Thank you David and Matthew, I have looked the yt webpage about derived Field. But, I can not find where in the script the definition goes. For example I wrote the script to make slice as follow ------------------------------------------------ from yt.mods import * from yt.analysis_modules.api import EnzoSimulation import matplotlib.pylab as pylab def _Temperature(field, data): DEFAULT_MU = 0.6 return data["Gas_Energy"]*(data.pf[Gamma]-1)*DEFAULT_MU add_field("Temperature", function=_Temperature) es = EnzoSimulation("RotatingSphere.enzo", initial_time=0.0, final_time=50.) time = [] i = 0 for output in es.allOutputs: # load up a dataset pf = load(output['filename']) # calculate the time of output time.append(0.1*i) i = i + 1 # create density slices pc = PlotCollection(pf, center=[0.5,0.5,0.5]) pc.add_slice("Temperature", 0) pc.add_slice("Temperature", 2) pc.save("t%05.2f" % time[i-1]) -------------------------------------------------------------------- But this python script crashed. How and where can I define new field in the script? Thank you Junhwan Matthew Turk wrote:

Hi Junhwan,

David wrote back earlier to your first email:

http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-April/00132...

Best,

Matt

On Mon, Apr 4, 2011 at 10:19 PM, wrote:

...

Hi YT uses,

I would like to know how make slice, projection, or volume rendering plots for derived Fields. For example, my enzo simulation output only has gas_energy (no temperature field in grid data) and I would like to make temperature map with add_slice, simply write add_slice("Temperature", 0) causes an error. Is there any way this visualization can be done with derived Field?

Thank you, Junhwan

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

_______________________________________________ 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

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

Thank you Matthew for quick reply, I made change from data.pf[Gamma] to data.pf["Gamma"], but it still crash with following report: yt INFO 2011-04-05 11:22:35,217 Loaded 501 total data outputs. yt INFO 2011-04-05 11:22:35,224 Parameters: current_time = 0.0 yt INFO 2011-04-05 11:22:35,224 Parameters: domain_dimensions = [32, 32, 32] yt INFO 2011-04-05 11:22:35,224 Parameters: domain_left_edge = [ 0. 0. 0.] yt INFO 2011-04-05 11:22:35,225 Parameters: domain_right_edge = [ 1. 1. 1.] yt INFO 2011-04-05 11:22:35,225 Parameters: cosmological_simulation = 0.0 yt INFO 2011-04-05 11:22:35,225 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt INFO 2011-04-05 11:22:35,231 Getting the binary hierarchy yt INFO 2011-04-05 11:22:35,236 Finished with binary hierarchy reading Warning: invalid value encountered in sqrt Warning: invalid value encountered in sqrt Traceback (most recent call last): File "plots.py", line 25, in <module> pc.add_slice("Temperature", 0) File "/home/jhchoi/common/src/yt-hg/yt/visualization/plot_collection.py", line 389, in add_slice center=center, **field_parameters) File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 732, in __init__ self._refresh_data() File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 267, in _refresh_data self.get_data() File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 615, in get_data if self._generate_field(field): File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 638, in _generate_field self.pf.field_info[field].check_available(self) File "/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", line 276, in check_available validator(data) File "/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", line 374, in __call__ raise NeedsDataField(doesnt_have) yt.data_objects.field_info_container.NeedsDataField: (['Temperature']) Thank you, Junhwan Matthew Turk wrote:

Hi Junhwan,

Your definition of the derived field looks okay to me, except that I think you need to do:

data.pf["Gamma"]

with the quotes around Gamma. Additionally, it's usually quite helpful to have the crash report when diagnosing issues like these. :)

-Matt

On Tue, Apr 5, 2011 at 10:54 AM, Jun-Hwan Choi wrote:

...

Thank you David and Matthew,

I have looked the yt webpage about derived Field. But, I can not find where in the script the definition goes. For example I wrote the script to make slice as follow ------------------------------------------------ from yt.mods import * from yt.analysis_modules.api import EnzoSimulation import matplotlib.pylab as pylab

def _Temperature(field, data): DEFAULT_MU = 0.6 return data["Gas_Energy"]*(data.pf[Gamma]-1)*DEFAULT_MU add_field("Temperature", function=_Temperature)

es = EnzoSimulation("RotatingSphere.enzo", initial_time=0.0, final_time=50.)

time = [] i = 0 for output in es.allOutputs: # load up a dataset pf = load(output['filename'])

# calculate the time of output time.append(0.1*i) i = i + 1

# create density slices pc = PlotCollection(pf, center=[0.5,0.5,0.5]) pc.add_slice("Temperature", 0) pc.add_slice("Temperature", 2) pc.save("t%05.2f" % time[i-1]) -------------------------------------------------------------------- But this python script crashed. How and where can I define new field in the script?

Thank you Junhwan

Matthew Turk wrote:

...

Hi Junhwan,

David wrote back earlier to your first email:

http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-April/00132...

Best,

Matt

On Mon, Apr 4, 2011 at 10:19 PM, wrote:

...

Hi YT uses,

I would like to know how make slice, projection, or volume rendering plots for derived Fields. For example, my enzo simulation output only has gas_energy (no temperature field in grid data) and I would like to make temperature map with add_slice, simply write add_slice("Temperature", 0) causes an error. Is there any way this visualization can be done with derived Field?

