Picciotto et al. 1960 isotopic temperature inference and [hydro]meteo…

…ric water line formulae (journal club paper); fixes in bibliography checks; code cleanups (#1498) Co-authored-by: Agnieszka Żaba <[email protected]> Co-authored-by: AgnieszkaZaba <[email protected]>
open-atmos · Jan 14, 2025 · 86ddb1d · 86ddb1d
1 parent 0219928
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diff --git a/PySDM/formulae.py b/PySDM/formulae.py
@@ -46,10 +46,11 @@ def __init__(  # pylint: disable=too-many-locals
         heterogeneous_ice_nucleation_rate: str = "Null",
         fragmentation_function: str = "AlwaysN",
         isotope_equilibrium_fractionation_factors: str = "Null",
-        isotope_meteoric_water_line_excess: str = "Null",
+        isotope_meteoric_water_line: str = "Null",
         isotope_ratio_evolution: str = "Null",
         isotope_diffusivity_ratios: str = "Null",
         isotope_relaxation_timescale: str = "Null",
+        isotope_temperature_inference: str = "Null",
         optical_albedo: str = "Null",
         optical_depth: str = "Null",
         particle_shape_and_density: str = "LiquidSpheres",
@@ -80,10 +81,11 @@ def __init__(  # pylint: disable=too-many-locals
         self.isotope_equilibrium_fractionation_factors = (
             isotope_equilibrium_fractionation_factors
         )
-        self.isotope_meteoric_water_line_excess = isotope_meteoric_water_line_excess
+        self.isotope_meteoric_water_line = isotope_meteoric_water_line
         self.isotope_ratio_evolution = isotope_ratio_evolution
         self.isotope_diffusivity_ratios = isotope_diffusivity_ratios
         self.isotope_relaxation_timescale = isotope_relaxation_timescale
+        self.isotope_temperature_inference = isotope_temperature_inference
         self.particle_shape_and_density = particle_shape_and_density
         self.air_dynamic_viscosity = air_dynamic_viscosity
         self.terminal_velocity = terminal_velocity

diff --git a/PySDM/physics/__init__.py b/PySDM/physics/__init__.py
@@ -29,10 +29,11 @@
     hygroscopicity,
     impl,
     isotope_equilibrium_fractionation_factors,
-    isotope_meteoric_water_line_excess,
+    isotope_meteoric_water_line,
     isotope_ratio_evolution,
     isotope_diffusivity_ratios,
     isotope_relaxation_timescale,
+    isotope_temperature_inference,
     latent_heat,
     optical_albedo,
     optical_depth,

