field gradients / vorticity / ghost cells
by Andrew Cunningham
I'd like to make a derived field that is the gradient of a primitive
field. Is there an example of how I can do this? I'm not sure how to
handle ghost cells for something like this.
I spoke with Jeff and he indicated that there was a vorticity example
somewhere, but I cannot find it.
Thanks.
8 years, 7 months
Change in behavior of smoothed covering grids and ghost zones
by Matthew Turk
Hi everyone,
After a bit of discussion on and off the yt-dev list, the mechanism
for interpolation in smoothed covering grids and vertex centered data
has changed in r1734. Previously, it would interpolate logged fields
in log-space -- so, for instance, Density would be interpolated in log
space between adjoining cells, rather than in linear space. At the
end of the interpolation it was restored.
This may result in small changes in results for a small set of
analysis types, but I believe that this change -- to interpolating
exclusively in linear space in the unmodified fields -- is the correct
change to make. To restore the old behavior, a derived field can be
created that operates by returning only the logged fields, and then
requesting smoothed or vertex centered data in that field.
Best,
Matt
8 years, 7 months
radial profile of the potential
by Jean-Claude Passy
Dear all,
I would like to access the gravitational potential and plot its radial
profile. Matthew told me that it was done in the clump finding algorithm
but I don't know how to use it.
I would really appreciate if someone could help me.
Thanks a lot,
Jean-Claude
8 years, 8 months
Quantities, hierarchy
by david collins
Hi, all--
I've used set_field_parameter for computing quantities, but that works
directly on a ExtractedRegions and whatnot. Is it possible to tie
something directly to the hierarchy or pf so that any new objects I
create can also see this value?
Thanks,
d.
--
Sent from my Stone Tablet and carried by my Pterodactyl.
8 years, 8 months
Plotting particles only above a certain mass
by Elizabeth Harper-Clark
Dear wonderful YT genii,
Within the star particle routine I am using, when star particles merge they
are kept and have mass set to tiny_mass rather than being deleted. This
makes keeping track of specific particles easier but makes plotting harder.
Does anyone have any good ideas for how to modify or create a new
p.modify["particles"] that will only plot particles above a certain mass?
many thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Astrophysics, UofT
www.astro.utoronto.ca/~h-clark
h-clark(a)cita.utoronto.ca
AIM: edphc1
MSN: edphc1(a)hotmail.com
Skype: eharperclark
Office phone: 416-978-5759
8 years, 8 months
clump finder
by Jean-Claude Passy
Dear all,
I want ultimately plot bound/unbound quantities such as mass, angular
momentum...
Britton suggested I used the clump finder. I have read the paragraph in
the Cookbook but did not manage to make it work. See below:
##########################################################################################
In [1]: from yt.mods import *
In [2]: import yt.raven as R
In [3]: fn = "DD0000/CommonEnvelope0000"
In [4]: field = "Density"
In [5]: step = 10.0
In [6]: pf = load(fn)
In [7]: whole_box = pf.h.all_data()
yt INFO 2010-05-19 13:47:49,272 Getting the binary hierarchy
yt INFO 2010-05-19 13:47:49,275 Finished with binary
hierarchy reading
In [8]: total_mass = whole_box.quantities['TotalQuantity']('CellMassMsun')
In [9]: data_source = pf.h.all_data()
In [10]: master_clump = Clump(data_source, None, field)
yt INFO 2010-05-19 13:47:49,371 Getting field Density from 1
In [11]: c_min = 10**na.floor(na.log10(data_source[field]).min() )
In [12]: c_max = 10**na.floor(na.log10(data_source[field]).max()+1)
In [13]: step = 10
In [14]: find_clumps(master_clump, c_min, c_max, step)
Finding clumps: min: 1.000000e-05, max: 1.000000e+03, step: 10.000000
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,908 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,910 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,916 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,920 Identified 1 contours
between 1.00000e-05 and 1.05005e+02
