From 1298b5d77ff9842f73aa5037c887aa4ca01d5e39 Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Wed, 3 Jun 2026 08:52:26 +0200 Subject: [PATCH 1/2] populate A&F example notebooks with output --- .../Arabas_and_Farhat_2020/fig_1.ipynb | 1935 ++++++++++++++++- .../Arabas_and_Farhat_2020/fig_2.ipynb | 1632 +++++++++++++- .../Arabas_and_Farhat_2020/fig_3.ipynb | 1578 +++++++++++++- 3 files changed, 5103 insertions(+), 42 deletions(-) diff --git a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_1.ipynb b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_1.ipynb index 230633fa2..14f281f50 100644 --- a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_1.ipynb +++ b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_1.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "pycharm": { "name": "#%%\n" @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -52,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -62,7 +62,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -74,9 +74,1924 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " 2026-06-03T08:44:10.776436\n", + " image/svg+xml\n", + " \n", + " \n", + " Matplotlib v3.10.8, https://matplotlib.org/\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " 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" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "04820d95f7344326a2a1bf1a7fbe071e", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "HBox(children=(HTML(value=\"./tmp3c5ffzq5.pdf
\"), HTML(value…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "fig, ax1 = pyplot.subplots()\n", "yscl = 1 / (settings.K2 - settings.K1)\n", @@ -100,7 +2015,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -110,7 +2025,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -120,7 +2035,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -155,7 +2070,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.2" + "version": "3.13.5" } }, "nbformat": 4, diff --git a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb index e3ad0131a..bd70e63a2 100644 --- a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb +++ b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "pycharm": { "name": "#%%\n" @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -51,9 +51,24 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[Parallel(n_jobs=-2)]: Using backend ThreadingBackend with 7 concurrent workers.\n", + "[Parallel(n_jobs=-2)]: Done 2 out of 9 | elapsed: 46.1s remaining: 2.7min\n", + "[Parallel(n_jobs=-2)]: Done 3 out of 9 | elapsed: 46.2s remaining: 1.5min\n", + "[Parallel(n_jobs=-2)]: Done 4 out of 9 | elapsed: 46.6s remaining: 58.2s\n", + "[Parallel(n_jobs=-2)]: Done 5 out of 9 | elapsed: 46.6s remaining: 37.3s\n", + "[Parallel(n_jobs=-2)]: Done 6 out of 9 | elapsed: 46.6s remaining: 23.3s\n", + "[Parallel(n_jobs=-2)]: Done 7 out of 9 | elapsed: 46.6s remaining: 13.3s\n", + "[Parallel(n_jobs=-2)]: Done 9 out of 9 | elapsed: 46.6s finished\n" + ] + } + ], "source": [ "# note: delete \"num=...\" for same number of points as in the paper\n", "data_C_err = convergence_in_space(num=3)" @@ -61,9 +76,1594 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " 2026-06-03T08:47:10.085911\n", + " image/svg+xml\n", + " \n", + " \n", + " Matplotlib v3.10.8, https://matplotlib.org/\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " 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\"), HTML(value…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "fig, ax = pyplot.subplots()\n", "x = np.array(next(iter(data_C_err.values()))[0])\n", @@ -87,7 +1687,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -101,7 +1701,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -113,20 +1713,6 @@ " assert np.mean(slope) >= 2.8" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, { "cell_type": "code", "execution_count": null, @@ -151,7 +1737,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.2" + "version": "3.13.5" } }, "nbformat": 4, diff --git a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb index ae9732809..9ad577f6a 100644 --- a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb +++ b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "pycharm": { "name": "#%%\n" @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -51,9 +51,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[Parallel(n_jobs=-2)]: Using backend ThreadingBackend with 7 concurrent workers.