[yt-svn] commit/yt-3.0: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Oct 29 06:48:39 PDT 2013
3 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/commits/1773e02166ca/
Changeset: 1773e02166ca
Branch: yt-3.0
User: scopatz
Date: 2013-10-29 02:02:55
Summary: fixed up PyneMoabHex8 to use updated pyne mesh tagging capabilities.
Affected #: 2 files
diff -r 9bc960be45cb0664d924523552460752a67c5325 -r 1773e02166caa9bf1042c029325bc761cc0a60d9 yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -157,11 +157,12 @@
#self.field_list = self.pyne_mesh.mesh.getAllTags(
# self.pyne_mesh.mesh.rootSet)
# So we have to look at each entity.
- tags = set([])
- for ent in self.pyne_mesh.mesh.rootSet:
- for tag in self.pyne_mesh.mesh.getAllTags(ent):
- tags.add(tag.name)
- self.field_list = list(tags)
+ #tags = set([])
+ #for ent in self.pyne_mesh.mesh.rootSet:
+ # for tag in self.pyne_mesh.mesh.getAllTags(ent):
+ # tags.add(tag.name)
+ #self.field_list = list(tags)
+ self.field_list = self.pyne_mesh.tags.keys()
def _count_grids(self):
self.num_grids = 1
diff -r 9bc960be45cb0664d924523552460752a67c5325 -r 1773e02166caa9bf1042c029325bc761cc0a60d9 yt/frontends/moab/io.py
--- a/yt/frontends/moab/io.py
+++ b/yt/frontends/moab/io.py
@@ -74,3 +74,28 @@
for g in chunk.objs:
ind += g.select(selector, ds, rv[field], ind) # caches
return rv
+
+ def _read_fluid_selection(self, chunks, selector, fields, size):
+ chunks = list(chunks)
+ assert(len(chunks) == 1)
+ tags = {}
+ rv = {}
+ pyne_mesh = self.pf.pyne_mesh
+ mesh = pyne_mesh.mesh
+ for field in fields:
+ rv[field] = np.empty(size, dtype="float64")
+ from itaps import iBase
+ ve_idx_tag = mesh.getTagHandle('ve_idx')
+ ents = pyne_mesh.structured_set.getEntities(iBase.Type.region)
+ ve_idx = ve_idx_tag[ents]
+ ngrids = sum(len(chunk.objs) for chunk in chunks)
+ mylog.debug("Reading %s cells of %s fields in %s blocks",
+ size, [fname for ftype, fname in fields], ngrids)
+ for field in fields:
+ ftype, fname = field
+ ds = np.asarray(getattr(pyne_mesh, fname)[ve_idx], 'float64')
+ ind = 0
+ for chunk in chunks:
+ for g in chunk.objs:
+ ind += g.select(selector, ds, rv[field], ind) # caches
+ return rv
https://bitbucket.org/yt_analysis/yt-3.0/commits/62e9d46abd61/
Changeset: 62e9d46abd61
Branch: yt-3.0
User: scopatz
Date: 2013-10-29 02:54:24
Summary: rm'd some commented and extraneous code
Affected #: 2 files
diff -r 1773e02166caa9bf1042c029325bc761cc0a60d9 -r 62e9d46abd61ee4ff02a8a33f6b9b8bf34da7cd9 yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -152,16 +152,6 @@
vind, coords, self)]
def _detect_fields(self):
- # Currently, I don't know a better way to do this. This code, for
- # example, does not work:
- #self.field_list = self.pyne_mesh.mesh.getAllTags(
- # self.pyne_mesh.mesh.rootSet)
- # So we have to look at each entity.
