From 9195e67a3ba6e541fc4257b2a2ecfcae27616449 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Agnieszka=20=C5=BBaba?= <azaba@agh.edu.pl>
Date: Mon, 14 Jul 2025 21:34:58 +0200
Subject: [PATCH 1/3] fractionation factors for different S and temp

---
 .../Zaba_et_al/fractionation_factors.ipynb    | 169 ++++++++++++++++++
 1 file changed, 169 insertions(+)
 create mode 100644 examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb

diff --git a/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb b/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
new file mode 100644
index 000000000..fefc5150a
--- /dev/null
+++ b/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
@@ -0,0 +1,169 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "id": "initial_id",
+   "metadata": {
+    "collapsed": true,
+    "ExecuteTime": {
+     "end_time": "2025-07-14T18:42:23.295115Z",
+     "start_time": "2025-07-14T18:42:23.287266Z"
+    }
+   },
+   "source": [
+    "import numpy as np\n",
+    "from matplotlib import pyplot\n",
+    "from functools import partial\n",
+    "from open_atmos_jupyter_utils import show_plot\n",
+    "\n",
+    "from PySDM import Formulae\n",
+    "from PySDM.physics import si"
+   ],
+   "outputs": [],
+   "execution_count": 71
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-07-14T19:16:41.463007Z",
+     "start_time": "2025-07-14T19:16:41.449038Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "formulae = Formulae(\n",
+    "    isotope_equilibrium_fractionation_factors=\"MerlivatAndNief1967+Majoube1970+Majoube1971\",\n",
+    "    isotope_kinetic_fractionation_factors=\"JouzelAndMerlivat1984\",\n",
+    "    isotope_diffusivity_ratios=\"Stewart1975\"\n",
+    ")\n",
+    "\n",
+    "saturation = np.linspace(.7, 1.1, 7)\n",
+    "temperature_C = np.linspace(-30, 0)\n",
+    "temperature = formulae.trivia.C2K(temperature_C) * si.K\n"
+   ],
+   "id": "5f8f76c80c1d2286",
+   "outputs": [],
+   "execution_count": 126
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-07-14T19:16:41.836941Z",
+     "start_time": "2025-07-14T19:16:41.833451Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "alpha_liquid = formulae.isotope_equilibrium_fractionation_factors.alpha_l_2H(temperature)\n",
+    "alpha_kinetic = partial(formulae.isotope_kinetic_fractionation_factors.alpha_kinetic, alpha_equilibrium=alpha, D_ratio_heavy_to_light=formulae.isotope_diffusivity_ratios.ratio_2H_heavy_to_light(temperature))\n",
+    "alpha_ice = formulae.isotope_equilibrium_fractionation_factors.alpha_i_2H(temperature)"
+   ],
+   "id": "810fcbb7b502850d",
+   "outputs": [],
+   "execution_count": 127
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-07-14T19:34:08.839335Z",
+     "start_time": "2025-07-14T19:34:07.644009Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "for S in saturation:\n",
+    "    alpha = alpha_liquid * alpha_kinetic(saturation=S)\n",
+    "    pyplot.plot(alpha, temperature_C, 'k', alpha=0.1)\n",
+    "    pyplot.annotate(f'{S:.3g}', xy=(alpha[4], temperature_C[4]), rotation=55, color='k', alpha=0.5, size=10)\n",
+    "\n",
+    "pyplot.plot(alpha_kinetic(saturation=1)*alpha_ice, temperature_C, label='wrt ice')\n",
+    "print(alpha[3]/alpha[0])\n",
+    "pyplot.plot(alpha_kinetic(saturation=1)*alpha_liquid, temperature_C, label='wrt liquid')\n",
+    "pyplot.gca().set(\n",
+    "    xlabel='Fractionation factor',\n",
+    "    ylabel=\"Temperature [K]\",\n",
+    ")\n",
+    "pyplot.gca().invert_yaxis()\n",
+    "pyplot.legend()\n",
+    "show_plot()\n"
+   ],
+   "id": "2f1aeb9076b01e6f",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.9965711674381411\n"
+     ]
+    },
+    {
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From 93a965f425b5836a8ddb8557f2ddef86ffec26a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Agnieszka=20=C5=BBaba?= <azaba@agh.edu.pl>
Date: Tue, 15 Jul 2025 21:06:08 +0200
Subject: [PATCH 2/3] fix args naming

