Source code for yt.frontends.enzo.simulation_handling

EnzoSimulation class and member functions.


# Copyright (c) 2013, yt Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file COPYING.txt, distributed with this software.

import numpy as np
import glob
import os

from math import ceil

from yt.convenience import \
from yt.funcs import \
from yt.data_objects.time_series import \
    SimulationTimeSeries, DatasetSeries
from yt.units import dimensions
from yt.units.unit_registry import \
from yt.units.yt_array import \
from yt.utilities.cosmology import \
from yt.utilities.exceptions import \
    InvalidSimulationTimeSeries, \
    MissingParameter, \
    NoStoppingCondition, \
from yt.utilities.logger import ytLogger as \
from yt.utilities.parallel_tools.parallel_analysis_interface import \

[docs]class EnzoSimulation(SimulationTimeSeries): r""" Initialize an Enzo Simulation object. Upon creation, the parameter file is parsed and the time and redshift are calculated and stored in all_outputs. A time units dictionary is instantiated to allow for time outputs to be requested with physical time units. The get_time_series can be used to generate a DatasetSeries object. parameter_filename : str The simulation parameter file. find_outputs : bool If True, subdirectories within the GlobalDir directory are searched one by one for datasets. Time and redshift information are gathered by temporarily instantiating each dataset. This can be used when simulation data was created in a non-standard way, making it difficult to guess the corresponding time and redshift information. Default: False. Examples -------- >>> import yt >>> es = yt.simulation("enzo_tiny_cosmology/32Mpc_32.enzo", "Enzo") >>> es.get_time_series() >>> for ds in es: ... print(ds.current_time) """ def __init__(self, parameter_filename, find_outputs=False): self.simulation_type = "grid" self.key_parameters = ["stop_cycle"] SimulationTimeSeries.__init__(self, parameter_filename, find_outputs=find_outputs) def _set_units(self): self.unit_registry = UnitRegistry() self.unit_registry.add("code_time", 1.0, dimensions.time) self.unit_registry.add("code_length", 1.0, dimensions.length) if self.cosmological_simulation: # Instantiate EnzoCosmology object for units and time conversions. self.cosmology = \ EnzoCosmology(self.parameters['CosmologyHubbleConstantNow'], self.parameters['CosmologyOmegaMatterNow'], self.parameters['CosmologyOmegaLambdaNow'], 0.0, self.parameters['CosmologyInitialRedshift'], unit_registry=self.unit_registry) self.time_unit = self.cosmology.time_unit.in_units("s") self.unit_registry.modify("h", self.hubble_constant) # Comoving lengths for my_unit in ["m", "pc", "AU", "au"]: new_unit = "%scm" % my_unit # technically not true, but should be ok self.unit_registry.add(new_unit, self.unit_registry.lut[my_unit][0], dimensions.length, "\\rm{%s}/(1+z)" % my_unit) self.length_unit = self.quan(self.box_size, "Mpccm / h", registry=self.unit_registry) else: self.time_unit = self.quan(self.parameters["TimeUnits"], "s") self.length_unit = self.quan(self.parameters["LengthUnits"], "cm") self.box_size = self.length_unit self.domain_left_edge = self.domain_left_edge * self.length_unit self.domain_right_edge = self.domain_right_edge * self.length_unit self.unit_registry.modify("code_time", self.time_unit) self.unit_registry.modify("code_length", self.length_unit) self.unit_registry.add("unitary", float(self.box_size.in_base()), self.length_unit.units.dimensions)
[docs] def get_time_series(self, time_data=True, redshift_data=True, initial_time=None, final_time=None, initial_redshift=None, final_redshift=None, initial_cycle=None, final_cycle=None, times=None, redshifts=None, tolerance=None, parallel=True, setup_function=None): """ Instantiate a DatasetSeries object for a set of outputs. If no additional keywords given, a DatasetSeries object will be created with all potential datasets created by the simulation. Outputs can be gather by specifying a time or redshift range (or combination of time and redshift), with a specific list of times or redshifts, a range of cycle numbers (for cycle based output), or by simply searching all subdirectories within the simulation directory. time_data : bool Whether or not to include time outputs when gathering