Problem with Units in a Derived Field
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field(): http://paste.yt-project.org/show/5833/ However, I get an error about being unable to add quantities with differing units: http://paste.yt-project.org/show/5834/ The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
Hi Jared, The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units. In your line, fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1). In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html I hope this helps! Cameron On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu <javascript:_e(%7B%7D,'cvml','Jared.W.Coughlin.29@nd.edu');>> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it. -Jared On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.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
That seemed to have worked, thanks! I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.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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Hi Jared, You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion: indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something* that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements. -Andrew On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I have a gadget snapshot for which the standard internal energy block has been replaced by one containing the temperature. I'm trying to calculate a derived field for the neutral hydrogen number density, but I'm getting an error when I try to do ds.add_field():
http://paste.yt-project.org/show/5833/
However, I get an error about being unable to add quantities with differing units:
http://paste.yt-project.org/show/5834/
The docs say not to do any unit conversion because that is apparently taken care of behind the scenes, so I didn't. I was just wondering if there was a way around this? Thanks! -Jared
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Thanks, I'll try that! -Jared On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jared,
The problem is one of units. In order to make common arithmetic work like addition, yt requires both arguments going into the addition operator to have the same units.
In your line,
fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
you're adding two things (gamma_HI) and (gamma_c*ne) that have different units--in this case, something with (code_mass/code_length**3) units and something with no units defined as (1).
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
In order to fix this, you can re-assign the appropriate units to different arrays or quantities with the YTArray and YTQuantity classes. In this case, make sure that the two arguments going into the addition have the same units. If you want to recast "ne" to have number density units, you can do this: from yt.units.yt_array import YTQuantity; ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out http://yt-project.org/docs/dev/analyzing/units/index.html
I hope this helps!
Cameron
On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> Hello! I have a gadget snapshot for which the standard internal > energy block has been replaced by one containing the temperature. I'm > trying to calculate a derived field for the neutral hydrogen number > density, but I'm getting an error when I try to do ds.add_field(): > > http://paste.yt-project.org/show/5833/ > > However, I get an error about being unable to add quantities with > differing units: > > http://paste.yt-project.org/show/5834/ > > The docs say not to do any unit conversion because that is > apparently taken care of behind the scenes, so I didn't. I was just > wondering if there was a way around this? Thanks! > -Jared > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
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Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne)) I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,) Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> wrote:
> Hi Jared, > > The problem is one of units. In order to make common arithmetic > work like addition, yt requires both arguments going into the addition > operator to have the same units. > > In your line, > > fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) > > you're adding two things (gamma_HI) and (gamma_c*ne) that have > different units--in this case, something with (code_mass/code_length**3) > units and something with no units defined as (1). >
Just a quick clarification: they need not have the same units, just the same dimensions. You can add two quantities with units of grams and solar masses (for example) but not grams and liters.
> > In order to fix this, you can re-assign the appropriate units to > different arrays or quantities with the YTArray and YTQuantity classes. In > this case, make sure that the two arguments going into the addition have > the same units. If you want to recast "ne" to have number density units, > you can do this: from yt.units.yt_array import YTQuantity; ne = > YTQuantity(ne, 'cm**-3'). For more info on units, check out > http://yt-project.org/docs/dev/analyzing/units/index.html > > I hope this helps! > > Cameron > > On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < > Jared.W.Coughlin.29@nd.edu> wrote: > >> Hello! I have a gadget snapshot for which the standard internal >> energy block has been replaced by one containing the temperature. I'm >> trying to calculate a derived field for the neutral hydrogen number >> density, but I'm getting an error when I try to do ds.add_field(): >> >> http://paste.yt-project.org/show/5833/ >> >> However, I get an error about being unable to add quantities with >> differing units: >> >> http://paste.yt-project.org/show/5834/ >> >> The docs say not to do any unit conversion because that is >> apparently taken care of behind the scenes, so I didn't. I was just >> wondering if there was a way around this? Thanks! >> -Jared >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > -- > Cameron Hummels > NSF Postdoctoral Fellow > Department of Astronomy > California Institute of Technology > http://chummels.org >
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On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared, I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now? Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu <javascript:_e(%7B%7D,'cvml','Jared.W.Coughlin.29@nd.edu');>> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com <javascript:_e(%7B%7D,'cvml','atmyers2@gmail.com');>> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu <javascript:_e(%7B%7D,'cvml','Jared.W.Coughlin.29@nd.edu');>> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <nathan12343@gmail.com <javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');>> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu <javascript:_e(%7B%7D,'cvml','Jared.W.Coughlin.29@nd.edu');>> wrote:
Great, thanks! I tried that, and it gave me the error: "YTQuantity instances must be scalars." I'm not sure what to do about that, since all of these quantities depend on either temperature or density, both of which are arrays. I tried looking at the doc page for YTQuantity, but I didn't see anything that looked like it could solve this problem, though it's possible I missed it.