---
 .../Zaba_et_al/fractionation_factors.ipynb    | 76 +++++++++----------
 1 file changed, 36 insertions(+), 40 deletions(-)

diff --git a/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb b/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
index fefc5150a..7193ed0cb 100644
--- a/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
+++ b/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
@@ -6,8 +6,8 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2025-07-14T18:42:23.295115Z",
-     "start_time": "2025-07-14T18:42:23.287266Z"
+     "end_time": "2025-07-15T18:53:32.653518Z",
+     "start_time": "2025-07-15T18:53:30.861075Z"
     }
    },
    "source": [
@@ -20,13 +20,13 @@
     "from PySDM.physics import si"
    ],
    "outputs": [],
-   "execution_count": 71
+   "execution_count": 1
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-14T19:16:41.463007Z",
-     "start_time": "2025-07-14T19:16:41.449038Z"
+     "end_time": "2025-07-15T18:53:33.014638Z",
+     "start_time": "2025-07-15T18:53:32.737631Z"
     }
    },
    "cell_type": "code",
@@ -38,47 +38,58 @@
     ")\n",
     "\n",
     "saturation = np.linspace(.7, 1.1, 7)\n",
+    "\n",
+    "# temperature_C might be replaced with temperature profile\n",
     "temperature_C = np.linspace(-30, 0)\n",
     "temperature = formulae.trivia.C2K(temperature_C) * si.K\n"
    ],
    "id": "5f8f76c80c1d2286",
    "outputs": [],
-   "execution_count": 126
+   "execution_count": 2
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-14T19:16:41.836941Z",
-     "start_time": "2025-07-14T19:16:41.833451Z"
+     "end_time": "2025-07-15T18:53:34.101574Z",
+     "start_time": "2025-07-15T18:53:33.022297Z"
     }
    },
    "cell_type": "code",
    "source": [
-    "alpha_liquid = formulae.isotope_equilibrium_fractionation_factors.alpha_l_2H(temperature)\n",
-    "alpha_kinetic = partial(formulae.isotope_kinetic_fractionation_factors.alpha_kinetic, alpha_equilibrium=alpha, D_ratio_heavy_to_light=formulae.isotope_diffusivity_ratios.ratio_2H_heavy_to_light(temperature))\n",
-    "alpha_ice = formulae.isotope_equilibrium_fractionation_factors.alpha_i_2H(temperature)"
+    "alpha_l = formulae.isotope_equilibrium_fractionation_factors.alpha_l_2H(temperature)\n",
+    "alpha_l_kinetic = partial(\n",
+    "    formulae.isotope_kinetic_fractionation_factors.alpha_kinetic,\n",
+    "    alpha_equilibrium=alpha_l,\n",
+    "    D_ratio_heavy_to_light=formulae.isotope_diffusivity_ratios.ratio_2H_heavy_to_light(temperature)\n",
+    ")\n",
+    "\n",
+    "alpha_i = formulae.isotope_equilibrium_fractionation_factors.alpha_i_2H(temperature)\n",
+    "alpha_i_kinetic = partial(\n",
+    "    formulae.isotope_kinetic_fractionation_factors.alpha_kinetic,\n",
+    "    alpha_equilibrium=alpha_i,\n",
