bounds() File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/visualization/volume_rendering/transfer_function_helper.py", line 66, in set_bounds bounds = self.ds.h.all_data().quantities['Extrema'](self.field, non_zero=True) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 510, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 67, in __call__ sto.result = self.process_chunk(ds, *args, **kwargs) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 518, in process_chunk fd = data[field] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1245, in _generate_fields raise YTFieldUnitParseError(fi) P015 yt : [ERROR ] 2016-11-01 16:11:53,572 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. --------------------------------------------------------------------------

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 4:03 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/ http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org http://paste.yt-project.org/ set up for this purpose.

-Nathan

The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...
On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Nathan Goldbaum

8:30 p.m.

Oh oops, I'm sorry my suggested test script had a typo, try this test script: http://paste.yt-project.org/show/6910/ I haven't actually tried to create an annotated volume rendering using a field with this kB unit yet, maybe there's a deeper issue. Unfortunately I need to work on a presentation for a conference right now and don't have time to dive in deeply on this. If you can create a test script that triggers this issue, using a publicly available dataset (e.g. one of the datasets on yt-project.org/data), that would be helpful. It might also be a lot easier to avoid this workaround and just specify the label by hand. You'll need to build yt from source and then modify the save_annotated function in yt/visualization/volume_rendering/scene.py to optionally accept a label instead of calculating one based on the plotted field. -Nathan On Tue, Nov 1, 2016 at 3:25 PM, Kuo-Chuan Pan wrote:

...

Dear Nathan,

It gives a different error message. http://paste.yt-project.org/show/6909/

I am using yt 3.3.2 installed from Anaconda on a Mac.

Many thanks, Kuo-Chuan

yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,280 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: current_time = 0.298820349993 yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: domain_dimensions = [80 80 80] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_left_edge = [ -1.00000000e+09 -1.00000000e+09 -1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_right_edge = [ 1.00000000e+09 1.00000000e+09 1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,304 Parameters: cosmological_simulation = 0.0 Traceback (most recent call last): File "test.py", line 15, in <module> print ad['Entropy'] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1243, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'Entropy')' returned data with units 'dimensionless' but was defined with units 'kB'.

On Nov 1, 2016, at 4:16 PM, Nathan Goldbaum wrote:

Which yt version is this? Can you reproduce it on yt 3.3.2?

Does the following simple test script work?

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ return data['ones'] ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

ad = ds.all_data()

print ad['Entropy']

On Tue, Nov 1, 2016 at 3:13 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your help. That was a stupid mistake and the error message is different with the previous one I said. If I changed to kb, the error message is:

P014 yt : [ERROR ] 2016-11-01 16:11:53,531 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. File "volume_rendering.py", line 164, in <module> plot_a_vr(fn,cycle,rotate=False) File "volume_rendering.py", line 101, in plot_a_vr tfh.set_bounds() File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/visuali zation/volume_rendering/transfer_function_helper.py", line 66, in set_bounds bounds = self.ds.h.all_data().quantities['Extrema'](self.field, non_zero=True) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_ objects/derived_quantities.py", line 510, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_ objects/derived_quantities.py", line 67, in __call__ sto.result = self.process_chunk(ds, *args, **kwargs) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_ objects/derived_quantities.py", line 518, in process_chunk fd = data[field] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1245, in _generate_fields raise YTFieldUnitParseError(fi) P015 yt : [ERROR ] 2016-11-01 16:11:53,572 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. ------------------------------------------------------------ --------------

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 4:03 PM, Nathan Goldbaum wrote:

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org set up for this purpose.

-Nathan

...
The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a 8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fil eviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan wrote:

...
Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/P NS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan wrote:

...
Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Kuo-Chuan Pan

8:33 p.m.

Dear Nathan, No problem and thank you very much for your great help. Many thanks, Kuo-Chuan

...

On Nov 1, 2016, at 4:30 PM, Nathan Goldbaum wrote:

Oh oops, I'm sorry my suggested test script had a typo, try this test script:

http://paste.yt-project.org/show/6910/ http://paste.yt-project.org/show/6910/

I haven't actually tried to create an annotated volume rendering using a field with this kB unit yet, maybe there's a deeper issue.

Unfortunately I need to work on a presentation for a conference right now and don't have time to dive in deeply on this. If you can create a test script that triggers this issue, using a publicly available dataset (e.g. one of the datasets on yt-project.org/data http://yt-project.org/data), that would be helpful.

It might also be a lot easier to avoid this workaround and just specify the label by hand. You'll need to build yt from source and then modify the save_annotated function in yt/visualization/volume_rendering/scene.py to optionally accept a label instead of calculating one based on the plotted field.

-Nathan

On Tue, Nov 1, 2016 at 3:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

It gives a different error message. http://paste.yt-project.org/show/6909/ http://paste.yt-project.org/show/6909/

I am using yt 3.3.2 installed from Anaconda on a Mac.

