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[Input] Add test of mechanism validation when using ck2yaml

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This commit is contained in:
Ray Speth
2020-06-18 12:03:45 -04:00
parent f8e80a08d1
commit 79a41633f6
3 changed files with 92 additions and 33 deletions
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77
interfaces/cython/cantera/ck2yaml.py
View File

@@ -61,6 +61,14 @@ except ImportError:
BlockMap = yaml.comments.CommentedMap
logger = logging.getLogger(__name__)
loghandler = logging.StreamHandler(sys.stdout)
logformatter = logging.Formatter('%(message)s')
loghandler.setFormatter(logformatter)
logger.handlers.clear()
logger.addHandler(loghandler)
logger.setLevel(logging.INFO)
def FlowMap(*args, **kwargs):
m = yaml.comments.CommentedMap(*args, **kwargs)
m.fa.set_flow_style()
@@ -757,7 +765,7 @@ class Parser:
if self.warning_as_error:
raise InputError(message)
else:
logging.warning(message)
logger.warning(message)
@staticmethod
def parse_composition(elements, nElements, width):
@@ -1562,7 +1570,7 @@ class Parser:
entry = []
if label not in self.species_dict:
if skip_undeclared_species:
logging.info('Skipping unexpected species "{0}" while reading thermodynamics entry.'.format(label))
logger.info('Skipping unexpected species "{0}" while reading thermodynamics entry.'.format(label))
continue
else:
# Add a new species entry
@@ -1612,7 +1620,7 @@ class Parser:
except Exception as e:
error_line_number = self.line_number - len(current) + 1
error_entry = ''.join(current).rstrip()
logging.info(
logger.info(
'Error while reading thermo entry starting on line {0}:\n'
'"""\n{1}\n"""'.format(error_line_number, error_entry)
)
@@ -1620,7 +1628,9 @@ class Parser:
if label not in self.species_dict:
if skip_undeclared_species:
logging.info('Skipping unexpected species "{0}" while reading thermodynamics entry.'.format(label))
logger.info(
'Skipping unexpected species "{0}" while'
' reading thermodynamics entry.'.format(label))
thermo = []
line, comment = readline()
current = []
@@ -1740,7 +1750,7 @@ class Parser:
reaction, revReaction = self.read_kinetics_entry(kinetics, surface)
except Exception as e:
self.line_number = line_number
logging.info('Error reading reaction starting on '
logger.info('Error reading reaction starting on '
'line {0}:\n"""\n{1}\n"""'.format(
line_number, kinetics.rstrip()))
raise
@@ -1970,9 +1980,9 @@ class Parser:
parser = Parser()
if quiet:
logging.basicConfig(level=logging.ERROR)
logger.setLevel(level=logging.ERROR)
else:
logging.basicConfig(level=logging.INFO)
logger.setLevel(level=logging.INFO)
if permissive is not None:
parser.warning_as_error = not permissive
@@ -1986,7 +1996,7 @@ class Parser:
# Read input mechanism files
parser.load_chemkin_file(input_file)
except Exception as err:
logging.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
logger.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
input_file, parser.line_number, err))
raise
else:
@@ -2001,8 +2011,8 @@ class Parser:
parser.load_chemkin_file(thermo_file,
skip_undeclared_species=bool(input_file))
except Exception:
logging.warning("\nERROR: Unable to parse '{0}' near line {1}:\n".format(
thermo_file, parser.line_number))
logger.warning("\nERROR: Unable to parse '{0}' near line {1}:\n".format(
thermo_file, parser.line_number))
raise
if transport_file:
@@ -2028,8 +2038,8 @@ class Parser:
# Read input mechanism files
parser.load_chemkin_file(surface_file, surface=True)
except Exception as err:
logging.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
surface_file, parser.line_number, err))
logger.warning("\nERROR: Unable to parse '{0}' near line {1}:\n{2}\n".format(
surface_file, parser.line_number, err))
raise
if extra_file:
@@ -2041,8 +2051,8 @@ class Parser:
# Read input mechanism files
parser.load_extra_file(extra_file)
except Exception as err:
logging.warning("\nERROR: Unable to parse '{0}':\n{1}\n".format(
extra_file, err))
logger.warning("\nERROR: Unable to parse '{0}':\n{1}\n".format(
extra_file, err))
raise
if out_name:
@@ -2054,8 +2064,9 @@ class Parser:
surface_names = parser.write_yaml(name=phase_name, out_name=out_name)
if not quiet:
nReactions = len(parser.reactions) + sum(len(surf.reactions) for surf in parser.surfaces)
print('Wrote YAML mechanism file to {0!r}.'.format(out_name))
print('Mechanism contains {0} species and {1} reactions.'.format(len(parser.species_list), nReactions))
logger.info('Wrote YAML mechanism file to {0!r}.'.format(out_name))
logger.info('Mechanism contains {0} species and {1} reactions.'.format(
len(parser.species_list), nReactions))
return parser, surface_names
def show_duplicate_reactions(self, error_message):
@@ -2071,15 +2082,15 @@ class Parser:
if len(reactions) != 2:
# Something went wrong while parsing the error message, so just
# display it as-is instead of trying to be clever.
print(error_message)
logger.warning(error_message)
return
# Give an error message that references the line numbers in the
# original input file.
equation = str(self.reactions[reactions[0]])
lines = [self.reactions[i].line_number for i in reactions]
print('Undeclared duplicate reaction {}\nfound on lines {} and {} of '
' the kinetics input file.'.format(equation, lines[0], lines[1]))
logger.warning('Undeclared duplicate reaction {}\nfound on lines {} and {} of '
'the kinetics input file.'.format(equation, lines[0], lines[1]))
def convert_mech(input_file, thermo_file=None, transport_file=None,
@@ -2108,13 +2119,13 @@ def main(argv):
repr(' '.join(args)))
except getopt.GetoptError as e:
print('ck2yaml.py: Error parsing arguments:')
print(e)
print('Run "ck2yaml.py --help" to see usage help.')
logger.error('ck2yaml.py: Error parsing arguments:')
logger.error(e)
logger.error('Run "ck2yaml.py --help" to see usage help.')
sys.exit(1)
if not options or '-h' in options or '--help' in options:
print(__doc__)
logger.info(__doc__)
sys.exit(0)
input_file = options.get('--input')
@@ -2126,14 +2137,14 @@ def main(argv):
if '--id' in options:
phase_name = options.get('--id', 'gas')
logging.warning("\nFutureWarning: "
"Option '--id=...' will be replaced by '--name=...'")
logger.warning("\nFutureWarning: "
"Option '--id=...' will be replaced by '--name=...'")
else:
phase_name = options.get('--name', 'gas')
if not input_file and not thermo_file:
print('At least one of the arguments "--input=..." or "--thermo=..."'
' must be provided.\nRun "ck2yaml.py --help" to see usage help.')
logger.error('At least one of the arguments "--input=..." or "--thermo=..."'
' must be provided.\nRun "ck2yaml.py --help" to see usage help.')
sys.exit(1)
extra_file = options.get('--extra')
@@ -2162,23 +2173,23 @@ def main(argv):
try:
import cantera as ct
except ImportError:
print('WARNING: Unable to import Cantera Python module. Output '
'mechanism has not been validated')
logger.warning('WARNING: Unable to import Cantera Python module. '
'Output mechanism has not been validated')
sys.exit(0)
try:
print('Validating mechanism...', end='')
logger.info('Validating mechanism...')
gas = ct.Solution(out_name)
for surf_name in surfaces:
phase = ct.Interface(out_name, surf_name, [gas])
print('PASSED.')
logger.info('PASSED')
except RuntimeError as e:
print('FAILED.')
logger.info('FAILED')
msg = str(e)
if 'Undeclared duplicate reactions' in msg:
parser.show_duplicate_reactions(msg)
else:
print(e)
logger.warning(e)
sys.exit(1)