yt INFO 2010-05-19 13:47:49,931 Getting field Density from 1
Finding clumps: min: 1.000000e-04, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,944 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,945 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,950 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,954 Identified 1 contours
between 1.00000e-04 and 1.05005e+02
yt INFO 2010-05-19 13:47:49,957 Getting field Density from 1
Finding clumps: min: 1.000000e-03, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,967 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,968 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,973 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,977 Identified 1 contours
between 1.00000e-03 and 1.05005e+02
yt INFO 2010-05-19 13:47:49,980 Getting field Density from 1
Finding clumps: min: 1.000000e-02, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,990 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:49,991 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:49,996 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,000 Identified 1 contours
between 1.00000e-02 and 1.05005e+02
yt INFO 2010-05-19 13:47:50,003 Getting field Density from 1
Finding clumps: min: 1.000000e-01, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,013 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,014 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,019 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,023 Identified 1 contours
between 1.00000e-01 and 1.05005e+02
yt INFO 2010-05-19 13:47:50,026 Getting field Density from 1
Finding clumps: min: 1.000000e+00, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,034 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,036 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,040 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,045 Identified 1 contours
between 1.00000e+00 and 1.05005e+02
yt INFO 2010-05-19 13:47:50,047 Getting field Density from 1
Finding clumps: min: 1.000000e+01, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,055 Coalescing 1 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,056 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,061 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,065 Identified 1 contours
between 1.00000e+01 and 1.05005e+02
yt INFO 2010-05-19 13:47:50,067 Getting field Density from 1
Finding clumps: min: 1.000000e+02, max: 1.000000e+03, step: 10.000000
Wiping out existing children clumps.
First pass100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
Calculating joins 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,073 Coalescing 0 joins
Joining 100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00
yt INFO 2010-05-19 13:47:50,075 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,080 Getting field tempContours
from 1
yt INFO 2010-05-19 13:47:50,084 Identified 0 contours
between 1.00000e+02 and 1.05005e+02
In [15]: p = R.PlotCollection(pf)
yt.lagos INFO 2010-05-19 13:47:50,918 Max Value is 1.05005e+02
at 0.4843750000000000 0.4843750000000000 0.4843750000000000 in grid
EnzoGrid_0001 at level 0 (15, 15, 15)
yt INFO 2010-05-19 13:47:50,919 Created plot collection
with default plot-center = [0.484375, 0.484375, 0.484375]
In [16]: p.add_slice("Density",2,center=[0.5, 0.5, 0.5])
yt INFO 2010-05-19 13:47:51,479 Added slice of Density at
z = 0.5 with 'center' = [0.5, 0.5, 0.5]
Out[16]: <yt.raven.PlotTypes.SlicePlot object at 0x42f1c10>
In [17]: p.plots[-1].modify["clumps"](master_clump)
Out[17]: 0
In [18]: p.save('testclumps', format = 'png')
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (10, 0))
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
----> 1
2
3
4
5
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/raven/PlotCollection.pyc in
save(self, basename, format, override, force_save)
81 fn.append(plot.save_image(basename, \
82 format=format, submit=self._run_id,
---> 83 override=override, force_save=force_save))
84 if self.submit:
85 im = plot.im.copy()
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/raven/PlotTypes.pyc in
save_image(self, prefix, format, submit, override, force_save)
116 *override* will force no filename generation beyond the
prefix.