Many thanks, Kuo-Chuan

yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,279 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,280 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: current_time = 0.298820349993 yt : [INFO ] 2016-11-01 16:23:01,302 Parameters: domain_dimensions = [80 80 80] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_left_edge = [ -1.00000000e+09 -1.00000000e+09 -1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,303 Parameters: domain_right_edge = [ 1.00000000e+09 1.00000000e+09 1.00000000e+09] yt : [INFO ] 2016-11-01 16:23:01,304 Parameters: cosmological_simulation = 0.0 Traceback (most recent call last): File "test.py", line 15, in <module> print ad['Entropy'] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1243, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'Entropy')' returned data with units 'dimensionless' but was defined with units 'kB'.

...
On Nov 1, 2016, at 4:16 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Which yt version is this? Can you reproduce it on yt 3.3.2?

Does the following simple test script work?

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ return data['ones'] ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

ad = ds.all_data()

print ad['Entropy']

On Tue, Nov 1, 2016 at 3:13 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. That was a stupid mistake and the error message is different with the previous one I said. If I changed to kb, the error message is:

P014 yt : [ERROR ] 2016-11-01 16:11:53,531 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. File "volume_rendering.py", line 164, in <module> plot_a_vr(fn,cycle,rotate=False) File "volume_rendering.py", line 101, in plot_a_vr tfh.set_bounds() File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/visualization/volume_rendering/transfer_function_helper.py", line 66, in set_bounds bounds = self.ds.h.all_data().quantities['Extrema'](self.field, non_zero=True) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 510, in __call__ rv = super(Extrema, self).__call__(fields, non_zero) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 67, in __call__ sto.result = self.process_chunk(ds, *args, **kwargs) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 518, in process_chunk fd = data[field] File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1192, in get_data self._generate_fields(fields_to_generate) File "/Users/pan/anaconda2/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 1245, in _generate_fields raise YTFieldUnitParseError(fi) P015 yt : [ERROR ] 2016-11-01 16:11:53,572 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB'. --------------------------------------------------------------------------

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 4:03 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thank you very much for your help. I was using ds.add_field()

I have pasted my script and error message here: http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/ http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your email and suggestions. I followed your suggested code but it is not working. yt gives an error message: yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field '('gas', 'Entropy')' has unparseable units 'kB’.

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field as you originally had in your last e-mail? You need to use ds.add_field as I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org http://paste.yt-project.org/ set up for this purpose.

-Nathan

The vales of my “entr” field is already in “kB/baryon” (specific entropy) but the unit is incorrect. Following your suggestions, I want to create two new units called “kB” and “baryon” (1.674e-24 g) and override the “entr” and “Entropy” units to “kB/baryon” (from dimensionless). Is it possible to do that?

Many thanks, Kuo-Chuan

...
On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

One could argue that it would be useful for save_annotated to optionally take a fully user-specified colorbar label. That's not the case now but it would be a relatively easy modification.

Your 'entr' field isn't being recognized by yt with units because it's not a field that is "known" by yt in the FLASH frontend:

https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43 https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9dd0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=file-view-default#fields.py-43

Specifically, it does not appear in the known_other_fields tuple in the flash fields.py file. If entr is not specific to your version of FLASH it may be worthwhile to add an entry there so that the entr field is read in with the correct units.

Similarly, kB isn't a unit that the yt unit system understands out of the box (although I think one could make a case that it's worth including). There is a way to add new units to the unit system though:

from yt.units import kb from yt.units.dimensions import energy, temperature

# load your dataset ds = yt.load(...)

ds.unit_registry.add('kB', 1.3806488e-16, dimensions=energy/temperature, tex_repr='k_{B}')

def _entrdens(field,data): """ create a new derived field to show both entropy and density """ dens = data["dens"] entr = data["entr"] entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR return kb*entrdens ds.add_field("Entropy",function=_entrdens, units="kB", display_name="Entropy per Baryon")

And then make your volume rendering as you were doing before. It should show up in the label as "Entropy per baryon" and with units of "kB".

Please feel free to open issues or pull requests about any of the things I raised above.

-Nathan

On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear Nathan,

Thanks very much for your help. entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon in the code but it is recognised as dimensionless in yt.

The field “entr" is the entropy in my dataset. The derived field “Entropy” is the one I want to visualise. PNS_DENSITY and PNS_ENTR are just constants.

Many thanks, Kuo-Chuan

11 def _entrdens(field,data): 12 """ 13 create a new derived field to show both entropy and density 14 """ 15 dens = data["dens"] 16 entr = data["entr"] 17 entrdens = entr*(np.exp(-(dens.in_cgs()/PNS_DENSITY)**5))+PNS_ENTR 18 return entrdens 19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")

...
On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Kuo-Chuan,

Can you show us how you've defined your derived field?

Is entropy a derived field as well or is it a field that's included in your dataset? This is the entropy per baryon, right?

-Nathan

On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan mailto:pankuoch@msu.edu> wrote: Dear all,

I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon).

Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()?

Many thanks, Kuo-Chuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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