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
-Jared
On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < nathan12343@gmail.com <javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');>> wrote:
> > > On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com > <javascript:_e(%7B%7D,'cvml','chummels@gmail.com');>> wrote: > >> Hi Jared, >> >> The problem is one of units. In order to make common arithmetic >> work like addition, yt requires both arguments going into the addition >> operator to have the same units. >> >> In your line, >> >> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >> >> you're adding two things (gamma_HI) and (gamma_c*ne) that have >> different units--in this case, something with (code_mass/code_length**3) >> units and something with no units defined as (1). >> > > Just a quick clarification: they need not have the same units, just > the same dimensions. You can add two quantities with units of grams and > solar masses (for example) but not grams and liters. > > >> >> In order to fix this, you can re-assign the appropriate units to >> different arrays or quantities with the YTArray and YTQuantity classes. In >> this case, make sure that the two arguments going into the addition have >> the same units. If you want to recast "ne" to have number density units, >> you can do this: from yt.units.yt_array import YTQuantity; ne = >> YTQuantity(ne, 'cm**-3'). For more info on units, check out >> http://yt-project.org/docs/dev/analyzing/units/index.html >> >> I hope this helps! >> >> Cameron >> >> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >> Jared.W.Coughlin.29@nd.edu> wrote: >> >>> Hello! I have a gadget snapshot for which the standard internal >>> energy block has been replaced by one containing the temperature. I'm >>> trying to calculate a derived field for the neutral hydrogen number >>> density, but I'm getting an error when I try to do ds.add_field(): >>> >>> http://paste.yt-project.org/show/5833/ >>> >>> However, I get an error about being unable to add quantities with >>> differing units: >>> >>> http://paste.yt-project.org/show/5834/ >>> >>> The docs say not to do any unit conversion because that is >>> apparently taken care of behind the scenes, so I didn't. I was just >>> wondering if there was a way around this? Thanks! >>> -Jared >>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> >> -- >> Cameron Hummels >> NSF Postdoctoral Fellow >> Department of Astronomy >> California Institute of Technology >> http://chummels.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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Sorry about that! Here's the script: http://paste.yt-project.org/show/5842/ And the traceback: http://paste.yt-project.org/show/5843/ Thanks! -Jared On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> Great, thanks! I tried that, and it gave me the error: "YTQuantity > instances must be scalars." I'm not sure what to do about that, since all > of these quantities depend on either temperature or density, both of which > are arrays. I tried looking at the doc page for YTQuantity, but I didn't > see anything that looked like it could solve this problem, though it's > possible I missed it. >
You need to use YTArray instead. YTQuantity is a subclass of YTArray that only holds scalars. YTArray can hold arrays of data with units.
> -Jared > > On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> >> >> On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> >> wrote: >> >>> Hi Jared, >>> >>> The problem is one of units. In order to make common arithmetic >>> work like addition, yt requires both arguments going into the addition >>> operator to have the same units. >>> >>> In your line, >>> >>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>> >>> you're adding two things (gamma_HI) and (gamma_c*ne) that have >>> different units--in this case, something with (code_mass/code_length**3) >>> units and something with no units defined as (1). >>> >> >> Just a quick clarification: they need not have the same units, just >> the same dimensions. You can add two quantities with units of grams and >> solar masses (for example) but not grams and liters. >> >> >>> >>> In order to fix this, you can re-assign the appropriate units to >>> different arrays or quantities with the YTArray and YTQuantity classes. In >>> this case, make sure that the two arguments going into the addition have >>> the same units. If you want to recast "ne" to have number density units, >>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>> http://yt-project.org/docs/dev/analyzing/units/index.html >>> >>> I hope this helps! >>> >>> Cameron >>> >>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>> Jared.W.Coughlin.29@nd.edu> wrote: >>> >>>> Hello! I have a gadget snapshot for which the standard internal >>>> energy block has been replaced by one containing the temperature. I'm >>>> trying to calculate a derived field for the neutral hydrogen number >>>> density, but I'm getting an error when I try to do ds.add_field(): >>>> >>>> http://paste.yt-project.org/show/5833/ >>>> >>>> However, I get an error about being unable to add quantities with >>>> differing units: >>>> >>>> http://paste.yt-project.org/show/5834/ >>>> >>>> The docs say not to do any unit conversion because that is >>>> apparently taken care of behind the scenes, so I didn't. I was just >>>> wondering if there was a way around this? Thanks! >>>> -Jared >>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> >>> -- >>> Cameron Hummels >>> NSF Postdoctoral Fellow >>> Department of Astronomy >>> California Institute of Technology >>> http://chummels.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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So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh. data['Gas', 'InternalEnergy'] ^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas'). data['gas', 'density'] ^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation. The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles. I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases. On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu
wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
That seemed to have worked, thanks!
