From da221515660542264ca6cee53c7414712d2dde4c Mon Sep 17 00:00:00 2001 From: "Felipe S. S. Schneider" Date: Wed, 27 Apr 2022 16:35:18 -0300 Subject: [PATCH] Write 'DOI' in lowercase --- overreact/_cli.py | 2 +- overreact/_constants.py | 6 ++-- overreact/api.py | 2 +- overreact/coords.py | 12 +++---- overreact/rates.py | 6 ++-- overreact/thermo/__init__.py | 2 +- overreact/thermo/_gas.py | 4 +-- overreact/thermo/_solv.py | 22 ++++++------- overreact/tunnel.py | 4 +-- tests/test_rates.py | 26 +++++++-------- tests/test_regressions.py | 64 ++++++++++++++++++------------------ tests/test_thermo_gas.py | 2 +- tests/test_thermo_solv.py | 8 ++--- tests/test_tunnel.py | 4 +-- 14 files changed, 82 insertions(+), 82 deletions(-) diff --git a/overreact/_cli.py b/overreact/_cli.py index 4f48b0ca..8dfbdc44 100644 --- a/overreact/_cli.py +++ b/overreact/_cli.py @@ -815,7 +815,7 @@ def main(arguments=None): "--no-qrrho", help="disable the quasi-rigid rotor harmonic oscillator (QRRHO) " "approximations to both enthalpies and entropies (see " - "DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497)", + "doi:10.1021/jp509921r and doi:10.1002/chem.201200497)", choices=["both", "enthalpy", "entropy", "none"], default="both", dest="qrrho_descriptor", diff --git a/overreact/_constants.py b/overreact/_constants.py index ab83c9d0..d73f31b4 100644 --- a/overreact/_constants.py +++ b/overreact/_constants.py @@ -171,14 +171,14 @@ def vdw_radius(atomno): This function returns van der Waals radii as recommended in the 95th edition of the "CRC Handbook of Chemistry and Physics" (2014). This consists of Bondi radii (A. Bondi. "van der Waals Volumes and Radii". J. - Phys. Chem. 1964, 68, 3, 441-451. DOI:10.1021/j100785a001) together with + Phys. Chem. 1964, 68, 3, 441-451. doi:10.1021/j100785a001) together with the values recommended by Truhlar (M. Mantina et al. "Consistent van der Waals Radii for the Whole Main Group". J. Phys. Chem. A 2009, 113, 19, - 5806-5812. DOI:10.1021/jp8111556). For hydrogen, the value recommended by + 5806-5812. doi:10.1021/jp8111556). For hydrogen, the value recommended by Taylor is employed (R. Rowland et al. "Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii". J. Phys. Chem. 1996, 100, 18, 7384-7391. - DOI:10.1021/jp953141+). Other elements receive values recommended by either + doi:10.1021/jp953141+). Other elements receive values recommended by either Hu (S.-Z., Hu. Kristallogr. 224, 375, 2009) or Guzei (Guzei, I. A. and Wendt, M., Dalton Trans., 2006, 3991, 2006). If neither are defined, we use 2.0 Å as default. diff --git a/overreact/api.py b/overreact/api.py index f8c47bc5..b43ebc3c 100644 --- a/overreact/api.py +++ b/overreact/api.py @@ -251,7 +251,7 @@ def get_entropies( if compounds[name].symmetry is not None: # The negative sign here seems correct. See equations (9) and (10) - # of DOI:10.1002/qua.25686. + # of doi:10.1002/qua.25686. entropy -= rx.change_reference_state( compounds[name].symmetry, 1, diff --git a/overreact/coords.py b/overreact/coords.py index 0558f9a5..74f142af 100644 --- a/overreact/coords.py +++ b/overreact/coords.py @@ -81,9 +81,9 @@ def get_molecular_volume( Notes ----- - For "izato", see equation 3 of DOI:10.1039/C9CP03226F for the conceptual + For "izato", see equation 3 of doi:10.1039/C9CP03226F for the conceptual details. There is theoretical support for the equation in the work of - Eyring (DOI:10.1021/j150380a007). + Eyring (doi:10.1021/j150380a007). Examples -------- @@ -189,7 +189,7 @@ def _garza( """Calculate cavity attributes according