+    "    D_ratio_heavy_to_light=formulae.isotope_diffusivity_ratios.ratio_2H_heavy_to_light(temperature)\n",
+    ")"
    ],
    "id": "810fcbb7b502850d",
    "outputs": [],
-   "execution_count": 127
+   "execution_count": 3
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-14T19:34:08.839335Z",
-     "start_time": "2025-07-14T19:34:07.644009Z"
+     "end_time": "2025-07-15T18:53:34.418783Z",
+     "start_time": "2025-07-15T18:53:34.110259Z"
     }
    },
    "cell_type": "code",
    "source": [
     "for S in saturation:\n",
-    "    alpha = alpha_liquid * alpha_kinetic(saturation=S)\n",
+    "    alpha = alpha_l * alpha_l_kinetic(saturation=S)\n",
     "    pyplot.plot(alpha, temperature_C, 'k', alpha=0.1)\n",
     "    pyplot.annotate(f'{S:.3g}', xy=(alpha[4], temperature_C[4]), rotation=55, color='k', alpha=0.5, size=10)\n",
     "\n",
-    "pyplot.plot(alpha_kinetic(saturation=1)*alpha_ice, temperature_C, label='wrt ice')\n",
-    "print(alpha[3]/alpha[0])\n",
-    "pyplot.plot(alpha_kinetic(saturation=1)*alpha_liquid, temperature_C, label='wrt liquid')\n",
+    "pyplot.plot(alpha_i_kinetic(saturation=1)*alpha_i, temperature_C, label='wrt ice')\n",
+    "pyplot.plot(alpha_l_kinetic(saturation=1)*alpha_l, temperature_C, label='wrt liquid')\n",
     "pyplot.gca().set(\n",
     "    xlabel='Fractionation factor',\n",
     "    ylabel=\"Temperature [K]\",\n",
@@ -89,19 +100,12 @@
    ],
    "id": "2f1aeb9076b01e6f",
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "0.9965711674381411\n"
-     ]
-    },
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@@ -109,40 +113,32 @@
     {
      "data": {
       "text/plain": [
-       "HBox(children=(HTML(value=\"<a href='./tmp_l8_pbgl.pdf' target='_blank'>./tmp_l8_pbgl.pdf</a><br>\"), HTML(value…"
+       "HBox(children=(HTML(value=\"<a href='./tmphss6ofj6.pdf' target='_blank'>./tmphss6ofj6.pdf</a><br>\"), HTML(value…"
       ],
       "application/vnd.jupyter.widget-view+json": {
        "version_major": 2,
        "version_minor": 0,
-       "model_id": "a8f58c2a3af844b08fb503e47f0af6f2"
+       "model_id": "99cfa7e0f64b411abb28c15e1bea5957"
       }
      },
      "metadata": {},
      "output_type": "display_data"
     }
    ],
-   "execution_count": 149
+   "execution_count": 4
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-14T19:23:49.618983Z",
-     "start_time": "2025-07-14T19:23:49.615602Z"
+     "end_time": "2025-07-15T18:53:34.461114Z",
+     "start_time": "2025-07-15T18:53:34.459575Z"
     }
    },
    "cell_type": "code",
    "source": "",
-   "id": "3a1b25d03fa7c846",
+   "id": "79642bd18579086a",
    "outputs": [],
    "execution_count": null
-  },
-  {
-   "metadata": {},
-   "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
-   "source": "",
-   "id": "79642bd18579086a"
   }
  ],
  "metadata": {