117 """
--> 118 self._redraw_image()
119 if not override:
120 self._generate_prefix(prefix)
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/raven/PlotTypes.pyc in
_redraw_image(self, *args)
404 self.norm.autoscale(na.array((newmin,newmax)))
405 self._reset_image_parameters()
--> 406 self._run_callbacks()
407
408 def _reset_image_parameters(self):
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/raven/PlotTypes.pyc in
_run_callbacks(self)
259 self._axes.texts = []
260 for cb in self._callbacks:
--> 261 cb(self)
262
263 def set_label(self, label):
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/raven/Callbacks.pyc in
__call__(self, plot)
451 nx, ny = plot.image._A.shape
452 buff = na.zeros((nx,ny),dtype='float64')
--> 453 for i,clump in enumerate(reversed(self.clumps)):
454 mylog.debug("Pixelizing contour %s", i)
455
TypeError: object of type 'Clump' has no len()
##########################################################################################
If I also try to reproduce the example in the cookbook:
##########################################################################################
In [19]: f = open('%s_clump_hierarchy.txt' % pf,'w')
In [20]: write_clump_hierarchy(master_clump,0,f)
yt INFO 2010-05-19 14:00:24,974 Getting field CellMassMsun
from 1
yt INFO 2010-05-19 14:00:24,974 Getting field CellVolume
from 1
yt INFO 2010-05-19 14:00:24,974 Getting field dx from 1
yt INFO 2010-05-19 14:00:24,978 Getting field dy from 1
yt INFO 2010-05-19 14:00:24,981 Getting field dz from 1
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (37, 0))
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (111, 0))
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (111, 0))
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (133, 0))
---------------------------------------------------------------------------
NeedsDataField Traceback (most recent call last)
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/scripts/iyt in <module>()
----> 1
2
3
4
5
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/Clump.pyc in
write_clump_hierarchy(clump, level, f_ptr)
196 f_ptr.write("\t")
197 f_ptr.write("Clump at level %d:\n" % level)
--> 198 clump.write_info(level,f_ptr)
199 f_ptr.write("\n")
200 f_ptr.flush()
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/Clump.pyc in
write_info(self, level, f_ptr)
102 value = item['quantity']()
103 else:
--> 104 value = eval(item['quantity'])
105 output = eval(item['format'])
106 f_ptr.write("%s%s" % ('\t'*level,output))
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/Clump.pyc in <module>()
----> 1
2
3
4
5
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc
in __call__(self, *args, **kwargs)
70 self._data_source.pf.h.io
<http://data_source.pf.h.io>)
71 if lazy_reader and not self.force_unlazy:
---> 72 return self._call_func_lazy(args, kwargs)
73 else:
74 return self._call_func_unlazy(args, kwargs)
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc
in _call_func_lazy(self, args, kwargs)
77 self.retvals = [ [] for i in range(self.n_ret)]
78 for gi,g in enumerate(self._get_grids()):
---> 79 rv = self.func(GridChildMaskWrapper(g,
self._data_source), *args, **kwargs)
80 for i in range(self.n_ret):
self.retvals[i].append(rv[i])
81 g.clear_data()
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc
in _WeightedAverageQuantity(data, field, weight)
151 :param weight: The field to weight by
152 """
--> 153 num = (data[field] * data[weight]).sum()
154 den = data[weight].sum()
155 return num, den
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc
in __getitem__(self, item)
41 return getattr(self.grid, attr)
42 def __getitem__(self, item):
---> 43 return self.data_source._get_data_from_grid(self.grid, item)
44
45 class DerivedQuantity(ParallelAnalysisInterface):
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseDataTypes.pyc in
save_state(self, grid, field)
41 old_keys = grid.data.keys()
42 grid.field_parameters = self.field_parameters
---> 43 tr = func(self, grid, field)
44 grid.field_parameters = old_params
45 grid.data = dict( [(k, grid.data[k]) for k in old_keys] )