to A. Garza. This is mainly a helper function for calculating solvation entropy - according to DOI:10.1021/acs.jctc.9b00214. + according to doi:10.1021/acs.jctc.9b00214. Parameters ---------- @@ -527,7 +527,7 @@ def _find_point_group_spheric( # http://web.mit.edu/5.03/www/readings/point_groups/point_groups.pdf # the following workflow is loosely inspired by some articles: - # 1. DOI:10.1016/0097-8485(76)80004-6 + # 1. doi:10.1016/0097-8485(76)80004-6 # elif _has_3_C4(atomcoords): # if _has_center_of_inversion(atomcoords): # return "oh" @@ -626,7 +626,7 @@ def _find_point_group_symmetric( ) # the following workflow is loosely inspired by some articles: - # 1. DOI:10.1016/0097-8485(76)80004-6 + # 1. doi:10.1016/0097-8485(76)80004-6 # if _has_proper_ax_of_highest_order(atomcoords): # if _has_proper_ax_larger_than_2_or_3_C2_perpendicular( # atomcoords @@ -1445,7 +1445,7 @@ def _operation(name, order=2, axis=None): def _classify_rotor(moments, rtol=0.0, atol=1.0e-2, slack=0.870): """Classify rotors based on moments of inertia. - See DOI:10.1002/jcc.23493. + See doi:10.1002/jcc.23493. Parameters ---------- diff --git a/overreact/rates.py b/overreact/rates.py index ddc1b43f..db584762 100644 --- a/overreact/rates.py +++ b/overreact/rates.py @@ -80,7 +80,7 @@ def smoluchowski( This is a work in progress! TODO(schneiderfelipe): THERE ARE DOUBTS ABOUT HOW TO SELECT - reactive_radius. DOI:10.1002/jcc.23409 HELPS CLARIFY SOME ASPECTS BUT + reactive_radius. doi:10.1002/jcc.23409 HELPS CLARIFY SOME ASPECTS BUT THERE'S STILL PROBLEMS. I BELIEVE THERE'S A RELATIONSHIP BETWEEN THE IMAGINARY FREQUENCY AND HOW FAR ATOMS MOVE CLOSE TO REACT, WHICH MIGHT GIVE SOME LIGHT. IN ANY CASE, I BELIEVE THAT THIS VALUE SHOULD BE LARGER @@ -132,7 +132,7 @@ def smoluchowski( def collins_kimball(k_tst, k_diff): """Calculate reaction rate constant inclusing diffusion effects. - This implementation is based on DOI:10.1016/0095-8522(49)90023-9. + This implementation is based on doi:10.1016/0095-8522(49)90023-9. Examples -------- @@ -152,7 +152,7 @@ def convert_rate_constant( ): r"""Convert a reaction rate constant between common units. - The reference paper used for developing this function is DOI:10.1021/ed046p54. + The reference paper used for developing this function is doi:10.1021/ed046p54. Parameters ---------- diff --git a/overreact/thermo/__init__.py b/overreact/thermo/__init__.py index 19eb0b0f..34e8937e 100644 --- a/overreact/thermo/__init__.py +++ b/overreact/thermo/__init__.py @@ -301,7 +301,7 @@ def calc_entropy( """Calculate entropy. Either the classical gas phase or solvation entropies are available. For - solvation entropies, the method of A. Garza (DOI:10.1021/acs.jctc.9b00214) + solvation entropies, the method of A. Garza (doi:10.1021/acs.jctc.9b00214) is available and recommended. Parameters diff --git a/overreact/thermo/_gas.py b/overreact/thermo/_gas.py index 9ec24f9b..c4e1a938 100644 --- a/overreact/thermo/_gas.py +++ b/overreact/thermo/_gas.py @@ -297,9 +297,9 @@ def calc_rot_entropy( exact for diatomics and approximate (?) for polyatomic molecules. For the liquid phase, the extra terms in the method of A. Garza are summed - (DOI:10.1021/acs.jctc.9b00214). This should be used together with + (doi:10.1021/acs.jctc.9b00214). This should be used together with ``method="garza"`` in `calc_trans_entropy`. I may implement the "izato" - method for rotational entropy in the future (DOI:10.1039/C9CP03226F), but + method for rotational entropy in the future (doi:10.1039/C9CP03226F), but this is *not* currently available. Parameters diff --git a/overreact/thermo/_solv.py b/overreact/thermo/_solv.py index 320b5ea7..7debd756 100644 --- a/overreact/thermo/_solv.py +++ b/overreact/thermo/_solv.py @@ -15,9 +15,9 @@ # TODO(schneiderfelipe): C-PCM already includes the whole Gibbs free energy -# associated with this (see DOI:10.1021/jp9716997 and references therein, e.g., -# DOI:10.1016/0009-2614(96)00349-1, DOI:10.1021/cr60304a002, -# DOI:10.1002/jcc.540100504). As such, including this in the total free energy +# associated with this (see doi:10.1021/jp9716997 and references therein, e.g., +# doi:10.1016/0009-2614(96)00349-1, doi:10.1021/cr60304a002, +# doi:10.1002/jcc.540100504). As such, including this in the total free energy # might overcount energy contributions. As an alternative, I might want to # a. remove this contribution, # b. keep this and remove the contribution from the cavity enthalpy, @@ -28,7 +28,7 @@ # c. implement something closer to the original and do one of the # cited in b. above. # -# See DOI:10.1021/cr60304a002. +# See doi:10.1021/cr60304a002. def calc_cav_entropy( atomnos, atomcoords, @@ -40,7 +40,7 @@ def calc_cav_entropy( ): r"""Calculate the cavity entropy from scaled particle theory. - This implements the method due to A. Garza, see DOI:10.1021/acs.jctc.9b00214. + This implements the method due to A. Garza, see doi:10.1021/acs.jctc.9b00214. Parameters ---------- @@ -130,17 +130,17 @@ def func(temperature, solvent): # TODO(schneiderfelipe): the concept of free volume in polymer and membrane # sciences are related to the difference between the specific volume (inverse # of density) and the van der Waals volume (oftentimes multiplied by a factor, -# normally 1.3), see DOI:10.1007/978-3-642-40872-4_279-5. This is very similar +# normally 1.3), see doi:10.1007/978-3-642-40872-4_279-5. This is very similar # to the thing done here with "izato". # # Further theoretical support is given for the exact equation -# used in the work of Eyring (DOI:10.1021/j150380a007), where it is also +# used in the work of Eyring (doi:10.1021/j150380a007), where it is also # suggested that that the self-solvation (solvent molecule solvated by itself) # outer volume (here called cavity volume) should match the specific volume of # the solvent at that temperature and pressure. # # Further evidence that the free volume should change with temperature can be -# found in DOI:10.1016/j.jct.2011.01.003. In fact, it is also shown there that +# found in doi:10.1016/j.jct.2011.01.003. In fact, it is also shown there that # the rotational entropy is almost the same as for the ideal gas for molecules # that don't do hydrogen bonding at their boiling temperature. For molecules # that do hydrogen bonding, the rotational entropy gain should be taken into @@ -151,7 +151,7 @@ def func(temperature, solvent): # up with an alpha that depends on temperature (and possibly pressure). # 2. I need to validate this by checking Trouton's and Hildebrand's laws for # apolar compounds, which should also give reasonable boiling temperatures and -# free volumes of around 1 ų (see again DOI:10.1016/j.jct.2011.01.003). +# free volumes of around 1 ų (see again doi:10.1016/j.jct.2011.01.003). # 3. Improve polar and hydrogen bonding molecules by adjusting their rotational # entropies. # 4. Some data evidence the possibility that the difference between gas and @@ -210,9 +210,9 @@ def molar_free_volume( Notes ----- - For "izato", see equation 3 of DOI:10.1039/C9CP03226F for the conceptual + For "izato", see equation 3 of