diff --git a/PySDM/physics/constants_defaults.py b/PySDM/physics/constants_defaults.py
@@ -437,3 +437,22 @@ def compute_derived_values(c: dict):
 isotopologue; in the paper timescale is calculated for tritium with assumption of no tritium
 in the environment around the drop (Table 1).
 """
+
+PICCIOTTO_18O_A = -0.9 * PER_MILLE / si.K
+""" linear fit coefficients from [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
+for atmospheric temperature inference from water isotopic composition
+(note that the sign of A coefficient is opposite to match the paper plot - typo in the paper?) """
+PICCIOTTO_18O_B = 6.4 * PER_MILLE
+"""〃"""
+PICCIOTTO_2H_A = -0.8 * PER_CENT / si.K
+"""〃"""
+PICCIOTTO_2H_B = 8 * PER_CENT
+"""〃"""
+
+PICCIOTTO_18O_TO_2H_SLOPE_COEFF = 0.8 * PER_CENT / PER_MILLE
+""" [hydro]meteoric water line [Picciotto et al. 1960](https://doi.org/10.1038/187857a0) coeffs
+(note that the delta-2H and delta-18O are swapped to match the paper plot - typo in the paper?)
+(note that the sign of INTERCEPT is opposite to match the paper plot - typo in the paper?)
+"""
+PICCIOTTO_18O_TO_2H_INTERCEPT_COEFF = -1.8 * PER_CENT
+"""〃"""
diff --git a/PySDM/physics/isotope_meteoric_water_line/__init__.py b/PySDM/physics/isotope_meteoric_water_line/__init__.py
@@ -0,0 +1,7 @@
+""" definitions of meteoric water line parameters
+and definitions of the excess quantities"""
+
+from PySDM.impl.null_physics_class import Null
+from .barkan_and_luz_2007 import BarkanAndLuz2007
+from .dansgaard_1964 import Dansgaard1964
+from .picciotto_et_al_1960 import PicciottoEtAl1960
diff --git a/..._water_line_excess/barkan_and_luz_2007.py → ...eteoric_water_line/barkan_and_luz_2007.py b/..._water_line_excess/barkan_and_luz_2007.py → ...eteoric_water_line/barkan_and_luz_2007.py
diff --git a/...eoric_water_line_excess/dansgaard_1964.py → ...ope_meteoric_water_line/dansgaard_1964.py b/...eoric_water_line_excess/dansgaard_1964.py → ...ope_meteoric_water_line/dansgaard_1964.py
diff --git a/PySDM/physics/isotope_meteoric_water_line/picciotto_et_al_1960.py b/PySDM/physics/isotope_meteoric_water_line/picciotto_et_al_1960.py
@@ -0,0 +1,15 @@
+""" based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
+ where delta(2H)= slope_coeff * delta(18O) + intercept_coeff formulae is given
+ with swapped 2H and 18O in a paper
+ """
+
+
+class PicciottoEtAl1960:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def d18O_of_d2H(const, delta_2H):
+        return (
+            delta_2H - const.PICCIOTTO_18O_TO_2H_INTERCEPT_COEFF
+        ) / const.PICCIOTTO_18O_TO_2H_SLOPE_COEFF
diff --git a/PySDM/physics/isotope_meteoric_water_line_excess/__init__.py b/PySDM/physics/isotope_meteoric_water_line_excess/__init__.py
diff --git a/PySDM/physics/isotope_temperature_inference/__init__.py b/PySDM/physics/isotope_temperature_inference/__init__.py
@@ -0,0 +1,8 @@
+"""
+formulae for inferring atmospheric temperatures from (ice core) water isotopic composition
+"""
+
+from PySDM.impl.null_physics_class import Null
+from PySDM.physics.isotope_temperature_inference.picciotto_et_al_1960 import (
+    PicciottoEtAl1960,
+)
diff --git a/PySDM/physics/isotope_temperature_inference/picciotto_et_al_1960.py b/PySDM/physics/isotope_temperature_inference/picciotto_et_al_1960.py
@@ -0,0 +1,15 @@
+""" based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
+ where delta(T)=-(a*T + b) formulae given, here cast as T(delta)=(-delta-b)/a """
+
+
+class PicciottoEtAl1960:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def temperature_from_delta_18O(const, delta_18O):
+        return const.T0 + (-delta_18O - const.PICCIOTTO_18O_B) / const.PICCIOTTO_18O_A
+
+    @staticmethod
+    def temperature_from_delta_2H(const, delta_2H):
+        return const.T0 + (-delta_2H - const.PICCIOTTO_2H_B) / const.PICCIOTTO_2H_A
diff --git a/docs/bibliography.json b/docs/bibliography.json
@@ -178,7 +178,7 @@
   },
   "https://doi.org/10.3402/tellusa.v16i4.8993": {
     "usages": [
-      "PySDM/physics/isotope_meteoric_water_line_excess/dansgaard_1964.py"
+      "PySDM/physics/isotope_meteoric_water_line/dansgaard_1964.py"
     ],
     "label": "Dansgaard 1964 (Tellus A 16)",
     "title": "Stable isotopes in precipitation"
@@ -481,7 +481,7 @@
   "https://doi.org/10.1002/rcm.3180": {
     "usages": [
       "PySDM/physics/constants_defaults.py",
-      "PySDM/physics/isotope_meteoric_water_line_excess/barkan_and_luz_2007.py"
+      "PySDM/physics/isotope_meteoric_water_line/barkan_and_luz_2007.py"
     ],
     "label": "Barkan & Luz 2007 (Rapid Commun. Mass Spectrom. 21)",
     "title": "Diffusivity fractionations of H<sub>2</sub><sup>16</sup>O/H<sub>2</sub><sup>17</sup>O and H<sub>2</sub><sup>16</sup>O/H<sub>2</sub><sup>18</sup>O in air and their implications for isotope hydrology"
@@ -616,7 +616,7 @@
   },
   "https://doi.org/10.1126/science.133.3465.1702": {
     "usages": [
-      "tests/unit_tests/physics/test_isotope_meteoric_water_line_excess.py",
+      "tests/unit_tests/physics/test_isotope_meteoric_water_line.py",
       "PySDM/physics/constants_defaults.py"
     ],
     "label": "Craig 1961 (Science 133)",
@@ -691,5 +691,15 @@
     "usages": ["PySDM/physics/saturation_vapour_pressure/wexler_1976.py"],
     "title": "Vapor Pressure Formulation for Water in Range 0 to f 00 °C. A Revision",
     "label": "Wexler 1976 (J. Res. NBS A Phys. Ch. 80A)"
+  },
+  "https://doi.org/10.1038/187857a0": {
+    "usages": [
+      "PySDM/physics/constants_defaults.py",
+      "PySDM/physics/isotope_temperature_inference/picciotto_et_al_1960.py",
+      "PySDM/physics/isotope_meteoric_water_line/picciotto_et_al_1960.py",
+      "tests/unit_tests/physics/test_isotope_temperature_inference.py"
+    ],
+    "title": "Isotopic Composition and Temperature of Formation of Antarctic Snows",
+    "label": "Picciotto et al. 1960 (Nature 187)"
   }
 }
diff --git a/docs/generate_html.py b/docs/generate_html.py
@@ -86,8 +86,10 @@ def check_urls(urls_from_json):
         for url in unique_urls_found
     }
     for url in unique_urls_read:
-        assert url_usages_found[url] == sorted(urls_from_json[url]["usages"]), (
-            f"{url} usages mismatch:\n"
+        assert set(url_usages_found[url]) == set(
+            sorted(urls_from_json[url]["usages"])
+        ), (
+            f"{url} usages mismatch (please fix docs/bibliography.json):\n"
             f"\texpected: {url_usages_found[url]}\n"
             f"\tactual:   {urls_from_json[url]['usages']}"
         )

