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Fix CLI tutorials for Colab #492

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Merged
alinelena merged 1 commit into from
Mar 25, 2025
Merged

Fix CLI tutorials for Colab #492

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32 changes: 10 additions & 22 deletions docs/source/tutorials/cli/geomopt.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,10 @@
"source": [
"# import locale\n",
"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
"# !python3 -m pip install janus-core[all] data-tutorials"
"\n",
"# ! pip uninstall torch torchaudio torchvision numpy -y\n",
"# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
"# get_ipython().kernel.do_shutdown(restart=True)"
]
},
{
Expand Down Expand Up @@ -84,10 +87,14 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"\n",
"from ase.build import bulk\n",
"from ase.io import write\n",
"from weas_widget import WeasWidget\n",
"\n",
"Path(\"data\").mkdir(exist_ok=True)\n",
"\n",
"NaCl = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n",
"NaCl[0].position = [1.5, 1.5, 1.5]\n",
"\n",
Expand Down Expand Up @@ -375,7 +382,7 @@
"<div class=\"alert alert-block alert-info\">\n",
"<b>Tip:</b> This is equivalent to:\n",
"\n",
"--struct data/NaCl-deformed.xyz --opt-cell-fully --filter-func ExpCellFilter --minimize-kwargs \"{'filter_kwargs': {'constant_volume' : True} --no-tracker\n",
"--struct data/NaCl-deformed.xyz --opt-cell-fully --filter-func ExpCellFilter --minimize-kwargs \"{'filter_kwargs': {'constant_volume' : True}\" --no-tracker\n",
"</div>\n"
]
},
Expand Down Expand Up @@ -494,33 +501,14 @@
"tracker: False"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%writefile geomopt_config_sevennet.yml\n",
"\n",
"struct: data/NaCl-deformed.xyz\n",
"arch: sevennet\n",
"opt_cell_fully: True\n",
"minimize_kwargs:\n",
" filter_kwargs:\n",
" constant_volume: True\n",
"pressure: 10\n",
"file_prefix: janus_results/NaCl-sevennet\n",
"tracker: False"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"! janus geomopt --config geomopt_config_mace.yml\n",
"! janus geomopt --config geomopt_config_sevennet.yml"
"! janus geomopt --config geomopt_config_mace.yml --arch sevennet --file-prefix janus_results/NaCl-sevennet"
]
},
{
Expand Down
16 changes: 10 additions & 6 deletions docs/source/tutorials/cli/md.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,10 @@
"source": [
"# import locale\n",
"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
"# !python3 -m pip install janus-core[all] data-tutorials"
"\n",
"# ! pip uninstall torch torchaudio torchvision numpy -y\n",
"# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
"# get_ipython().kernel.do_shutdown(restart=True)"
]
},
{
Expand Down Expand Up @@ -121,6 +124,8 @@
"traj_every: 10\n",
"restart_every: 50\n",
"\n",
"tracker: False\n",
"\n",
"# If you have an Nvidia GPU.\n",
"#device: cuda"
]
Expand Down Expand Up @@ -373,6 +378,8 @@
" a_kwargs: {'components': ['xy', 'yz', 'zx']}\n",
" points: 250\n",
"\n",
"tracker: False\n",
"\n",
"# If you have an Nvidia GPU.\n",
"#device: cuda"
]
Expand Down Expand Up @@ -491,6 +498,8 @@
"stats_every: 10\n",
"traj_every: 10\n",
"\n",
"tracker: False\n",
"\n",
"# If you have an Nvidia GPU.\n",
"#device: cuda"
]
Expand Down Expand Up @@ -543,11 +552,6 @@
"\n",
"Experimentally NaCl melts at about 1074 Kelvin at atmospheric pressure."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
],
"metadata": {
Expand Down
27 changes: 8 additions & 19 deletions docs/source/tutorials/cli/neb.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,10 @@
"source": [
"# import locale\n",
"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
"# !python3 -m pip install janus-core[all] data-tutorials"
"\n",
"# ! pip uninstall torch torchaudio torchvision numpy -y\n",
"# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
"# get_ipython().kernel.do_shutdown(restart=True)"
]
},
{
Expand All @@ -77,7 +80,7 @@
"from data_tutorials.data import get_data\n",
"\n",
"get_data(\n",
" url=\"https://raw.githubusercontent.com/stfc/janus-tutorials/main/data/\",\n",
" url=\"https://raw.githubusercontent.com/stfc/janus-core/main/docs/source/tutorials/data/\",\n",
" filename=[\"ethanol_reactants.extxyz\", \"ethanol_products.extxyz\",\"ethanol_reactants_1water.extxyz\",\"ethanol_products_1water.extxyz\",\"ethanol_reactants_2water.extxyz\",\"ethanol_products_2water.extxyz\"],\n",
" folder=\"data\",\n",
")"
Expand Down Expand Up @@ -131,9 +134,10 @@
"minimize: True\n",
"plot_band: True\n",
"write_band: True\n",
"calc-kwargs:\n",
"calc_kwargs:\n",
" dispersion: True\n",
" model: medium-omat-0"
" model: medium-omat-0\n",
"tracker: False"
]
},
{
Expand Down Expand Up @@ -302,11 +306,6 @@
"w2"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -317,16 +316,6 @@
"- analyse the barrier height trend.\n",
"- consider redoing the same exercise with a different potential... remember if you use mace-off dispersion needs to be off.\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
],
"metadata": {
