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feature/SOF-8063 SE: Formation Energy + Band Structure for N3-substitution + Vacancy in graphene #372

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Merged
VsevolodX merged 11 commits into from
Oct 8, 2026
Merged

feature/SOF-8063 SE: Formation Energy + Band Structure for N3-substitution + Vacancy in graphene #372

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f1c0978
SOF-8063: formation energy beside the band structure for graphene C28N3
VsevolodX Sep 19, 2026
0c416d6
SOF-8063: NOTE lines saying what a result close to the manuscript needs
VsevolodX Sep 19, 2026
c90cf3c
SOF-8063: prefer an exact name in load_material_from_folder
VsevolodX Sep 19, 2026
a704c55
SOF-8063: scope the Total Energy reuse to this notebook's own workflow
VsevolodX Sep 19, 2026
34ef46a
SOF-8063: reuse an existing Band Structure job instead of submitting …
VsevolodX Sep 19, 2026
e0ef207
Merge remote-tracking branch 'origin/main' into feature/SOF-8063
VsevolodX Oct 2, 2026
374f750
SOF-8063: TIME_LIMIT 4 h — 12 h x 16 ppn is refused at submission
VsevolodX Oct 2, 2026
bf9c3a7
SOF-8063: RUN_TIER fast|production replaces RELAX — one tier sets k-g…
VsevolodX Oct 2, 2026
44a85c0
SOF-8063: model-scoped total energy reuse, a source switch, and one p…
VsevolodX Oct 2, 2026
46d8367
SOF-8063: default the total-energy source to public, safe now that gr…
VsevolodX Oct 2, 2026
09f45a6
Merge remote-tracking branch 'origin/main' into feature/SOF-8063
VsevolodX Oct 8, 2026
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12 changes: 8 additions & 4 deletions other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,10 @@
"id": "16",
"metadata": {},
"source": [
"## 4. Write resulting material to the folder"
"## 4. Write resulting materials to the folder\n",
"\n",
"Both materials are saved to `uploads` under the names the simulation notebook loads by exact name:\n",
"`graphene 4x4` is the reference cell, `graphene 4x4 N3V pyridinic (C28N3)` is the defective one."
]
},
{
Expand All @@ -235,9 +238,10 @@
"from mat3ra.notebooks_utils.io import download_content_to_file\n",
"from mat3ra.notebooks_utils.material import set_materials\n",
"\n",
"material_with_defect.name = \"N-doped Graphene\"\n",
"set_materials(material_with_defect)\n",
"download_content_to_file(material_with_defect.to_json(), \"N-doped_Graphene.json\")"
"supercell.name = \"graphene 4x4\"\n",
"material_with_defect.name = \"graphene 4x4 N3V pyridinic (C28N3)\"\n",
"set_materials([supercell, material_with_defect])\n",
"download_content_to_file(material_with_defect.to_json(), \"graphene_4x4_N3V_pyridinic.json\")"
]
}
],
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