I just have another quick question, if you wouldn't mind? In my function to generate my new field, there's an if statement that looks at the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: However, I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to loop over the elements of the array to access a specific element, or if that's even possible? Using a.any() or a.all() don't seem to fit the bill for this particular problem, either. Thanks! -Jared
On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> > > On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < > Jared.W.Coughlin.29@nd.edu> wrote: > >> Great, thanks! I tried that, and it gave me the error: "YTQuantity >> instances must be scalars." I'm not sure what to do about that, since all >> of these quantities depend on either temperature or density, both of which >> are arrays. I tried looking at the doc page for YTQuantity, but I didn't >> see anything that looked like it could solve this problem, though it's >> possible I missed it. >> > > You need to use YTArray instead. YTQuantity is a subclass of YTArray > that only holds scalars. YTArray can hold arrays of data with units. > > >> -Jared >> >> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >> nathan12343@gmail.com> wrote: >> >>> >>> >>> On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> >>> wrote: >>> >>>> Hi Jared, >>>> >>>> The problem is one of units. In order to make common arithmetic >>>> work like addition, yt requires both arguments going into the addition >>>> operator to have the same units. >>>> >>>> In your line, >>>> >>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>> >>>> you're adding two things (gamma_HI) and (gamma_c*ne) that have >>>> different units--in this case, something with (code_mass/code_length**3) >>>> units and something with no units defined as (1). >>>> >>> >>> Just a quick clarification: they need not have the same units, >>> just the same dimensions. You can add two quantities with units of grams >>> and solar masses (for example) but not grams and liters. >>> >>> >>>> >>>> In order to fix this, you can re-assign the appropriate units to >>>> different arrays or quantities with the YTArray and YTQuantity classes. In >>>> this case, make sure that the two arguments going into the addition have >>>> the same units. If you want to recast "ne" to have number density units, >>>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>> >>>> I hope this helps! >>>> >>>> Cameron >>>> >>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>> >>>>> Hello! I have a gadget snapshot for which the standard internal >>>>> energy block has been replaced by one containing the temperature. I'm >>>>> trying to calculate a derived field for the neutral hydrogen number >>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>> >>>>> http://paste.yt-project.org/show/5833/ >>>>> >>>>> However, I get an error about being unable to add quantities >>>>> with differing units: >>>>> >>>>> http://paste.yt-project.org/show/5834/ >>>>> >>>>> The docs say not to do any unit conversion because that is >>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>> wondering if there was a way around this? Thanks! >>>>> -Jared >>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> >>>> >>>> >>>> -- >>>> Cameron Hummels >>>> NSF Postdoctoral Fellow >>>> Department of Astronomy >>>> California Institute of Technology >>>> http://chummels.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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My ultimate goal is to make an absorption spectrum, so I was trying to add an HI number density field. I don't have any experience working with grid based codes, only sph, so I was assuming that I was using the particle positions. -Jared On Wed, Aug 26, 2015 at 11:25 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh.
data['Gas', 'InternalEnergy']
^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas').
data['gas', 'density']
^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation.
The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles.
I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases.
On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Jared,
You probably don't want to loop over the entire array in pure python; that could be very slow for large datasets. One thing you can do is use slicing to select the elements of the array that meet your criterion:
indices = data['gas','InternalEnergy'] <= 1e4 data['gas', 'InternalEnergy'][indices] = *something*
that would set all the elements where the InternalEnergy field is less than or equal to 1e4 to *something*. Usually you can express most operations you'd want to do this way without explicitly looping over the elements.
-Andrew
On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> That seemed to have worked, thanks! > > I just have another quick question, if you wouldn't mind? In my > function to generate my new field, there's an if statement that looks at > the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: > However, I get the error: "The truth value of an array with more > than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how > to loop over the elements of the array to access a specific element, or if > that's even possible? Using a.any() or a.all() don't seem to fit the bill > for this particular problem, either. Thanks! > -Jared > > On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> >> >> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < >> Jared.W.Coughlin.29@nd.edu> wrote: >> >>> Great, thanks! I tried that, and it gave me the error: "YTQuantity >>> instances must be scalars." I'm not sure what to do about that, since all >>> of these quantities depend on either temperature or density, both of which >>> are arrays. I tried looking at the doc page for YTQuantity, but I didn't >>> see anything that looked like it could solve this problem, though it's >>> possible I missed it. >>> >> >> You need to use YTArray instead. YTQuantity is a subclass of >> YTArray that only holds scalars. YTArray can hold arrays of data with units. >> >> >>> -Jared >>> >>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >>> nathan12343@gmail.com> wrote: >>> >>>> >>>> >>>> On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> >>>> wrote: >>>> >>>>> Hi Jared, >>>>> >>>>> The problem is one of units. In order to make common arithmetic >>>>> work like addition, yt requires both arguments going into the addition >>>>> operator to have the same units. >>>>> >>>>> In your line, >>>>> >>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>>> >>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that have >>>>> different units--in this case, something with (code_mass/code_length**3) >>>>> units and something with no units defined as (1). >>>>> >>>> >>>> Just a quick clarification: they need not have the same units, >>>> just the same dimensions. You can add two quantities with units of grams >>>> and solar masses (for example) but not grams and liters. >>>> >>>> >>>>> >>>>> In order to fix this, you can re-assign the appropriate units to >>>>> different arrays or quantities with the YTArray and YTQuantity classes. In >>>>> this case, make sure that the two arguments going into the addition have >>>>> the same units. If you want to recast "ne" to have number density units, >>>>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>>>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>>> >>>>> I hope this helps! >>>>> >>>>> Cameron >>>>> >>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>> >>>>>> Hello! I have a gadget snapshot for which the standard internal >>>>>> energy block has been replaced by one containing the temperature. I'm >>>>>> trying to calculate a derived field for the neutral hydrogen number >>>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>>> >>>>>> http://paste.yt-project.org/show/5833/ >>>>>> >>>>>> However, I get an error about being unable to add quantities >>>>>> with differing units: >>>>>> >>>>>> http://paste.yt-project.org/show/5834/ >>>>>> >>>>>> The docs say not to do any unit conversion because that is >>>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>>> wondering if there was a way around this? Thanks! >>>>>> -Jared >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> yt-users mailing list >>>>>> yt-users@lists.spacepope.org >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Cameron Hummels >>>>> NSF Postdoctoral Fellow >>>>> Department of Astronomy >>>>> California Institute of Technology >>>>> http://chummels.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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The best way to do this would be to make the HI number density field from the particle fields and then deposit it on the grid and sample that. The absorption spectrum infrastructure requires the fields it samples to be grid-based fields. On Wed, Aug 26, 2015 at 8:34 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
My ultimate goal is to make an absorption spectrum, so I was trying to add an HI number density field. I don't have any experience working with grid based codes, only sph, so I was assuming that I was using the particle positions. -Jared
On Wed, Aug 26, 2015 at 11:25 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh.
data['Gas', 'InternalEnergy']
^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas').
data['gas', 'density']
^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation.