33
interfaces/cython/cantera/test/test_convert.py
View File

@@ -2,6 +2,9 @@ import os
from os.path import join as pjoin
import itertools
from pathlib import Path
import logging
import io
import sys
from . import utilities
import cantera as ct
@@ -475,6 +478,36 @@ class ck2yamlTest(converterTestCommon, utilities.CanteraTest):
for key in ['foo', 'bar']:
self.assertIn(key, yml.keys())
def test_duplicate_reactions(self):
# Running a test this way instead of using the convertMech function
# tests the behavior of the ck2yaml.main function and the mechanism
# validation step.
# clear global handler created by logging.basicConfig() in ck2cti
logging.getLogger().handlers.clear()
# Replace the ck2yaml logger with our own in order to capture the output
log_stream = io.StringIO()
logger = logging.getLogger('cantera.ck2yaml')
original_handler = logger.handlers.pop()
logformatter = logging.Formatter('%(message)s')
handler = logging.StreamHandler(log_stream)
handler.setFormatter(logformatter)
logger.addHandler(handler)
with self.assertRaises(SystemExit):
ck2yaml.main([
'--input={}/undeclared-duplicate-reactions.inp'.format(self.test_data_dir),
'--thermo={}/dummy-thermo.dat'.format(self.test_data_dir)])
# Put the original logger back in place
logger.handlers.clear()
logger.addHandler(original_handler)
message = log_stream.getvalue()
for token in ('FAILED', 'lines 12 and 14', 'R1A', 'R1B'):
self.assertIn(token, message)
class CtmlConverterTest(utilities.CanteraTest):
def test_sofc(self):

15
test/data/undeclared-duplicate-reactions.inp Normal file
View File

@@ -0,0 +1,15 @@
ELEMENTS
H C
END
SPECIES
H
R1A R1B P1 R3 P3A P3B
END
REACTIONS
R3+H <=> P3A+P3B 1.0e19 0.0 5000.0
R1A+R1B <=> P1+H 1.0e19 0.0 5000.0
R1A+R1B+M <=> P1+H+M 1.0e-2 0.0 5000.0
P1+H => R1A+R1B 1.0e19 0.0 5000.0
END