datasets for time series. Default: True. redshift_data : bool Whether or not to include redshift outputs when gathering datasets for time series. Default: True. initial_time : tuple of type (float, str) The earliest time for outputs to be included. This should be given as the value and the string representation of the units. For example, (5.0, "Gyr"). If None, the initial time of the simulation is used. This can be used in combination with either final_time or final_redshift. Default: None. final_time : tuple of type (float, str) The latest time for outputs to be included. This should be given as the value and the string representation of the units. For example, (13.7, "Gyr"). If None, the final time of the simulation is used. This can be used in combination with either initial_time or initial_redshift. Default: None. times : tuple of type (float array, str) A list of times for which outputs will be found and the units of those values. For example, ([0, 1, 2, 3], "s"). Default: None. initial_redshift : float The earliest redshift for outputs to be included. If None, the initial redshift of the simulation is used. This can be used in combination with either final_time or final_redshift. Default: None. final_redshift : float The latest redshift for outputs to be included. If None, the final redshift of the simulation is used. This can be used in combination with either initial_time or initial_redshift. Default: None. redshifts : array_like A list of redshifts for which outputs will be found. Default: None. initial_cycle : float The earliest cycle for outputs to be included. If None, the initial cycle of the simulation is used. This can only be used with final_cycle. Default: None. final_cycle : float The latest cycle for outputs to be included. If None, the final cycle of the simulation is used. This can only be used in combination with initial_cycle. Default: None. tolerance : float Used in combination with "times" or "redshifts" keywords, this is the tolerance within which outputs are accepted given the requested times or redshifts. If None, the nearest output is always taken. Default: None. parallel : bool/int If True, the generated DatasetSeries will divide the work such that a single processor works on each dataset. If an integer is supplied, the work will be divided into that number of jobs. Default: True. setup_function : callable, accepts a ds This function will be called whenever a dataset is loaded. Examples -------- >>> import yt >>> es = yt.simulation("enzo_tiny_cosmology/32Mpc_32.enzo", "Enzo") >>> es.get_time_series(initial_redshift=10, final_time=(13.7, "Gyr"), redshift_data=False) >>> for ds in es: ... print(ds.current_time) >>> es.get_time_series(redshifts=[3, 2, 1, 0]) >>> for ds in es: ... print(ds.current_time) """ if (initial_redshift is not None or \ final_redshift is not None) and \ not self.cosmological_simulation: raise InvalidSimulationTimeSeries( "An initial or final redshift has been given for a " + "noncosmological simulation.") if time_data and redshift_data: my_all_outputs = self.all_outputs elif time_data: my_all_outputs = self.all_time_outputs elif redshift_data: my_all_outputs = self.all_redshift_outputs else: raise InvalidSimulationTimeSeries('Both time_data and redshift_data are False.') if not my_all_outputs: DatasetSeries.__init__(self, outputs=[], parallel=parallel)"0 outputs loaded into time series.") return # Apply selection criteria to the set. if times is not None: my_outputs = self._get_outputs_by_key("time", times, tolerance=tolerance, outputs=my_all_outputs) elif redshifts is not None: my_outputs = self._get_outputs_by_key("redshift", redshifts, tolerance=tolerance, outputs=my_all_outputs) elif initial_cycle is not None or final_cycle is not None: if initial_cycle is None: initial_cycle = 0 else: initial_cycle = max(initial_cycle, 0) if final_cycle is None: final_cycle = self.parameters['StopCycle'] else: final_cycle = min(final_cycle, self.parameters['StopCycle']) my_outputs = my_all_outputs[int(ceil(float(initial_cycle) / self.parameters['CycleSkipDataDump'])): (final_cycle / self.parameters['CycleSkipDataDump'])+1] else: if initial_time is not None: if isinstance(initial_time, float): initial_time = self.quan(initial_time, "code_time") elif