def test_bad_reactant():
"""test that input parser correctly handles reactants not matching the species array"""
try:
reactions = chemkin('tests/test_xml/rxns_bad_reactants.xml')
except ValueError as e:
assert type(e) == ValueError
print(e)
def start(self):
global myFileString
print("start")
T = 273.15
x_init = np.array([100, 1, 1, 1]) #initial concentration
t_max = 300 #integration end time in seconds
dt = 0.01 #step size in seconds
cs = ChemSolver(chemkin('TaskD.xml'))
cs.solve(x_init, T, t_max, dt, algorithm='vode', nsteps=5000)
#time_array, conc_array, rxnrate_array = cs.get_results()
cs.save_results('SimulationData/TaskDSimulationData' + myFileString +
'.csv')
cv = ChemViz(cs)
cv.plot_time_series(
'concentration',
tmin=0,
tmax=300,
species=['a', 'b', 'c', 'd'],
outputfile='ConcentrationGraphs/TaskDConcentrationSeries' +
myFileString + '.png')
#cv.html_report('HTMLReports/TaskDHTMLReport' + myFileString + '.html')
self.iterate()
return
def test_singlereversible():
reactions = chemkin('tests/test_xml/rxns_singlereversible.xml')
x = np.array([2., 1., 0.5, 1.])
T = 1500
expect = np.array(
[2.97178272e+14, 2.97178272e+14, -2.97178272e+14, -2.97178272e+14])
assert str(reactions.reaction_rate(x, T)) == str(expect)
def test_not_implement():
"""Test that input parser correctly handles reaction types and rate coefficients that are not implemented"""
try:
reactions = chemkin('tests/test_xml/rxns_bad_not_implement.xml')
except NotImplementedError as e:
assert type(e) == NotImplementedError
print(e)
def run(myFileString):
global file_name
T = 273.15
x_init = np.array([100, 0, 1, 1]) #initial concentration
t_max = 300 #integration end time in seconds
dt = 0.1 #step size in seconds
#rxn_system = chemkin(filename)
cs = ChemSolver(chemkin(file_name))
cs.solve(x_init, T, t_max, dt, algorithm='lsoda')
#time_array, conc_array, rxnrate_array = cs.get_results()
cs.save_results('SimulationData/TaskDSimulationData' + myFileString +
'.csv')
cv = ChemViz(cs)
cv.plot_time_series(
'concentration',
tmin=0,
tmax=300,
species=['a', 'b', 'c', 'd'],
outputfile='ConcentrationGraphs/TaskDConcentrationSeries' +
myFileString + '.png')
#cv.plot_time_series('reactionrate', tmin=1.e-13, tmax=300, outputfile='TaskDReactionRateSeries' + str(number) + '.png')
#cv.html_report('HTMLReports/TaskDHTMLReport' + myFileString + '.html')
# simpleIO('cs.pkl').to_pickle(cs)
# cs2 = simpleIO('cs.pkl').read_pickle()
return
def test_reversible():
reactions = chemkin('tests/test_xml/rxns_reversible.xml')
x = np.array([2., 1., 0.5, 1., 1., 0., 0., 0.25])
T = 1500
expect = np.array([
3.77689350e+14, -3.81148508e+14, -4.18872924e+14, 6.96275658e+12,
3.07172197e+13, 3.93416746e+14, 1.66470991e+13, -2.54117388e+13
])
assert str(reactions.reaction_rate(x, T)) == str(expect)
def test_mixedreversible():
reactions = chemkin('tests/test_xml/rxnset_mixedreversible_long.xml')
x = np.array([2., 1., 0.5, 1., 1., 0., 0., 0.25])
T = 1500
expect = np.array([
-1.51420660e+13, 1.22682375e+13, -2.60415020e+13, 6.37742014e+12,
3.13025562e+13, 0.00000000e+00, 1.66470929e+13, -2.54117388e+13
])
assert str(reactions.reaction_rate(x, T)) == str(expect)
def test_singlerxnxml():
"""testing that single reaction systems are handled correctly"""
reactions = chemkin('tests/test_xml/rxns_single.xml')
expect = np.array([-1.e4, -1.e4, 1.e4, 1.e4])
assert all(
reactions.reaction_rate([1, 1, 1, 1], 1000).astype(int) ==
expect.astype(int))
return reactions
def test_dimension_error():
"""
check that inconsistencies in input params are handled correctly
"""
try:
reactions = chemkin('tests/test_xml/rxns_dimensionerror.xml')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_long():
reactions = chemkin('tests/test_xml/rxnset_long.xml')
x = np.array([2., 1., 0.5, 1., 1., 0., 0., 0.25])
T = 1500
print(reactions.reaction_rate(x, T))
expect = np.array([
-7.10942556e+12, -1.58164670e+13, 2.20952666e+13, -1.65522031e+12,
1.12504921e+13, 0.00000000e+00, 1.66470929e+13, -2.54117388e+13
])
assert str(reactions.reaction_rate(x, T)) == str(expect)
def test_invalid_reversible():
"""
test that chemkin object handles invalid reversible input as expected
"""
try:
