[Yt-svn] yt: * Initial import of sketch of direct Grid Data Format reader
hg at spacepope.org
hg at spacepope.org
Wed Sep 15 09:18:52 PDT 2010
hg Repository: yt
details: yt/rev/2b532c6e0153
changeset: 3400:2b532c6e0153
user: Matthew Turk <matthewturk at gmail.com>
date:
Wed Sep 15 09:18:39 2010 -0700
description:
* Initial import of sketch of direct Grid Data Format reader
* Added option flag variables for MPL compilation in install_script.sh
diffstat:
doc/install_script.sh | 31 +++++-
yt/frontends/gdf/api.py | 42 ++++++++
yt/frontends/gdf/data_structures.py | 205 +++++++++++++++++++++++++++++++++++++++++
yt/frontends/gdf/definitions.py | 25 +++++
yt/frontends/gdf/fields.py | 113 ++++++++++++++++++++++
yt/frontends/gdf/io.py | 68 +++++++++++++
yt/frontends/gdf/setup.py | 12 ++
7 files changed, 494 insertions(+), 2 deletions(-)
diffs (truncated from 552 to 300 lines):
diff -r d448849e70a4 -r 2b532c6e0153 doc/install_script.sh
--- a/doc/install_script.sh Mon Sep 13 21:29:07 2010 -0700
+++ b/doc/install_script.sh Wed Sep 15 09:18:39 2010 -0700
@@ -41,6 +41,11 @@
# If you've got YT some other place, set this to point to it.
YT_DIR=""
+# If you need to pass anything to matplotlib, do so here:
+#MPL_SUPP_LDFLAGS=""
+#MPL_SUPP_CCFLAGS=""
+#MPL_SUPP_CXXFLAGS=""
+
#------------------------------------------------------------------------------#
# #
# Okay, the script starts here. Feel free to play with it, but hopefully #
@@ -100,7 +105,7 @@
echo "Looks like you're on Abe."
echo "We're going to have to set some supplemental environment"
echo "variables to get this to work..."
- MPL_SUPP_LDFLAGS="-L${DEST_DIR}/lib -L${DEST_DIR}/lib64 -L/usr/local/lib64 -L/usr/local/lib"
+ MPL_SUPP_LDFLAGS="${MPL_SUPP_LDFLAGS} -L${DEST_DIR}/lib -L${DEST_DIR}/lib64 -L/usr/local/lib64 -L/usr/local/lib"
fi
if [ "${MYHOST##steele}" != "${MYHOST}" ]
then
@@ -353,11 +358,30 @@
if [ -n "${MPL_SUPP_LDFLAGS}" ]
then
+ OLD_LDFLAGS=${LDFLAGS}
export LDFLAGS="${MPL_SUPP_LDFLAGS}"
echo "Setting LDFLAGS ${LDFLAGS}"
fi
+if [ -n "${MPL_SUPP_CXXFLAGS}" ]
+then
+ OLD_CXXFLAGS=${CXXFLAGS}
+ export CXXFLAGS="${MPL_SUPP_CXXFLAGS}"
+ echo "Setting CXXFLAGS ${CXXFLAGS}"
+fi
+if [ -n "${MPL_SUPP_CCFLAGS}" ]
+then
+ OLD_CCFLAGS=${CCFLAGS}
+ export CCFLAGS="${MPL_SUPP_CCFLAGS}"
+ echo "Setting CCFLAGS ${CCFLAGS}"
+fi
do_setup_py matplotlib-0.99.3
-unset LDFLAGS
+if [-n "${OLD_LDFLAGS}" ]
+then
+ export LDFLAG=${OLD_LDFLAGS}
+fi
+[-n "${OLD_LDFLAGS}" ] && export LDFLAGS=${OLD_LDFLAGS}
+[-n "${OLD_CXXFLAGS}" ] && export CXXFLAGS=${OLD_CXXFLAGS}
+[-n "${OLD_CCFLAGS}" ] && export CCFLAGS=${OLD_CCFLAGS}
do_setup_py ipython-0.10
do_setup_py h5py-1.2.0
@@ -417,3 +441,6 @@
echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
echo
echo "========================================================================"
+echo
+echo "Oh, look at me, still talking when there's science to do!"
