[yt-svn] commit/yt: 3 new changesets
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Thu Mar 29 12:55:20 PDT 2012
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/changeset/02bd133c677b/
changeset: 02bd133c677b
branch: yt
user: jzuhone
date: 2012-03-28 23:19:52
summary: Redefining "TotalEnergy" and "ThermalEnergy" as in units of erg/g. Including a few fallbacks in case some fields are not defined.
affected #: 1 file
diff -r 48de2f60f2a2ddfe01a85b904934c82cc886d9de -r 02bd133c677b0998d82a7b235bcfad8f1b937813 yt/frontends/flash/fields.py
--- a/yt/frontends/flash/fields.py
+++ b/yt/frontends/flash/fields.py
@@ -34,7 +34,8 @@
ValidateSpatial, \
ValidateGridType
import yt.data_objects.universal_fields
-
+from yt.utilities.physical_constants import \
+ kboltz
KnownFLASHFields = FieldInfoContainer()
add_flash_field = KnownFLASHFields.add_field
@@ -62,8 +63,6 @@
"y-velocity": "vely",
"z-velocity": "velz",
"Density": "dens",
- "TotalEnergy": "ener",
- "GasEnergy": "eint",
"Temperature": "temp",
"Pressure" : "pres",
"particle_position_x" : "particle_posx",
@@ -214,15 +213,43 @@
particle_type=True, convert_function=_convertParticleMassMsun,
particle_convert_function=_ParticleMassMsun)
-def _ThermalEnergy(fields,data):
- te = data["TotalEnergy"] - 0.5 * data["Density"] * (
- data["x-velocity"]**2.0 +
- data["y-velocity"]**2.0 +
- data["z-velocity"]**2.0 )
+def _ThermalEnergy(fields, data) :
try:
- te -= data['magp']
- except:
+ return data["eint"]
+ except:
pass
- return te
+ try:
+ return data["Pressure"] / (data.pf["Gamma"] - 1.0) / data["Density"]
+ except:
+ pass
+ if data.has_field_parameter("mu") :
+ mu = data.get_field_parameter("mu")
+ else:
+ mu = 0.6
+ return kboltz*data["Density"]*data["Temperature"]/(mu*mh) / (data.pf["Gamma"] - 1.0)
+
add_field("ThermalEnergy", function=_ThermalEnergy,
- units=r"\rm{ergs}/\rm{cm^3}")
+ units=r"\rm{ergs}/\rm{g}")
+
+def _TotalEnergy(fields, data) :
+ try:
+ etot = data["ener"]
+ except:
+ etot = data["ThermalEnergy"] + 0.5 * (
+ data["x-velocity"]**2.0 +
+ data["y-velocity"]**2.0 +
+ data["z-velocity"]**2.0)
+ try:
+ etot += data['magp']/data["Density"]
+ except:
+ pass
+ return etot
+
+add_field("TotalEnergy", function=_TotalEnergy,
+ units=r"\rm{ergs}/\rm{g}")
+
+def _GasEnergy(fields, data) :
+ return data["ThermalEnergy"]
+
+add_field("GasEnergy", function=_GasEnergy,
+ units=r"\rm{ergs}/\rm{g}")
https://bitbucket.org/yt_analysis/yt/changeset/41585d0a8eef/
changeset: 41585d0a8eef
branch: yt
user: ngoldbaum
date: 2012-03-29 21:47:05
summary: Fixes parameter file parsing for FLASH2.5 and some fixes for 2D data.
