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alinelena merged 1 commit into from
Oct 3, 2025
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Remove SevenNet from tutorials #615

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12 changes: 6 additions & 6 deletions docs/source/tutorials/cli/geomopt.ipynb
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Expand Up @@ -50,7 +50,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,visualise] data-tutorials --system # Install janus-core with MACE, Orb, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -502,14 +502,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Comparing MACE to SevenNet"
"## Comparing MACE to Orb"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Finally, let's compare to the structure optimised by SevenNet:"
"Finally, let's compare to the structure optimised by Orb:"
]
},
{
Expand Down Expand Up @@ -538,7 +538,7 @@
"outputs": [],
"source": [
"! janus geomopt --config geomopt_config_mace.yml\n",
"! janus geomopt --config geomopt_config_mace.yml --arch sevennet --file-prefix janus_results/NaCl-sevennet"
"! janus geomopt --config geomopt_config_mace.yml --arch orb --file-prefix janus_results/NaCl-orb"
]
},
{
Expand All @@ -558,8 +558,8 @@
"from weas_widget import WeasWidget\n",
"\n",
"mace_opt = read(\"janus_results/NaCl-mace-opt.extxyz\")\n",
"sevennet_opt = read(\"janus_results/NaCl-sevennet-opt.extxyz\")\n",
"opt_comparison = [mace_opt, sevennet_opt]\n",
"orb_opt = read(\"janus_results/NaCl-orb-opt.extxyz\")\n",
"opt_comparison = [mace_opt, orb_opt]\n",
"\n",
"v=WeasWidget()\n",
"v.from_ase(opt_comparison)\n",
Expand Down
10 changes: 5 additions & 5 deletions docs/source/tutorials/cli/singlepoint.ipynb
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Expand Up @@ -23,7 +23,7 @@
"id": "4vcbRxmIhHLL"
},
"source": [
"`janus-core` contains various machine learnt interatomic potentials (MLIPs), including MACE based models (MACE-MP, MACE-OFF), CHGNet, SevenNet and more, full list on https://github.com/stfc/janus-core.\n",
"`janus-core` contains various machine learnt interatomic potentials (MLIPs), including MACE based models (MACE-MP, MACE-OFF), CHGNet, Orb and more, full list on https://github.com/stfc/janus-core.\n",
"\n",
"Other will be added as their utility is proven beyond a specific material."
]
Expand Down Expand Up @@ -59,7 +59,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,visualise] data-tutorials --system # Install janus-core with MACE, Orb, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -450,7 +450,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"For example, if we re-run the calculation using SevenNet, saving the results to a new output file, we see that \"mace_mp_energy\" is still saved, other unlabelled results are updated:"
"For example, if we re-run the calculation using Orb, saving the results to a new output file, we see that \"mace_mp_energy\" is still saved, other unlabelled results are updated:"
]
},
{
Expand All @@ -459,7 +459,7 @@
"metadata": {},
"outputs": [],
"source": [
"! janus singlepoint --struct janus_results/NaCl-results.extxyz --arch sevennet --out janus_results/NaCl-updated-results.extxyz --no-tracker"
"! janus singlepoint --struct janus_results/NaCl-results.extxyz --arch orb --out janus_results/NaCl-updated-results.extxyz --no-tracker"
]
},
{
Expand All @@ -483,7 +483,7 @@
"\n",
"print()\n",
"print(updated_results.info[\"mace_mp_energy\"])\n",
"print(updated_results.info[\"sevennet_energy\"])\n",
"print(updated_results.info[\"orb_energy\"])\n",
"print(updated_results.calc.results[\"energy\"])\n",
"print(updated_results.get_potential_energy())\n",
"print(updated_results.get_total_energy())"
Expand Down
16 changes: 8 additions & 8 deletions docs/source/tutorials/python/eos.ipynb
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Expand Up @@ -50,7 +50,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, CHGNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, Orb, CHGNet, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -292,7 +292,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Comparing MACE to CHGNeT and SevenNet"
"### Comparing MACE to CHGNeT and Orb"
]
},
{
Expand All @@ -301,14 +301,14 @@
"metadata": {},
"outputs": [],
"source": [
"sevennet_eos = EoS(\n",
"orb_eos = EoS(\n",
" struct=α_quartz.copy(),\n",
" arch=\"sevennet\",\n",
" arch=\"orb\",\n",
" device=\"cpu\",\n",
" minimize_kwargs={\"filter_class\": None},\n",
").run()\n",
"\n",
"sevennet_eos[\"eos\"].plot(show=True)"
"orb_eos[\"eos\"].plot(show=True)"
]
},
{
Expand All @@ -334,19 +334,19 @@
"outputs": [],
"source": [
"print(f\"MACE energy [eV]: {mace_eos['e_0']}\")\n",
