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Allow mole fractions to be normalized if they do not sum to one #1809

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Dec 9, 2019
Merged

Allow mole fractions to be normalized if they do not sum to one #1809

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629ea74
Normalize mole fractions for simpleReactor
kspieks Dec 6, 2019
c3d6d3b
Add unit tests for initial composition handling in reactor input blocks
mliu49 Dec 7, 2019
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17 changes: 17 additions & 0 deletions rmgpy/rmg/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,6 +226,23 @@ def simple_reactor(temperature,
[not isinstance(x, list) for x in initialMoleFractions.values()]):
nSims = 1

# normalize mole fractions if not using a mole fraction range
if all([not isinstance(x, list) for x in initialMoleFractions.values()]):
total_initial_moles = sum(initialMoleFractions.values())
if total_initial_moles != 1:
logging.warning('Initial mole fractions do not sum to one; normalizing.')
logging.info('')
logging.info('Original composition:')
for spec, molfrac in initialMoleFractions.items():
logging.info('{0} = {1}'.format(spec, molfrac))
for spec in initialMoleFractions:
initialMoleFractions[spec] /= total_initial_moles
logging.info('')
logging.info('Normalized mole fractions:')
for spec, molfrac in initialMoleFractions.items():
logging.info('{0} = {1}'.format(spec, molfrac))
logging.info('')
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This is really minor, but I think it would be nice to put the blank lines before Original composition and Normalized mole fractions like before.


termination = []
if terminationConversion is not None:
for spec, conv in terminationConversion.items():
Expand Down
238 changes: 236 additions & 2 deletions rmgpy/rmg/inputTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,14 +28,15 @@
###############################################################################

import unittest
from unittest.mock import patch

import rmgpy.rmg.input as inp
from rmgpy.rmg.main import RMG


###################################################

def setUpModule(self):
def setUpModule():
"""
A method that is run before the class.
"""
Expand All @@ -46,7 +47,7 @@ def setUpModule(self):
inp.set_global_rmg(rmg)


def tearDownModule(self):
def tearDownModule():
# remove RMG object
global rmg
rmg = None
Expand Down Expand Up @@ -146,5 +147,238 @@ def test_themo_central_database(self):
self.assertEqual(rmg.thermo_central_database.client, None)


class TestInputReactors(unittest.TestCase):
"""
Contains unit tests for reactor input classes
"""

def setUp(self):
"""This method is run before every test in this class"""
# Create a mock species dictionary
# In reality, the values would be Species objects, but it doesn't matter for testing
species_dict = {
'A': 'A',
'B': 'B',
'C': 'C',
'X': 'X',
}

# Assign to global variable in the input module
inp.species_dict = species_dict

# Initialize the rmg.reaction_systems attribute
global rmg
rmg.reaction_systems = []

def tearDown(self):
"""This method is run after every test in this class"""
# Reset the global species_dict variable in the input module
inp.species_dict = {}

# Reset the rmg.reaction_systems attribute
global rmg
rmg.reaction_systems = []

def test_simple_reactor_mole_fractions(self):
"""Test that SimpleReactor mole fractions are set properly"""
inp.simple_reactor(
temperature=(1000, 'K'),
pressure=(1, 'atm'),
initialMoleFractions={
'A': 0.5,
'B': 0.3,
'C': 0.2,
},
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_mole_fractions['C'], 0.2)

@patch('rmgpy.rmg.input.logging')
def test_simple_reactor_mole_fractions_normalize_1(self, mock_logging):
"""Test that SimpleReactor mole fractions are normalized properly"""
inp.simple_reactor(
temperature=(1000, 'K'),
pressure=(1, 'atm'),
initialMoleFractions={
'A': 5,
'B': 3,
'C': 2,
},
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_mole_fractions['C'], 0.2)

mock_logging.warning.assert_called_with(
'Initial mole fractions do not sum to one; normalizing.'
)

