def test_arr_A():
"""Test when parameter A (for computing
Arrrhenius reaction rate coeff)
is missing from xml file"""
with pytest.raises(ValueError):
xml_filename = os.path.join(DATA_DIRECTORY, "A_arr.xml")
parser = Parser.ReactionParser(xml_filename)
def test_graphics_dict():
"""Test if No# of Reactions consistent with No# of Specie Lists"""
xml_filename = os.path.join(DATA_DIRECTORY, "rxnset_long.xml")
parser = Parser.ReactionParser(xml_filename)
concentration = ({
'H': 1,
'H2': 1,
'H2O': 0,
'H2O2': 1,
'HO2': 1,
'O': 1,
"O2": 1,
"OH": 1
})
temperature = 1000
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs,
temperature, concentration)
target = "final/results"
graphics_dict = {
'node_color': "hello",
'rate': False,
'arrow_size': False,
'arrow_color': True,
'init_con': True,
'prod_con': True
}
obj = visualizer.ReactionPathDiagram(target,
rxnsys,
integrate=False,
time=None,
cluster=False)
obj.fit()
with pytest.raises(ValueError):
obj.connect(graphics_dict, size=5, separate=False)
def test_const_k():
"""Test when k (for computing
constant reaction rate coeff)
is missing from xml file"""
with pytest.raises(ValueError):
xml_filename = os.path.join(DATA_DIRECTORY, "k_const.xml")
parser = Parser.ReactionParser(xml_filename)
def test_RxnParser_rate_coeffs_components():
"""Test get_rate_coeffs_components for reaction 1."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert (parser.reaction_list[0].rate_coeffs_components == {
'A': 35200000000.0,
'E': 71400.0
})
def test_rxn_sys():
"""Returns a valid reaction system"""
xml_filename = os.path.join(DATA_DIRECTORY, "rxn.xml")
parser = Parser.ReactionParser(xml_filename)
temp = 500 # "low" temperature range in NASA coeffs database
concentrations = {'H': 1, 'O2': 1, 'H2O': 1}
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
return rxnsys
def test_RxnParser_product_stoich_coeffs():
"""Test get_product_stoich_coeffs for reaction 1."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert (parser.reaction_list[0].product_stoich_coeffs == {
'H': 0,
'H2': 0,
'H2O': 0,
'O': 1,
'O2': 0,
'OH': 1
})
def test_RxnParser_species():
"""Test when reaction rate coefficient is modified
Arrhenius but R is changed by user"""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert parser.get_species() == ({
'H': None,
'O': None,
'OH': None,
'H2': None,
'H2O': None,
'O2': None
})
def test_rxn_sys_invalid_temperature():
"""Tests setting up reaction system with invalid temperatures."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns_mixed.xml")
parser = Parser.ReactionParser(xml_filename)
concentrations = {'H': 1, 'O2': 2, 'OH': 1, 'O': 4, 'H2O': 0, 'H2': 1}
temp = 0
with pytest.raises(ValueError):
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
temp = -100
with pytest.raises(ValueError):
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
def test_rxn_sys_get_reaction_rate_for_3_rxns():
"""Tests function to get reaction rate for a given system of reactions (more than 1 reaction)."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxnsys.xml")
parser = Parser.ReactionParser(xml_filename)
temp = 10
concentrations = {'H': 1, 'O2': 1, 'OH': 1, 'O': 1, 'H2O': 1, 'H2': 1}
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
# assert rxnsys.get_reaction_rate() == -10.
assert rates['H'] == -10.
assert rates['O2'] == -15.
assert rates['H2O'] == 40.
assert rates['H2'] == -20.
assert rates['O'] == -10.
assert rates['OH'] == 0.
def test_rxn_sys_rev_reaction():
"""Tests setting up reaction system with reversible reaction."""