doi:10.1039/C9CP03226F for the conceptual details. There is theoretical support for the equation in the work of - Eyring (DOI:10.1021/j150380a007). + Eyring (doi:10.1021/j150380a007). Examples -------- diff --git a/overreact/tunnel.py b/overreact/tunnel.py index 2283a2f5..0d1914c1 100644 --- a/overreact/tunnel.py +++ b/overreact/tunnel.py @@ -202,7 +202,7 @@ def eckart( def _eckart(u: float, alpha1: float, alpha2: float | None = None) -> float: """Implement of the (unsymmetrical) Eckart tunneling approximation. - This is based on DOI:10.1021/j100809a040 and DOI:10.6028/jres.086.014. + This is based on doi:10.1021/j100809a040 and doi:10.6028/jres.086.014. Parameters ---------- @@ -224,7 +224,7 @@ def _eckart(u: float, alpha1: float, alpha2: float | None = None) -> float: distribution using a mixed set of quadratures (Gauss quadrature for values below zero and Laguerre quadrature for values from zero to infinity). The orders for both quadratures are fixed and are the smallest numbers that - allow us to reproduce values from the literature (DOI:10.1021/j100809a040). + allow us to reproduce values from the literature (doi:10.1021/j100809a040). Both alpha1 and alpha2 should be non-negative. diff --git a/tests/test_rates.py b/tests/test_rates.py index a6317b96..d8e60a99 100644 --- a/tests/test_rates.py +++ b/tests/test_rates.py @@ -118,7 +118,7 @@ def test_liquid_viscosities_are_correct(): viscosity, 4e-3 ) - # - hexane (DOI:10.1063/1.555943): + # - hexane (doi:10.1063/1.555943): # TODO(schneiderfelipe): hexane: 178 K -- 340 K temperature = 273.15 + np.array([25]) viscosity = 1e-3 * np.array([0.295]) @@ -126,14 +126,14 @@ def test_liquid_viscosities_are_correct(): viscosity, 5e-3 ) - # - acetone (DOI:10.1021/je00017a031): + # - acetone (doi:10.1021/je00017a031): temperature = 273.15 + np.array([25]) viscosity = 1e-3 * np.array([0.302]) assert rx.rates.liquid_viscosity("acetone", temperature) == pytest.approx( viscosity, 2e-2 ) - # - heptane (DOI:10.1063/1.555943): + # - heptane (doi:10.1063/1.555943): # TODO(schneiderfelipe): heptane: 183 K -- 370 K temperature = 273.15 + np.array([25]) viscosity = 1e-3 * np.array([0.389]) @@ -141,7 +141,7 @@ def test_liquid_viscosities_are_correct(): viscosity, 9e-5 ) - # - octane (DOI:10.1063/1.555943): + # - octane (doi:10.1063/1.555943): # TODO(schneiderfelipe): octane: 217 K -- 398 K temperature = 273.15 + np.array([25]) viscosity = 1e-3 * np.array([0.509]) @@ -165,7 +165,7 @@ def test_liquid_viscosities_are_correct(): viscosity, 3e-2 ) - # - water (DOI:10.1002/9781118131473): + # - water (doi:10.1002/9781118131473): temperature = 273.15 + np.array( [0, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100] ) @@ -191,7 +191,7 @@ def test_liquid_viscosities_are_correct(): viscosity, 6e-2 ) - # - water (DOI:10.1002/qua.25686): + # - water (doi:10.1002/qua.25686): temperature = np.array([298.15, 300, 310, 320, 330, 340, 350]) viscosity = 1e-4 * np.array([8.90, 8.54, 6.94, 5.77, 4.90, 4.22, 3.69]) assert rx.rates.liquid_viscosity("water", temperature) == pytest.approx( @@ -205,7 +205,7 @@ def test_liquid_viscosities_are_correct(): viscosity, 4e-3 ) - # - 2-propanol (DOI:10.1021/je00058a025): + # - 2-propanol (doi:10.1021/je00058a025): temperature = 273.15 + np.array([25]) viscosity = 1e-3 * np.array([2.052]) assert rx.rates.liquid_viscosity("2-propanol", temperature) == pytest.approx( @@ -280,7 +280,7 @@ def test_second_order_conversion_rates_match_literature(): References are given in the comments.""" for temperature in [200.0, 273.15, 298.15, 300.0, 