"print(f\"SevenNet energy [eV]: {sevennet_eos['e_0']}\")\n",
"print(f\"Orb energy [eV]: {orb_eos['e_0']}\")\n",
"print(f\"CHGNeT energy [eV]: {chgnet_eos['e_0']}\")\n",
"\n",
"print()\n",
"\n",
"print(f\"MACE volume [Å^3]: {mace_eos['v_0']}\")\n",
"print(f\"SevenNet volume [Å^3]: {sevennet_eos['v_0']}\")\n",
"print(f\"Orb volume [Å^3]: {orb_eos['v_0']}\")\n",
"print(f\"CHGNeT volume [Å^3]: {chgnet_eos['v_0']}\")\n",
"\n",
"print()\n",
"\n",
"print(f\"MACE bulk_modulus [GPa]: {mace_eos['bulk_modulus']}\")\n",
"print(f\"SevenNet bulk_modulus [GPa]: {sevennet_eos['bulk_modulus']}\")\n",
"print(f\"Orb bulk_modulus [GPa]: {orb_eos['bulk_modulus']}\")\n",
"print(f\"CHGNeT bulk_modulus [GPa]: {chgnet_eos['bulk_modulus']}\")"
]
}
Expand Down
13 changes: 6 additions & 7 deletions docs/source/tutorials/python/geom_opt.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, CHGNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, Orb, CHGNet, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -317,7 +317,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Comparing MACE to CHGNet and SevenNet"
"## Comparing MACE to CHGNet and Orb"
]
},
{
Expand Down Expand Up @@ -345,14 +345,13 @@
")\n",
"optimized_NaCl_chgnet.run()\n",
"\n",
"optimized_NaCl_sevennet = GeomOpt(\n",
"optimized_NaCl_orb = GeomOpt(\n",
" struct=NaCl.copy(),\n",
" arch=\"sevennet\",\n",
" arch=\"orb\",\n",
" device=\"cpu\",\n",
" calc_kwargs={\"default_dtype\": \"float64\"},\n",
" fmax=0.01,\n",
")\n",
"optimized_NaCl_sevennet.run()"
"optimized_NaCl_orb.run()"
]
},
{
Expand All @@ -365,7 +364,7 @@
"\n",
"print(f\"Final energy (MACE): {optimized_NaCl_mace.struct.get_potential_energy()}\")\n",
"print(f\"Final energy (CHGNet): {optimized_NaCl_chgnet.struct.get_potential_energy()}\")\n",
"print(f\"Final energy (SevenNet): {optimized_NaCl_sevennet.struct.get_potential_energy()}\")"
"print(f\"Final energy (Orb): {optimized_NaCl_orb.struct.get_potential_energy()}\")"
]
}
],
Expand Down
4 changes: 2 additions & 2 deletions docs/source/tutorials/python/neb.ipynb
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Expand Up @@ -63,7 +63,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, CHGNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, Orb, CHGNet, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -110,7 +110,7 @@
"# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-mpa-0\"}\n",
"# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-omat-0\"}\n",
"# model_params = {\"arch\": \"chgnet\"}\n",
"# model_params = {\"arch\": \"sevennet\"}"
"# model_params = {\"arch\": \"orb\"}"
]
},
{
Expand Down
14 changes: 7 additions & 7 deletions docs/source/tutorials/python/phonons.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, CHGNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, Orb, CHGNet, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -373,7 +373,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Comparing the band structure from MACE to CHGNet and SevenNet:"
"## Comparing the band structure from MACE to CHGNet and Orb:"
]
},
{
Expand Down Expand Up @@ -421,7 +421,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Calculate band structure using SevenNet"
"### Calculate band structure using Orb"
]
},
{
Expand All @@ -430,9 +430,9 @@
"metadata": {},
"outputs": [],
"source": [
"phonons_sevennet = Phonons(\n",
"phonons_orb = Phonons(\n",
" struct=NaCl.copy(),\n",
" arch=\"sevennet\",\n",
" arch=\"orb\",\n",
" device=\"cpu\",\n",
" supercell=[2, 2, 2],\n",
" displacement=0.01,\n",
Expand All @@ -455,7 +455,7 @@
"metadata": {},
"outputs": [],
"source": [
"phonons_sevennet.calc_bands(write_bands=True)"
"phonons_orb.calc_bands(write_bands=True)"
]
},
{
Expand All @@ -473,7 +473,7 @@
"source": [
"phonons_mace.write_bands(plot_file=\"MACE.svg\")\n",
"phonons_chgnet.write_bands(plot_file=\"chgnet.svg\")\n",
"phonons_sevennet.write_bands(plot_file=\"sevennet.svg\")"
"phonons_orb.write_bands(plot_file=\"orb.svg\")"
]
},
{
Expand Down
20 changes: 10 additions & 10 deletions docs/source/tutorials/python/single_point.ipynb
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Expand Up @@ -23,7 +23,7 @@
"id": "4vcbRxmIhHLL"
},
"source": [
"`janus-core` contains various machine learnt interatomic potentials (MLIPs), including MACE based models (MACE-MP, MACE-OFF), CHGNet, SevenNet and more, full list on https://github.com/stfc/janus-core.\n",
"`janus-core` contains various machine learnt interatomic potentials (MLIPs), including MACE based models (MACE-MP, MACE-OFF), CHGNet, Orb and more, full list on https://github.com/stfc/janus-core.\n",
"\n",
"Other will be added as their utility is proven beyond a specific material."