The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles.
I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases.
On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Thanks, I'll try that! -Jared
On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> wrote:
> Hi Jared, > > You probably don't want to loop over the entire array in pure > python; that could be very slow for large datasets. One thing you can do is > use slicing to select the elements of the array that meet your criterion: > > indices = data['gas','InternalEnergy'] <= 1e4 > data['gas', 'InternalEnergy'][indices] = *something* > > that would set all the elements where the InternalEnergy field is > less than or equal to 1e4 to *something*. Usually you can express most > operations you'd want to do this way without explicitly looping over the > elements. > > -Andrew > > On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < > Jared.W.Coughlin.29@nd.edu> wrote: > >> That seemed to have worked, thanks! >> >> I just have another quick question, if you wouldn't mind? In my >> function to generate my new field, there's an if statement that looks at >> the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: >> However, I get the error: "The truth value of an array with more >> than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how >> to loop over the elements of the array to access a specific element, or if >> that's even possible? Using a.any() or a.all() don't seem to fit the bill >> for this particular problem, either. Thanks! >> -Jared >> >> On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < >> nathan12343@gmail.com> wrote: >> >>> >>> >>> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < >>> Jared.W.Coughlin.29@nd.edu> wrote: >>> >>>> Great, thanks! I tried that, and it gave me the error: >>>> "YTQuantity instances must be scalars." I'm not sure what to do about that, >>>> since all of these quantities depend on either temperature or density, both >>>> of which are arrays. I tried looking at the doc page for YTQuantity, but I >>>> didn't see anything that looked like it could solve this problem, though >>>> it's possible I missed it. >>>> >>> >>> You need to use YTArray instead. YTQuantity is a subclass of >>> YTArray that only holds scalars. YTArray can hold arrays of data with units. >>> >>> >>>> -Jared >>>> >>>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >>>> nathan12343@gmail.com> wrote: >>>> >>>>> >>>>> >>>>> On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi Jared, >>>>>> >>>>>> The problem is one of units. In order to make common >>>>>> arithmetic work like addition, yt requires both arguments going into the >>>>>> addition operator to have the same units. >>>>>> >>>>>> In your line, >>>>>> >>>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>>>> >>>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that have >>>>>> different units--in this case, something with (code_mass/code_length**3) >>>>>> units and something with no units defined as (1). >>>>>> >>>>> >>>>> Just a quick clarification: they need not have the same units, >>>>> just the same dimensions. You can add two quantities with units of grams >>>>> and solar masses (for example) but not grams and liters. >>>>> >>>>> >>>>>> >>>>>> In order to fix this, you can re-assign the appropriate units >>>>>> to different arrays or quantities with the YTArray and YTQuantity classes. >>>>>> In this case, make sure that the two arguments going into the addition have >>>>>> the same units. If you want to recast "ne" to have number density units, >>>>>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>>>>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>>>> >>>>>> I hope this helps! >>>>>> >>>>>> Cameron >>>>>> >>>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>>> >>>>>>> Hello! I have a gadget snapshot for which the standard >>>>>>> internal energy block has been replaced by one containing the temperature. >>>>>>> I'm trying to calculate a derived field for the neutral hydrogen number >>>>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>>>> >>>>>>> http://paste.yt-project.org/show/5833/ >>>>>>> >>>>>>> However, I get an error about being unable to add quantities >>>>>>> with differing units: >>>>>>> >>>>>>> http://paste.yt-project.org/show/5834/ >>>>>>> >>>>>>> The docs say not to do any unit conversion because that is >>>>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>>>> wondering if there was a way around this? Thanks! >>>>>>> -Jared >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> yt-users mailing list >>>>>>> yt-users@lists.spacepope.org >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Cameron Hummels >>>>>> NSF Postdoctoral Fellow >>>>>> Department of Astronomy >>>>>> California Institute of Technology >>>>>> http://chummels.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 > >
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Ok. I'm really new to yt, so I apologize for the stupid question, but: how do I access the particle field explicitly and then convert to a grid? -Jared On Wed, Aug 26, 2015 at 11:37 AM, Cameron Hummels <chummels@gmail.com> wrote:
The best way to do this would be to make the HI number density field from the particle fields and then deposit it on the grid and sample that. The absorption spectrum infrastructure requires the fields it samples to be grid-based fields.
On Wed, Aug 26, 2015 at 8:34 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
My ultimate goal is to make an absorption spectrum, so I was trying to add an HI number density field. I don't have any experience working with grid based codes, only sph, so I was assuming that I was using the particle positions. -Jared
On Wed, Aug 26, 2015 at 11:25 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh.
data['Gas', 'InternalEnergy']
^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas').
data['gas', 'density']
^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation.
The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles.
I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases.