@patch('rmgpy.rmg.input.logging')
def test_simple_reactor_mole_fractions_normalize_2(self, mock_logging):
"""Test that SimpleReactor mole fractions are normalized properly"""
inp.simple_reactor(
temperature=[(1000, 'K'), (2000, 'K')],
pressure=[(1, 'atm'), (10, 'atm')],
initialMoleFractions={
'A': 5,
'B': 3,
'C': 2,
},
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_mole_fractions['C'], 0.2)

mock_logging.warning.assert_called_with(
'Initial mole fractions do not sum to one; normalizing.'
)

def test_simple_reactor_mole_fractions_ranged(self):
"""Test that SimpleReactor ranged mole fractions are not normalized"""
inp.simple_reactor(
temperature=[(1000, 'K'), (2000, 'K')],
pressure=[(1, 'atm'), (10, 'atm')],
initialMoleFractions={
'A': [5, 8],
'B': 3,
'C': 2,
},
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], [5, 8])
self.assertEqual(reactor.initial_mole_fractions['B'], 3)
self.assertEqual(reactor.initial_mole_fractions['C'], 2)

def test_liquid_reactor_concentrations(self):
"""Test that LiquidReactor concentrations are set properly"""
inp.liquid_reactor(
temperature=(1000, 'K'),
initialConcentrations={
'A': (0.3, 'mol/L'),
'B': (0.2, 'mol/L'),
'C': (0.1, 'mol/L'),
},
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]

# Values get converted to default SI units, mol/m^3
self.assertEqual(reactor.initial_concentrations['A'], 300)
self.assertEqual(reactor.initial_concentrations['B'], 200)
self.assertEqual(reactor.initial_concentrations['C'], 100)

def test_surface_reactor_mole_fractions(self):
"""Test that SurfaceReactor mole fractions are set properly"""
inp.surface_reactor(
temperature=(1000, 'K'),
initialPressure=(1, 'atm'),
initialGasMoleFractions={
'A': 0.5,
'B': 0.3,
'C': 0.2,
},
initialSurfaceCoverages={'X': 1.0},
surfaceVolumeRatio=(1e1, 'm^-1'),
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_gas_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_gas_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_gas_mole_fractions['C'], 0.2)

@patch('rmgpy.rmg.input.logging')
def test_surface_reactor_mole_fractions_normalize_1(self, mock_logging):
"""Test that SurfaceReactor mole fractions are normalized properly"""
inp.surface_reactor(
temperature=(1000, 'K'),
initialPressure=(1, 'atm'),
initialGasMoleFractions={
'A': 5,
'B': 3,
'C': 2,
},
initialSurfaceCoverages={'X': 1.0},
surfaceVolumeRatio=(1e1, 'm^-1'),
terminationTime=(1, 's'),
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_gas_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_gas_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_gas_mole_fractions['C'], 0.2)

mock_logging.warning.assert_called_with(
'Initial gas mole fractions do not sum to one; renormalizing.'
)

def test_mb_sampled_reactor_mole_fractions(self):
"""Test that MBSampledReactor mole fractions are set properly"""
inp.mb_sampled_reactor(
temperature=(1000, 'K'),
pressure=(1, 'atm'),
initialMoleFractions={
'A': 0.5,
'B': 0.3,
'C': 0.2,
},
mbsamplingRate=3500,
terminationTime=(1, 's'),
constantSpecies=['B', 'C'],
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_mole_fractions['C'], 0.2)

@patch('rmgpy.rmg.input.logging')
def test_mb_sampled_reactor_mole_fractions_normalize_1(self, mock_logging):
"""Test that MBSampledReactor mole fractions are normalized properly"""
inp.mb_sampled_reactor(
temperature=(1000, 'K'),
pressure=(1, 'atm'),
initialMoleFractions={
'A': 5,
'B': 3,
'C': 2,
},
mbsamplingRate=3500,
terminationTime=(1, 's'),
constantSpecies=['B', 'C'],
)

global rmg
reactor = rmg.reaction_systems[0]
self.assertEqual(reactor.initial_mole_fractions['A'], 0.5)
self.assertEqual(reactor.initial_mole_fractions['B'], 0.3)
self.assertEqual(reactor.initial_mole_fractions['C'], 0.2)

mock_logging.warning.assert_called_with(
'Initial mole fractions do not sum to one; normalizing.'
)


if __name__ == '__main__':
unittest.main()