Thank you, Junhwan

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

_______________________________________________ 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

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

_______________________________________________ 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

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

Hi Junhwan, I think I have figured out the issue, but I am not sure because I don't have access to your data. If you run this inside your loop: print pf.h.field_list You may see that you are missing the field "Gas_Energy", and you may in its place have "TotalEnergy" or "Total_Energy" and possibly "GasEnergy". My guess is that what's happening is that the derived field you defined can't be created, so rather than adding that to the list of "known fields" it's falling back on the default definition for Temperature, which is to read it from a file. One option would be to switch on Gas_Energy in your problem definition (from your parameter file I would guess you are using a homegrown problem type) and you may even be able to have Enzo output the temperature by examining how the OutputTemperatuer parameter works. -Matt On Tue, Apr 5, 2011 at 1:11 PM, Matthew Turk wrote:

Hi Junhwan,

This is confusing to me.  Could you run:

yt_lodgeit.py plots.py

and then send me the location that it returns?  I'd like to investigate your script in detail, and I believe the best way to do that woul be to replicate it here.

-Matt

On Tue, Apr 5, 2011 at 11:23 AM, Jun-Hwan Choi wrote:

...

Thank you Matthew for quick reply,

I made change from data.pf[Gamma] to data.pf["Gamma"], but it still crash with following report: yt         INFO       2011-04-05 11:22:35,217 Loaded 501 total data outputs. yt         INFO       2011-04-05 11:22:35,224 Parameters: current_time        = 0.0 yt         INFO       2011-04-05 11:22:35,224 Parameters: domain_dimensions         = [32, 32, 32] yt         INFO       2011-04-05 11:22:35,224 Parameters: domain_left_edge        = [ 0.  0.  0.] yt         INFO       2011-04-05 11:22:35,225 Parameters: domain_right_edge         = [ 1.  1.  1.] yt         INFO       2011-04-05 11:22:35,225 Parameters: cosmological_simulation   = 0.0 yt         INFO       2011-04-05 11:22:35,225 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt         INFO       2011-04-05 11:22:35,231 Getting the binary hierarchy yt         INFO       2011-04-05 11:22:35,236 Finished with binary hierarchy reading Warning: invalid value encountered in sqrt Warning: invalid value encountered in sqrt Traceback (most recent call last):  File "plots.py", line 25, in <module>   pc.add_slice("Temperature", 0)  File "/home/jhchoi/common/src/yt-hg/yt/visualization/plot_collection.py", line 389, in add_slice   center=center, **field_parameters)  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 732, in __init__   self._refresh_data()  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 267, in _refresh_data   self.get_data()  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 615, in get_data   if self._generate_field(field):  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 638, in _generate_field   self.pf.field_info[field].check_available(self)  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", line 276, in check_available   validator(data)  File "/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", line 374, in __call__   raise NeedsDataField(doesnt_have) yt.data_objects.field_info_container.NeedsDataField: (['Temperature'])

Thank you, Junhwan

Matthew Turk wrote:

...

Hi Junhwan,

Your definition of the derived field looks okay to me, except that I think you need to do:

data.pf["Gamma"]

with the quotes around Gamma.  Additionally, it's usually quite helpful to have the crash report when diagnosing issues like these. :)

-Matt

On Tue, Apr 5, 2011 at 10:54 AM, Jun-Hwan Choi wrote:

...

Thank you David and Matthew,

I have looked the yt webpage about derived Field. But, I can not find where in the script the definition goes. For example I wrote the script to make slice as follow ------------------------------------------------ from yt.mods import * from yt.analysis_modules.api import EnzoSimulation import matplotlib.pylab as pylab

def _Temperature(field, data):  DEFAULT_MU = 0.6  return data["Gas_Energy"]*(data.pf[Gamma]-1)*DEFAULT_MU add_field("Temperature", function=_Temperature)

es = EnzoSimulation("RotatingSphere.enzo", initial_time=0.0, final_time=50.)

time = [] i = 0 for output in es.allOutputs:  # load up a dataset  pf = load(output['filename'])

 # calculate the time of output  time.append(0.1*i)  i = i + 1

 # create density slices  pc = PlotCollection(pf, center=[0.5,0.5,0.5])  pc.add_slice("Temperature", 0)  pc.add_slice("Temperature", 2)  pc.save("t%05.2f" % time[i-1]) -------------------------------------------------------------------- But this python script crashed. How and where can I define new field in the script?

Thank you Junhwan

Matthew Turk wrote:

...

Hi Junhwan,

David wrote back earlier to your first email:

http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-April/00132...

Best,

Matt

On Mon, Apr 4, 2011 at 10:19 PM,   wrote:

...

Hi YT uses,

I would like to know how make slice, projection, or volume rendering plots for derived Fields. For example, my enzo simulation output only has gas_energy (no temperature field in grid data) and I would like to make temperature map with add_slice, simply write add_slice("Temperature", 0) causes an error. Is there any way this visualization can be done with derived Field?

Thank you, Junhwan

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737        Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

_______________________________________________ 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

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737        Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

_______________________________________________ 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

-- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737        Fax: (859) 323-2846 Email: jhchoi@pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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