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Previously, there were two spots where a list of temperatures was created for fitting high pressure kinetics in Arkane. One fit using inverse temperature spacing and the other one fit with linear temperature spacing. See #1671 This commit moves the location for creating a listing of temperatures to the __init__ method, so there is only one spot where temperatures are initialized. The default min and max in `generateKinetics` was moved into the __init__ method. Three unittests were written for obtaining the proper temperatures in the __init__ method. `generateKinetics` previously accepted an arguement Tlist, which is already an attribute of KineticsJob, creating redundancy. The Tlist argument was removed and self.Tlist was used in this method instead, simplifying the code. Calls to quantity.Quantity in the __init__ method were unnecessary before setting them with quantity.Temperature, so the __init__ code was simplified by setting attributes with (value, 'K') instead. Documentation was updated to better describe the three methods of specifying temperature when calling `kinetics` in Arkane
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| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
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| ############################################################################### | ||
| # # | ||
| # RMG - Reaction Mechanism Generator # | ||
| # # | ||
| # Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu), # | ||
| # Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # | ||
| # # | ||
| # Permission is hereby granted, free of charge, to any person obtaining a # | ||
| # copy of this software and associated documentation files (the 'Software'), # | ||
| # to deal in the Software without restriction, including without limitation # | ||
| # the rights to use, copy, modify, merge, publish, distribute, sublicense, # | ||
| # and/or sell copies of the Software, and to permit persons to whom the # | ||
| # Software is furnished to do so, subject to the following conditions: # | ||
| # # | ||
| # The above copyright notice and this permission notice shall be included in # | ||
| # all copies or substantial portions of the Software. # | ||
| # # | ||
| # THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # | ||
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # | ||
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # | ||
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # | ||
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # | ||
| # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # | ||
| # DEALINGS IN THE SOFTWARE. # | ||
| # # | ||
| ############################################################################### | ||
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| import unittest | ||
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| from rmgpy.species import TransitionState | ||
| from rmgpy.reaction import Reaction | ||
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| from arkane.kinetics import KineticsJob | ||
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| ################################################################################ | ||
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| class KineticsTest(unittest.TestCase): | ||
| """ | ||
| Contains unit tests for the Arkane Kinetics module | ||
| """ | ||
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| def test_give_tlist_for_kineticsjob(self): | ||
| """ | ||
| Ensures that the proper temperature ranges are set when Tlist is specified | ||
| """ | ||
| rxn = Reaction(transitionState=TransitionState()) | ||
| Tlist = [50.7, 100, 300, 800, 1255] | ||
| kjob = KineticsJob(rxn, Tlist=(Tlist, 'K')) | ||
| self.assertEqual(min(Tlist), kjob.Tmin.value_si) | ||
| self.assertEqual(max(Tlist), kjob.Tmax.value_si) | ||
| self.assertEqual(len(Tlist), kjob.Tcount) | ||
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| def test_give_Trange_for_kineticsjob(self): | ||
| """ | ||
| Ensures that Tlist is set when a range of temperatures is specified | ||
| """ | ||
| rxn = Reaction(transitionState=TransitionState()) | ||
| kjob = KineticsJob(rxn, Tmin=(50, 'K'), Tmax=(4000, 'K'), Tcount=5) | ||
| self.assertEqual(5, len(kjob.Tlist.value_si)) | ||
| self.assertEqual(50, min(kjob.Tlist.value_si)) | ||
| self.assertAlmostEqual(4000, max(kjob.Tlist.value_si)) | ||
| inverse_tlist = 1 / kjob.Tlist.value_si | ||
| self.assertAlmostEqual(inverse_tlist[1] - inverse_tlist[0], | ||
| inverse_tlist[-1] - inverse_tlist[-2], | ||
| msg='The points for fitting do not appear 1/T spaced. ' | ||
| 'Obtained values of {0} and {1}'.format(inverse_tlist[1] - inverse_tlist[0], | ||
| inverse_tlist[-1] - inverse_tlist[-2])) | ||
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| def test_get_tlist_for_kineticsjob(self): | ||
| """ | ||
| Ensures that Tlist is set when no range is specified | ||
| """ | ||
| rxn = Reaction(transitionState=TransitionState()) | ||
| kjob = KineticsJob(rxn) | ||
| self.assertAlmostEqual(298, kjob.Tmin.value_si) | ||
| self.assertAlmostEqual(2500, kjob.Tmax.value_si) | ||
| self.assertEqual(50, kjob.Tcount) | ||
| self.assertEqual(50, len(kjob.Tlist.value_si)) | ||
| self.assertAlmostEqual(298, min(kjob.Tlist.value_si)) | ||
| self.assertAlmostEqual(2500, max(kjob.Tlist.value_si)) | ||
| inverse_tlist = 1 / kjob.Tlist.value_si | ||
| self.assertAlmostEqual(inverse_tlist[1] - inverse_tlist[0], | ||
| inverse_tlist[-1] - inverse_tlist[-2], | ||
| msg='The points for fitting do not appear 1/T spaced. ' | ||
| 'Obtained values of {0} and {1}'.format(inverse_tlist[1] - inverse_tlist[0], | ||
| inverse_tlist[-1] - inverse_tlist[-2])) | ||
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| if __name__ == '__main__': | ||
| unittest.main(testRunner=unittest.TextTestRunner(verbosity=2)) |
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