xml_filename = os.path.join(DATA_DIRECTORY, "rev_rxn.xml")
parser = Parser.ReactionParser(xml_filename)
temp = 500 # "low" temperature range in NASA coeffs database
concentrations = {'H': 1, 'O2': 1, 'H2O': 1}
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
# expected_nasa = numpy.array([[2.50000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
# 0.00000000e+00, 2.54716270e+04, -4.60117608e-01],
# [3.38684249e+00, 3.47498246e-03, -6.35469633e-06, 6.96858127e-09,
# -2.50658847e-12, -3.02081133e+04, 2.59023285e+00],
# [3.21293640e+00, 1.12748635e-03, -5.75615047e-07, 1.31387723e-09,
# -8.76855392e-13, -1.00524902e+03, 6.03473759e+00]])
expected_nasa = {
'O2':
numpy.array([
3.28253784e+00, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10,
-2.16717794e-14, -1.08845772e+03, 5.45323129e+00
]),
'H2O':
numpy.array([
3.03399249e+00, 2.17691804e-03, -1.64072518e-07, -9.70419870e-11,
1.68200992e-14, -3.00042971e+04, 4.96677010e+00
]),
'H':
numpy.array([
2.50000001e+00, -2.30842973e-11, 1.61561948e-14, -4.73515235e-18,
4.98197357e-22, 2.54736599e+04, -4.46682914e-01
])
}
rev_rxn_obj = parser.reaction_list[0]
#assert numpy.isclose(rev_rxn_obj.NASA_poly_coefs, expected_nasa).all()
assert (numpy.isclose(rev_rxn_obj.NASA_poly_coefs_dict['H2O'],
expected_nasa['H2O'])).all()
assert (numpy.isclose(rev_rxn_obj.NASA_poly_coefs_dict['O2'],
expected_nasa['O2'])).all()
assert (numpy.isclose(rev_rxn_obj.NASA_poly_coefs_dict['H'],
expected_nasa['H'])).all()
def test_rxn_sys_get_highT_nasa_matrix():
"""Tests function to fetch NASA coefficients of appropriate T and appropriate species in reaction."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxn.xml")
parser = Parser.ReactionParser(xml_filename)
temp = 5000 # "high" temperature range in NASA coeffs database
concentrations = {'H': 1, 'O2': 1, 'H2O': 1}
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temp,
concentrations)
# Order of high T range NASA coefficients: H, H2O, O2
expected_nasa = {
'O2':
numpy.array([
3.78245636e+00, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09,
3.24372837e-12, -1.06394356e+03, 3.65767573e+00
]),
'H2O':
numpy.array([
4.19864056e+00, -2.03643410e-03, 6.52040211e-06, -5.48797062e-09,
1.77197817e-12, -3.02937267e+04, -8.49032208e-01
]),
'H':
numpy.array([
2.50000000e+00, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 2.54736599e+04, -4.46682853e-01
])
}
# expected_nasa = numpy.array([[2.50000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
# 0.00000000e+00, 2.54716270e+04, -4.60117608e-01],
# [2.67214561e+00, 3.05629289e-03, -8.73026011e-07, 1.20099639e-10,
# -6.39161787e-15, -2.98992090e+04, 6.86281681e+00],
# [3.69757819e+00, 6.13519689e-04, -1.25884199e-07, 1.77528148e-11,
# -1.13643531e-15, -1.23393018e+03, 3.18916559e+00]])
#assert numpy.isclose(rxnsys.NASA_matrix, expected_nasa).all()
assert (numpy.isclose(rxnsys.NASA_matrix['H2O'],
expected_nasa['H2O'])).all()
assert (numpy.isclose(rxnsys.NASA_matrix['O2'], expected_nasa['O2'])).all()
assert (numpy.isclose(rxnsys.NASA_matrix['H'], expected_nasa['H'])).all()
def test_RxnParser_rxn_equation():
"""Test get_rxn_equation for reaction 1."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert parser.reaction_list[0].rxn_equation == 'H + O2 =] OH + O'
def test_RxnParser_is_reversible():
"""Test get_is_reversible for reaction irreversible reaction."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert parser.reaction_list[0].is_reversible == False
def test_RxnParser_type():
"""Test get_rxn_type() for an elementary reaction."""
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
assert parser.reaction_list[0].rxn_type == 'Elementary'
def test_get_coeffs_invalid_temp_range():
"""Test when invalid temperature range inputed"""
with pytest.raises(ValueError):
xml_filename = os.path.join(DATA_DIRECTORY, "rxns.xml")
parser = Parser.ReactionParser(xml_filename)
parser.get_coeffs('H', 'invalid_range')
"""Example of irreversible reaction."""
import os
from chemkinlib.utils import Parser
from chemkinlib.reactions import ReactionSystems
from chemkinlib.config import DATA_DIRECTORY
import numpy
# USER INPUT: reaction (xml) file
xml_filename = os.path.join(DATA_DIRECTORY, "rxnset_long.xml")
parser = Parser.ReactionParser(xml_filename)
# USER INPUTS (concentrations and temperatures)
concentration = ({
'H': 1,
'H2': 1,
'H2O': 0,
'H2O2': 1,
'HO2': 1,
'O': 1,
"O2": 1,
"OH": 1
})
temperature = 1000
# Set up reaction system
rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
parser.NASA_poly_coefs, temperature,
concentration)
def test_RxnParser_file_not_found():
"""Test when xml file is nonexistent"""
with pytest.raises(IOError):
parser = Parser.ReactionParser("no_such_file")