From 3c7b987ed7ca90bae3984327dbaf7bb509d104db Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Agnieszka=20=C5=BBaba?= <azaba@agh.edu.pl>
Date: Mon, 17 Nov 2025 16:40:58 +0100
Subject: [PATCH 3/3] move to HOWTOs, start description; add badges

---
 .../fractionation_factors.ipynb               | 108 ++++++++++++++----
 1 file changed, 83 insertions(+), 25 deletions(-)
 rename examples/PySDM_examples/{Zaba_et_al => _HOWTOs}/fractionation_factors.ipynb (81%)

diff --git a/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb b/examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb
similarity index 81%
rename from examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
rename to examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb
index 7193ed0cb..5e5065e42 100644
--- a/examples/PySDM_examples/Zaba_et_al/fractionation_factors.ipynb
+++ b/examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb
@@ -1,13 +1,53 @@
 {
  "cells": [
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "[![preview notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb)\n",
+    "[![launch on mybinder.org](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb)\n",
+    "[![launch on Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/fractionation_factors.ipynb)"
+   ],
+   "id": "be4d0663e92430ea"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "# Isotopic fractionation factors (kinetic and equilibrium) HOWTO\n",
+    "- $\\alpha(T)$ is a fractionation factor for water isotopologues, factors are different wrt ice and liquid phase\n",
+    "- effective, equilibrium and kinetic\n",
+    "- plot description"
+   ],
+   "id": "b7a9153ddefcdf76"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-11-17T15:35:49.920503Z",
+     "start_time": "2025-11-17T15:35:49.917010Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "import sys\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    !pip --quiet install open-atmos-jupyter-utils\n",
+    "    from open_atmos_jupyter_utils import pip_install_on_colab\n",
+    "    pip_install_on_colab('PySDM-examples')"
+   ],
+   "id": "dbb2b5f1c8d451d6",
+   "outputs": [],
+   "execution_count": 3
+  },
   {
    "cell_type": "code",
    "id": "initial_id",
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2025-07-15T18:53:32.653518Z",
-     "start_time": "2025-07-15T18:53:30.861075Z"
+     "end_time": "2025-11-17T15:39:18.823256Z",
+     "start_time": "2025-11-17T15:39:18.756973Z"
     }
    },
    "source": [
@@ -20,13 +60,19 @@
     "from PySDM.physics import si"
    ],
    "outputs": [],
-   "execution_count": 1
+   "execution_count": 8
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "formulae, considered saturation range, temperature profile (here linear)",
+   "id": "7011f12adc2d5dbd"
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-15T18:53:33.014638Z",
-     "start_time": "2025-07-15T18:53:32.737631Z"
+     "end_time": "2025-11-17T15:35:53.370217Z",
+     "start_time": "2025-11-17T15:35:52.792830Z"
     }
    },
    "cell_type": "code",
@@ -39,19 +85,24 @@
     "\n",
     "saturation = np.linspace(.7, 1.1, 7)\n",
     "\n",
-    "# temperature_C might be replaced with temperature profile\n",
     "temperature_C = np.linspace(-30, 0)\n",
-    "temperature = formulae.trivia.C2K(temperature_C) * si.K\n"
+    "temperature = formulae.trivia.C2K(temperature_C) * si.K"
    ],
    "id": "5f8f76c80c1d2286",
    "outputs": [],
-   "execution_count": 2
+   "execution_count": 5
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "fractionation factors for $^2$H in given temperature range (wrt ice and liquid, kinetic and equilibrium)",
+   "id": "e6d93020d01aefbd"
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-15T18:53:34.101574Z",
-     "start_time": "2025-07-15T18:53:33.022297Z"
+     "end_time": "2025-11-17T15:35:55.364926Z",
+     "start_time": "2025-11-17T15:35:53.375406Z"
     }
    },
    "cell_type": "code",
@@ -72,29 +123,30 @@
    ],
    "id": "810fcbb7b502850d",
    "outputs": [],
-   "execution_count": 3
+   "execution_count": 6
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-07-15T18:53:34.418783Z",
-     "start_time": "2025-07-15T18:53:34.110259Z"
+     "end_time": "2025-11-17T15:35:56.081460Z",
+     "start_time": "2025-11-17T15:35:55.392476Z"
     }
    },
    "cell_type": "code",
    "source": [
     "for S in saturation:\n",
-    "    alpha = alpha_l * alpha_l_kinetic(saturation=S)\n",
-    "    pyplot.plot(alpha, temperature_C, 'k', alpha=0.1)\n",
+    "    alpha_eff = alpha_l * alpha_l_kinetic(saturation=S)\n",
+    "    pyplot.plot(alpha_eff, temperature_C, 'k', alpha=0.1)\n",
     "    pyplot.annotate(f'{S:.3g}', xy=(alpha[4], temperature_C[4]), rotation=55, color='k', alpha=0.5, size=10)\n",
     "\n",
-    "pyplot.plot(alpha_i_kinetic(saturation=1)*alpha_i, temperature_C, label='wrt ice')\n",
-    "pyplot.plot(alpha_l_kinetic(saturation=1)*alpha_l, temperature_C, label='wrt liquid')\n",
+    "pyplot.plot(alpha_i_kinetic(saturation=1)*alpha_i, temperature_C, label=r'$\\alpha_\\text{eff}$ wrt ice')\n",
+    "pyplot.plot(alpha_l_kinetic(saturation=1)*alpha_l, temperature_C, label=r'$\\alpha_\\text{eff}$ wrt liquid')\n",
     "pyplot.gca().set(\n",
     "    xlabel='Fractionation factor',\n",
     "    ylabel=\"Temperature [K]\",\n",
     ")\n",
     "pyplot.gca().invert_yaxis()\n",
+    "pyplot.title(\"Effective fractionation factors wrt ice and liquid\")\n",
     "pyplot.legend()\n",
     "show_plot()\n"
    ],
@@ -105,33 +157,39 @@
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