On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
On Tuesday, August 25, 2015, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Hello! I'm really sorry for the barrage of questions; hopefully this will be the last one! I now get the error: operands could not be broadcast together with shapes (2072685,) (2153824,) on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
I printed the shapes of all of those arrays, and this is what I get: nH.shape (16, 16, 16) ne.shape (16, 16, 16) gamma_c.shape (1,) recomb.shape (1,) nH.shape (2153824,) ne.shape (2153824,) gamma_c.shape (2072685,) recomb.shape (2072685,)
Firstly, I'm a little confused as to why their dimensions change, but what really matters are the bottom ones. I know how many gas particles are in my gadget simulation: 2072685. All of the arrays were created from either data["Gas", "InternalEnergy"] or data["gas", "density"], which should, I would imagine, have the same dimensions: the number of gas particles. I was just wondering if anyone had seen something like this before? The function in question was posted to a pastebin in an earlier email on this thread, and I have since made all of the arrays YTArrays, as suggested above. Thanks! -Jared
Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> Thanks, I'll try that! > -Jared > > On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> > wrote: > >> Hi Jared, >> >> You probably don't want to loop over the entire array in pure >> python; that could be very slow for large datasets. One thing you can do is >> use slicing to select the elements of the array that meet your criterion: >> >> indices = data['gas','InternalEnergy'] <= 1e4 >> data['gas', 'InternalEnergy'][indices] = *something* >> >> that would set all the elements where the InternalEnergy field is >> less than or equal to 1e4 to *something*. Usually you can express most >> operations you'd want to do this way without explicitly looping over the >> elements. >> >> -Andrew >> >> On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < >> Jared.W.Coughlin.29@nd.edu> wrote: >> >>> That seemed to have worked, thanks! >>> >>> I just have another quick question, if you wouldn't mind? In my >>> function to generate my new field, there's an if statement that looks at >>> the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: >>> However, I get the error: "The truth value of an array with more >>> than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how >>> to loop over the elements of the array to access a specific element, or if >>> that's even possible? Using a.any() or a.all() don't seem to fit the bill >>> for this particular problem, either. Thanks! >>> -Jared >>> >>> On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < >>> nathan12343@gmail.com> wrote: >>> >>>> >>>> >>>> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < >>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>> >>>>> Great, thanks! I tried that, and it gave me the error: >>>>> "YTQuantity instances must be scalars." I'm not sure what to do about that, >>>>> since all of these quantities depend on either temperature or density, both >>>>> of which are arrays. I tried looking at the doc page for YTQuantity, but I >>>>> didn't see anything that looked like it could solve this problem, though >>>>> it's possible I missed it. >>>>> >>>> >>>> You need to use YTArray instead. YTQuantity is a subclass of >>>> YTArray that only holds scalars. YTArray can hold arrays of data with units. >>>> >>>> >>>>> -Jared >>>>> >>>>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >>>>> nathan12343@gmail.com> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Monday, August 24, 2015, Cameron Hummels <chummels@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi Jared, >>>>>>> >>>>>>> The problem is one of units. In order to make common >>>>>>> arithmetic work like addition, yt requires both arguments going into the >>>>>>> addition operator to have the same units. >>>>>>> >>>>>>> In your line, >>>>>>> >>>>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>>>>> >>>>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that have >>>>>>> different units--in this case, something with (code_mass/code_length**3) >>>>>>> units and something with no units defined as (1). >>>>>>> >>>>>> >>>>>> Just a quick clarification: they need not have the same units, >>>>>> just the same dimensions. You can add two quantities with units of grams >>>>>> and solar masses (for example) but not grams and liters. >>>>>> >>>>>> >>>>>>> >>>>>>> In order to fix this, you can re-assign the appropriate units >>>>>>> to different arrays or quantities with the YTArray and YTQuantity classes. >>>>>>> In this case, make sure that the two arguments going into the addition have >>>>>>> the same units. If you want to recast "ne" to have number density units, >>>>>>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>>>>>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>>>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>>>>> >>>>>>> I hope this helps! >>>>>>> >>>>>>> Cameron >>>>>>> >>>>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>>>> >>>>>>>> Hello! I have a gadget snapshot for which the standard >>>>>>>> internal energy block has been replaced by one containing the temperature. >>>>>>>> I'm trying to calculate a derived field for the neutral hydrogen number >>>>>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>>>>> >>>>>>>> http://paste.yt-project.org/show/5833/ >>>>>>>> >>>>>>>> However, I get an error about being unable to add quantities >>>>>>>> with differing units: >>>>>>>> >>>>>>>> http://paste.yt-project.org/show/5834/ >>>>>>>> >>>>>>>> The docs say not to do any unit conversion because that is >>>>>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>>>>> wondering if there was a way around this? Thanks! >>>>>>>> -Jared >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> yt-users mailing list >>>>>>>> yt-users@lists.spacepope.org >>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Cameron Hummels >>>>>>> NSF Postdoctoral Fellow >>>>>>> Department of Astronomy >>>>>>> California Institute of Technology >>>>>>> http://chummels.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 >> >> >
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There are no stupid questions. This is a help list, so you're free to ask as much as you need, but it is recommended for you to read some of the documentation on how this all works. Additionally, it might make sense for you to connect to the IRC or slack channels in order to get more interaction with other developers at low latency: http://yt-project.org/community.html To answer your questions: you are actually already accessing some of the particle fields. For instance, ("Gas", "InternalEnergy") is a particle field--it's a field which is tied to the specific particles as written out by Gadget. Whereas ("gas", "density") is a grid-based field, as it is aliased to ("deposit", "smoothed_Gas_Density") in the case of the the gadget outputs, I think. You can read up more on fields here: http://yt-project.org/docs/dev/analyzing/fields.html "Deposition" is how particle fields are put on to the grid for further use (for example, in the AbsorptionSpectrum analysis module). I actually don't know if there is a standard route for triggering the deposition infrastructure on a user-defined derived particle field, as it appears you want to do. Incidentally, there are a few yt developers who are building a code that sits on top of yt and does what you're trying to do for any simulation output: generate a spectrum. We're planning to release this code by halloween, so it will help with what you want to do shortly. Check out: http://trident-project.org. Cameron On Wed, Aug 26, 2015 at 8:43 AM, Jared Coughlin <Jared.W.Coughlin.29@nd.edu> wrote:
Ok. I'm really new to yt, so I apologize for the stupid question, but: how do I access the particle field explicitly and then convert to a grid? -Jared
On Wed, Aug 26, 2015 at 11:37 AM, Cameron Hummels <chummels@gmail.com> wrote:
The best way to do this would be to make the HI number density field from the particle fields and then deposit it on the grid and sample that. The absorption spectrum infrastructure requires the fields it samples to be grid-based fields.
