troubles with derived field: 1+1 is not equal to 2
Hello, I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on. I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields: def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB'] Then I add them to my yt object: ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False) and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots. I must be missing something here but I really don’t get it. Many thanks in advance for your help! Antoine Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
Hi Antoine, I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data? On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file)
ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log= False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log= False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log= False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Nathan, Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue. I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem. I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help! Antoine Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Antoine, I'm having some trouble reproducing your issue. When I run the attached script on the TurbBoxLowRes dataset, I get the following png files, the last of which is different than yours. Could you tell us what version of yt you're running? Thanks, Andrew Myers On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log= False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log= False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log= False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Antoine, Actually, on closer inspection I think you may have found a bug in the Chombo frontend. Thanks for bringing this to our attention. Would you mind checking whether these <https://bitbucket.org/yt_analysis/yt/pull-request/1137/a-patch-that-fixes-an-issue-uncovered-by> changes fix the problem for you? Thanks, Andrew On Thu, Aug 7, 2014 at 11:28 AM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Antoine,
I'm having some trouble reproducing your issue. When I run the attached script on the TurbBoxLowRes dataset, I get the following png files, the last of which is different than yours. Could you tell us what version of yt you're running?
Thanks, Andrew Myers
On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log= False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log= False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log= False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Nathan and Andrew, Many thanks for your help, the fix from Andrew indeed fixed my problem! Nathan, originally I wanted to use the geometrical field that were automatically computed by yt, but in my case the cylindrical coordinates are not correct. They do not use the shifted version of the original axes, meaning that it seems they supposed the origin (0,0,0) was at the bottom left of the simulation box. I’m not sure if this is the expected behaviour when reading my data set, but I had to recompute them anyway to derive my fields. Best regards, Antoine Le 2014-08-07 à 19:16 , Andrew Myers <atmyers2@gmail.com> a écrit :
Hi Antoine,
Actually, on closer inspection I think you may have found a bug in the Chombo frontend. Thanks for bringing this to our attention. Would you mind checking whether these changes fix the problem for you?
Thanks, Andrew
On Thu, Aug 7, 2014 at 11:28 AM, Andrew Myers <atmyers2@gmail.com> wrote: Hi Antoine,
I'm having some trouble reproducing your issue. When I run the attached script on the TurbBoxLowRes dataset, I get the following png files, the last of which is different than yours. Could you tell us what version of yt you're running?
Thanks, Andrew Myers
On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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On Fri, Aug 8, 2014 at 4:31 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hi Nathan and Andrew,
Many thanks for your help, the fix from Andrew indeed fixed my problem!
Excellent! Glad to hear things are working now. Hopefully we will have Andrew's fix merged in soon.
Nathan, originally I wanted to use the geometrical field that were automatically computed by yt, but in my case the cylindrical coordinates are not correct. They do not use the shifted version of the original axes, meaning that it seems they supposed the origin (0,0,0) was at the bottom left of the simulation box. I’m not sure if this is the expected behaviour when reading my data set, but I had to recompute them anyway to derive my fields.
By default yt uses coordinate system the simulation was run with. Is it not doing that in this case? You should be able to supply parameters to the coordinate system using a field parameter: http://yt-project.org/docs/3.0/analyzing/fields.html#field-parameters In yt 3.0 both SlicePlot and ProjectionPlot take field parameters as keyword arguments. You can also create a custom data object (e.g. ds.slice, ds.proj), set your field parameters, and then use the to_pw method to get back a SlicePlot or ProjectionPlot created using your custom data source.
Best regards,
Antoine
Le 2014-08-07 à 19:16 , Andrew Myers <atmyers2@gmail.com> a écrit :
Hi Antoine,
Actually, on closer inspection I think you may have found a bug in the Chombo frontend. Thanks for bringing this to our attention. Would you mind checking whether these <https://bitbucket.org/yt_analysis/yt/pull-request/1137/a-patch-that-fixes-an-issue-uncovered-by> changes fix the problem for you?
Thanks, Andrew
On Thu, Aug 7, 2014 at 11:28 AM, Andrew Myers <atmyers2@gmail.com> wrote:
Hi Antoine,
I'm having some trouble reproducing your issue. When I run the attached script on the TurbBoxLowRes dataset, I get the following png files, the last of which is different than yours. Could you tell us what version of yt you're running?
Thanks, Andrew Myers
On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log= False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log= False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log= False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Nathan, Le 2014-08-08 à 13:22 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
On Fri, Aug 8, 2014 at 4:31 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hi Nathan and Andrew,
Many thanks for your help, the fix from Andrew indeed fixed my problem!
Excellent! Glad to hear things are working now. Hopefully we will have Andrew's fix merged in soon.
