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

/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

/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

/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)

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)

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