373.15, 400.0]: - # to cm3 mol-1 s-1 (DOI:10.1021/ed046p54) + # to cm3 mol-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "cm3 mol-1 s-1", @@ -340,7 +340,7 @@ def test_second_order_conversion_rates_match_literature(): temperature=temperature, ) == pytest.approx(82.06 * temperature, 4e-5) - # to l mol-1 s-1 (DOI:10.1021/ed046p54) + # to l mol-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "l mol-1 s-1", @@ -400,7 +400,7 @@ def test_second_order_conversion_rates_match_literature(): temperature=temperature, ) == pytest.approx(8.206e-2 * temperature, 4e-5) - # to m3 mol-1 s-1 (DOI:10.1021/ed046p54) + # to m3 mol-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "m3 mol-1 s-1", @@ -460,7 +460,7 @@ def test_second_order_conversion_rates_match_literature(): temperature=temperature, ) == pytest.approx(8.206e-5 * temperature, 4e-5) - # to cm3 particle-1 s-1 (DOI:10.1021/ed046p54) + # to cm3 particle-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "cm3 particle-1 s-1", @@ -520,7 +520,7 @@ def test_second_order_conversion_rates_match_literature(): temperature=temperature, ) == pytest.approx(1.362e-22 * temperature) - # to mmHg-1 s-1 (DOI:10.1021/ed046p54) + # to mmHg-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "mmHg-1 s-1", @@ -595,7 +595,7 @@ def test_second_order_conversion_rates_match_literature(): temperature=temperature, ) == pytest.approx(9.658e18 / temperature, 2e-4) - # to atm-1 s-1 (DOI:10.1021/ed046p54) + # to atm-1 s-1 (doi:10.1021/ed046p54) assert rx.rates.convert_rate_constant( 1.0, "atm-1 s-1", diff --git a/tests/test_regressions.py b/tests/test_regressions.py index 4ed57c9a..c3643521 100644 --- a/tests/test_regressions.py +++ b/tests/test_regressions.py @@ -19,12 +19,12 @@ def test_basic_example_for_solvation_equilibria(): """Reproduce literature data for AcOH(g) <=> AcOH(aq). - Data is as cited in DOI:10.1021/jp810292n and DOI:10.1063/1.1416902, and + Data is as cited in doi:10.1021/jp810292n and doi:10.1063/1.1416902, and is experimental except when otherwise indicated in the comments. """ model = rx.parse_model("data/acetate/Orca4/model.k") temperature = 298.15 - pK = 4.756 # DOI:10.1063/1.1416902 + pK = 4.756 # doi:10.1063/1.1416902 acid_energy = -constants.R * temperature * np.log(10**-pK) / constants.kcal solv_energy = ( @@ -64,12 +64,12 @@ def test_basic_example_for_solvation_equilibria(): delta_freeenergies_ref, 7e-3 ) - # the following tests the solvation free energy from DOI:10.1021/jp810292n + # the following tests the solvation free energy from doi:10.1021/jp810292n assert delta_freeenergies[2] / constants.kcal == pytest.approx( -6.70 + concentration_correction / constants.kcal, 1.5e-1 ) - # the following tests the reaction free energy from DOI:10.1063/1.1416902 + # the following tests the reaction free energy from doi:10.1063/1.1416902 assert delta_freeenergies[0] == pytest.approx(27.147 * constants.kilo, 7e-3) assert delta_freeenergies[0] == pytest.approx( -constants.R * temperature * np.log(10**-pK), 7e-3 @@ -84,7 +84,7 @@ def test_basic_example_for_solvation_equilibria(): def test_basic_example_for_solvation_phase_kinetics(): """Reproduce literature data for NH3(w) + OH·(w) -> NH2·(w) + H2O(w). - This uses raw data from from DOI:10.1002/qua.25686 and no calls from + This uses raw data from from doi:10.1002/qua.25686 and no calls from overreact.api. """ temperatures = np.array([298.15, 300, 310, 320, 330, 340, 350]) @@ -146,7 +146,7 @@ def test_basic_example_for_solvation_phase_kinetics(): def test_basic_example_for_gas_phase_kinetics(): """Reproduce