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Merge pull request #1596 from ReactionMechanismGenerator/arkane_style
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Improved coding style in Arkane
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@mliu49
mliu49 authored May 13, 2019
2 parents fe57caa + 0982f57 commit baed747
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Showing 21 changed files with 1,501 additions and 1,164 deletions.
4 changes: 4 additions & 0 deletions arkane/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
initialize imports
"""

###############################################################################
# #
# RMG - Reaction Mechanism Generator #
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303 changes: 192 additions & 111 deletions arkane/common.py
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114 changes: 61 additions & 53 deletions arkane/commonTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,21 +49,23 @@
from arkane.statmech import InputError, StatMechJob
from arkane.input import jobList


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


class CommonTest(unittest.TestCase):
"""
Contains unit tests of Arkane's common functions.
"""

def test_check_conformer_energy(self):
"""
test the check_conformer_energy function with an list of energies.
"""
v_list = [-272.2779012225, -272.2774933703, -272.2768397635, -272.2778432059, -272.278645477, -272.2789602654,
-272.2788749196, -272.278496709, -272.2779350675, -272.2777008843, -272.2777167286, -272.2780937643,
-272.2784838846, -272.2788050464, -272.2787865352, -272.2785091607, -272.2779977452, -272.2777957743,
-272.2779134906, -272.2781827547, -272.278443339, -272.2788244214, -272.2787748749]
-272.2788749196, -272.278496709, -272.2779350675, -272.2777008843, -272.2777167286, -272.2780937643,
-272.2784838846, -272.2788050464, -272.2787865352, -272.2785091607, -272.2779977452, -272.2777957743,
-272.2779134906, -272.2781827547, -272.278443339, -272.2788244214, -272.2787748749]
v_list = numpy.array(v_list, numpy.float64)
v_diff = (v_list[0] - numpy.min(v_list)) * constants.E_h * constants.Na / 1000
self.assertAlmostEqual(v_diff / 2.7805169838282797, 1, 5)
Expand All @@ -73,160 +75,163 @@ class TestArkaneJob(unittest.TestCase):
"""
Contains unit tests of the Arkane module and its interactions with other RMG modules.
"""

@classmethod
def setUp(self):
def setUp(cls):
"""A method that is run before each unit test in this class"""
arkane = Arkane()
jobList = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'methoxy.py'))
'data', 'methoxy.py'))
pdepjob = jobList[-1]
self.kineticsjob = jobList[0]
cls.kineticsjob = jobList[0]
pdepjob.activeJRotor = True
network = pdepjob.network
self.Nisom = len(network.isomers)
self.Nreac = len(network.reactants)
self.Nprod = len(network.products)
self.Npath = len(network.pathReactions)
self.PathReaction2 = network.pathReactions[2]
self.TminValue = pdepjob.Tmin.value
self.Tmaxvalue = pdepjob.Tmax.value
self.TmaxUnits = pdepjob.Tmax.units
self.TlistValue = pdepjob.Tlist.value
self.PminValue = pdepjob.Pmin.value
self.Pcount = pdepjob.Pcount
self.Tcount = pdepjob.Tcount
self.GenTlist = pdepjob.generateTemperatureList()
self.PlistValue = pdepjob.Plist.value
self.maximumGrainSizeValue = pdepjob.maximumGrainSize.value
self.method = pdepjob.method
self.rmgmode = pdepjob.rmgmode
cls.Nisom = len(network.isomers)
cls.Nreac = len(network.reactants)
cls.Nprod = len(network.products)
cls.Npath = len(network.pathReactions)
cls.PathReaction2 = network.pathReactions[2]
cls.TminValue = pdepjob.Tmin.value
cls.Tmaxvalue = pdepjob.Tmax.value
cls.TmaxUnits = pdepjob.Tmax.units
cls.TlistValue = pdepjob.Tlist.value
cls.PminValue = pdepjob.Pmin.value
cls.Pcount = pdepjob.Pcount
cls.Tcount = pdepjob.Tcount
cls.GenTlist = pdepjob.generateTemperatureList()
cls.PlistValue = pdepjob.Plist.value
cls.maximumGrainSizeValue = pdepjob.maximumGrainSize.value
cls.method = pdepjob.method
cls.rmgmode = pdepjob.rmgmode

# test Arkane's interactions with the network module
def testNisom(self):
"""
Test the number of isomers identified.
"""
self.assertEqual(self.Nisom, 2, msg=None)
self.assertEqual(self.Nisom, 2)

def testNreac(self):
"""
Test the number of reactants identified.
"""
self.assertEqual(self.Nreac, 1, msg=None)
self.assertEqual(self.Nreac, 1)

def testNprod(self):
"""
Test the number of products identified.
"""
self.assertEqual(self.Nprod, 1, msg=None)
self.assertEqual(self.Nprod, 1)

def testNpathReactions(self):
"""
Test the whether or not RMG mode is turned on.
"""
self.assertEqual(self.Npath, 3, msg=None)
self.assertEqual(self.Npath, 3)

def testPathReactions(self):
"""
Test a path reaction label
"""
self.assertEqual(str(self.PathReaction2), 'CH2OH <=> methoxy', msg=None)
self.assertEqual(str(self.PathReaction2), 'CH2OH <=> methoxy')