isinstance(initial_time, tuple) and len(initial_time) == 2: initial_time = self.quan(*initial_time) elif not isinstance(initial_time, YTArray): raise RuntimeError( "Error: initial_time must be given as a float or " + "tuple of (value, units).") elif initial_redshift is not None: my_initial_time = self.cosmology.t_from_z(initial_redshift) else: my_initial_time = self.initial_time if final_time is not None: if isinstance(final_time, float): final_time = self.quan(final_time, "code_time") elif isinstance(final_time, tuple) and len(final_time) == 2: final_time = self.quan(*final_time) elif not isinstance(final_time, YTArray): raise RuntimeError( "Error: final_time must be given as a float or " + "tuple of (value, units).") my_final_time = final_time.in_units("s") elif final_redshift is not None: my_final_time = self.cosmology.t_from_z(final_redshift) else: my_final_time = self.final_time my_initial_time.convert_to_units("s") my_final_time.convert_to_units("s") my_times = np.array([a['time'] for a in my_all_outputs]) my_indices = np.digitize([my_initial_time, my_final_time], my_times) if my_initial_time == my_times[my_indices[0] - 1]: my_indices[0] -= 1 my_outputs = my_all_outputs[my_indices[0]:my_indices[1]] init_outputs = [] for output in my_outputs: if os.path.exists(output['filename']): init_outputs.append(output['filename']) DatasetSeries.__init__(self, outputs=init_outputs, parallel=parallel, setup_function=setup_function)"%d outputs loaded into time series.", len(init_outputs))
def _parse_parameter_file(self): """ Parses the parameter file and establishes the various dictionaries. """ self.conversion_factors = {} redshift_outputs = [] # Let's read the file lines = open(self.parameter_filename).readlines() for line in (l.strip() for l in lines): if '#' in line: line = line[0:line.find('#')] if '//' in line: line = line[0:line.find('//')] if len(line) < 2: continue param, vals = (i.strip() for i in line.split("=", 1)) # First we try to decipher what type of value it is. vals = vals.split() # Special case approaching. if "(do" in vals: vals = vals[:1] if len(vals) == 0: pcast = str # Assume NULL output else: v = vals[0] # Figure out if it's castable to floating point: try: float(v) except ValueError: pcast = str else: if any("." in v or "e" in v for v in vals): pcast = float elif v == "inf": pcast = str else: pcast = int # Now we figure out what to do with it. if param.endswith("Units") and not param.startswith("Temperature"): dataType = param[:-5] # This one better be a float. self.conversion_factors[dataType] = float(vals[0]) if param.startswith("CosmologyOutputRedshift["): index = param[param.find("[")+1:param.find("]")] redshift_outputs.append({'index':int(index), 'redshift':float(vals[0])}) elif len(vals) == 0: vals = "" elif len(vals) == 1: vals = pcast(vals[0]) else: vals = np.array([pcast(i) for i in vals if i != "-99999"]) self.parameters[param] = vals self.refine_by = self.parameters["RefineBy"] self.dimensionality = self.parameters["TopGridRank"] if self.dimensionality > 1: self.domain_dimensions = self.parameters["TopGridDimensions"] if len(self.domain_dimensions) < 3: tmp = self.domain_dimensions.tolist() tmp.append(1) self.domain_dimensions = np.array(tmp) self.domain_left_edge = np.array(self.parameters["DomainLeftEdge"], "float64").copy() self.domain_right_edge = np.array(self.parameters["DomainRightEdge"], "float64").copy() else: self.domain_left_edge = np.array(self.parameters["DomainLeftEdge"], "float64") self.domain_right_edge = np.array(self.parameters["DomainRightEdge"], "float64") self.domain_dimensions = np.array([self.parameters["TopGridDimensions"],1,1]) if self.parameters["ComovingCoordinates"]: cosmo_attr = {'box_size': 'CosmologyComovingBoxSize', 'omega_lambda': 'CosmologyOmegaLambdaNow', 'omega_matter': 'CosmologyOmegaMatterNow', 'hubble_constant': 'CosmologyHubbleConstantNow', 'initial_redshift': 'CosmologyInitialRedshift', 'final_redshift': 'CosmologyFinalRedshift'} self.cosmological_simulation = 1 for a, v in cosmo_attr.items(): if v not in self.parameters: raise MissingParameter(self.parameter_filename, v) setattr(self, a, self.parameters[v]) else: self.cosmological_simulation = 0 self.omega_lambda = self.omega_matter = \ self.hubble_constant = 0.0 # make