Nathan, originally I wanted to use the geometrical field that were automatically computed by yt, but in my case the cylindrical coordinates are not correct. They do not use the shifted version of the original axes, meaning that it seems they supposed the origin (0,0,0) was at the bottom left of the simulation box. I’m not sure if this is the expected behaviour when reading my data set, but I had to recompute them anyway to derive my fields.
By default yt uses coordinate system the simulation was run with. Is it not doing that in this case?
You should be able to supply parameters to the coordinate system using a field parameter: http://yt-project.org/docs/3.0/analyzing/fields.html#field-parameters
In yt 3.0 both SlicePlot and ProjectionPlot take field parameters as keyword arguments. You can also create a custom data object (e.g. ds.slice, ds.proj), set your field parameters, and then use the to_pw method to get back a SlicePlot or ProjectionPlot created using your custom data source.
I would be glad to use this but I’m not sure I quite understand how to. Ideally what I first tried using yt is to (a) do a load and (b) check the various fields that were automatically computed (cylindrical_r, spherical_r, radius, etc…). When I check the value of the parameter ‘center’ right after doing a load and doing ad=ds.all_data(), it is indeed set to the center of my grid (in my case, the point [20,20,20] since my cube is [0,40]^3. The axes are correct for my slices (e.g., x goes from -20 to 20 as it should be) and the field (‘index’,’radius’) indeed corresponds to the spherical radius. Though the fields label ‘cylindrical_*’ and ’spherical_*’ are not correct and seem to use the upper right corner of my simulation box as the ‘center’ (as if the ‘center’ parameter was applied twice to compute them?). I don’t know if it’s a bug in my chombo file, or a bug in the chombo frontend in yt? It seems strange to me that the axes and ‘radius’ fields are correct but not the other geometrical components. Thanks again for your help! Antoine
Best regards,
Antoine
Le 2014-08-07 à 19:16 , Andrew Myers <atmyers2@gmail.com> a écrit :
Hi Antoine,
Actually, on closer inspection I think you may have found a bug in the Chombo frontend. Thanks for bringing this to our attention. Would you mind checking whether these changes fix the problem for you?
Thanks, Andrew
On Thu, Aug 7, 2014 at 11:28 AM, Andrew Myers <atmyers2@gmail.com> wrote: Hi Antoine,
I'm having some trouble reproducing your issue. When I run the attached script on the TurbBoxLowRes dataset, I get the following png files, the last of which is different than yours. Could you tell us what version of yt you're running?
Thanks, Andrew Myers
On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek <strugarek@astro.umontreal.ca> wrote: Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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Hi Antoine, I think there were some unit issues in your derived fields. Note that simply specifying that a field is in CGS doesn't necessarily mean that the returned data is in CGS. It's up to the derived field author to make sure that data is returned in the units specified in the add_field call. I've pasted a script that generates what I believe are correct results here: http://paste.yt-project.org/show/4997/ Note the calls to .in_cgs() in the derived field definition. In particular the 'x', 'y', and 'z' fields are in *code units* by default in yt. Also note that many of the geometric fields you are defining are already defined inside yt, so no need to redefine them. See the "index" fields on this page: http://yt-project.org/docs/3.0/reference/field_list.html#index-cell-volume -Nathan On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hi Nathan,
Many thanks for the fast answer. I just tried to reproduce my problem with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data) and I get the same issue.
I just attached at the end of this email the small script I use to generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes case. I also tried your suggestions of not adding my derived field as type ‘chombo’, but it did not solve the problem.
I also attached the same snapshots from the TurbBoxLowRes case, VVR should be the sum of the two other and as you can see the blue negative patch on the right should clearly not be there (the color scale is the same in all the plots). It does not seem overall far off so I guess this is really dumb on my side, thanks again for your help!
Antoine
Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343@gmail.com> a écrit :
Hi Antoine,
I'm not sure what's going wrong here. I have a few ideas below. If the dataset is small enough it would probably help if you could share it using e.g. dropbox or google drive along with your full analysis script. Alternately, can you reproduce the issue using one of the public datasets on yt-project.org/data?
On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek < strugarek@astro.umontreal.ca> wrote:
Hello,
I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on.
I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields:
def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB']
Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as well? If so, can you share their definitions?
Then I add them to my yt object:
ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log= False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log= False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log= False)
and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots.
What happens if instead of passing in the field tuple ('chombo', 'VRA'), you instead pass in 'VRA' or ('gas', 'VRA'). Saying the field type is 'chombo' for a derived field doesn't really make much sense. For a chombo dataset, a 'chombo' field must be on-disk and is always in code units. By creating a derived field with explicit CGS units you might be confusing yt's field system.
I must be missing something here but I really don’t get it. Many thanks in advance for your help!
Antoine
Antoine STRUGAREK ------------------------------------------------------------------- Webpage <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
Département de physique, Université de Montréal strugarek@astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek@cea.fr --------------------------------------------------------------------
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participants (3)
-
Andrew Myers -
Antoine Strugarek -
Nathan Goldbaum