+echo "Good luck, and email the user list if you run into any problems."
diff -r d448849e70a4 -r 2b532c6e0153 yt/frontends/gdf/api.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/yt/frontends/gdf/api.py Wed Sep 15 09:18:39 2010 -0700
@@ -0,0 +1,42 @@
+"""
+API for yt.frontends.chombo
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: UCSD
+Author: J.S. Oishi <jsoishi at gmail.com>
+Affiliation: KIPAC/SLAC/Stanford
+Author: Britton Smith <brittonsmith at gmail.com>
+Affiliation: MSU
+Homepage: http://yt.Chombotools.org/
+License:
+ Copyright (C) 2010 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+from .data_structures import \
+ ChomboGrid, \
+ ChomboHierarchy, \
+ ChomboStaticOutput
+
+from .fields import \
+ ChomboFieldContainer, \
+ ChomboFieldInfo, \
+ add_chombo_field
+
+from .io import \
+ IOHandlerChomboHDF5
diff -r d448849e70a4 -r 2b532c6e0153 yt/frontends/gdf/data_structures.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/yt/frontends/gdf/data_structures.py Wed Sep 15 09:18:39 2010 -0700
@@ -0,0 +1,205 @@
+"""
+Data structures for Chombo.
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Author: J. S. Oishi <jsoishi at gmail.com>
+Affiliation: KIPAC/SLAC/Stanford
+Homepage: http://yt.enzotools.org/
+License:
+ Copyright (C) 2008-2010 Matthew Turk, J. S. Oishi. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from yt.funcs import *
+from yt.data_objects.grid_patch import \
+ AMRGridPatch
+from yt.data_objects.hierarchy import \
+ AMRHierarchy
+from yt.data_objects.static_output import \
+ StaticOutput
+
+from .fields import GDFFieldContainer
+
+class GDFGrid(AMRGridPatch):
+ _id_offset = 0
+ def __init__(self, id, hierarchy, level, start, dimensions):
+ AMRGridPatch.__init__(self, id, filename = hierarchy.hierarchy_filename,
+ hierarchy = hierarchy)
+ self.Parent = []
+ self.Children = []
+ self.Level = level
+ self.start_index = start.copy()
+ self.stop_index = self.start_index + dimensions
+ self.ActiveDimensions = dimensions.copy()
+
+ def _setup_dx(self):
+ # So first we figure out what the index is. We don't assume
+ # that dx=dy=dz , at least here. We probably do elsewhere.
+ id = self.id - self._id_offset
+ if len(self.Parent) > 0:
+ self.dds = self.Parent[0].dds / self.pf.refine_by
+ else:
+ LE, RE = self.hierarchy.grid_left_edge[id,:], \
+ self.hierarchy.grid_right_edge[id,:]
+ self.dds = na.array((RE-LE)/self.ActiveDimensions)
+ if self.pf.dimensionality < 2: self.dds[1] = 1.0
+ if self.pf.dimensionality < 3: self.dds[2] = 1.0
+ self.data['dx'], self.data['dy'], self.data['dz'] = self.dds
+
+class GDFHierarchy(AMRHierarchy):
+
+ grid = GDFGrid
+
+ def __init__(self, pf, data_style='grid_data_format'):
+ self.parameter_file = weakref.proxy(pf)
+ # for now, the hierarchy file is the parameter file!