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseDataTypes.pyc in
_get_data_from_grid(self, grid, field)
1670 else:
1671 pointI = self._get_point_indices(grid)
-> 1672 if grid[field].size == 1: # dx, dy, dz, cellvolume
1673 t = grid[field] * na.ones(grid.ActiveDimensions,
dtype='float64')
1674 return t[pointI].ravel()
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
__getitem__(self, key)
133 """
134 if not self.data.has_key(key):
--> 135 self.get_data(key)
136 return self.data[key]
137
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
get_data(self, field)
176 else: raise
177 else:
--> 178 self._generate_field(field)
179 return self.data[field]
180
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
_generate_field(self, field)
121 self[field] = temp_array[sl]
122 else:
--> 123 self[field] = self.pf.field_info[field](self)
124 else: # Can't find the field, try as it might
125 raise exceptions.KeyError, field
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/FieldInfoContainer.pyc
in __call__(self, data)
316 ii = self.check_available(data)
317 original_fields = data.keys() # Copy
--> 318 dd = self._function(self, data)
319 dd *= self._convert_function(data)
320 for field_name in data.keys():
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/UniversalFields.pyc
in _JeansMassMsun(field, data)
769
770 return (MJ_constant *
--> 771
((data["Temperature"]/data["MeanMolecularWeight"])**(1.5)) *
772 (data["Density"]**(-0.5)))
773 add_field("JeansMassMsun",function=_JeansMassMsun,
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
__getitem__(self, key)
133 """
134 if not self.data.has_key(key):
--> 135 self.get_data(key)
136 return self.data[key]
137
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
get_data(self, field)
176 else: raise
177 else:
--> 178 self._generate_field(field)
179 return self.data[field]
180
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in
_generate_field(self, field)
111 # First we check the validator
112 try:
--> 113 self.pf.field_info[field].check_available(self)
114 except NeedsGridType, ngt_exception:
115 # This is only going to be raised if n_gz > 0
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/FieldInfoContainer.pyc
in check_available(self, data)
283 """
284 for validator in self.validators:
--> 285 validator(data)
286 # If we don't get an exception, we're good to go
287 return True
/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/FieldInfoContainer.pyc
in __call__(self, data)
381 doesnt_have.append(f)
382 if len(doesnt_have) > 0:
--> 383 raise NeedsDataField(doesnt_have)
384 return True
385
NeedsDataField: (['Temperature'])
##########################################################################################
Also, if I correctly understand the Cookbook and the reference, the tree
of clumps in contained in master_clump. It contains only the bound
clumps so if I do :
##########################################################################################
In [31]: master_clump.data.fields
Out[31]: ['Density', 'tempContours', 'CellMassMsun']
In [32]: a = master_clump.data['CellMassMsun']
In [33]: sum(a)
Out[33]: 0.98881452898337696
##########################################################################################
this will be the total bound mass. Does it automatically take into
account the thermal energy to determine whether a clump is bound or not ?
I would really appreciate if someone could give me a hint.
Thanks a lot,
Jean-Claude
8 years, 8 months
Adding Coordinate axes
by Elizabeth Harper-Clark
Dear all,
I am trying to add coordinate axes to a slice. Here is my code:
from yt.mods import *
import pylab
import sys
import cmath
frame_template = "aaWoC/%s/Density_slice_zoom_%01i_%04i"
for n in range(370,500): # make density slice with particles on
pf = lagos.EnzoStaticOutput("WOCOUT/%s/DD%04i/data%04i" %
(sys.argv[-1],n, n))
pc = raven.PlotCollection(pf)
for ax in range(3):
p = pc.add_slice("Density", ax, weight_field="Density")
p.set_width(0.05,1)
p.modify["coord_axes"](unit=None, coords=False)
if na.any(pf.h.grid_particle_count):
