[Yt-svn] commit/yt: 2 new changesets
Bitbucket
commits-noreply at bitbucket.org
Thu Mar 10 13:25:35 PST 2011
2 new changesets in yt:
http://bitbucket.org/yt_analysis/yt/changeset/8e66b2684b99/
changeset: r3809:8e66b2684b99
branch: yt
user: atmyers
date: 2011-03-10 22:01:41
summary: patch for Chombo reader. Attemps to read pluto/orion2 input files if present
affected #: 3 files (4.6 KB)
--- a/yt/frontends/chombo/data_structures.py Thu Mar 10 12:33:13 2011 -0800
+++ b/yt/frontends/chombo/data_structures.py Thu Mar 10 13:01:41 2011 -0800
@@ -24,13 +24,34 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import h5py
+import re
+import os
+import weakref
+import numpy as na
+
+from collections import \
+ defaultdict
+from string import \
+ strip, \
+ rstrip
+from stat import \
+ ST_CTIME
+
+from .definitions import \
+ pluto2enzoDict, \
+ yt2plutoFieldsDict, \
+ parameterDict \
+
from yt.funcs import *
from yt.data_objects.grid_patch import \
- AMRGridPatch
+ AMRGridPatch
from yt.data_objects.hierarchy import \
- AMRHierarchy
+ AMRHierarchy
from yt.data_objects.static_output import \
- StaticOutput
+ StaticOutput
+from yt.utilities.definitions import \
+ mpc_conversion
from .fields import ChomboFieldContainer
@@ -66,12 +87,15 @@
grid = ChomboGrid
def __init__(self,pf,data_style='chombo_hdf5'):
+ self.domain_left_edge = pf.domain_left_edge # need these to determine absolute grid locations
+ self.domain_right_edge = pf.domain_right_edge # need these to determine absolute grid locations
self.data_style = data_style
self.field_info = ChomboFieldContainer()
self.field_indexes = {}
self.parameter_file = weakref.proxy(pf)
# for now, the hierarchy file is the parameter file!
self.hierarchy_filename = self.parameter_file.parameter_filename
+ self.hierarchy = os.path.abspath(self.hierarchy_filename)
self.directory = os.path.dirname(self.hierarchy_filename)
self._fhandle = h5py.File(self.hierarchy_filename)
@@ -117,8 +141,8 @@
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_left_edge[i] = dx*si.astype(self.float_type) + self.domain_left_edge
+ self.grid_right_edge[i] = dx*(ei.astype(self.float_type)+1) + self.domain_left_edge
self.grid_particle_count[i] = 0
self.grid_dimensions[i] = ei - si + 1
i += 1
@@ -152,18 +176,13 @@
_fieldinfo_class = ChomboFieldContainer
def __init__(self, filename, data_style='chombo_hdf5',
- storage_filename = None):
+ storage_filename = None, ini_filename = None):
+ # hardcoded for now
+ self.current_time = 0.0
+ self.ini_filename = ini_filename
StaticOutput.__init__(self,filename,data_style)
self.storage_filename = storage_filename
-
self.field_info = self._fieldinfo_class()
- # hardcoded for now
- self.current_time = 0.0
- # These should be explicitly obtained from the file, but for now that
- # will wait until a reorganization of the source tree and better
- # generalization.
- self.dimensionality = 3
- self.refine_by = 2
def _set_units(self):
"""
@@ -177,11 +196,11 @@
self.conversion_factors = defaultdict(lambda: 1.0)
self.time_units['1'] = 1
self.units['1'] = 1.0
- self.units['unitary'] = 1.0 / (self["DomainRightEdge"] - self["DomainLeftEdge"]).max()
+ self.units['unitary'] = 1.0 / (self.domain_right_edge - self.domain_left_edge).max()
seconds = 1 #self["Time"]
self.time_units['years'] = seconds / (365*3600*24.0)
self.time_units['days'] = seconds / (3600*24.0)
- for key in yt2orionFieldsDict:
+ for key in yt2plutoFieldsDict:
self.conversion_factors[key] = 1.0
def _setup_nounits_units(self):
@@ -194,13 +213,79 @@
self.units[unit] = mpc_conversion[unit] / mpc_conversion["cm"]
+ def _localize(self, f, default):
+ if f is None:
+ return os.path.join(self.directory, default)
+ return f
+
def _parse_parameter_file(self):
+ """
+ Check to see whether a 'pluto.ini' or 'orion2.ini' file
+ exists in the plot file directory. If one does, attempt to parse it.
+ Otherwise, assume the left edge starts at 0 and get the right edge
+ from the hdf5 file.
+ """
+ if os.path.isfile('pluto.ini'):
+ self._parse_pluto_file('pluto.ini')
+ elif os.path.isfile('orion2.ini'):
+ self._parse_pluto_file('orion2.ini')
+ else:
+ self.unique_identifier = \
+ int(os.stat(self.parameter_filename)[ST_CTIME])
+ self.domain_left_edge = na.array([0.,0.,0.])
+ self.domain_right_edge = self.__calc_right_edge()
+
+ def _parse_pluto_file(self, ini_filename):
+ """
+ Reads in an inputs file in the 'pluto.ini' format. Probably not
+ especially robust at the moment.