list of redshift outputs self.all_redshift_outputs = [] if not self.cosmological_simulation: return for output in redshift_outputs: output['filename'] = os.path.join(self.parameters['GlobalDir'], "%s%04d" % (self.parameters['RedshiftDumpDir'], output['index']), "%s%04d" % (self.parameters['RedshiftDumpName'], output['index'])) del output['index'] self.all_redshift_outputs = redshift_outputs def _calculate_time_outputs(self): """ Calculate time outputs and their redshifts if cosmological. """ self.all_time_outputs = [] if self.final_time is None or \ 'dtDataDump' not in self.parameters or \ self.parameters['dtDataDump'] <= 0.0: return [] index = 0 current_time = self.initial_time.copy() dt_datadump = self.quan(self.parameters['dtDataDump'], "code_time") while current_time <= self.final_time + dt_datadump: filename = os.path.join(self.parameters['GlobalDir'], "%s%04d" % (self.parameters['DataDumpDir'], index), "%s%04d" % (self.parameters['DataDumpName'], index)) output = {'index': index, 'filename': filename, 'time': current_time.copy()} output['time'] = min(output['time'], self.final_time) if self.cosmological_simulation: output['redshift'] = self.cosmology.z_from_t(current_time) self.all_time_outputs.append(output) if np.abs(self.final_time - current_time) / self.final_time < 1e-4: break current_time += dt_datadump index += 1 def _calculate_cycle_outputs(self): """ Calculate cycle outputs. """ mylog.warn('Calculating cycle outputs. Dataset times will be unavailable.') if self.stop_cycle is None or \ 'CycleSkipDataDump' not in self.parameters or \ self.parameters['CycleSkipDataDump'] <= 0.0: return [] self.all_time_outputs = [] index = 0 for cycle in range(0, self.stop_cycle+1, self.parameters['CycleSkipDataDump']): filename = os.path.join(self.parameters['GlobalDir'], "%s%04d" % (self.parameters['DataDumpDir'], index), "%s%04d" % (self.parameters['DataDumpName'], index)) output = {'index': index, 'filename': filename, 'cycle': cycle} self.all_time_outputs.append(output) index += 1 def _get_all_outputs(self, find_outputs=False): """ Get all potential datasets and combine into a time-sorted list. """ # Create the set of outputs from which further selection will be done. if find_outputs: self._find_outputs() elif self.parameters['dtDataDump'] > 0 and \ self.parameters['CycleSkipDataDump'] > 0: "Simulation %s has both dtDataDump and CycleSkipDataDump set.", self.parameter_filename ) " Unable to calculate datasets. " + "Attempting to search in the current directory") self._find_outputs() else: # Get all time or cycle outputs. if self.parameters['CycleSkipDataDump'] > 0: self._calculate_cycle_outputs() else: self._calculate_time_outputs() # Calculate times for redshift outputs. if self.cosmological_simulation: for output in self.all_redshift_outputs: output["time"] = self.cosmology.t_from_z(output["redshift"]) self.all_redshift_outputs.sort(key=lambda obj:obj["time"]) self.all_outputs = self.all_time_outputs + self.all_redshift_outputs if self.parameters['CycleSkipDataDump'] <= 0: self.all_outputs.sort(key=lambda obj:obj['time'].to_ndarray()) def _calculate_simulation_bounds(self): """ Figure out the starting and stopping time and redshift for the simulation. """ if 'StopCycle' in self.parameters: self.stop_cycle = self.parameters['StopCycle'] # Convert initial/final redshifts to times. if self.cosmological_simulation: self.initial_time = self.cosmology.t_from_z(self.initial_redshift) self.initial_time.units.registry = self.unit_registry self.final_time = self.cosmology.t_from_z(self.final_redshift) self.final_time.units.registry = self.unit_registry # If not a cosmology simulation, figure out the stopping criteria. else: if 'InitialTime' in self.parameters: self.initial_time = self.quan(self.parameters['InitialTime'], "code_time") else: self.initial_time = self.quan(0., "code_time") if 'StopTime' in self.parameters: self.final_time = self.quan(self.parameters['StopTime'], "code_time") else: self.final_time = None if not ('StopTime' in self.parameters or 'StopCycle' in self.parameters): raise NoStoppingCondition(self.parameter_filename) if self.final_time is None: mylog.warn( "Simulation %s has no stop time set, stopping condition " + "will be based only on cycles.", self.parameter_filename) def _set_parameter_defaults(self): """ Set some default parameters to avoid problems if they are not in the parameter file. """ self.parameters['GlobalDir'] = self.parameters['DataDumpName'] = "data" self.parameters['DataDumpDir'] = "DD" self.parameters['RedshiftDumpName'] = "RedshiftOutput" self.parameters['RedshiftDumpDir'] = "RD" self.parameters['ComovingCoordinates'] = 0 self.parameters['TopGridRank'] = 3 self.parameters['DomainLeftEdge'] = np.zeros(self.parameters['TopGridRank']) self.parameters['DomainRightEdge'] = np.ones(self.parameters['TopGridRank']) self.parameters['RefineBy'] = 2 # technically not the enzo default self.parameters['StopCycle'] = 100000 self.parameters['dtDataDump'] = 0. self.parameters['CycleSkipDataDump'] = 0. self.parameters['LengthUnits'] = 1. self.parameters['TimeUnits'] = 1. def _find_outputs(self): """ Search for directories matching the data dump keywords. If found, get dataset times py opening the ds. """ # look for time outputs. potential_time_outputs = \ glob.glob(os.path.join(self.parameters['GlobalDir'], "%s*" % self.parameters['DataDumpDir'])) self.all_time_outputs = \ self._check_for_outputs(potential_time_outputs) self.all_time_outputs.sort(key=lambda obj: obj['time']) # look for redshift outputs. potential_redshift_outputs = \ glob.glob(os.path.join(self.parameters['GlobalDir'], "%s*" % self.parameters['RedshiftDumpDir'])) self.all_redshift_outputs = \ self._check_for_outputs(potential_redshift_outputs) self.all_redshift_outputs.sort(key=lambda obj: obj['time']) self.all_outputs = self.all_time_outputs + self.all_redshift_outputs self.all_outputs.sort(key=lambda obj: obj['time']) only_on_root(, "Located %d total outputs.", len(self.all_outputs)) # manually set final time and redshift with last output if self.all_outputs: self.final_time = self.all_outputs[-1]['time'] if self.cosmological_simulation: self.final_redshift = self.all_outputs[-1]['redshift'] def _check_for_outputs(self, potential_outputs): """ Check a list of files to see if they are valid datasets. """ only_on_root(, "Checking %d potential outputs.", len(potential_outputs)) my_outputs = {} llevel = mylog.level # suppress logging as we load every dataset, unless set to debug if llevel > 10 and llevel < 40: mylog.setLevel(40) for my_storage, output in parallel_objects(potential_outputs, storage=my_outputs): if self.parameters['DataDumpDir'] in output: dir_key = self.parameters['DataDumpDir'] output_key = self.parameters['DataDumpName'] else: dir_key = self.parameters['RedshiftDumpDir'] output_key = self.parameters['RedshiftDumpName'] index = output[output.find(dir_key) + len(dir_key):] filename = os.path.join(self.parameters['GlobalDir'], "%s%s" % (dir_key, index), "%s%s" % (output_key, index)) if os.path.exists(filename): try: ds = load(filename) if ds is not None: my_storage.result = {'filename': filename, 'time': ds.current_time.in_units("s")} if ds.cosmological_simulation: my_storage.result['redshift'] = ds.current_redshift except YTOutputNotIdentified: mylog.error('Failed to load %s', filename) mylog.setLevel(llevel) my_outputs = [my_output for my_output in my_outputs.values() \ if my_output is not None] return my_outputs def _write_cosmology_outputs(self, filename, outputs, start_index, decimals=3): """ Write cosmology output parameters for a cosmology splice. """"Writing redshift output list to %s.", filename) f = open(filename, 'w') for q, output in enumerate(outputs): f.write(("CosmologyOutputRedshift[%d] = %." + str(decimals) + "f\n") % ((q + start_index), output['redshift'])) f.close()
[docs]class EnzoCosmology(Cosmology): def __init__(self, hubble_constant, omega_matter, omega_lambda, omega_curvature, initial_redshift, unit_registry = None): Cosmology.__init__(self, hubble_constant=hubble_constant, omega_matter=omega_matter, omega_lambda=omega_lambda, omega_curvature=omega_curvature, unit_registry=unit_registry) self.initial_redshift = initial_redshift self.initial_time = self.t_from_z(self.initial_redshift) # time units = 1 / sqrt(4 * pi * G rho_0 * (1 + z_i)**3), # rho_0 = (3 * Omega_m * h**2) / (8 * pi * G) self.time_unit = ((1.5 * self.omega_matter * self.hubble_constant**2 * (1 + self.initial_redshift)**3)**-0.5).in_units("s") self.time_unit.units.registry = self.unit_registry