Write 'DOI' in lowercase

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",

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.

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,

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
     ----------

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
     ----------

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

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

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
     --------

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.
 

tests/test_rates.py

@@ -118,30 +118,30 @@ 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])
     assert rx.rates.liquid_viscosity("hexane", temperature) == pytest.approx(
         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])
     assert rx.rates.liquid_viscosity("heptane", temperature) == pytest.approx(
         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",