reactions = chemkin('tests/test_xml/rxns_invalid_reversible.xml')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_solve():
chem = chemkin("tests/test_xml/rxns.xml")
y0 = np.ones(len(chem.species))
T = 300
t1 = 0.003
dt = 5e-4
cs = ChemSolver(chem).solve(y0, T, t1, dt, algorithm='lsoda')
t, y, rr = cs.get_results(return_reaction_rate=False)
assert rr is None
t, y, rr = cs.get_results()
print(y)
def test_construct_nonelementary():
"""
test that chemkin object handles non-elementary reactions as expected
"""
try:
reactions = chemkin('tests/test_xml/rxns_pseudononelementary.xml')
reactions.reaction_rate_T(np.ones(1), 1000)
except NotImplementedError as e:
assert type(e) == NotImplementedError
print(e)
def test_grid_search():
chem = chemkin("tests/test_xml/rxns.xml")
t1 = 0.003
dt = 5e-4
y0s = [np.ones(len(chem.species)) * i for i in range(1, 4)]
Ts = [300, 400]
gs = ChemSolver(chem).grid_solve(y0s, Ts, t1, dt, algorithm='lsoda')
_y1 = gs.get_grid_results()[1][300][0][1]
_y2 = ChemSolver(chem).solve(y0s[0], Ts[0], t1, dt,
algorithm='lsoda').get_results()[1]
assert str(_y1) == str(_y2)
print(_y1)
gs.save_grid_results('abc')
def test_from_xml():
"""
testing normal reaction rate calculations from xml input
"""
reactions = chemkin('tests/test_xml/rxns.xml')
expect = np.array([
-6.28889929e+06, 6.28989929e+06, 6.82761528e+06, -2.70357993e+05,
1.00000000e+03, -6.55925729e+06
])
assert all(
reactions.reaction_rate([1, 1, 1, 1, 1, 1], 1000).astype(int) ==
expect.astype(int))
return reactions
def test_IO():
chem = chemkin("tests/test_xml/rxns.xml")
y0 = np.ones(len(chem.species))
T = 300
t1 = 0.003
dt = 5e-4
cs = ChemSolver(chem).solve(y0, T, t1, dt, algorithm='lsoda')
cs.save_results('tests/test_data/test.csv')
cs.save_results('tests/test_data/test.h5')
cs1 = ChemSolver(chem).load_results('tests/test_data/test.csv')
cs2 = ChemSolver(chem).load_results('tests/test_data/test.h5')
assert str(cs.get_results()) == str(cs1.get_results())
assert str(cs1.get_results()) == str(cs2.get_results())
def test_wrong_file_name():
chem = chemkin("tests/test_xml/rxns.xml")
cs = ChemSolver(chem)
try:
cs.save_results('test.pdf')
except ValueError as e:
assert type(e) == ValueError
print(e)
try:
cs.load_results('test.pdf')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_ODE_not_solved():
chem = chemkin("tests/test_xml/rxns.xml")
cs = ChemSolver(chem)
try:
t, y, rr = cs.get_results()
except ValueError as e:
assert type(e) == ValueError
print(e)
try:
cs.save_results('tests/test_data/test.csv')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_reversible():
x_init = np.ones(8)
T = 1000
# integration end time
t_max = 5.e-13
# step size
dt = 1.e-16
cs = ChemSolver(chemkin('tests/test_xml/rxns_reversible.xml')).solve(
x_init, T, t_max, dt)
assert not cs.is_equilibrium()
t, y, rr = cs.get_results(return_reaction_rate=False)
assert rr is None
t, y, rr = cs.get_results()
assert rr is not None
print(y)
def test_simpleIO():
chem2 = chemkin("tests/test_xml/rxns_reversible.xml")
# initial concentration
x_init = np.ones(8)
T = 2000
t_final = 3.e-13
t_step = 1.e-16
cs = ChemSolver(chem2).solve(x_init, T, t_final, t_step, algorithm='lsoda')
r1 = cs.get_results()
simpleIO('tests/test_data/test.pkl').to_pickle(cs)
cs2 = simpleIO('tests/test_data/test.pkl').read_pickle()
r2 = cs2.get_results()
for i in range(len(r1)):
assert np.any(r1[i] == r2[i])
assert repr(cs.chem) == repr(cs2.chem)
import pandas
import numpy as np
from pychemkin import chemkin, ChemSolver, ChemViz, simpleIO
T = 1000
x_init = np.ones(8) #initial concentration
t_max = 5.e-13 #integration end time in seconds
dt = 1.e-16 #step size in seconds
cs = ChemSolver(chemkin('rxns_reversible.xml'))
cs.solve(x_init, T, t_max, dt, algorithm='vode', method='bdf', nsteps=500)
time_array, conc_array, rxnrate_array = cs.get_results()
df = cs.to_df()
cs.save_results('simulationdata.csv')
cv = ChemViz(cs)
cv.plot_time_series('concentration',
tmin=0,
tmax=4.5e-13,
species=['H', 'OH', 'O2', 'H2O'],
outputfile='modeldocfig1.png')
cv.plot_time_series('reactionrate',
tmin=1.e-13,
tmax=4.5e-13,
outputfile='modeldocfig2.png')
cv.plot_network([0, 1.5e-13, 3e-13],
figsize=(8, 15),
outputfile='modeldocfig3.png')