]
Expand Down Expand Up @@ -59,7 +59,7 @@
"# ! pip uninstall torch torchaudio torchvision transformers -y # Uninstall pre-installed torch\n",
"# ! uv pip install torch==2.5.1 # Install pinned version of torch\n",
"\n",
"# ! uv pip install janus-core[mace,sevennet,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, SevenNet, CHGNet, and WeasWidget, and data-tutorials\n",
"# ! uv pip install janus-core[mace,orb,chgnet,visualise] data-tutorials --system # Install janus-core with MACE, Orb, CHGNet, and WeasWidget, and data-tutorials\n",
"\n",
"# get_ipython().kernel.do_shutdown(restart=True) # Restart kernel to update libraries. This may warn that your session has crashed."
]
Expand Down Expand Up @@ -148,10 +148,10 @@
"NaCl = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n",
"sp = SinglePoint(\n",
" struct=NaCl,\n",
" arch=\"sevennet\",\n",
" arch=\"orb\",\n",
" device=device,\n",
")\n",
"res_sevennet = sp.run()\n",
"res_orb = sp.run()\n",
"\n",
"NaCl = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n",
"sp = SinglePoint(\n",
Expand All @@ -162,7 +162,7 @@
"res_chgnet = sp.run()\n",
"\n",
"print(f\" MACE[eV]: {res_mace['energy']}\")\n",
"print(f\"SevenNet[eV]: {res_sevennet['energy']}\")\n",
"print(f\"Orb[eV]: {res_orb['energy']}\")\n",
"print(f\" CHGNeT[eV]: {res_chgnet['energy']}\")"
]
},
Expand Down Expand Up @@ -288,21 +288,21 @@
"chgnet_energy = np.array([s.info[\"chgnet_energy\"] / len(s) for s in sp.struct])\n",
"rmse_chgnet = np.linalg.norm(chgnet_energy - dft_energy) / np.sqrt(len(dft_energy))\n",
"\n",
"sp = SinglePoint(struct=\"data/NaCl-set.xyz\", arch=\"sevennet\", device=device)\n",
"sp = SinglePoint(struct=\"data/NaCl-set.xyz\", arch=\"orb\", device=device)\n",
"sp.run()\n",
"\n",
"sevennet_energy = np.array([s.info[\"sevennet_energy\"] / len(s) for s in sp.struct])\n",
"rmse_sevennet = np.linalg.norm(sevennet_energy - dft_energy) / np.sqrt(len(dft_energy))\n",
"orb_energy = np.array([s.info[\"orb_energy\"] / len(s) for s in sp.struct])\n",
"rmse_orb = np.linalg.norm(orb_energy - dft_energy) / np.sqrt(len(dft_energy))\n",
"\n",
"print(\n",
" f\"rmse: mace_mp = {rmse_mace}, chgnet = {rmse_chgnet}, \"\n",
" f\"sevennet = {rmse_sevennet} eV/atom\"\n",
" f\"orb = {rmse_orb} eV/atom\"\n",
")\n",
"\n",
"fig, ax = plt.subplots()\n",
"\n",
"ax.scatter(dft_energy, mace_mp_energy, marker=\"o\", label=\"mace-mp-0\")\n",
"ax.scatter(dft_energy, sevennet_energy, marker=\"x\", label=\"sevennet\")\n",
"ax.scatter(dft_energy, orb_energy, marker=\"x\", label=\"orb\")\n",
"ax.scatter(dft_energy, chgnet_energy, marker=\"+\", label=\"chgnet\")\n",
"ax.legend()\n",
"plt.xlabel(\"MLIP [eV/atom]\")\n",
Expand Down