[Yt-svn] yt-commit r1338 - trunk/yt/extensions
britton at wrangler.dreamhost.com
britton at wrangler.dreamhost.com
Tue Jun 16 08:59:04 PDT 2009
Author: britton
Date: Tue Jun 16 08:59:04 2009
New Revision: 1338
URL: http://yt.spacepope.org/changeset/1338
Log:
Added EnzoSimulation superclass for performing the same operation over
multiple datasets in one simulation. Also added an example sub class for
running the halo profiler in this way. I'm looking forward to seeing a more
general way to do this.
Added:
trunk/yt/extensions/EnzoSimulation.py
trunk/yt/extensions/SimulationHaloProfiler.py
Added: trunk/yt/extensions/EnzoSimulation.py
==============================================================================
--- (empty file)
+++ trunk/yt/extensions/EnzoSimulation.py Tue Jun 16 08:59:04 2009
@@ -0,0 +1,206 @@
+import yt.lagos as lagos
+import numpy as na
+
+class EnzoSimulation(object):
+ """
+ Super class for performing the same operation over all data dumps in
+ a simulation from one redshift to another.
+ """
+ def __init__(self,EnzoParameterFile,initial_time=None,final_time=None,initial_redshift=None,final_redshift=None):
+ self.EnzoParameterFile = EnzoParameterFile
+ self.enzoParameters = {}
+ self.redshiftOutputs = []
+ self.timeOutputs = []
+ self.allOutputs = []
+ self.InitialTime = initial_time
+ self.FinalTime = final_time
+ self.InitialRedshift = initial_redshift
+ self.FinalRedshift = final_redshift
+
+ # Set some parameter defaults.
+ self._SetParameterDefaults()
+
+ # Read parameters.
+ self._ReadEnzoParameterFile()
+
+ # Check for sufficient starting/ending parameters.
+ if self.InitialTime is None and self.InitialRedshift is None:
+ if self.enzoParameters['ComovingCoordinates'] and \
+ self.enzoParameters.has_key('CosmologyInitialRedshift'):
+ self.InitialRedshift = self.enzoParameters['CosmologyInitialRedshift']
+ elif self.enzoParameters.has_key('InitialTime'):
+ self.InitialTime = self.enzoParameters['InitialTime']
+ else:
+ mylog.error("Couldn't find parameter for initial time or redshift from parameter file.")
+ return None
+ if self.FinalTime is None and self.FinalRedshift is None:
+ if self.enzoParameters['ComovingCoordinates'] and \
+ self.enzoParameters.has_key('CosmologyFinalRedshift'):
+ self.FinalRedshift = self.enzoParameters['CosmologyFinalRedshift']
+ elif self.enzoParameters.has_key('StopTime'):
+ self.FinalTime = self.enzoParameters['StopTime']
+ else:
+ mylog.error("Couldn't find parameter for final time or redshift from parameter file.")
+ return None
+
+ # Calculate redshifts for dt data dumps.
+ if self.enzoParameters.has_key('dtDataDump'):
+ self._CalculateTimeDumps()
+
+ # Calculate times for redshift dumps.
+ if self.enzoParameters['ComovingCoordinates']:
+ self._CalculateRedshiftDumpTimes()
+
+ # Combine all data dumps.
+ self._CombineDataOutputs()
+
+ def _CalculateRedshiftDumpTimes(self):
+ "Calculates time from redshift of redshift dumps."
+
+ ec = lagos.EnzoCosmology(HubbleConstantNow = \
+ (100.0 * self.enzoParameters['CosmologyHubbleConstantNow']),
+ OmegaMatterNow = self.enzoParameters['CosmologyOmegaMatterNow'],
+ OmegaLambdaNow = self.enzoParameters['CosmologyOmegaLambdaNow'],
+ InitialRedshift = self.enzoParameters['CosmologyInitialRedshift'])
+
+ for output in self.redshiftOutputs:
+ output['time'] = ec.ComputeTimeFromRedshift(output['redshift']) / ec.TimeUnits
+
+ def _CalculateTimeDumps(self):
+ "Calculates time dumps and their redshifts if cosmological."
+
+ initial_time = self.InitialTime
+ final_time = self.FinalTime
+
+ if self.enzoParameters['ComovingCoordinates']:
+ ec = lagos.EnzoCosmology(HubbleConstantNow = \
+ (100.0 * self.enzoParameters['CosmologyHubbleConstantNow']),
+ OmegaMatterNow = self.enzoParameters['CosmologyOmegaMatterNow'],
+ OmegaLambdaNow = self.enzoParameters['CosmologyOmegaLambdaNow'],
+ InitialRedshift = self.enzoParameters['CosmologyInitialRedshift'])
+ if initial_time is None:
+ initial_time = ec.ComputeTimeFromRedshift(self.InitialRedshift) / ec.TimeUnits
+ if final_time is None:
+ final_time = ec.ComputeTimeFromRedshift(self.FinalRedshift) / ec.TimeUnits
+
+ index = 0
+ t_Tolerance = 1e-3
+ current_time = initial_time
+ while ((current_time <= final_time) and
+ (na.fabs(current_time - final_time) > t_Tolerance)):
+ filename = "%s/%s%04d/%s%04d" % (self.enzoParameters['GlobalDir'],
+ self.enzoParameters['DataDumpDir'],index,
+ self.enzoParameters['DataDumpName'],index)
+
+ self.timeOutputs.append({'index':index,'filename':filename,'time':current_time})
+ if self.enzoParameters['ComovingCoordinates']:
+ t = ec.InitialTime + (self.enzoParameters['dtDataDump'] * ec.TimeUnits * index)
+ self.timeOutputs[-1]['redshift'] = ec.ComputeRedshiftFromTime(t)
+
+ current_time += self.enzoParameters['dtDataDump']
+ index += 1
+
+ def _CombineDataOutputs(self):
+ "Combines redshift and time data into one sorted list."