# test Arkane's interactions with the pdep module
def testTemperaturesUnits(self):
"""
Test the Temperature Units.
"""
self.assertEqual(str(self.TmaxUnits), 'K', msg=None)
self.assertEqual(str(self.TmaxUnits), 'K')

def testTemperaturesValue(self):
"""
Test the temperature value.
"""
self.assertEqual(self.TminValue, 450.0, msg=None)
self.assertEqual(self.TminValue, 450.0)

def testTemperaturesList(self):
"""
Test the temperature list.
"""
self.assertEqual(numpy.array_equal(self.TlistValue, numpy.array([450, 500, 678, 700])), True, msg=None)
self.assertTrue(numpy.array_equal(self.TlistValue, numpy.array([450, 500, 678, 700])))

def testPminValue(self):
"""
Test the minimum pressure value.
"""
self.assertEqual("%0.7f" % self.PminValue, str(0.0101325), msg=None)
self.assertEqual("%0.7f" % self.PminValue, str(0.0101325))

def testPcount(self):
"""
Test the number pressures specified.
"""
self.assertEqual(self.Pcount, 7, msg=None)
self.assertEqual(self.Pcount, 7)

def testTcount(self):
"""
Test the number temperatures specified.
"""
self.assertEqual(self.Tcount, 4, msg=None)
self.assertEqual(self.Tcount, 4)

def testPressureList(self):
"""
Test the pressure list.
"""
self.assertEqual(numpy.array_equal(self.PlistValue, numpy.array([0.01, 0.1, 1, 3, 10, 100, 1000])), True, msg=None)
self.assertTrue(numpy.array_equal(self.PlistValue, numpy.array([0.01, 0.1, 1, 3, 10, 100, 1000])))

def testGenerateTemperatureList(self):
"""
Test the generated temperature list.
"""
self.assertEqual(list(self.GenTlist), [450.0, 500.0, 678.0, 700.0], msg=None)
self.assertEqual(list(self.GenTlist), [450.0, 500.0, 678.0, 700.0])

def testmaximumGrainSizeValue(self):
"""
Test the max grain size value.
"""
self.assertEqual(self.maximumGrainSizeValue, 0.5, msg=None)
self.assertEqual(self.maximumGrainSizeValue, 0.5)

def testMethod(self):
"""
Test the master equation solution method chosen.
"""
self.assertEqual(self.method, 'modified strong collision', msg=None)
self.assertEqual(self.method, 'modified strong collision')

def testRmgmode(self):
"""
Test the whether or not RMG mode is turned on.
"""
self.assertEqual(self.rmgmode, False, msg=None)
self.assertEqual(self.rmgmode, False)

# Test Arkane's interactions with the kinetics module
def testCalculateTSTRateCoefficient(self):
"""
Test the calculation of the high-pressure limit rate coef for one of the kinetics jobs at Tmin and Tmax.
"""
self.assertEqual("%0.7f" % self.kineticsjob.reaction.calculateTSTRateCoefficient(self.TminValue),
str(46608.5904933), msg=None)
str(46608.5904933))
self.assertEqual("%0.5f" % self.kineticsjob.reaction.calculateTSTRateCoefficient(self.Tmaxvalue),
str(498796.64535), msg=None)
str(498796.64535))

def testTunneling(self):
"""
Test the whether or not tunneling has been included in a specific kinetics job.
"""
self.assertEqual(self.kineticsjob.reaction.transitionState.tunneling, None, msg=None)
self.assertEqual(self.kineticsjob.reaction.transitionState.tunneling, None)


class TestArkaneInput(unittest.TestCase):
"""
Contains unit tests for loading and processing Arkane input files.
"""

@classmethod
def setUp(self):
def setUp(cls):
"""Preparation for all unit tests in this class."""
self.directory = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)), 'examples', 'arkane')
self.modelChemistry = "cbs-qb3"
self.frequencyScaleFactor = 0.99
self.useHinderedRotors = False
self.useBondCorrections = True
cls.directory = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)), 'examples', 'arkane')
cls.modelChemistry = "cbs-qb3"
cls.frequencyScaleFactor = 0.99
cls.useHinderedRotors = False
cls.useBondCorrections = True

def testSpecies(self):
"""Test loading of species input file."""
Expand Down Expand Up @@ -262,7 +267,7 @@ def testTransitionState(self):
"""Test loading of transition state input file."""
ts = input.transitionState('TS', os.path.join(self.directory, 'reactions', 'H+C2H4=C2H5', 'TS.py'))
self.assertTrue(isinstance(ts, TransitionState))

def testTransitionStateStatmech(self):
"""Test loading of statmech job from transition state input file."""
job = jobList[-1]
Expand All @@ -278,11 +283,13 @@ class TestStatmech(unittest.TestCase):
"""
Contains unit tests of statmech.py
"""

@classmethod
def setUp(self):
def setUp(cls):
"""A method that is run before each unit test in this class"""
arkane = Arkane()
self.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'Benzyl', 'input.py'))
cls.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'Benzyl', 'input.py'))

def test_gaussian_log_file_error(self):
"""Test that the proper error is raised if gaussian geometry and frequency file paths are the same"""
Expand Down Expand Up @@ -364,7 +371,7 @@ def tearDownClass(cls):
item_path = os.path.join(path, name)
if os.path.isfile(item_path):
extension = name.split('.')[-1]
if name in cls.files_to_delete or\
if name in cls.files_to_delete or \
(extension in cls.extensions_to_delete and name not in cls.files_to_keep):
os.remove(item_path)
else:
Expand All @@ -376,6 +383,7 @@ class TestGetMass(unittest.TestCase):
"""
Contains unit tests of common.py
"""

def test_get_mass(self):
"""Test that the correct mass/number/isotop is returned from get_element_mass"""
self.assertEquals(get_element_mass(1), (1.00782503224, 1)) # test input by integer
Expand Down
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