[yt-svn] commit/yt: 4 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sat Apr 19 01:29:31 PDT 2014
4 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/4e98001dadde/
Changeset: 4e98001dadde
Branch: yt-3.0
User: jmoloney
Date: 2014-04-16 23:39:09
Summary: Various bugfixes for reading and writing saved hop halos.
Affected #: 1 file
diff -r 3d28859d2cec38a349e7335fc04e62978ffcc1a8 -r 4e98001daddeacb5461067e6322242bd92d9b2c3 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -110,7 +110,9 @@
if self._name == "RockstarHalo":
ds = self.pf.sphere(self.CoM, self._radjust * self.max_radius)
elif self._name == "LoadedHalo":
- ds = self.pf.sphere(self.CoM, self._radjust * self.max_radius)
+ ds = self.pf.sphere(self.CoM, np.maximum(self._radjust * \
+ self.pf.quan(self.max_radius, 'code_length'), \
+ self.pf.index.get_smallest_dx()))
sp_pid = ds['particle_index']
self._ds_sort = sp_pid.argsort()
sp_pid = sp_pid[self._ds_sort]
@@ -217,7 +219,7 @@
vx = (self["particle_velocity_x"] * pm).sum()
vy = (self["particle_velocity_y"] * pm).sum()
vz = (self["particle_velocity_z"] * pm).sum()
- return np.array([vx, vy, vz]) / pm.sum()
+ return YTArray([vx, vy, vz], vx.units) / pm.sum()
def rms_velocity(self):
r"""Returns the mass-weighted RMS velocity for the halo
@@ -331,9 +333,11 @@
handle.create_group("/%s" % gn)
for field in ["particle_position_%s" % ax for ax in 'xyz'] \
+ ["particle_velocity_%s" % ax for ax in 'xyz'] \
- + ["particle_index"] + ["particle_mass"].in_units('Msun'):
+ + ["particle_index"]:
handle.create_dataset("/%s/%s" % (gn, field), data=self[field])
- if 'creation_time' in self.data.pf.field_list:
+ handle.create_dataset("/%s/particle_mass" % gn,
+ data=self["particle_mass"].in_units('Msun'))
+ if ('io','creation_time') in self.data.pf.field_list:
handle.create_dataset("/%s/creation_time" % gn,
data=self['creation_time'])
n = handle["/%s" % gn]
@@ -848,6 +852,7 @@
self._saved_fields = {}
self._ds_sort = None
self._particle_mask = None
+ self._pid_sort = None
def __getitem__(self, key):
@@ -865,14 +870,28 @@
self.size, key)
if field_data is not None:
if key == 'particle_index':
- field_data = field_data[field_data.argsort()]
+ #this is an index for turning data sorted by particle index
+ #into the same order as the fields on disk
+ self._pid_sort = field_data.argsort().argsort()
+ #convert to YTArray using the data from disk
+ if key == 'particle_mass':
+ field_data = YTArray(field_data, 'Msun')
+ else:
+ field_data = self.pf.arr(field_data,
+ self.pf._get_field_info('unknown',key).units)
self._saved_fields[key] = field_data
return self._saved_fields[key]
# We won't store this field below in saved_fields because
# that would mean keeping two copies of it, one in the yt
# machinery and one here.
- ds = self.pf.sphere(self.CoM, 1.05 * self.max_radius)
- return np.take(ds[key][self._ds_sort], self.particle_mask)
+ ds = self.pf.sphere(self.CoM, np.maximum(self._radjust * \
+ self.pf.quan(self.max_radius, 'code_length'), \
+ self.pf.index.get_smallest_dx()))
+ # If particle_mask hasn't been called once then _ds_sort won't have
+ # the proper values set yet
+ if self._particle_mask is None:
+ self.particle_mask
+ return ds[key][self._ds_sort][self.particle_mask][self._pid_sort]
def _get_particle_data(self, halo, fnames, size, field):
# Given a list of file names, a halo, its size, and the desired field,
@@ -1087,10 +1106,10 @@
gc.collect()
def _get_dm_indices(self):
- if 'creation_time' in self._data_source.index.field_list:
+ if ('io','creation_time') in self._data_source.index.field_list:
mylog.debug("Differentiating based on creation time")
return (self._data_source["creation_time"] <= 0)
- elif 'particle_type' in self._data_source.index.field_list:
+ elif ('io','particle_type') in self._data_source.index.field_list:
mylog.debug("Differentiating based on particle type")
return (self._data_source["particle_type"] == 1)
else:
@@ -2388,7 +2407,7 @@
total_mass = \
self.comm.mpi_allreduce((self._data_source['all', "particle_mass"][select].in_units('Msun')).sum(dtype='float64'), op='sum')
else:
- total_mass = self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("particle_mass")[0].in_units('Msun'), op='sum')
+ total_mass = self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("particle_mass").in_units('Msun'), op='sum')
# MJT: Note that instead of this, if we are assuming that the particles
# are all on different processors, we should instead construct an
# object representing the entire domain and sum it "lazily" with
@@ -2412,7 +2431,7 @@
sub_mass = self._data_source["particle_mass"][select].in_units('Msun').sum(dtype='float64')
else:
sub_mass = \
- self._data_source.quantities["TotalQuantity"]("particle_mass")[0].in_units('Msun')
+ self._data_source.quantities["TotalQuantity"]("particle_mass").in_units('Msun')
HOPHaloList.__init__(self, self._data_source,
threshold * total_mass / sub_mass, dm_only)
self._parse_halolist(total_mass / sub_mass)
https://bitbucket.org/yt_analysis/yt/commits/607b84bdc6ee/
Changeset: 607b84bdc6ee
Branch: yt-3.0
User: jmoloney
Date: 2014-04-17 00:41:54
Summary: Fixes for new units in parallel_hop.