diff --git a/examples/PySDM_examples/Gedzelman_and_Arnold_1994/fig_2.ipynb b/examples/PySDM_examples/Gedzelman_and_Arnold_1994/fig_2.ipynb
@@ -11496,11 +11496,11 @@
     "formulae = Formulae(\n",
     "    isotope_equilibrium_fractionation_factors='BarkanAndLuz2005+HoritaAndWesolowski1994',\n",
     "    isotope_diffusivity_ratios='HellmannAndHarvey2020',\n",
-    "    isotope_meteoric_water_line_excess='BarkanAndLuz2007+Dansgaard1964',\n",
+    "    isotope_meteoric_water_line='BarkanAndLuz2007+Dansgaard1964',\n",
     "    isotope_ratio_evolution='GedzelmanAndArnold1994',\n",
     ")\n",
-    "deltas_18O = [formulae.isotope_meteoric_water_line_excess.d18O_of_d2H(d2H) for d2H in DELTAS_2H]\n",
-    "deltas_17O = [formulae.isotope_meteoric_water_line_excess.d17O_of_d18O(d18O) for d18O in deltas_18O]\n",
+    "deltas_18O = [formulae.isotope_meteoric_water_line.d18O_of_d2H(d2H) for d2H in DELTAS_2H]\n",
+    "deltas_17O = [formulae.isotope_meteoric_water_line.d17O_of_d18O(d18O) for d18O in deltas_18O]\n",
     "\n",
     "fig, axs = pyplot.subplots(3, 3, figsize=(10,8), sharex=False, sharey=True, tight_layout=True) \n",
     "\n",

diff --git a/examples/PySDM_examples/Graf_et_al_2019/Table_1.ipynb b/examples/PySDM_examples/Graf_et_al_2019/Table_1.ipynb
@@ -80,7 +80,7 @@
    "source": [
     "formulae = Formulae(\n",
     "    isotope_equilibrium_fractionation_factors='Majoube1970+Majoube1971+MerlivatAndNief1967',\n",
-    "    isotope_meteoric_water_line_excess='Dansgaard1964'\n",
+    "    isotope_meteoric_water_line='Dansgaard1964'\n",
     ")\n",
     "const = formulae.constants\n",
     "\n",
@@ -90,7 +90,7 @@
     "    '18O_s': formulae.isotope_equilibrium_fractionation_factors.alpha_i_18O,\n",
     "    '2H_s': formulae.isotope_equilibrium_fractionation_factors.alpha_i_2H\n",
     "}\n",
-    "excess_d = formulae.isotope_meteoric_water_line_excess.excess_d\n",
+    "excess_d = formulae.isotope_meteoric_water_line.excess_d\n",
     "\n",
     "CASES = {\n",
     "    'A': {'18O': -10 * const.PER_MILLE, '2H': -80 * const.PER_MILLE},\n",

diff --git a/examples/PySDM_examples/Pierchala_et_al_2022/fig_3.ipynb b/examples/PySDM_examples/Pierchala_et_al_2022/fig_3.ipynb
@@ -71,7 +71,7 @@
    "source": [
     "formulae = Formulae(\n",
     "    isotope_equilibrium_fractionation_factors='BarkanAndLuz2005+HoritaAndWesolowski1994',\n",
-    "    isotope_meteoric_water_line_excess='Dansgaard1964+BarkanAndLuz2007',\n",
+    "    isotope_meteoric_water_line='Dansgaard1964+BarkanAndLuz2007',\n",
     "    isotope_ratio_evolution='RayleighDistillation'\n",
     ")\n",
     "const = formulae.constants\n",
@@ -118,7 +118,7 @@
     "alpha_l_2H = alphas.alpha_l_2H(T=T)\n",
     "alpha_l_17O = alphas.alpha_l_17O(np.nan, alpha_l_18O=alpha_l_18O)\n",
     "\n",
-    "excess = formulae.isotope_meteoric_water_line_excess\n",
+    "excess = formulae.isotope_meteoric_water_line\n",
     "\n",
     "deltas = {}\n",
     "enrichments = {}\n",