+ """
+ self.fullplotdir = os.path.abspath(self.parameter_filename)
+ self.ini_filename = self._localize( \
+ self.ini_filename, ini_filename)
self.unique_identifier = \
- int(os.stat(self.parameter_filename)[ST_CTIME])
- self.domain_left_edge = na.array([0.,0.,0.])
- self.domain_right_edge = self.__calc_right_edge()
-
+ int(os.stat(self.parameter_filename)[ST_CTIME])
+ lines = open(self.ini_filename).readlines()
+ # read the file line by line, storing important parameters
+ for lineI, line in enumerate(lines):
+ try:
+ param, sep, vals = map(rstrip,line.partition(' '))
+ except ValueError:
+ mylog.error("ValueError: '%s'", line)
+ if pluto2enzoDict.has_key(param):
+ paramName = pluto2enzoDict[param]
+ t = map(parameterDict[paramName], vals.split())
+ if len(t) == 1:
+ self.parameters[paramName] = t[0]
+ else:
+ if paramName == "RefineBy":
+ self.parameters[paramName] = t[0]
+ else:
+ self.parameters[paramName] = t
+ # assumes 3D for now
+ elif param.startswith("X1-grid"):
+ t = vals.split()
+ low1 = float(t[1])
+ high1 = float(t[4])
+ N1 = int(t[2])
+ elif param.startswith("X2-grid"):
+ t = vals.split()
+ low2 = float(t[1])
+ high2 = float(t[4])
+ N2 = int(t[2])
+ elif param.startswith("X3-grid"):
+ t = vals.split()
+ low3 = float(t[1])
+ high3 = float(t[4])
+ N3 = int(t[2])
+
+ self.dimensionality = 3
+ self.domain_left_edge = na.array([low1,low2,low3])
+ self.domain_right_edge = na.array([high1,high2,high3])
+ self.domain_dimensions = na.array([N1,N2,N3])
+ self.refine_by = self.parameters["RefineBy"]
+
def __calc_right_edge(self):
fileh = h5py.File(self.parameter_filename,'r')
dx0 = fileh['/level_0'].attrs['dx']
--- a/yt/frontends/chombo/definitions.py Thu Mar 10 12:33:13 2011 -0800
+++ b/yt/frontends/chombo/definitions.py Thu Mar 10 13:01:41 2011 -0800
@@ -23,3 +23,43 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+
+parameterDict = {"CosmologyCurrentRedshift": float,
+ "CosmologyComovingBoxSize": float,
+ "CosmologyOmegaMatterNow": float,
+ "CosmologyOmegaLambdaNow": float,
+ "CosmologyHubbleConstantNow": float,
+ "CosmologyInitialRedshift": float,
+ "DualEnergyFormalismEta1": float,
+ "DualEnergyFormalismEta2": float,
+ "MetaDataString": str,
+ "HydroMethod": int,
+ "DualEnergyFormalism": int,
+ "InitialTime": float,
+ "ComovingCoordinates": int,
+ "DensityUnits": float,
+ "LengthUnits": float,
+ "LengthUnit": float,
+ "TemperatureUnits": float,
+ "TimeUnits": float,
+ "GravitationalConstant": float,
+ "Gamma": float,
+ "MultiSpecies": int,
+ "CompilerPrecision": str,
+ "CurrentTimeIdentifier": int,
+ "RefineBy": int,
+ "BoundaryConditionName": str,
+ "TopGridRank": int,
+ "TopGridDimensions": int,
+ "EOSSoundSpeed": float,
+ "EOSType": int,
+ "NumberOfParticleAttributes": int,
+ }
+
+pluto2enzoDict = {"GAMMA": "Gamma",
+ "Ref_ratio": "RefineBy"
+ }
+
+yt2plutoFieldsDict = {}
+pluto2ytFieldsDict = {}
+
--- a/yt/frontends/chombo/io.py Thu Mar 10 12:33:13 2011 -0800
+++ b/yt/frontends/chombo/io.py Thu Mar 10 13:01:41 2011 -0800
@@ -23,6 +23,9 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import h5py
+import re
+
from yt.utilities.io_handler import \
BaseIOHandler
http://bitbucket.org/yt_analysis/yt/changeset/44ef2576918c/
changeset: r3810:44ef2576918c
branch: yt
user: atmyers
date: 2011-03-10 22:18:32
summary: need to assume a dimensionality and refinement ratio if no inputs file found
affected #: 1 file (67 bytes)
--- a/yt/frontends/chombo/data_structures.py Thu Mar 10 13:01:41 2011 -0800
+++ b/yt/frontends/chombo/data_structures.py Thu Mar 10 13:18:32 2011 -0800
@@ -234,6 +234,8 @@
int(os.stat(self.parameter_filename)[ST_CTIME])
self.domain_left_edge = na.array([0.,0.,0.])
self.domain_right_edge = self.__calc_right_edge()
+ self.dimensionality = 3
+ self.refine_by = 2
def _parse_pluto_file(self, ini_filename):
"""
Repository URL: https://bitbucket.org/yt_analysis/yt/
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