\n", + "[Parallel(n_jobs=-2)]: Done 2 out of 9 | elapsed: 46.4s remaining: 2.7min\n", + "[Parallel(n_jobs=-2)]: Done 3 out of 9 | elapsed: 46.5s remaining: 1.5min\n", + "/home/user/devel/PySDM/venv/lib/python3.13/site-packages/numba/core/utils.py:621: NumbaExperimentalFeatureWarning: [Parallel(n_jobs=-2)]: Done 4 out of 9 | elapsed: 46.5s remaining: 58.1s\n", + "[Parallel(n_jobs=-2)]: Done 5 out of 9 | elapsed: 46.5s remaining: 37.2s\n", + "First-class function type feature is experimental[Parallel(n_jobs=-2)]: Done 6 out of 9 | elapsed: 46.5s remaining: 23.2s\n", + "\n", + " warnings.warn(\"First-class function type feature is experimental\",\n", + "[Parallel(n_jobs=-2)]: Done 7 out of 9 | elapsed: 46.5s remaining: 13.3s\n", + "[Parallel(n_jobs=-2)]: Done 9 out of 9 | elapsed: 46.5s finished\n" + ] + } + ], "source": [ "# note: delete \"num=...\" for same number of points as in the paper\n", "data_l2_err = convergence_in_time(num=3)" @@ -61,9 +78,1552 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "image/svg+xml": 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\"), HTML(value…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "fig, ax = pyplot.subplots()\n", "x = np.array(next(iter(data_l2_err.values()))[0])\n", @@ -87,7 +1647,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -101,7 +1661,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -137,7 +1697,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.2" + "version": "3.13.5" } }, "nbformat": 4, From 7ab98d165e0342d56d820b97e70e869e24e5bcfc Mon Sep 17 00:00:00 2001 From: Sylwester Arabas Date: Wed, 3 Jun 2026 08:59:46 +0200 Subject: [PATCH 2/2] remove stderr stream output --- .../Arabas_and_Farhat_2020/fig_2.ipynb | 17 +---------------- .../Arabas_and_Farhat_2020/fig_3.ipynb | 19 +------------------ 2 files changed, 2 insertions(+), 34 deletions(-) diff --git a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb index bd70e63a2..599a702e4 100644 --- a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb +++ b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb @@ -53,22 +53,7 @@ "cell_type": "code", "execution_count": 3, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[Parallel(n_jobs=-2)]: Using backend ThreadingBackend with 7 concurrent workers.\n", - "[Parallel(n_jobs=-2)]: Done 2 out of 9 | elapsed: 46.1s remaining: 2.7min\n", - "[Parallel(n_jobs=-2)]: Done 3 out of 9 | elapsed: 46.2s remaining: 1.5min\n", - "[Parallel(n_jobs=-2)]: Done 4 out of 9 | elapsed: 46.6s remaining: 58.2s\n", - "[Parallel(n_jobs=-2)]: Done 5 out of 9 | elapsed: 46.6s remaining: 37.3s\n", - "[Parallel(n_jobs=-2)]: Done 6 out of 9 | elapsed: 46.6s remaining: 23.3s\n", - "[Parallel(n_jobs=-2)]: Done 7 out of 9 | elapsed: 46.6s remaining: 13.3s\n", - "[Parallel(n_jobs=-2)]: Done 9 out of 9 | elapsed: 46.6s finished\n" - ] - } - ], + "outputs": [], "source": [ "# note: delete \"num=...\" for same number of points as in the paper\n", "data_C_err = convergence_in_space(num=3)" diff --git a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb index 9ad577f6a..a2d2549dd 100644 --- a/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb +++ b/examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb @@ -53,24 +53,7 @@ "cell_type": "code", "execution_count": 3, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[Parallel(n_jobs=-2)]: Using backend ThreadingBackend with 7 concurrent workers.\n", - "[Parallel(n_jobs=-2)]: Done 2 out of 9 | elapsed: 46.4s remaining: 2.7min\n", - "[Parallel(n_jobs=-2)]: Done 3 out of 9 | elapsed: 46.5s remaining: 1.5min\n", - "/home/user/devel/PySDM/venv/lib/python3.13/site-packages/numba/core/utils.py:621: NumbaExperimentalFeatureWarning: [Parallel(n_jobs=-2)]: Done 4 out of 9 | elapsed: 46.5s remaining: 58.1s\n", - "[Parallel(n_jobs=-2)]: Done 5 out of 9 | elapsed: 46.5s remaining: 37.2s\n", - "First-class function type feature is experimental[Parallel(n_jobs=-2)]: Done 6 out of 9 | elapsed: 46.5s remaining: 23.2s\n", - "\n", - " warnings.warn(\"First-class function type feature is experimental\",\n", - "[Parallel(n_jobs=-2)]: Done 7 out of 9 | elapsed: 46.5s remaining: 13.3s\n", - "[Parallel(n_jobs=-2)]: Done 9 out of 9 | elapsed: 46.5s finished\n" - ] - } - ], + "outputs": [], "source": [ "# note: delete \"num=...\" for same number of points as in the paper\n", "data_l2_err = convergence_in_time(num=3)"