Expand Down
29 changes: 13 additions & 16 deletions docs/source/tutorials/cli/phonons.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,10 @@
"source": [
"# import locale\n",
"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
"# !python3 -m pip install janus-core[all] data-tutorials"
"\n",
"# ! pip uninstall torch torchaudio torchvision numpy -y\n",
"# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
"# get_ipython().kernel.do_shutdown(restart=True)"
]
},
{
Expand Down Expand Up @@ -153,7 +156,7 @@
"calc-kwargs:\n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand Down Expand Up @@ -243,7 +246,7 @@
" skin: 0 \n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand Down Expand Up @@ -316,7 +319,7 @@
" skin: 0 \n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand Down Expand Up @@ -380,7 +383,7 @@
" skin: 0 \n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand Down Expand Up @@ -419,7 +422,7 @@
"outputs": [],
"source": [
"get_data(\n",
" url=\"https://raw.githubusercontent.com/stfc/janus-tutorials/main/data/\",\n",
" url=\"https://raw.githubusercontent.com/stfc/janus-core/main/docs/source/tutorials/data/\",\n",
" filename=[\"mof-5.cif\",\"paths.yaml\"],\n",
" folder=\"data\",\n",
")"
Expand All @@ -431,7 +434,6 @@
"metadata": {},
"outputs": [],
"source": [
"\n",
"mof5 = read(\"data/mof-5.cif\")\n",
"v=WeasWidget()\n",
"v.from_ase(mof5)\n",
Expand Down Expand Up @@ -471,7 +473,7 @@
" skin: 0 \n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand Down Expand Up @@ -506,7 +508,7 @@
"outputs": [],
"source": [
"from IPython.display import SVG, display\n",
"display(SVG(\"janus_results/mof-5-bs-dos.svg\"))\n"
"display(SVG(\"janus_results/mof-5-bs-dos.svg\"))"
]
},
{
Expand Down Expand Up @@ -542,7 +544,7 @@
" skin: 0 \n",
" model: medium-mpa-0\n",
"device: cpu\n",
"\n"
"tracker: False"
]
},
{
Expand All @@ -569,7 +571,7 @@
"metadata": {},
"outputs": [],
"source": [
"display(SVG(\"janus_results/mof-5-bs-dos.svg\"))\n"
"display(SVG(\"janus_results/mof-5-bs-dos.svg\"))"
]
},
{
Expand All @@ -584,11 +586,6 @@
"\n",
"this is part of this paper if you want to know more: https://arxiv.org/abs/2412.02877"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
],
"metadata": {
Expand Down
49 changes: 41 additions & 8 deletions docs/source/tutorials/cli/singlepoint.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,10 @@
"source": [
"# import locale\n",
"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
"# !python3 -m pip install janus-core[all] data-tutorials"
"\n",
"# ! pip uninstall torch torchaudio torchvision numpy -y\n",
"# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
"# get_ipython().kernel.do_shutdown(restart=True)"
]
},
{
Expand Down Expand Up @@ -214,11 +217,11 @@
"metadata": {},
"outputs": [],
"source": [
"print(f\"Energy: {results.info[\"mace_mp_energy\"]}\")\n",
"print(f\"Energy: {results.info['mace_mp_energy']}\")\n",
"print()\n",
"print(f\"Stress: {results.info[\"mace_mp_stress\"]}\")\n",
"print(f\"Stress: {results.info['mace_mp_stress']}\")\n",
"print()\n",
"print(f\"Forces: {results.arrays[\"mace_mp_forces\"]}\")"
"print(f\"Forces: {results.arrays['mace_mp_forces']}\")"
]
},
{
Expand Down Expand Up @@ -284,6 +287,15 @@
"tracker: False"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"! cat singlepoint_config_1.yml"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -341,7 +353,8 @@
"metadata": {},
"source": [
"<div class=\"alert alert-block alert-info\">\n",
"<b>Note:</b> In the CLI, arguments are separated by \"-\", while in configuration files, they are specified by \"_\"\n",
"<b>Note:</b> In the CLI, multi-word arguments must be separated by \"-\".\n",
"In configuration files, they are preferably separated by \"_\", although \"-\" should be converted automatically.\n",
"</div>"
]
},
Expand Down Expand Up @@ -619,7 +632,7 @@
"metadata": {},
"outputs": [],
"source": [
"! janus singlepoint --config singlepoint_config_1.yml --calc-kwargs \"{'dispersion': True}\""
"! janus singlepoint --config singlepoint_config_1.yml --calc-kwargs \"{'dispersion': True}\" --out janus_results/NaCl-dispersion-results.extxyz"
]
},
{
Expand All @@ -640,7 +653,24 @@
"struct: data/NaCl.xyz\n",
"tracker: False\n",
"calc_kwargs:\n",
" dispersion: True"
" dispersion: True\n",
"out: janus_results/NaCl-dispersion-results.extxyz"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"! janus singlepoint --config singlepoint_config_4.yml"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Comparing the results before and after the correction:"
]
},
{
Expand All @@ -649,7 +679,10 @@
"metadata": {},
"outputs": [],
"source": [
"! janus singlepoint --config singlepoint_config_4.yml --calc-kwargs \"{'dispersion': True}\""
"dispersion_results = read(\"janus_results/NaCl-dispersion-results.extxyz\")\n",
"\n",
"print(f\"Original results: {results.info['mace_mp_energy']}\")\n",
"print(f\"Results with dispersion correction: {dispersion_results.info['mace_mp_energy']}\")"
]
}
],
Expand Down
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