literature data for CH4 + Cl⋅ -> CH3· + HCl. - This uses raw data from from DOI:10.1002/qua.25686 and no calls from + This uses raw data from from doi:10.1002/qua.25686 and no calls from overreact.api. """ temperatures = np.array([200, 298.15, 300, 400]) @@ -216,7 +216,7 @@ def test_basic_example_for_gas_phase_kinetics(): def test_rate_constants_for_hickel1992(): """Reproduce literature data for NH3(w) + OH·(w) -> NH2·(w) + H2O(w). - Data is as cited in DOI:10.1002/qua.25686 and is experimental except when + Data is as cited in doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for consistency with the literature in terms of @@ -280,7 +280,7 @@ def test_rate_constants_for_hickel1992(): def test_rate_constants_for_tanaka1996(): """Reproduce literature data for CH4 + Cl⋅ -> CH3· + HCl. - Data is as cited in DOI:10.1007/BF00058703 and DOI:10.1002/qua.25686 and + Data is as cited in doi:10.1007/BF00058703 and doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for consistency with the literature in terms of @@ -395,7 +395,7 @@ def test_rate_constants_for_tanaka1996(): def test_delta_energies_for_hickel1992(): """Reproduce literature data for NH3(w) + OH·(w) -> NH2·(w) + H2O(w). - Data is as cited in DOI:10.1002/qua.25686 and is experimental except when + Data is as cited in doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for consistency with the literature in terms of @@ -428,7 +428,7 @@ def test_delta_energies_for_hickel1992(): * rx.change_reference_state(temperature=temperatures) / constants.kcal, 2e-2, - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 # extra symmetry is required for this reaction since the transition state # is nonsymmetric @@ -437,13 +437,13 @@ def test_delta_energies_for_hickel1992(): delta_freeenergies_ref = [7.9, 7.9, 8.1, 8.3, 8.5, 8.7, 8.8] assert delta_freeenergies / constants.kcal == pytest.approx( delta_freeenergies_ref, 2e-2 - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 def test_delta_energies_for_tanaka1996(): """Reproduce literature data for CH4 + Cl⋅ -> CH3· + HCl. - Data is as cited in DOI:10.1007/BF00058703 and DOI:10.1002/qua.25686 and + Data is as cited in doi:10.1007/BF00058703 and doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for consistency with the literature in terms of @@ -470,7 +470,7 @@ def test_delta_energies_for_tanaka1996(): assert delta_freeenergies / constants.kcal == pytest.approx( delta_freeenergies_ref, 4e-2 - ) # UMP2/6-311G(2d,p) DOI:10.1007/BF00058703 + ) # UMP2/6-311G(2d,p) doi:10.1007/BF00058703 # testing now another level of theory! basisset = "cc-pVTZ" # not the basis used in the ref., but close enough @@ -497,13 +497,13 @@ def test_delta_energies_for_tanaka1996(): assert delta_freeenergies / constants.kcal == pytest.approx( delta_freeenergies_ref, 2e-2 - ) # UMP2/6-311G(3d,2p) from DOI:10.1002/qua.25686 + ) # UMP2/6-311G(3d,2p) from doi:10.1002/qua.25686 def test_logfiles_for_hickel1992(): """Reproduce literature data for NH3(w) + OH·(w) -> NH2·(w) + H2O(w). - Data is as cited in DOI:10.1002/qua.25686 and is experimental except when + Data is as cited in doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for details in the logfiles such as point group symmetry @@ -519,20 +519,20 @@ def test_logfiles_for_hickel1992(): assert data.vibfreqs == pytest.approx( [1022, 1691, 1691, 3506, 3577, 3577], 5e-2 - ) # DOI:10.1002/qua.25686 + ) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [1065.8, 1621.5, 1620.6, 3500.2, 3615.5, 3617.3], 4e-2 - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 # OH·(w) data = datasets.logfiles["hickel1992"][f"OH·@{theory}/{basisset}"] point_group = rx.coords.find_point_group(data.atommasses, data.atomcoords) assert rx.coords.symmetry_number(point_group) == 1 - assert data.vibfreqs == pytest.approx([3737.8], 2e-2) # DOI:10.1002/qua.25686 + assert data.vibfreqs == pytest.approx([3737.8], 2e-2) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [3724.3], 2e-2 - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 # NH2·(w) data = datasets.logfiles["hickel1992"][f"NH2·@{theory}/{basisset}"] @@ -541,10 +541,10 @@ def test_logfiles_for_hickel1992(): assert data.vibfreqs == pytest.approx( [1497.3, 3220.0, 3301.1], 7e-2 - ) # DOI:10.1002/qua.25686 + ) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [1471.2, 3417.6, 3500.8], 9e-3 - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 # H2O(w) data = datasets.logfiles["hickel1992"][f"H2O@{theory}/{basisset}"] @@ -553,10 +553,10 @@ def test_logfiles_for_hickel1992(): assert data.vibfreqs == pytest.approx( [1594.6, 3656.7, 3755.8], 6e-2 - ) # DOI:10.1002/qua.25686 + ) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [1570.4, 3847.9, 3928.9], 6e-3 - ) # M06-2X/6-311++G(d,p) from DOI:10.1002/qua.25686 + ) # M06-2X/6-311++G(d,p) from doi:10.1002/qua.25686 # NH3·OH#(w) data = datasets.logfiles["hickel1992"][f"NH3·OH@{theory}/{basisset}"] @@ -570,7 +570,7 @@ def test_logfiles_for_hickel1992(): def test_logfiles_for_tanaka1996(): """Reproduce literature data for CH4 + Cl⋅ -> CH3· + HCl. - Data is as cited in DOI:10.1007/BF00058703 and DOI:10.1002/qua.25686 and + Data is as cited in doi:10.1007/BF00058703 and doi:10.1002/qua.25686 and is experimental except when otherwise indicated in the comments. Those tests check for details in the logfiles such as point group symmetry @@ -586,10 +586,10 @@ def test_logfiles_for_tanaka1996(): assert data.vibfreqs == pytest.approx( [1306, 1306, 1306, 1534, 1534, 2917, 3019, 3019, 3019], 7e-2 - ) # DOI:10.1002/qua.25686 + ) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [1367, 1367, 1367, 1598, 1598, 3070, 3203, 3203, 3205], 8e-3 - ) # UMP2/6-311G(3d,2p) from DOI:10.1002/qua.25686 + ) # UMP2/6-311G(3d,2p) from doi:10.1002/qua.25686 # CH3· data = datasets.logfiles["tanaka1996"][f"CH3·@{theory}/{basisset}"] @@ -598,20 +598,20 @@ def test_logfiles_for_tanaka1996(): assert data.vibfreqs == pytest.approx( [580, 1383, 1383, 3002, 3184, 3184], 1.4e-1 - ) # DOI:10.1002/qua.25686 + ) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [432, 1454, 1454, 3169, 3360, 3360], 1.7e-1 - ) # UMP2/6-311G(3d,2p) from DOI:10.1002/qua.25686 + ) # UMP2/6-311G(3d,2p) from doi:10.1002/qua.25686 # HCl data = datasets.logfiles["tanaka1996"][f"HCl@{theory}/{basisset}"] point_group = rx.coords.find_point_group(data.atommasses, data.atomcoords) assert rx.coords.symmetry_number(point_group) == 1 - assert data.vibfreqs == pytest.approx([2991], 3e-2) # DOI:10.1002/qua.25686 + assert data.vibfreqs == pytest.approx([2991], 3e-2) # doi:10.1002/qua.25686 assert data.vibfreqs == pytest.approx( [3028], 9e-3 - ) # UMP2/6-311G(3d,2p) from DOI:10.1002/qua.25686 + ) # UMP2/6-311G(3d,2p) from doi:10.1002/qua.25686 # Cl· data = datasets.logfiles["tanaka1996"][f"Cl·@{theory}/{basisset}"] @@ -624,7 +624,7 @@ def test_logfiles_for_tanaka1996(): assert rx.coords.symmetry_number(point_group) == 3 # NOTE(schneiderfelipe): vibrations are from an UMP2/6-311G(3d,2p) - # calculation, see the reference in DOI:10.1007/BF00058703 + # calculation, see the reference in doi:10.1007/BF00058703 