Adding method for class generation from a SON file. Adding options to run for... (95dede16) · Commits · Shriwise, Patrick / PyGriffin

pygriffin/pygriffin.py

+79 −5

Original line number	Diff line number	Diff line
		from collections import Iterable
		from numbers import Integral
		import os
		from pathlib import Path
		import subprocess
		from collections import Iterable
		import warnings

		from . import checkvalue as cv
		@@ -25,7 +26,12 @@ class PyGriffin:
		self.mesh = mesh
		self.n_procs = n_procs

		def run(self, input=None, mesh=None, cwd=None, other_args=None, color=True):
		def run(self, input=None,
		mesh=None,
		cwd=None,
		other_args=None,
		color=True,
		logfile=None):
		"""
		Execute Griffin

		@@ -42,6 +48,8 @@ class PyGriffin:
		color : bool
		Removes posix terminal color characters from Griffin output
		if False
		logfile : str or pathlib.Path object
		Write output to screen if True. Write to file if false.

		Returns
		-------
		@@ -90,8 +98,13 @@ class PyGriffin:
		if not color:
		cmd += ['--color', 'off']

		p = subprocess.Popen(cmd, universal_newlines=True, cwd=str(cwd))

		if logfile is not None:
		with open(logfile, 'w') as OUT:
		p = subprocess.Popen(cmd,
		universal_newlines=True,
		cwd=str(cwd),
		stdout=OUT,
		stderr=OUT)
		return p.wait()

		def process_xs(self, overwrite=False, particle='neutron', cwd=None):
		@@ -132,7 +145,6 @@ class PyGriffin:
		# run isoxml executable on the current xs file
		cmd = [str(self.config.isoxml_exec), p_flag, str(self.xs)]
		p = subprocess.Popen(cmd, universal_newlines=True, cwd=str(cwd))

		p.wait()

		# construct the name of the new xs file and return it
		@@ -211,4 +223,66 @@ class PyGriffin:
		cv.check_greater_than('Griffin processes', procs, 0)
		self._n_procs = procs

		@classmethod
		def from_son(cls, son_input, sonvalidxml_path=None):
		# generate an XML from the SON input
		import subprocess
		schema = Path(__file__).parent / "../etc/pygriffin.sch"
		# if explicit path to the sonvalidxml executable is
		# provided, assume it is in the environment's PATH
		if sonvalidxml_path is None:
		sonvalidxml_path = 'sonvalidxml'
		cmd = ' '.join([sonvalidxml_path, str(schema), son_input])
		xml_file = subprocess.check_output(cmd, shell=True)

		# generate a Python object from the XML file
		from wasppy import xml2obj
		xml_obj = xml2obj.xml2obj(xml_file)

		def _wasp_attr_to_str(attr):
		return str(attr.value).replace('"','')

		griffin_block = xml_obj.griffin

		if griffin_block is None:
		raise RuntimeError("No griffin block is present in the iput file")

		mesh = None
		if griffin_block.mesh_input is not None:
		mesh = _wasp_attr_to_str(griffin_block.mesh_input)
		elif griffin_block.mesh_exodus is not None:
		mesh = _wasp_attr_to_str(griffin_block.mesh_exodus)
		elif griffin_block.shift_input is not None:
		raise NotImplementedError("Shift input is not yet supported")
		else:
		raise RuntimeError("No mesh input provided in the SON file")

		options_file = None
		if griffin_block.griffin_input is not None:
		options_file = _wasp_attr_to_str(griffin_block.griffin_input)
		elif griffin_block.griffin_solver_options is not None:
		raise NotImplementedError("Support for option specification "
		"is not yet supported")
		else:
		raise RuntimeError("No griffin options provided in the SON file")

		# create a new PyGriffin class instance
		pyg = cls(input=options_file, mesh=mesh)

		if griffin_block.isoxml is not None:
		pyg.xs = _wasp_attr_to_str(griffin_block.isoxml)
		if griffin_block.macro_isotxs:
		pyg.xs = _wasp_attr_to_str(griffin_block.macro_isotxs)
		pyg.xs = pyg.process_xs()
		else:
		raise RuntimeError("No cross section data provided in the SON file")

		if griffin_block.num_cpu_max_griffin is not None:
		if pyg.mpi_enabled:
		pyg.n_procs = _wasp_attr_to_str(griffin_block.num_cpu_max_griffin)
		else:
		warnings.warn("Griffin executable was not compiled with MPI enabled. "
		"Setting number of cpus/procs to 1.")
		pyg.n_procs = 1

		return pyg