Affected #: 2 files
diff -r 4e98001daddeacb5461067e6322242bd92d9b2c3 -r 607b84bdc6ee5d949ef9b13a5cd8e09162a5029a yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -2160,7 +2160,7 @@
elif fancy_padding and self._distributed:
LE_padding = np.empty(3, dtype='float64')
RE_padding = np.empty(3, dtype='float64')
- avg_spacing = (float(vol) / data.size) ** (1. / 3.)
+ avg_spacing = (vol / data.size) ** (1. / 3.)
base_padding = (self.num_neighbors) ** (1. / 3.) * self.safety * \
avg_spacing
for dim in xrange(3):
diff -r 4e98001daddeacb5461067e6322242bd92d9b2c3 -r 607b84bdc6ee5d949ef9b13a5cd8e09162a5029a yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -53,7 +53,7 @@
self.zpos = particle_fields.pop("particle_position_z")
self.real_size = len(self.xpos)
self.index = particle_fields.pop("particle_index")
- self.mass = particle_fields.pop("ParticleMassMsun")
+ self.mass = particle_fields.pop("particle_mass")
self.padded_particles = []
self.nMerge = 4
self.tree = tree
https://bitbucket.org/yt_analysis/yt/commits/634d6721073e/
Changeset: 634d6721073e
Branch: yt-3.0
User: jmoloney
Date: 2014-04-17 21:39:28
Summary: Replaced YTArray with pf.arr.
Affected #: 1 file
diff -r 607b84bdc6ee5d949ef9b13a5cd8e09162a5029a -r 634d6721073e99c77f213003c35f924e32041226 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -219,7 +219,7 @@
vx = (self["particle_velocity_x"] * pm).sum()
vy = (self["particle_velocity_y"] * pm).sum()
vz = (self["particle_velocity_z"] * pm).sum()
- return YTArray([vx, vy, vz], vx.units) / pm.sum()
+ return self.pf.arr([vx, vy, vz], vx.units) / pm.sum()
def rms_velocity(self):
r"""Returns the mass-weighted RMS velocity for the halo
@@ -875,7 +875,7 @@
self._pid_sort = field_data.argsort().argsort()
#convert to YTArray using the data from disk
if key == 'particle_mass':
- field_data = YTArray(field_data, 'Msun')
+ field_data = self.pf.arr(field_data, 'Msun')
else:
field_data = self.pf.arr(field_data,
self.pf._get_field_info('unknown',key).units)
https://bitbucket.org/yt_analysis/yt/commits/7de0dd178c22/
Changeset: 7de0dd178c22
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-19 10:29:24
Summary: Merged in jmoloney/yt/yt-3.0 (pull request #835)
Bug fixes for saving and loading hop halos
Affected #: 2 files
diff -r 0c0a0b6f8dca9b1536efe6032b6854a43d092079 -r 7de0dd178c22e32b843a58494d5bd6b1ffc2112c yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -110,7 +110,9 @@
if self._name == "RockstarHalo":
ds = self.pf.sphere(self.CoM, self._radjust * self.max_radius)
elif self._name == "LoadedHalo":
- ds = self.pf.sphere(self.CoM, self._radjust * self.max_radius)
+ ds = self.pf.sphere(self.CoM, np.maximum(self._radjust * \
+ self.pf.quan(self.max_radius, 'code_length'), \
+ self.pf.index.get_smallest_dx()))
sp_pid = ds['particle_index']
self._ds_sort = sp_pid.argsort()
sp_pid = sp_pid[self._ds_sort]
@@ -217,7 +219,7 @@
vx = (self["particle_velocity_x"] * pm).sum()
vy = (self["particle_velocity_y"] * pm).sum()
vz = (self["particle_velocity_z"] * pm).sum()
- return np.array([vx, vy, vz]) / pm.sum()
+ return self.pf.arr([vx, vy, vz], vx.units) / pm.sum()
def rms_velocity(self):
r"""Returns the mass-weighted RMS velocity for the halo
@@ -331,9 +333,11 @@
handle.create_group("/%s" % gn)
for field in ["particle_position_%s" % ax for ax in 'xyz'] \
+ ["particle_velocity_%s" % ax for ax in 'xyz'] \
- + ["particle_index"] + ["particle_mass"].in_units('Msun'):
+ + ["particle_index"]:
handle.create_dataset("/%s/%s" % (gn, field), data=self[field])
- if 'creation_time' in self.data.pf.field_list:
+ handle.create_dataset("/%s/particle_mass" % gn,
+ data=self["particle_mass"].in_units('Msun'))
+ if ('io','creation_time') in self.data.pf.field_list:
handle.create_dataset("/%s/creation_time" % gn,
data=self['creation_time'])
n = handle["/%s" % gn]
@@ -848,6 +852,7 @@
self._saved_fields = {}
self._ds_sort = None
self._particle_mask = None