On Wed, Aug 26, 2015 at 8:34 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
My ultimate goal is to make an absorption spectrum, so I was trying to add an HI number density field. I don't have any experience working with grid based codes, only sph, so I was assuming that I was using the particle positions. -Jared
On Wed, Aug 26, 2015 at 11:25 AM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh.
data['Gas', 'InternalEnergy']
^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas').
data['gas', 'density']
^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation.
The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles.
I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases.
On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
On Tuesday, August 25, 2015, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
> Hello! I'm really sorry for the barrage of questions; hopefully this > will be the last one! > I now get the error: operands could not be broadcast together with > shapes (2072685,) (2153824,) > on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne)) > > I printed the shapes of all of those arrays, and this is what I get: > nH.shape > (16, 16, 16) > ne.shape > (16, 16, 16) > gamma_c.shape > (1,) > recomb.shape > (1,) > nH.shape > (2153824,) > ne.shape > (2153824,) > gamma_c.shape > (2072685,) > recomb.shape > (2072685,) > > Firstly, I'm a little confused as to why their dimensions change, > but what really matters are the bottom ones. I know how many gas particles > are in my gadget simulation: 2072685. All of the arrays were created from > either data["Gas", "InternalEnergy"] or data["gas", "density"], which > should, I would imagine, have the same dimensions: the number of gas > particles. I was just wondering if anyone had seen something like this > before? The function in question was posted to a pastebin in an earlier > email on this thread, and I have since made all of the arrays YTArrays, as > suggested above. Thanks! > -Jared > > Hey Jared,
I looked above but can't seem to find the correct link for the script you're using. Can you pastebin your updated script and the full error tracrback you're seeing now?
Nathan
> > On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < > Jared.W.Coughlin.29@nd.edu> wrote: > >> Thanks, I'll try that! >> -Jared >> >> On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> >> wrote: >> >>> Hi Jared, >>> >>> You probably don't want to loop over the entire array in pure >>> python; that could be very slow for large datasets. One thing you can do is >>> use slicing to select the elements of the array that meet your criterion: >>> >>> indices = data['gas','InternalEnergy'] <= 1e4 >>> data['gas', 'InternalEnergy'][indices] = *something* >>> >>> that would set all the elements where the InternalEnergy field is >>> less than or equal to 1e4 to *something*. Usually you can express most >>> operations you'd want to do this way without explicitly looping over the >>> elements. >>> >>> -Andrew >>> >>> On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < >>> Jared.W.Coughlin.29@nd.edu> wrote: >>> >>>> That seemed to have worked, thanks! >>>> >>>> I just have another quick question, if you wouldn't mind? In my >>>> function to generate my new field, there's an if statement that looks at >>>> the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: >>>> However, I get the error: "The truth value of an array with more >>>> than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how >>>> to loop over the elements of the array to access a specific element, or if >>>> that's even possible? Using a.any() or a.all() don't seem to fit the bill >>>> for this particular problem, either. Thanks! >>>> -Jared >>>> >>>> On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < >>>> nathan12343@gmail.com> wrote: >>>> >>>>> >>>>> >>>>> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < >>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>> >>>>>> Great, thanks! I tried that, and it gave me the error: >>>>>> "YTQuantity instances must be scalars." I'm not sure what to do about that, >>>>>> since all of these quantities depend on either temperature or density, both >>>>>> of which are arrays. I tried looking at the doc page for YTQuantity, but I >>>>>> didn't see anything that looked like it could solve this problem, though >>>>>> it's possible I missed it. >>>>>> >>>>> >>>>> You need to use YTArray instead. YTQuantity is a subclass of >>>>> YTArray that only holds scalars. YTArray can hold arrays of data with units. >>>>> >>>>> >>>>>> -Jared >>>>>> >>>>>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >>>>>> nathan12343@gmail.com> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> On Monday, August 24, 2015, Cameron Hummels < >>>>>>> chummels@gmail.com> wrote: >>>>>>> >>>>>>>> Hi Jared, >>>>>>>> >>>>>>>> The problem is one of units. In order to make common >>>>>>>> arithmetic work like addition, yt requires both arguments going into the >>>>>>>> addition operator to have the same units. >>>>>>>> >>>>>>>> In your line, >>>>>>>> >>>>>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>>>>>> >>>>>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that >>>>>>>> have different units--in this case, something with (code_mass/code_length**3) >>>>>>>> units and something with no units defined as (1). >>>>>>>> >>>>>>> >>>>>>> Just a quick clarification: they need not have the same units, >>>>>>> just the same dimensions. You can add two quantities