Mailman 3 May 2010 - yt-users

field gradients / vorticity / ghost cells
by Andrew Cunningham 02 Jun '10

02 Jun '10

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.

6 18

Thickness of slices
by Agarwal, Shankar 28 May '10

28 May '10

Hi, http://yt.enzotools.org/doc/cookbook/recipes.html#simple-slice Is there a way to figure out the approximate thickness of a slice (given the overall size of the simulation box). Shankar Agarwal Department of Physics and Astronomy University of Kansas

2 2

Change in behavior of smoothed covering grids and ghost zones
by Matthew Turk 27 May '10

27 May '10

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

1 0

radial profile of the potential
by Jean-Claude Passy 26 May '10

26 May '10

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

3 2

Quantities, hierarchy
by david collins 26 May '10

26 May '10

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.

3 5

Plotting particles only above a certain mass
by Elizabeth Harper-Clark 24 May '10

24 May '10

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

2 1

clump finder
by Jean-Claude Passy 21 May '10

21 May '10

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

3 3

Adding Coordinate axes
by Elizabeth Harper-Clark 19 May '10

19 May '10

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

3 2

Re: [yt-users] .yt files
by j s oishi 15 May '10

15 May '10

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

2 1

dynamic derived fields
by Charles Hansen 12 May '10

12 May '10

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

3 2

tracking the masses
by Jean-Claude Passy 11 May '10

11 May '10

Dear all, what I would like to do is tracking bound/lost/unbound quantities. For instance, I would like to be able to plot as a function of time: - the total mass in the grid - the mass lost by the grid - the bound mass in the grid - the unbound mass in the grid Is there a way to get these quantities with the output files only, or do I have to track them during the simulation - which will be bad news :-) ? Thanks for your help, Jean-Claude

2 1

undefined symbol: _intel_fast_memcpy
by Jean-Claude Passy 06 May '10

06 May '10

Dear all, an error occurred when I try to launch yt: [ 9:30:33] seawolf2:$ iyt Traceback (most recent call last): File "/global/home/jcpassy/yt-x86_64/bin/iyt", line 7, in <module> execfile(__file__) File "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3, in <module> from yt.mods import * File "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/__init__.py", line 58, in <module> import yt.amr_utils as amr_utils ImportError: /global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/amr_utils.so: undefined symbol: _intel_fast_memcpy I am loading the intel module at start (see my bashrc). Any help much appreciated. Thanks, Jean-Claude # .bashrc # user functions and aliases # Environment stuff goes in .profile # # Read a common system Bashrc file first if [ -f /global/system/common/Bashrc ] ; then . /global/system/common/Bashrc fi # set bash variable to keep 50 command in history HSTSIZE=100 # Include any personal modifications below # modification can include the aliases functions etc. # PS1 export PS1="[\$(date +%k:%M:%S)] \h:\$ " # Path export PATH=/global/home/jcpassy/orcinus_jc/hdf5-1.8.4/bin:/global/home/jcpassy/orcinus_jc/openmpi-1.4.1/bin:/global/home/jcpassy/yt-x86_64/bin/:/global/home/jcpassy/hg/bin:${PATH} export PYTHONPATH=/global/home/jcpassy/yt-x86_64/lib/python2.6/site-packages/:/global/home/jcpassy/hg/lib64/python2.4/site-packages:${PYTHONPATH} export LD_LIBRARY_PATH=/global/home/jcpassy/orcinus_jc/hdf5-1.8.4/lib:/global/home/jcpassy/orcinus_jc/openmpi-1.4.1/lib:/global/home/jcpassy/yt-x86_64/lib/:${LD_LIBRARY_PATH} export LD_LIBRARY_PATH=/global/home/jcpassy/orcinus_jc/szip-2.1/lib:${LD_LIBRARY_PATH} # Linux aliases alias rm='rm -f' alias rmjc='rm *~ *#' alias lsd='ls -d' alias ed='emacs -nw' alias ls2='ls -s -h -CF -G' alias df='df -h' alias dus='du -s -h' alias tarcvzf='tar -cvzf' alias tarzxvf='tar -zxvf' # Loading modules module load intel/11.0.074 # Some small programs alias calc_orbit='/global/home/jcpassy/TOOLS/orbit/calc_orbit.exe' alias clean_enzo='/global/home/jcpassy/TOOLS/enzo/clean_enzo_output.exe' alias print_units='/global/home/jcpassy/TOOLS/units/print_units.exe' #From falk alias qjc='qstat -u jcpassy' alias mjobs='showq -u jcpassy' alias qjobs='showq -i | more'

4 6

error in submitting script to cluster
by Christine Simpson 05 May '10

05 May '10

Hi, I am trying to run yt scripts on a computing cluster that uses condor. I have installed yt and successfully run scripts from the command line, but I get an error when I try to submit scripts to the cluster. I think the problem lies in how I submit the script through condor, however, I am trying to get a better understanding of the python error to help me figure it out. I was hoping you yt/python folks could give me some insight. The script I'm testing out is the one that does a simple radial profile, I copied it from the wiki: from yt.mods import * # set up our namespace fn= "output_0064" # parameter file to load pf = load(fn) # load data pc = PlotCollection(pf) # defaults to center at most dense point pc.add_profile_sphere(50.0, "kpc", # how many of which unit at pc.center ["RadiusMpc", "Density"], weight="CellMassMsun", # x, y, weight x_bounds = (1e-3, 10.0)) # cut out zero-radius and tiny-radius cells # But ... weight defaults to CellMassMsun, so we're being redundant here! pc.save(fn) # save all plots I get this error: Traceback (most recent call last): File "simple_radial_profile.py", line 3, in <module> from yt.mods import * # set up our namespace File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/lagos/__init__.py", line 29, in <module> from yt.config import ytcfg File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/config.py", line 33, in <module> 'RunDir': os.path.join(os.getenv("HOME"),'.yt/EnzoRuns/'), File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt///lib/python2.6/posixpath.py", line 67, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' The problem is with the line that imports the yt module, but I'm not sure exactly what the issue is. I thought that maybe it was an issue with not finding PYTHONPATH, but I'm not sure. If anyone has any ideas about this error, I'd appreciate them. Thanks Christine Simpson

3 2

Smoothed Covering Grid
by david collins 04 May '10

04 May '10

Hi-- What interpolation does smoothed_covering_grid use? Does it smooth from the top down or the bottom up? Thanks, d. -- Sent from my Stone Tablet and carried by my Pterodactyl.

3 2

Function Generator Warning
by robyn 01 May '10

01 May '10

I get the following message starting up iyt and wonder if it could cause any problems: robyn@rscp4:~iyt yt INFO 2010-05-01 09:16:53,866 The Fortran kD-Tree did not import correctly. The structure function generator will not work correctly. yt INFO 2010-05-01 09:16:56,113 Setting default colormap to algae WARNING: Readline services not available on this platform. WARNING: The auto-indent feature requires the readline library WARNING: Readline services not available on this platform. WARNING: The auto-indent feature requires the readline library Welcome to yt! Everything seems to work okay otherwise, though no good pictures yet. I presume that's my data refinement. -Thanks.

2 1