+ self.allOutputs = self.redshiftOutputs + self.timeOutputs
+ self.allOutputs.sort(reverse=True,key=lambda obj:obj['redshift'])
+ start_index = None
+ end_index = None
+ for q in range(len(self.allOutputs)):
+ del self.allOutputs[q]['index']
+ # set beginning and end indices from redshift limits
+ if start_index is None:
+ if self.InitialRedshift is not None and \
+ self.allOutputs[q]['redshift'] <= self.InitialRedshift:
+ start_index = q
+ else:
+ self.allOutputs[q]['time'] >= self.InitialTime
+ if end_index is None:
+ if self.FinalRedshift is not None:
+ if self.allOutputs[q]['redshift'] < self.FinalRedshift:
+ end_index = q - 1
+ elif self.allOutputs[q]['redshift'] == self.FinalRedshift:
+ end_index = q
+ else:
+ if self.allOutputs[q]['time'] > self.FinalTime:
+ end_index = q - 1
+ elif self.allOutputs[q]['time'] == self.FinalTime:
+ end_index = q
+
+# if (q == 0):
+# self.allOutputs[q]['previous'] = None
+# self.allOutputs[q]['next'] = self.allOutputs[q+1]
+# elif (q == len(self.allOutputs) - 1):
+# self.allOutputs[q]['previous'] = self.allOutputs[q-1]
+# self.allOutputs[q]['next'] = None
+# else:
+# self.allOutputs[q]['previous'] = self.allOutputs[q-1]
+# self.allOutputs[q]['next'] = self.allOutputs[q+1]
+
+ del self.redshiftOutputs
+ del self.timeOutputs
+ if end_index is None:
+ end_index = len(self.allOutputs)-1
+
+ self.allOutputs = self.allOutputs[start_index:end_index+1]
+
+ def _ReadEnzoParameterFile(self):
+ "Reads an Enzo parameter file looking for cosmology and output parameters."
+ lines = open(self.EnzoParameterFile).readlines()
+ for line in lines:
+ if line.find("#") >= 0: # Keep the commented lines
+ line=line[:line.find("#")]
+ line=line.strip()
+ if len(line) < 2:
+ continue
+ try:
+ param, vals = map(str,line.split("="))
+ param = param.strip()
+ vals = vals.strip()
+ except ValueError:
+ if self.verbose: mylog.error("Skipping line: %s" % line)
+ continue
+ if EnzoParameterDict.has_key(param):
+ t = map(EnzoParameterDict[param], vals.split())
+ if len(t) == 1:
+ self.enzoParameters[param] = t[0]
+ else:
+ self.enzoParameters[param] = t
+ elif param.startswith("CosmologyOutputRedshift["):
+ index = param[param.find("[")+1:param.find("]")]
+ self.redshiftOutputs.append({'index':int(index),
+ 'redshift':float(vals)})
+
+ # Add filenames to redshift outputs.
+ for output in self.redshiftOutputs:
+ output["filename"] = "%s/%s%04d/%s%04d" % (self.enzoParameters['GlobalDir'],
+ self.enzoParameters['RedshiftDumpDir'],output['index'],
+ self.enzoParameters['RedshiftDumpName'],output['index'])
+
+ def _SetParameterDefaults(self):
+ "Set some default parameters to avoid problems if they are not in the parameter file."
+ self.enzoParameters['GlobalDir'] = ""
+ self.enzoParameters['RedshiftDumpName'] = "RD"
+ self.enzoParameters['RedshiftDumpDir'] = "RD"
+ self.enzoParameters['DataDumpName'] = "DD"
+ self.enzoParameters['DataDumpDir'] = "DD"
+ self.enzoParameters['ComovingCoordinates'] = 0
+
+EnzoParameterDict = {"CosmologyCurrentRedshift": float,
+ "CosmologyComovingBoxSize": float,
+ "CosmologyOmegaMatterNow": float,
+ "CosmologyOmegaLambdaNow": float,
+ "CosmologyHubbleConstantNow": float,
+ "CosmologyInitialRedshift": float,
+ "CosmologyFinalRedshift": float,
+ "ComovingCoordinates": int,
+ "InitialTime": float,
+ "StopTime": float,
+ "TopGridDimensions": float,
+ "dtDataDump": float,
+ "RedshiftDumpName": str,
+ "RedshiftDumpDir": str,
+ "DataDumpName": str,
+ "DataDumpDir": str,
+ "GlobalDir" : str}
+
Added: trunk/yt/extensions/SimulationHaloProfiler.py
==============================================================================
--- (empty file)
+++ trunk/yt/extensions/SimulationHaloProfiler.py Tue Jun 16 08:59:04 2009
@@ -0,0 +1,16 @@
+import yt.lagos as lagos
+import numpy as na
+import yt.extensions.HaloProfiler as HP
+from EnzoSimulation import *
+
+class SimulationHaloProfiler(EnzoSimulation):
+ def __init__(self,EnzoParameterFile,HaloProfilerParameterFile,**kwargs):
+ EnzoSimulation.__init__(self,EnzoParameterFile,**kwargs)
+ self.HaloProfilerParameterFile = HaloProfilerParameterFile
+
+ def runHaloProfiler(self):
+ for output in self.allOutputs:
+ halo_profiler = HP.HaloProfiler(output['filename'],self.HaloProfilerParameterFile)
+ halo_profiler.makeProfiles()
+ #halo_profiler.makeProjections()
+ del halo_profiler
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