p.modify["particles"](0.05, p_size=10.0, col='k')
print " XXXXX Particles present XXXXX"
p.modify["text"]((0.101,0.899),"Time = %8.4f Myr" %
(pf["InitialTime"]*pf["years"]/1.e6), text_args = {'color':'k'})
p.modify["text"]((0.1,0.9),"Time = %8.4f Myr" %
(pf["InitialTime"]*pf["years"]/1.e6), text_args = {'color':'w'})
pc.save(frame_template % (sys.argv[-1],ax,n), override=True)
and here is the output I get:
[h-clark@tpb92-chroot my_scripts]$ python2.6 Density_slices_zoom.py
experiments2
0.35 0.45 0.7
yt INFO 2010-05-17 11:03:57,243 Getting the binary hierarchy
yt INFO 2010-05-17 11:03:57,291 Finished with binary hierarchy
reading
yt INFO 2010-05-17 11:03:57,295 Adding PotentialField to list
of fields
yt INFO 2010-05-17 11:03:57,295 Adding AccelerationField2 to
list of fields
yt INFO 2010-05-17 11:03:57,295 Adding AccelerationField3 to
list of fields
yt INFO 2010-05-17 11:03:57,296 Adding AccelerationField1 to
list of fields
yt.lagos INFO 2010-05-17 11:03:57,518 Max Value is 7.53287e-17 at
0.6984863281250000 0.3586425781250000 0.3889160156250000 in grid
EnzoGrid_0037 at level 4 (4, 4, 6)
yt INFO 2010-05-17 11:03:57,518 Created plot collection with
default plot-center = [0.698486328125, 0.358642578125, 0.388916015625]
yt INFO 2010-05-17 11:03:58,136 Added slice of Density at x =
0.698486328125 with 'center' = [0.698486328125, 0.358642578125,
0.388916015625]
Traceback (most recent call last):
File "Density_slices_zoom.py", line 34, in <module>
pc.save(frame_template % (sys.argv[-1],ax,n), override=True)
File
"/mnt/raid-project/murray/h-clark/YT/src/yt-trunk-svn/yt/raven/PlotCollection.py",
line 83, in save
override=override, force_save=force_save))
File
"/mnt/raid-project/murray/h-clark/YT/src/yt-trunk-svn/yt/raven/PlotTypes.py",
line 118, in save_image
self._redraw_image()
File
"/mnt/raid-project/murray/h-clark/YT/src/yt-trunk-svn/yt/raven/PlotTypes.py",
line 406, in _redraw_image
self._run_callbacks()
File
"/mnt/raid-project/murray/h-clark/YT/src/yt-trunk-svn/yt/raven/PlotTypes.py",
line 261, in _run_callbacks
cb(self)
File
"/mnt/raid-project/murray/h-clark/YT/src/yt-trunk-svn/yt/raven/Callbacks.py",
line 737, in __call__
unit_conversion = plot.data.hierarchy[plot.im["Unit"]]
TypeError: 'EnzoHierarchy' object is unsubscriptable
Does anyone see what I am doing wrong?
many thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Astrophysics, UofT
www.astro.utoronto.ca/~h-clark
h-clark(a)cita.utoronto.ca
AIM: edphc1
MSN: edphc1(a)hotmail.com
Skype: eharperclark
Office phone: 416-978-5759
8 years, 8 months
Re: [yt-users] .yt files
by j s oishi
Hi Andy,
On Thu, May 13, 2010 at 6:44 PM, Andrew Cunningham
<ajc4(a)pas.rochester.edu> wrote:
> For some reason I get .yt files on kraken, but on ranger .yt files are never
> saved. ... Do you have any pointers to diagnose why the .yt files aren't
> working on ranger?
This is a weird one. I don't have a good idea. Did you build yt on
Ranger from the install script? Does it mention anything about
serialization when you run scripts? It's possible, I suppose that
seralization has been turned off somehow. Can you add
from yt.config import ytcfg
ytcfg["lagos","serialize"] = 'True'
to your script on ranger to explicitly turn on serialization?
I'm bouncing this to the yt-users list in case someone else might have
had a similar issue on Ranger. I don't use the machine myself, so I
don't have a feel for anything specific to that machine.
Jeff
8 years, 8 months
dynamic derived fields
by Charles Hansen
Hi all,
Is it possible to make something like a derived field in yt that takes
passed variables? A simple example would be extracting gas density
above a certain temperature, but changing that temperature threshold on
the fly
def _hotgas(field, data, temperature_threshold):
reutrn data["density"]*(data["Temperature"] > temperature_threshold)
add_field("hotgas", function=_hotgas, Something else goes here?)
In this particular case I only need a few temperatures and can make a
new derived quantity each time, but it seems like a generally useful
ability.
Thanks,
Charles
8 years, 8 months