diff --git a/examples/PySDM_examples/Pierchala_et_al_2022/fig_4.ipynb b/examples/PySDM_examples/Pierchala_et_al_2022/fig_4.ipynb
@@ -72,7 +72,7 @@
     "\n",
     "formulae = Formulae(\n",
     "    isotope_equilibrium_fractionation_factors='BarkanAndLuz2005+HoritaAndWesolowski1994',\n",
-    "    isotope_meteoric_water_line_excess='Dansgaard1964+BarkanAndLuz2007',\n",
+    "    isotope_meteoric_water_line='Dansgaard1964+BarkanAndLuz2007',\n",
     "    isotope_ratio_evolution='RayleighDistillation'\n",
     ")\n",
     "const = formulae.constants\n",
@@ -165,7 +165,7 @@
     "    axs[1].plot(\n",
     "        x,\n",
     "        in_unit(\n",
-    "            formulae.isotope_meteoric_water_line_excess.excess_17O(deltas['17O'], deltas['18O']),\n",
+    "            formulae.isotope_meteoric_water_line.excess_17O(deltas['17O'], deltas['18O']),\n",
     "            const.PER_MEG\n",
     "        ),\n",
     "        **kwargs\n",

diff --git a/examples/PySDM_examples/Rozanski_and_Sonntag_1982/figs_4_5_6.ipynb b/examples/PySDM_examples/Rozanski_and_Sonntag_1982/figs_4_5_6.ipynb
@@ -76,7 +76,7 @@
    "source": [
     "formulae = Formulae(\n",
     "    isotope_equilibrium_fractionation_factors='HoritaAndWesolowski1994',\n",
-    "    isotope_meteoric_water_line_excess='Dansgaard1964',\n",
+    "    isotope_meteoric_water_line='Dansgaard1964',\n",
     "    isotope_ratio_evolution='MerlivatAndJouzel1979',\n",
     ")\n",
     "BACKEND = CPU(formulae, override_jit_flags={'parallel': False})\n",
@@ -96,7 +96,7 @@
     "}\n",
     "\n",
     "ARBITRARY_PARAMS = {\n",
-    "    'delta_18O_init': formulae.isotope_meteoric_water_line_excess.d18O_of_d2H(\n",
+    "    'delta_18O_init': formulae.isotope_meteoric_water_line.d18O_of_d2H(\n",
     "        delta_2H=FIG4_CAPTION_PARAMS['delta_2H_init']\n",
     "    ),\n",
     "    'N_SUPER_DROPLETS': 1,\n",
@@ -12299,7 +12299,7 @@
     "            )\n",
     "        axs[plot_row, 3].plot(\n",
     "            in_unit(\n",
-    "                formulae.isotope_meteoric_water_line_excess.excess_d(delta_2H=deltas[\"2H\"], delta_18O=deltas[\"18O\"]),\n",
+    "                formulae.isotope_meteoric_water_line.excess_d(delta_2H=deltas[\"2H\"], delta_18O=deltas[\"18O\"]),\n",
     "                const.PER_MILLE\n",
     "            ),\n",
     "            temp_C[level_indices['CB']:],\n",

diff --git a/tests/smoke_tests/no_env/pierchala_et_al_2022/test_fig_4.py b/tests/smoke_tests/no_env/pierchala_et_al_2022/test_fig_4.py
@@ -62,7 +62,7 @@ def test_bottom_panel(notebook_local_variables, RH, delta_18O, excess_17O):
         np.testing.assert_approx_equal(
             actual=notebook_local_variables[
                 "formulae"
-            ].isotope_meteoric_water_line_excess.excess_17O(
+            ].isotope_meteoric_water_line.excess_17O(
                 deltas_per_rh[RH]["17O"][index], deltas_per_rh[RH]["18O"][index]
             ),
             desired=excess_17O,

diff --git a/tests/smoke_tests/no_env/pierchala_et_al_2022/test_supplement.py b/tests/smoke_tests/no_env/pierchala_et_al_2022/test_supplement.py
@@ -9,10 +9,8 @@
 def test_cracow_water_excesses():
     """checking if d-excess and 17O-excess values match those computed from deltas"""
     # arrange
-    formulae = Formulae(
-        isotope_meteoric_water_line_excess="Dansgaard1964+BarkanAndLuz2007"
-    )
-    sut = formulae.isotope_meteoric_water_line_excess
+    formulae = Formulae(isotope_meteoric_water_line="Dansgaard1964+BarkanAndLuz2007")
+    sut = formulae.isotope_meteoric_water_line
 
     # act/assert
     np.testing.assert_approx_equal(