affected #: 1 file
diff -r 02bd133c677b0998d82a7b235bcfad8f1b937813 -r 41585d0a8eef8751db79e588d9bb7203174346bc yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -99,14 +99,22 @@
f = self._handle # shortcut
pf = self.parameter_file # shortcut
- self.grid_left_edge[:] = f["/bounding box"][:,:,0]
- self.grid_right_edge[:] = f["/bounding box"][:,:,1]
+ # Initialize to the domain left / domain right
+ ND = self.parameter_file.dimensionality
+ DLE = self.parameter_file.domain_left_edge
+ DRE = self.parameter_file.domain_left_edge
+ for i in range(3):
+ self.grid_left_edge[:,i] = DLE[i]
+ self.grid_right_edge[:,i] = DRE[i]
+ # We only go up to ND for 2D datasets
+ self.grid_left_edge[:,:ND] = f["/bounding box"][:,:,0]
+ self.grid_right_edge[:,:ND] = f["/bounding box"][:,:,1]
# Move this to the parameter file
try:
- nxb = pf._find_parameter("integer", "nxb", True)
- nyb = pf._find_parameter("integer", "nyb", True)
- nzb = pf._find_parameter("integer", "nzb", True)
+ nxb = pf.parameters['nxb']
+ nyb = pf.parameters['nyb']
+ nzb = pf.parameters['nzb']
except KeyError:
nxb, nyb, nzb = [int(f["/simulation parameters"]['n%sb' % ax])
for ax in 'xyz']
@@ -325,21 +333,39 @@
# note the ordering here is important: runtime parameters should
# ovewrite scalars with the same name.
for ptype in ['scalars', 'runtime parameters']:
- for vtype in ['integer', 'real', 'logical','string']:
+ for vtype in ['integer', 'real', 'logical', 'string']:
hns.append("%s %s" % (vtype, ptype))
- for hn in hns:
- if hn not in self._handle:
- continue
- for varname, val in zip(self._handle[hn][:,'name'],
- self._handle[hn][:,'value']):
- vn = varname.strip()
- if hn.startswith("string") :
- pval = val.strip()
- else :
- pval = val
- if vn in self.parameters and self.parameters[vn] != pval:
- mylog.warning("{0} {1} overwrites a simulation scalar of the same name".format(hn[:-1],vn))
- self.parameters[vn] = pval
+ if self._flash_version > 7:
+ for hn in hns:
+ if hn not in self._handle:
+ continue
+ for varname, val in zip(self._handle[hn][:,'name'],
+ self._handle[hn][:,'value']):
+ vn = varname.strip()
+ if hn.startswith("string") :
+ pval = val.strip()
+ else :
+ pval = val
+ if vn in self.parameters and self.parameters[vn] != pval:
+ mylog.warning("{0} {1} overwrites a simulation scalar of the same name".format(hn[:-1],vn))
+ self.parameters[vn] = pval
+ if self._flash_version == 7:
+ for hn in hns:
+ if hn not in self._handle:
+ continue
+ if hn is 'simulation parameters':
+ zipover = zip(self._handle[hn].dtype.names,self._handle[hn][0])
+ else:
+ zipover = zip(self._handle[hn][:,'name'],self._handle[hn][:,'value'])
+ for varname, val in zipover:
+ vn = varname.strip()
+ if hn.startswith("string") :
+ pval = val.strip()
+ else :
+ pval = val
+ if vn in self.parameters and self.parameters[vn] != pval:
+ mylog.warning("{0} {1} overwrites a simulation scalar of the same name".format(hn[:-1],vn))
+ self.parameters[vn] = pval
self.domain_left_edge = na.array(
[self.parameters["%smin" % ax] for ax in 'xyz']).astype("float64")
self.domain_right_edge = na.array(
https://bitbucket.org/yt_analysis/yt/changeset/54c597a3e8b8/
changeset: 54c597a3e8b8
branch: yt
user: ngoldbaum
date: 2012-03-29 21:54:56
summary: Oops, left -> right.
affected #: 1 file
diff -r 41585d0a8eef8751db79e588d9bb7203174346bc -r 54c597a3e8b813031c2f499b8e7844d1d6bacf5e yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -102,7 +102,7 @@
# Initialize to the domain left / domain right
ND = self.parameter_file.dimensionality
DLE = self.parameter_file.domain_left_edge
- DRE = self.parameter_file.domain_left_edge
+ DRE = self.parameter_file.domain_right_edge
for i in range(3):
self.grid_left_edge[:,i] = DLE[i]
self.grid_right_edge[:,i] = DRE[i]
Repository URL: https://bitbucket.org/yt_analysis/yt/
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