+ self.hierarchy_filename = self.parameter_file.parameter_filename
+ self.directory = os.path.dirname(self.hierarchy_filename)
+ self._fhandle = h5py.File(self.hierarchy_filename)
+ AMRHierarchy.__init__(self,pf,data_style)
+
+ self._fhandle.close()
+
+ def _initialize_data_storage(self):
+ pass
+
+ def _detect_fields(self):
+ ncomp = int(self._fhandle['/'].attrs['num_components'])
+ self.field_list = [c[1] for c in self._fhandle['/'].attrs.listitems()[-ncomp:]]
+
+ def _setup_classes(self):
+ dd = self._get_data_reader_dict()
+ AMRHierarchy._setup_classes(self, dd)
+ self.object_types.sort()
+
+ def _count_grids(self):
+ self.num_grids = 0
+ for lev in self._levels:
+ self.num_grids += self._fhandle[lev]['Processors'].len()
+
+ def _parse_hierarchy(self):
+ f = self._fhandle # shortcut
+
+ # this relies on the first Group in the H5 file being
+ # 'Chombo_global'
+ levels = f.listnames()[1:]
+ self.grids = []
+ i = 0
+ for lev in levels:
+ level_number = int(re.match('level_(\d+)',lev).groups()[0])
+ boxes = f[lev]['boxes'].value
+ dx = f[lev].attrs['dx']
+ for level_id, box in enumerate(boxes):
+ si = na.array([box['lo_%s' % ax] for ax in 'ijk'])
+ ei = na.array([box['hi_%s' % ax] for ax in 'ijk'])
+ pg = self.grid(len(self.grids),self,level=level_number,
+ start = si, stop = ei)
+ self.grids.append(pg)
+ self.grids[-1]._level_id = level_id
+ self.grid_left_edge[i] = dx*si.astype(self.float_type)
+ self.grid_right_edge[i] = dx*(ei.astype(self.float_type) + 1)
+ self.grid_particle_count[i] = 0
+ self.grid_dimensions[i] = ei - si + 1
+ i += 1
+ self.grids = na.array(self.grids, dtype='object')
+
+ def _populate_grid_objects(self):
+ for g in self.grids:
+ g._prepare_grid()
+ g._setup_dx()
+
+ for g in self.grids:
+ g.Children = self._get_grid_children(g)
+ for g1 in g.Children:
+ g1.Parent.append(g)
+ self.max_level = self.grid_levels.max()
+
+ def _setup_unknown_fields(self):
+ pass
+
+ def _setup_derived_fields(self):
+ self.derived_field_list = []
+
+ def _get_grid_children(self, grid):
+ mask = na.zeros(self.num_grids, dtype='bool')
+ grids, grid_ind = self.get_box_grids(grid.LeftEdge, grid.RightEdge)
+ mask[grid_ind] = True
+ return [g for g in self.grids[mask] if g.Level == grid.Level + 1]
+
+class GDFStaticOutput(StaticOutput):
+ _hierarchy_class = GDFHierarchy
+ _fieldinfo_class = GDFFieldContainer
+
+ def __init__(self, filename, data_style='grid_data_format',
+ storage_filename = None):
+ StaticOutput.__init__(self, filename, data_style)
+ self._handle = h5py.File(self.filename, "r")
+ self.storage_filename = storage_filename
+ self.field_info = self._fieldinfo_class()
+ self._handle.close()
+ del self._handle
+
+ def _set_units(self):
+ """
+ Generates the conversion to various physical _units based on the parameter file
+ """
+ self.units = {}
+ self.time_units = {}
+ if len(self.parameters) == 0:
+ self._parse_parameter_file()
+ self.time_units['1'] = 1
+ self.units['1'] = 1.0
+ self.units['unitary'] = 1.0 / (self.domain_right_edge - self.domain_right_edge).max()
+ seconds = 1
+ self.time_units['years'] = seconds / (365*3600*24.0)
+ self.time_units['days'] = seconds / (3600*24.0)
+ # This should be improved.
+ for field_name in self._handle["/field_types"]:
+ self.units[field_name] = self._handle["/%s/field_to_cgs" % field_name]
+
+ def _parse_parameter_file(self):
+ sp = self._handle["/simulation_parameters"].attrs
+ self.domain_left_edge = sp["domain_left_edge"][:]
+ self.domain_right_edge = sp["domain_right_edge"][:]
+ self.refine_by = sp["refine_by"][:]
+ self.dimensionality = sp["dimensionality"][:]
+ self.current_time = sp["current_time"][:]
+ self.unique_identifier = sp["unique_identifier"]
+ self.cosmological_simulation = sp["cosmological_simulation"]
+ if sp["num_ghost_zones"] != 0: raise RuntimeError
+ self.field_ordering = sp["field_ordering"]
+ self.boundary_conditions = sp["boundary_conditions"][:]
+ if self.cosmological_simulation:
+ self.current_redshift = sp["current_redshift"]
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