- #tags = set([])
- #for ent in self.pyne_mesh.mesh.rootSet:
- # for tag in self.pyne_mesh.mesh.getAllTags(ent):
- # tags.add(tag.name)
- #self.field_list = list(tags)
self.field_list = self.pyne_mesh.tags.keys()
def _count_grids(self):
diff -r 1773e02166caa9bf1042c029325bc761cc0a60d9 -r 62e9d46abd61ee4ff02a8a33f6b9b8bf34da7cd9 yt/frontends/moab/io.py
--- a/yt/frontends/moab/io.py
+++ b/yt/frontends/moab/io.py
@@ -55,31 +55,6 @@
assert(len(chunks) == 1)
tags = {}
rv = {}
- mesh = self.pf.pyne_mesh.mesh
- for field in fields:
- ftype, fname = field
- rv[field] = np.empty(size, dtype="float64")
- tags[field] = mesh.getTagHandle(fname)
- from itaps import iBase
- ents = self.pf.pyne_mesh.structured_set.getEntities(
- iBase.Type.region)
- ngrids = sum(len(chunk.objs) for chunk in chunks)
- mylog.debug("Reading %s cells of %s fields in %s blocks",
- size, [fname for ftype, fname in fields], ngrids)
- for field in fields:
- ftype, fname = field
- ds = tags[field][ents]
- ind = 0
- for chunk in chunks:
- for g in chunk.objs:
- ind += g.select(selector, ds, rv[field], ind) # caches
- return rv
-
- def _read_fluid_selection(self, chunks, selector, fields, size):
- chunks = list(chunks)
- assert(len(chunks) == 1)
- tags = {}
- rv = {}
pyne_mesh = self.pf.pyne_mesh
mesh = pyne_mesh.mesh
for field in fields:
https://bitbucket.org/yt_analysis/yt-3.0/commits/75ffc619a1d7/
Changeset: 75ffc619a1d7
Branch: yt-3.0
User: scopatz
Date: 2013-10-29 03:31:50
Summary: further improvements to make field access faster
Affected #: 2 files
diff -r 62e9d46abd61ee4ff02a8a33f6b9b8bf34da7cd9 -r 75ffc619a1d7bee7cbfbe795e62107e4485e9a6f yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -141,9 +141,9 @@
def _initialize_mesh(self):
from itaps import iBase, iMesh
- ent = self.pyne_mesh.structured_set.getEntities(iBase.Type.vertex)
- coords = self.pyne_mesh.mesh.getVtxCoords(ent).astype("float64")
- vind = self.pyne_mesh.structured_set.getAdjEntIndices(
+ ents = self.pyne_mesh.mesh.rootSet.getEntities(iBase.Type.vertex)
+ coords = self.pyne_mesh.mesh.getVtxCoords(ents).astype("float64")
+ vind = self.pyne_mesh.mesh.rootSet.getAdjEntIndices(
iBase.Type.region, iMesh.Topology.hexahedron,
iBase.Type.vertex)[1].indices.data.astype("int64")
# Divide by float so it throws an error if it's not 8
@@ -192,8 +192,8 @@
def _parse_parameter_file(self):
from itaps import iBase
- ent = self.pyne_mesh.structured_set.getEntities(iBase.Type.vertex)
- coords = self.pyne_mesh.mesh.getVtxCoords(ent)
+ ents = self.pyne_mesh.mesh.rootSet.getEntities(iBase.Type.vertex)
+ coords = self.pyne_mesh.mesh.getVtxCoords(ents)
self.domain_left_edge = coords[0]
self.domain_right_edge = coords[-1]
self.domain_dimensions = self.domain_right_edge - self.domain_left_edge
diff -r 62e9d46abd61ee4ff02a8a33f6b9b8bf34da7cd9 -r 75ffc619a1d7bee7cbfbe795e62107e4485e9a6f yt/frontends/moab/io.py
--- a/yt/frontends/moab/io.py
+++ b/yt/frontends/moab/io.py
@@ -59,16 +59,12 @@
mesh = pyne_mesh.mesh
for field in fields:
rv[field] = np.empty(size, dtype="float64")
- from itaps import iBase
- ve_idx_tag = mesh.getTagHandle('ve_idx')
- ents = pyne_mesh.structured_set.getEntities(iBase.Type.region)
- ve_idx = ve_idx_tag[ents]
ngrids = sum(len(chunk.objs) for chunk in chunks)
mylog.debug("Reading %s cells of %s fields in %s blocks",
size, [fname for ftype, fname in fields], ngrids)
for field in fields:
ftype, fname = field
- ds = np.asarray(getattr(pyne_mesh, fname)[ve_idx], 'float64')
+ ds = np.asarray(getattr(pyne_mesh, fname)[:], 'float64')
ind = 0
for chunk in chunks:
for g in chunk.objs:
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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