def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise
logging.info('Reading input file "{0}"...'.format(full_path))
rmg = rmg0
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'catalystProperties': catalystProperties,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'solvation': solvation,
'adjacencyList': adjacencyList,
'quantumMechanics': quantumMechanics,
'mlEstimator': mlEstimator,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError) as e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
def testSaveOutputHTML(self): """ This example is to test if an HTML file can be generated for the provided chemkin model. """ folder = os.path.join(os.getcwd(),'rmgpy/rmg/test_data/saveOutputHTML/') chemkinPath = os.path.join(folder, 'eg6', 'chem_annotated.inp') dictionaryPath = os.path.join(folder,'eg6', 'species_dictionary.txt') # loadChemkinFile species, reactions = loadChemkinFile(chemkinPath, dictionaryPath) # convert it into a reaction model: core = ReactionModel(species, reactions) cerm = CoreEdgeReactionModel(core) out = os.path.join(folder, 'output.html') saveOutputHTML(out, cerm) self.assertTrue(os.path.isfile(out)) os.remove(out) shutil.rmtree(os.path.join(folder,'species'))
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError, e:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise e
logging.info('Reading input file "{0}"...'.format(full_path))
logging.info(f.read())
f.seek(0)# return to beginning of file
rmg = rmg0
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'adjacencyList': adjacencyList,
def readInputFile(path, rmg0):
"""
Read an RMG input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise
logging.info('Reading input file "{0}"...'.format(full_path))
logging.info(f.read())
f.seek(0)# return to beginning of file
setGlobalRMG(rmg0)
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'catalystProperties': catalystProperties,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'adjacencyList': adjacencyList,
'simpleReactor': simpleReactor,
'liquidReactor': liquidReactor,
'surfaceReactor': surfaceReactor,
'simulator': simulator,
'solvation': solvation,
'model': model,
'quantumMechanics': quantumMechanics,
'mlEstimator': mlEstimator,
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
'thermoCentralDatabase': thermoCentralDatabase
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError) as e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