with units of grams >>>>>>> and solar masses (for example) but not grams and liters. >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> In order to fix this, you can re-assign the appropriate units >>>>>>>> to different arrays or quantities with the YTArray and YTQuantity classes. >>>>>>>> In this case, make sure that the two arguments going into the addition have >>>>>>>> the same units. If you want to recast "ne" to have number density units, >>>>>>>> you can do this: from yt.units.yt_array import YTQuantity; ne = >>>>>>>> YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>>>>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>>>>>> >>>>>>>> I hope this helps! >>>>>>>> >>>>>>>> Cameron >>>>>>>> >>>>>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>>>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>>>>> >>>>>>>>> Hello! I have a gadget snapshot for which the standard >>>>>>>>> internal energy block has been replaced by one containing the temperature. >>>>>>>>> I'm trying to calculate a derived field for the neutral hydrogen number >>>>>>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>>>>>> >>>>>>>>> http://paste.yt-project.org/show/5833/ >>>>>>>>> >>>>>>>>> However, I get an error about being unable to add quantities >>>>>>>>> with differing units: >>>>>>>>> >>>>>>>>> http://paste.yt-project.org/show/5834/ >>>>>>>>> >>>>>>>>> The docs say not to do any unit conversion because that is >>>>>>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>>>>>> wondering if there was a way around this? Thanks! >>>>>>>>> -Jared >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> yt-users mailing list >>>>>>>>> yt-users@lists.spacepope.org >>>>>>>>> >>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Cameron Hummels >>>>>>>> NSF Postdoctoral Fellow >>>>>>>> Department of Astronomy >>>>>>>> California Institute of Technology >>>>>>>> http://chummels.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
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.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
-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
Thanks! The trident project looks really interesting, and I look forward to it! -Jared On Wed, Aug 26, 2015 at 12:05 PM, Cameron Hummels <chummels@gmail.com> wrote:
There are no stupid questions. This is a help list, so you're free to ask as much as you need, but it is recommended for you to read some of the documentation on how this all works. Additionally, it might make sense for you to connect to the IRC or slack channels in order to get more interaction with other developers at low latency: http://yt-project.org/community.html
To answer your questions: you are actually already accessing some of the particle fields. For instance, ("Gas", "InternalEnergy") is a particle field--it's a field which is tied to the specific particles as written out by Gadget. Whereas ("gas", "density") is a grid-based field, as it is aliased to ("deposit", "smoothed_Gas_Density") in the case of the the gadget outputs, I think. You can read up more on fields here:
http://yt-project.org/docs/dev/analyzing/fields.html
"Deposition" is how particle fields are put on to the grid for further use (for example, in the AbsorptionSpectrum analysis module). I actually don't know if there is a standard route for triggering the deposition infrastructure on a user-defined derived particle field, as it appears you want to do.
Incidentally, there are a few yt developers who are building a code that sits on top of yt and does what you're trying to do for any simulation output: generate a spectrum. We're planning to release this code by halloween, so it will help with what you want to do shortly. Check out: http://trident-project.org.
Cameron
On Wed, Aug 26, 2015 at 8:43 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Ok. I'm really new to yt, so I apologize for the stupid question, but: how do I access the particle field explicitly and then convert to a grid? -Jared
On Wed, Aug 26, 2015 at 11:37 AM, Cameron Hummels <chummels@gmail.com> wrote:
The best way to do this would be to make the HI number density field from the particle fields and then deposit it on the grid and sample that. The absorption spectrum infrastructure requires the fields it samples to be grid-based fields.
On Wed, Aug 26, 2015 at 8:34 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
My ultimate goal is to make an absorption spectrum, so I was trying to add an HI number density field. I don't have any experience working with grid based codes, only sph, so I was assuming that I was using the particle positions. -Jared
On Wed, Aug 26, 2015 at 11:25 AM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
So the issue is that you're combining particle fields, which are defined at the location of your SPH particles, with fields that are defined on the octree mesh.
data['Gas', 'InternalEnergy']
^ is a particle field defined at the locations of your SPH particles (particles of type 'Gas').
data['gas', 'density']
^ is a mesh field defined at the cell centers of the octree mesh yt constructs in memory. It's specifically generated an SPH smoothing operation.
The reasons the shapes of the arrays you're getting back are different is that the number of leaf octree cells is not the same as the number of Gas particles.
I'm not sure if what you're trying to do is supposed to use the mesh locations or the particle locations. The correct way to modify your script would be different in the two cases.