assert data.vibfreqs == pytest.approx( [ -1214.38, @@ -645,4 +645,4 @@ def test_logfiles_for_tanaka1996(): assert data.vibfreqs == pytest.approx( [-1218, 369, 369, 516, 962, 962, 1217, 1460, 1460, 3123, 3294, 3294], 7e-2, - ) # UMP2/6-311G(3d,2p) from DOI:10.1002/qua.25686 + ) # UMP2/6-311G(3d,2p) from doi:10.1002/qua.25686 diff --git a/tests/test_thermo_gas.py b/tests/test_thermo_gas.py index 4e20e682..c6b71e8a 100644 --- a/tests/test_thermo_gas.py +++ b/tests/test_thermo_gas.py @@ -1078,7 +1078,7 @@ def test_equilibrium_constant_works(): 0.0 ) - # The following reproduces some data from DOI:10.1021/ic202081z for equilibria + # The following reproduces some data from doi:10.1021/ic202081z for equilibria # relevant to the decomposition of aqueous nitrous acid. Table 2 gives Gibbs free # energies at 298 K for two methods (G3B3 and CBS-QB3), whose average is used for # the calculation of equilibrium constants. The authors could not reproduce diff --git a/tests/test_thermo_solv.py b/tests/test_thermo_solv.py index 3dfca394..93024231 100644 --- a/tests/test_thermo_solv.py +++ b/tests/test_thermo_solv.py @@ -11,7 +11,7 @@ def test_entropy_liquid_phase(): - """Validate selected values from Table 1 of DOI:10.1021/acs.jctc.9b00214. + """Validate selected values from Table 1 of doi:10.1021/acs.jctc.9b00214. Experimental values are actually used as reference. """ @@ -218,13 +218,13 @@ def test_entropy_liquid_phase(): def test_translational_entropy_liquid_phase(): - """Validate calculated volumes from Table S3 of DOI:10.1039/C9CP03226F. + """Validate calculated volumes from Table S3 of doi:10.1039/C9CP03226F. The original data seems to have errors, some severe. I *assumed* this is due to too few decimal places in the free volume and adjusted the precision for some entries accordingly. - The same systems are probed for the method of DOI:10.1021/acs.jctc.9b00214 + The same systems are probed for the method of doi:10.1021/acs.jctc.9b00214 in water and the gas phase translational entropy is also tested. """ # H2O @@ -870,7 +870,7 @@ def test_translational_entropy_liquid_phase(): def test_sackur_tetrode_given_free_volumes(): - """Reproduce calculated values from Table S3 of DOI:10.1039/C9CP03226F. + """Reproduce calculated values from Table S3 of doi:10.1039/C9CP03226F. The original data seems to have errors, some severe. I assumed this is due to too few decimal places in the free volume and adjusted the precision for diff --git a/tests/test_tunnel.py b/tests/test_tunnel.py index 8f480ee8..73cba6ed 100644 --- a/tests/test_tunnel.py +++ b/tests/test_tunnel.py @@ -36,7 +36,7 @@ def test_eckart_tunneling_corrections_are_correct(): assert rx.tunnel.eckart(59, 15781.6) == pytest.approx(1.01679385) assert rx.tunnel.eckart(158, 56813.61, 94689.35) == pytest.approx(1.02392807) - # a selection for testing higher precision from DOI:10.1021/j100809a040 + # a selection for testing higher precision from doi:10.1021/j100809a040 assert rx.tunnel.eckart(414.45, 15781.6, 15781.6) == pytest.approx(1.2, 9e-3) assert rx.tunnel.eckart(414.45, 1578.16, 1578.16) == pytest.approx(1.32, 2e-3) assert rx.tunnel.eckart(1243.35, 9468.94, 28406.81) == pytest.approx(3.39, 2e-4) @@ -54,7 +54,7 @@ def test_eckart_is_symmetric(): def test_low_level_eckart_against_johnston1962(): - """Reproduce all values from Table 1 of DOI:10.1021/j100809a040.""" + """Reproduce all values from Table 1 of doi:10.1021/j100809a040.""" us = [2, 3, 4, 5, 6, 8, 10, 12, 16] # columns # The first examples have very low barriers and comprise the "imaginary