Define a field of spacial derivatives for FLASH4 2D cylindrical uniform grid
Hi, I would like to compute some spacial derivatives for FLASH4 2D cylindrical uniform grid datafile with YT. For simplicity, I tried the example given in YT docs, although I know the derivative form is only valid for Cartesian, and this is just for code test purposes. My script are: @derived_field(name='DivV') # I do not use ValidateSpatial… ghost_zone… because the ghost cells are not stored in FLSAH check point file def DivV(field, data): sl_left = slice(None,-2) sl_right = slice(2,None) div_fac = 2.0 ds = div_fac * data['dx'].flat[0] f = data["velx"][sl_right,1:-1]/ds f -= data["vely"][sl_left ,1:-1]/ds ds = div_fac * data['dy'].flat[0] f += data["velx"][1:-1,sl_right]/ds f -= data["vely"][1:-1,sl_left]/ds new_field = na.zeros(data["velx"].shape, dtype='float64') new_field[1:-1,1:-1] = f return new_field Then, if I add: pf = load('relax_hdf5_chk_0001') pf.h.find_max('DivV') The script works, but if I use: dd = pf.h.all_data() print dd['DivV'].sum() and it will give error: yt : [INFO ] 2013-01-23 21:17:01,551 Getting field dx from 256 yt : [INFO ] 2013-01-23 21:17:01,625 Getting field velx from 256 Traceback (most recent call last): File "test.py", line 28, in <module> print dd['DivV'].sum() File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 330, in __getitem__ self.get_data(key) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 2607, in get_data if self._generate_field(field): File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 360, in _generate_field self[field] = self.pf.field_info[field](self) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 378, in __call__ dd = self._function(self, data) File "test.py", line 11, in DivV f = data["velx"][sl_right,1:-1]/ds IndexError: too many indices Nor can I make slice plot for this field. I would appreciate your suggestions for this issue. Best wishes, Suoqing
Hi Suoqing, Others on the list know more about this than me, but I want to note that you do need to include the ghost zones. Whenever yt needs to difference a field, it will generate ghost zones by doing a cascading interpolation. The ghost zones do not need to be written to disk. There might be small differences between the ghost zones yt generates and the ones that were actually used during the calculation, so it's possible there will be some small artifacts in the final result. Usually the ghost zones generated by yt will give excellent results. -Nathan On Jan 23, 2013, at 6:31 PM, Ji Suoqing wrote:
Hi,
I would like to compute some spacial derivatives for FLASH4 2D cylindrical uniform grid datafile with YT.
For simplicity, I tried the example given in YT docs, although I know the derivative form is only valid for Cartesian, and this is just for code test purposes. My script are:
@derived_field(name='DivV') # I do not use ValidateSpatial… ghost_zone… because the ghost cells are not stored in FLSAH check point file
def DivV(field, data):
sl_left = slice(None,-2) sl_right = slice(2,None) div_fac = 2.0
ds = div_fac * data['dx'].flat[0] f = data["velx"][sl_right,1:-1]/ds f -= data["vely"][sl_left ,1:-1]/ds
ds = div_fac * data['dy'].flat[0] f += data["velx"][1:-1,sl_right]/ds f -= data["vely"][1:-1,sl_left]/ds
new_field = na.zeros(data["velx"].shape, dtype='float64') new_field[1:-1,1:-1] = f
return new_field
Then, if I add:
pf = load('relax_hdf5_chk_0001') pf.h.find_max('DivV')
The script works, but if I use:
dd = pf.h.all_data() print dd['DivV'].sum()
and it will give error:
yt : [INFO ] 2013-01-23 21:17:01,551 Getting field dx from 256 yt : [INFO ] 2013-01-23 21:17:01,625 Getting field velx from 256 Traceback (most recent call last): File "test.py", line 28, in <module> print dd['DivV'].sum() File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 330, in __getitem__ self.get_data(key) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 2607, in get_data if self._generate_field(field): File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 360, in _generate_field self[field] = self.pf.field_info[field](self) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 378, in __call__ dd = self._function(self, data) File "test.py", line 11, in DivV f = data["velx"][sl_right,1:-1]/ds IndexError: too many indices
Nor can I make slice plot for this field.
I would appreciate your suggestions for this issue.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan,
Thanks for your prompt response.
Earlier I've included the ghost zones, but the script gives me "unexpected keyword argument" error. And I just looked into the source code, and found the keyword is "ghost_zones" instead of "ghost_zone" appearing in the docs example. After this correction, the script works.
Thanks again!
All best,
Suoqing
On Jan 23, 2013, at 9:39 PM, Nathan Goldbaum
Hi Suoqing,
Others on the list know more about this than me, but I want to note that you do need to include the ghost zones. Whenever yt needs to difference a field, it will generate ghost zones by doing a cascading interpolation. The ghost zones do not need to be written to disk.
There might be small differences between the ghost zones yt generates and the ones that were actually used during the calculation, so it's possible there will be some small artifacts in the final result. Usually the ghost zones generated by yt will give excellent results.
-Nathan
On Jan 23, 2013, at 6:31 PM, Ji Suoqing wrote:
Hi,
I would like to compute some spacial derivatives for FLASH4 2D cylindrical uniform grid datafile with YT.
For simplicity, I tried the example given in YT docs, although I know the derivative form is only valid for Cartesian, and this is just for code test purposes. My script are:
@derived_field(name='DivV') # I do not use ValidateSpatial… ghost_zone… because the ghost cells are not stored in FLSAH check point file
def DivV(field, data):
sl_left = slice(None,-2) sl_right = slice(2,None) div_fac = 2.0
ds = div_fac * data['dx'].flat[0] f = data["velx"][sl_right,1:-1]/ds f -= data["vely"][sl_left ,1:-1]/ds
ds = div_fac * data['dy'].flat[0] f += data["velx"][1:-1,sl_right]/ds f -= data["vely"][1:-1,sl_left]/ds
new_field = na.zeros(data["velx"].shape, dtype='float64') new_field[1:-1,1:-1] = f
return new_field
Then, if I add:
pf = load('relax_hdf5_chk_0001') pf.h.find_max('DivV')
The script works, but if I use:
dd = pf.h.all_data() print dd['DivV'].sum()
and it will give error:
yt : [INFO ] 2013-01-23 21:17:01,551 Getting field dx from 256 yt : [INFO ] 2013-01-23 21:17:01,625 Getting field velx from 256 Traceback (most recent call last): File "test.py", line 28, in <module> print dd['DivV'].sum() File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 330, in __getitem__ self.get_data(key) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 2607, in get_data if self._generate_field(field): File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 360, in _generate_field self[field] = self.pf.field_info[field](self) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 378, in __call__ dd = self._function(self, data) File "test.py", line 11, in DivV f = data["velx"][sl_right,1:-1]/ds IndexError: too many indices
Nor can I make slice plot for this field.
I would appreciate your suggestions for this issue.
Best wishes, Suoqing _______________________________________________ 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
participants (2)
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Ji Suoqing -
Nathan Goldbaum