From 9f34e98f0f6c93d193ef5a5cad9585d03eb742f6 Mon Sep 17 00:00:00 2001
From: Sylwester Arabas <sylwester.arabas@agh.edu.pl>
Date: Sat, 17 Aug 2024 17:15:25 +0200
Subject: [PATCH] Smolarkiewicz 2006 example: add missing badge, regenerate
 plots, fix rectangular signal width (#438)

---
 .../demo.ipynb                                | 2995 ++++++++++++++++-
 .../settings.py                               |    2 +-
 2 files changed, 2966 insertions(+), 31 deletions(-)

diff --git a/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb b/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb
index 68ccc4dc..9402f744 100644
--- a/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb
+++ b/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb
@@ -1,20 +1,23 @@
 {
  "cells": [
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "metadata": {
     "pycharm": {
      "name": "#%% raw\n"
     }
    },
    "source": [
+    "[![View notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PyMPDATA/blob/main/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb)\n",
     "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PyMPDATA.git/main?filepath=examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyMPDATA/blob/main/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb)"
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PyMPDATA/blob/main/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb)\n",
+    "\n",
+    "example based on basic 1D advection test from [Smolarkiewicz 2006](https://doi.org/10.1002/fld.1071)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,11 +30,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "from matplotlib import pyplot\n",
     "from open_atmos_jupyter_utils import show_plot\n",
     "from PyMPDATA import Options\n",
     "from PyMPDATA_examples.Smolarkiewicz_2006_Figs_3_4_10_11_12.simulation import Simulation\n",
@@ -40,71 +44,3002 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "def plot(simulation):\n",
+    "def plot(simulation, filename, yshift=0):\n",
     "    psi_0 = simulation.state\n",
     "    simulation.run()\n",
     "    psi_T = simulation.state\n",
-    "    plt.plot(psi_0)\n",
-    "    plt.plot(psi_T)\n",
-    "    show_plot()"
+    "    x, dx = np.linspace(-250, 250, len(psi_T), retstep=True, endpoint=False)\n",
+    "    x += dx/2\n",
+    "    pyplot.figure(figsize=(7,4))\n",
+    "    pyplot.grid()\n",
+    "    pyplot.ylim(-2 + yshift, 4 + yshift)\n",
+    "    pyplot.xlim(-250, 250)\n",
+    "    pyplot.yticks(np.linspace(-2 + yshift, 4 + yshift, 4))\n",
+    "    pyplot.xticks(np.linspace(-250, 250, 6))\n",
+    "    pyplot.plot(x, psi_0)\n",
+    "    pyplot.plot(x, psi_T)\n",
+    "    show_plot(filename)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
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    "source": [
-    "plot(Simulation(Settings(\"cosine\"), Options(n_iters=1)))"
+    "plot(Simulation(Settings(\"cosine\"), Options(n_iters=1)), filename='fig_3')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
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    "source": [
-    "plot(Simulation(Settings(\"cosine\"), Options(n_iters=2)))"
+    "plot(Simulation(Settings(\"cosine\"), Options(n_iters=2)), filename='fig_4')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
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    "source": [
-    "plot(Simulation(Settings(\"cosine\"), Options(infinite_gauge=True, n_iters=2)))"
+    "plot(Simulation(Settings(\"cosine\"), Options(infinite_gauge=True, n_iters=2)), filename='fig_10')"
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   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
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    "source": [
-    "plot(Simulation(Settings(\"rect\"), Options(infinite_gauge=True, n_iters=2)))"
+    "plot(Simulation(Settings(\"rect\"), Options(infinite_gauge=True, n_iters=2)), filename='fig_11', yshift=2)"
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   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [],
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+      ],
+      "text/plain": [
+       "<Figure size 700x400 with 1 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
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+    }
+   ],
    "source": [
-    "plot(Simulation(Settings(\"rect\"), Options(n_iters=2, infinite_gauge=True, nonoscillatory=True)))"
+    "plot(Simulation(Settings(\"rect\"), Options(n_iters=2, infinite_gauge=True, nonoscillatory=True)), filename='fig_12', yshift=2)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
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+       "  </clipPath>\n",
+       " </defs>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "<Figure size 700x400 with 1 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "931d0755a7be4e0a9ed2b76275c2a308",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(HTML(value=\"<a href='./fig_12_3_iters.pdf' target='_blank'>./fig_12_3_iters.pdf</a><br>\"), HTML…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
-    "plot(Simulation(Settings(\"rect\"), Options(n_iters=3, infinite_gauge=True, nonoscillatory=True)))"
+    "plot(Simulation(Settings(\"rect\"), Options(n_iters=3, infinite_gauge=True, nonoscillatory=True)), filename='fig_12_3_iters', yshift=2)"
    ]
   },
   {
@@ -117,7 +3052,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -131,7 +3066,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,
diff --git a/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/settings.py b/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/settings.py
index 02054462..a6855063 100644
--- a/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/settings.py
+++ b/examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/settings.py
@@ -34,5 +34,5 @@ def cdf_rect(x):
         amplitude = 2
         offset = 2
 
-        pdf = offset + np.where(np.abs(x - x_mid) <= 10, amplitude, 0)
+        pdf = offset + np.where(np.abs(x - x_mid) <= 12, amplitude, 0)
         return np.cumsum(pdf)