On Wed, Aug 26, 2015 at 10:17 AM, Jared Coughlin < Jared.W.Coughlin.29@nd.edu> wrote:
Sorry about that! Here's the script:
http://paste.yt-project.org/show/5842/
And the traceback:
http://paste.yt-project.org/show/5843/
Thanks! -Jared
On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> > > On Tuesday, August 25, 2015, Jared Coughlin < > Jared.W.Coughlin.29@nd.edu> wrote: > >> Hello! I'm really sorry for the barrage of questions; hopefully >> this will be the last one! >> I now get the error: operands could not be broadcast together with >> shapes (2072685,) (2153824,) >> on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne)) >> >> I printed the shapes of all of those arrays, and this is what I >> get: >> nH.shape >> (16, 16, 16) >> ne.shape >> (16, 16, 16) >> gamma_c.shape >> (1,) >> recomb.shape >> (1,) >> nH.shape >> (2153824,) >> ne.shape >> (2153824,) >> gamma_c.shape >> (2072685,) >> recomb.shape >> (2072685,) >> >> Firstly, I'm a little confused as to why their dimensions change, >> but what really matters are the bottom ones. I know how many gas particles >> are in my gadget simulation: 2072685. All of the arrays were created from >> either data["Gas", "InternalEnergy"] or data["gas", "density"], which >> should, I would imagine, have the same dimensions: the number of gas >> particles. I was just wondering if anyone had seen something like this >> before? The function in question was posted to a pastebin in an earlier >> email on this thread, and I have since made all of the arrays YTArrays, as >> suggested above. Thanks! >> -Jared >> >> > Hey Jared, > > I looked above but can't seem to find the correct link for the > script you're using. Can you pastebin your updated script and the > full error tracrback you're seeing now? > > Nathan > > > >> >> On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin < >> Jared.W.Coughlin.29@nd.edu> wrote: >> >>> Thanks, I'll try that! >>> -Jared >>> >>> On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2@gmail.com> >>> wrote: >>> >>>> Hi Jared, >>>> >>>> You probably don't want to loop over the entire array in pure >>>> python; that could be very slow for large datasets. One thing you can do is >>>> use slicing to select the elements of the array that meet your criterion: >>>> >>>> indices = data['gas','InternalEnergy'] <= 1e4 >>>> data['gas', 'InternalEnergy'][indices] = *something* >>>> >>>> that would set all the elements where the InternalEnergy field is >>>> less than or equal to 1e4 to *something*. Usually you can express most >>>> operations you'd want to do this way without explicitly looping over the >>>> elements. >>>> >>>> -Andrew >>>> >>>> On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin < >>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>> >>>>> That seemed to have worked, thanks! >>>>> >>>>> I just have another quick question, if you wouldn't mind? In my >>>>> function to generate my new field, there's an if statement that looks at >>>>> the value of the temperature: if data['gas','InternalEnergy'] <= 1e4: >>>>> However, I get the error: "The truth value of an array with more >>>>> than one element is ambiguous. Use a.any() or a.all()." I wasn't sure how >>>>> to loop over the elements of the array to access a specific element, or if >>>>> that's even possible? Using a.any() or a.all() don't seem to fit the bill >>>>> for this particular problem, either. Thanks! >>>>> -Jared >>>>> >>>>> On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum < >>>>> nathan12343@gmail.com> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin < >>>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>>> >>>>>>> Great, thanks! I tried that, and it gave me the error: >>>>>>> "YTQuantity instances must be scalars." I'm not sure what to do about that, >>>>>>> since all of these quantities depend on either temperature or density, both >>>>>>> of which are arrays. I tried looking at the doc page for YTQuantity, but I >>>>>>> didn't see anything that looked like it could solve this problem, though >>>>>>> it's possible I missed it. >>>>>>> >>>>>> >>>>>> You need to use YTArray instead. YTQuantity is a subclass of >>>>>> YTArray that only holds scalars. YTArray can hold arrays of data with units. >>>>>> >>>>>> >>>>>>> -Jared >>>>>>> >>>>>>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum < >>>>>>> nathan12343@gmail.com> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Monday, August 24, 2015, Cameron Hummels < >>>>>>>> chummels@gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi Jared, >>>>>>>>> >>>>>>>>> The problem is one of units. In order to make common >>>>>>>>> arithmetic work like addition, yt requires both arguments going into the >>>>>>>>> addition operator to have the same units. >>>>>>>>> >>>>>>>>> In your line, >>>>>>>>> >>>>>>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne)) >>>>>>>>> >>>>>>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that >>>>>>>>> have different units--in this case, something with (code_mass/code_length**3) >>>>>>>>> units and something with no units defined as (1). >>>>>>>>> >>>>>>>> >>>>>>>> Just a quick clarification: they need not have the same >>>>>>>> units, just the same dimensions. You can add two quantities with units of >>>>>>>> grams and solar masses (for example) but not grams and liters. >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> In order to fix this, you can re-assign the appropriate >>>>>>>>> units to different arrays or quantities with the YTArray and YTQuantity >>>>>>>>> classes. In this case, make sure that the two arguments going into the >>>>>>>>> addition have the same units. If you want to recast "ne" to have number >>>>>>>>> density units, you can do this: from yt.units.yt_array import YTQuantity; >>>>>>>>> ne = YTQuantity(ne, 'cm**-3'). For more info on units, check out >>>>>>>>> http://yt-project.org/docs/dev/analyzing/units/index.html >>>>>>>>> >>>>>>>>> I hope this helps! >>>>>>>>> >>>>>>>>> Cameron >>>>>>>>> >>>>>>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin < >>>>>>>>> Jared.W.Coughlin.29@nd.edu> wrote: >>>>>>>>> >>>>>>>>>> Hello! I have a gadget snapshot for which the standard >>>>>>>>>> internal energy block has been replaced by one containing the temperature. >>>>>>>>>> I'm trying to calculate a derived field for the neutral hydrogen number >>>>>>>>>> density, but I'm getting an error when I try to do ds.add_field(): >>>>>>>>>> >>>>>>>>>> http://paste.yt-project.org/show/5833/ >>>>>>>>>> >>>>>>>>>> However, I get an error about being unable to add >>>>>>>>>> quantities with differing units: >>>>>>>>>> >>>>>>>>>> http://paste.yt-project.org/show/5834/ >>>>>>>>>> >>>>>>>>>> The docs say not to do any unit conversion because that is >>>>>>>>>> apparently taken care of behind the scenes, so I didn't. I was just >>>>>>>>>> wondering if there was a way around this? Thanks! >>>>>>>>>> -Jared >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> yt-users mailing list >>>>>>>>>> yt-users@lists.spacepope.org >>>>>>>>>> >>>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Cameron Hummels >>>>>>>>> NSF Postdoctoral Fellow >>>>>>>>> Department of Astronomy >>>>>>>>> California Institute of Technology >>>>>>>>> http://chummels.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 > >
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-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
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-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
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participants (4)
-
Andrew Myers -
Cameron Hummels -
Jared Coughlin -
Nathan Goldbaum