+ self._pid_sort = None
def __getitem__(self, key):
@@ -865,14 +870,28 @@
self.size, key)
if field_data is not None:
if key == 'particle_index':
- field_data = field_data[field_data.argsort()]
+ #this is an index for turning data sorted by particle index
+ #into the same order as the fields on disk
+ self._pid_sort = field_data.argsort().argsort()
+ #convert to YTArray using the data from disk
+ if key == 'particle_mass':
+ field_data = self.pf.arr(field_data, 'Msun')
+ else:
+ field_data = self.pf.arr(field_data,
+ self.pf._get_field_info('unknown',key).units)
self._saved_fields[key] = field_data
return self._saved_fields[key]
# We won't store this field below in saved_fields because
# that would mean keeping two copies of it, one in the yt
# machinery and one here.
- ds = self.pf.sphere(self.CoM, 1.05 * self.max_radius)
- return np.take(ds[key][self._ds_sort], self.particle_mask)
+ ds = self.pf.sphere(self.CoM, np.maximum(self._radjust * \
+ self.pf.quan(self.max_radius, 'code_length'), \
+ self.pf.index.get_smallest_dx()))
+ # If particle_mask hasn't been called once then _ds_sort won't have
+ # the proper values set yet
+ if self._particle_mask is None:
+ self.particle_mask
+ return ds[key][self._ds_sort][self.particle_mask][self._pid_sort]
def _get_particle_data(self, halo, fnames, size, field):
# Given a list of file names, a halo, its size, and the desired field,
@@ -1087,10 +1106,10 @@
gc.collect()
def _get_dm_indices(self):
- if 'creation_time' in self._data_source.index.field_list:
+ if ('io','creation_time') in self._data_source.index.field_list:
mylog.debug("Differentiating based on creation time")
return (self._data_source["creation_time"] <= 0)
- elif 'particle_type' in self._data_source.index.field_list:
+ elif ('io','particle_type') in self._data_source.index.field_list:
mylog.debug("Differentiating based on particle type")
return (self._data_source["particle_type"] == 1)
else:
@@ -2141,7 +2160,7 @@
elif fancy_padding and self._distributed:
LE_padding = np.empty(3, dtype='float64')
RE_padding = np.empty(3, dtype='float64')
- avg_spacing = (float(vol) / data.size) ** (1. / 3.)
+ avg_spacing = (vol / data.size) ** (1. / 3.)
base_padding = (self.num_neighbors) ** (1. / 3.) * self.safety * \
avg_spacing
for dim in xrange(3):
@@ -2388,7 +2407,7 @@
total_mass = \
self.comm.mpi_allreduce((self._data_source['all', "particle_mass"][select].in_units('Msun')).sum(dtype='float64'), op='sum')
else:
- total_mass = self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("particle_mass")[0].in_units('Msun'), op='sum')
+ total_mass = self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("particle_mass").in_units('Msun'), op='sum')
# MJT: Note that instead of this, if we are assuming that the particles
# are all on different processors, we should instead construct an
# object representing the entire domain and sum it "lazily" with
@@ -2412,7 +2431,7 @@
sub_mass = self._data_source["particle_mass"][select].in_units('Msun').sum(dtype='float64')
else:
sub_mass = \
- self._data_source.quantities["TotalQuantity"]("particle_mass")[0].in_units('Msun')
+ self._data_source.quantities["TotalQuantity"]("particle_mass").in_units('Msun')
HOPHaloList.__init__(self, self._data_source,
threshold * total_mass / sub_mass, dm_only)
self._parse_halolist(total_mass / sub_mass)
diff -r 0c0a0b6f8dca9b1536efe6032b6854a43d092079 -r 7de0dd178c22e32b843a58494d5bd6b1ffc2112c yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -53,7 +53,7 @@
self.zpos = particle_fields.pop("particle_position_z")
self.real_size = len(self.xpos)
self.index = particle_fields.pop("particle_index")
- self.mass = particle_fields.pop("ParticleMassMsun")
+ self.mass = particle_fields.pop("particle_mass")
self.padded_particles = []
self.nMerge = 4
self.tree = tree
Repository URL: https://bitbucket.org/yt_analysis/yt/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the yt-svn
mailing list