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feature/SOF-8075 Update: a description above every code cell of the SrTiO3 notebooks #404

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e2b0ebc
SOF-8075: review (TB) - a description above every code cell
VsevolodX Oct 26, 2026
948400e
SOF-8075: review (TB) - description wording: no reuse mechanics, term…
VsevolodX Oct 26, 2026
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31 changes: 21 additions & 10 deletions other/materials_designer/specific_examples/slab_strontium_titanate.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -156,8 +156,9 @@
"metadata": {},
"source": [
"## 3. Create the cleaved slabs\n",
"### 3.1. Get the formula of a plane\n",
"\n",
"A slab of whole unit cells holds an even number of planes, alternating SrTiO and O2 on (011) and SrO and TiO2 on (001), so its two faces differ."
"A plane's formula is written as in `TERMINATIONS_BY_MILLER_INDICES`, such as SrTiO and O2."
]
},
{
Expand All @@ -179,10 +180,20 @@
" return \"\".join(f\"{element}{count if count > 1 else ''}\" for element, count in counts.items())"
]
},
{
"cell_type": "markdown",
"id": "13",
"metadata": {},
"source": [
"### 3.2. Create a cleaved slab per Miller indices\n",
"\n",
"A slab of whole unit cells holds an even number of planes, alternating SrTiO and O2 on (011) and SrO and TiO2 on (001), so its two faces differ."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "13",
"id": "14",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -206,7 +217,7 @@
},
{
"cell_type": "markdown",
"id": "14",
"id": "15",
"metadata": {},
"source": [
"## 4. Cut the seven-plane slabs and remove atoms from each surface\n",
Expand All @@ -217,7 +228,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "15",
"id": "16",
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -251,7 +262,7 @@
},
{
"cell_type": "markdown",
"id": "16",
"id": "17",
"metadata": {},
"source": [
"Each slab is printed with its formula, atom count, nominal charge, face equivalence, vacuum and planes from bottom to top. The nominal charge (Sr +2, Ti +4, O -2) shows why the manuscript removes atoms from the cleaved (011) slabs: they carry ±4 e, the nonpolar ones none."
Expand All @@ -260,7 +271,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "17",
"id": "18",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -286,7 +297,7 @@
},
{
"cell_type": "markdown",
"id": "18",
"id": "19",
"metadata": {},
"source": [
"## 5. Visualize the slabs"
Expand All @@ -295,7 +306,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "19",
"id": "20",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -304,7 +315,7 @@
},
{
"cell_type": "markdown",
"id": "20",
"id": "21",
"metadata": {},
"source": [
"## 6. Download materials"
Expand All @@ -313,7 +324,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "21",
"id": "22",
"metadata": {},
"outputs": [],
"source": [
Expand Down
83 changes: 54 additions & 29 deletions other/materials_designer/specific_examples/slab_strontium_titanate_SIMULATION.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -212,10 +212,18 @@
"client.list_accounts()\n"
]
},
{
"cell_type": "markdown",
"id": "15",
"metadata": {},
"source": [
"The materials, jobs and project below belong to this account."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "15",
"id": "16",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -230,7 +238,7 @@
},
{
"cell_type": "markdown",
"id": "16",
"id": "17",
"metadata": {},
"source": [
"### 2.4. Select project"
Expand All @@ -239,7 +247,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "17",
"id": "18",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -250,7 +258,7 @@
},
{
"cell_type": "markdown",
"id": "18",
"id": "19",
"metadata": {},
"source": [
"## 3. Load the materials\n",
Expand All @@ -260,7 +268,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "19",
"id": "20",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -278,7 +286,7 @@
},
{
"cell_type": "markdown",
"id": "20",
"id": "21",
"metadata": {},
"source": [
"### 3.2. Save the materials to the platform"
Expand All @@ -287,7 +295,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "21",
"id": "22",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -299,7 +307,7 @@
},
{
"cell_type": "markdown",
"id": "22",
"id": "23",
"metadata": {},
"source": [
"## 4. Configure the shared DFT model and k-grid\n",
Expand All @@ -309,7 +317,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "23",
"id": "24",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -329,7 +337,7 @@
},
{
"cell_type": "markdown",
"id": "24",
"id": "25",
"metadata": {},
"source": [
"### 4.2. k-grid per material"
Expand All @@ -338,7 +346,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "25",
"id": "26",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -352,7 +360,7 @@
},
{
"cell_type": "markdown",
"id": "26",
"id": "27",
"metadata": {},
"source": [
"## 5. Create the compute configuration\n",
Expand All @@ -362,7 +370,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "27",
"id": "28",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -372,7 +380,7 @@
},
{
"cell_type": "markdown",
"id": "28",
"id": "29",
"metadata": {},
"source": [
"### 5.2. Create the compute configuration for the jobs"
Expand All @@ -381,7 +389,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "29",
"id": "30",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -401,16 +409,17 @@
},
{
"cell_type": "markdown",
"id": "30",
"id": "31",
"metadata": {},
"source": [
"## 6. Total energy of every cell as cut"
"## 6. Total energy of every cell as cut\n",
"### 6.1. Find or create a job"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "31",
"id": "32",
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -441,10 +450,18 @@
" return job[\"_id\"], True"
]
},
{
"cell_type": "markdown",
"id": "33",
"metadata": {},
"source": [
"### 6.2. One Total Energy job per material"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "32",
"id": "34",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -459,10 +476,18 @@
" new_job_ids.append(energy_job_ids[name])"
]
},
{
"cell_type": "markdown",
"id": "35",
"metadata": {},
"source": [
"### 6.3. Submit the new jobs and wait for all to finish"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "33",
"id": "36",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -476,7 +501,7 @@
},
{
"cell_type": "markdown",
"id": "34",
"id": "37",
"metadata": {},
"source": [
"## 7. Relax the slabs (optional)\n",
Expand All @@ -487,7 +512,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "35",
"id": "38",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -513,7 +538,7 @@
},
{
"cell_type": "markdown",
"id": "36",
"id": "39",
"metadata": {},
"source": [
"## 8. Retrieve the results\n",
Expand All @@ -523,7 +548,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "37",
"id": "40",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -544,7 +569,7 @@
},
{
"cell_type": "markdown",
"id": "38",
"id": "41",
"metadata": {},
"source": [
"### 8.2. Cleavage, relaxation and surface energies\n",
Expand All @@ -564,7 +589,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "39",
"id": "42",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -591,7 +616,7 @@
},
{
"cell_type": "markdown",
"id": "40",
"id": "43",
"metadata": {},
"source": [
"## 9. Comparison with Eglitis & Vanderbilt (2008)\n",
Expand All @@ -602,7 +627,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "41",
"id": "44",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -627,7 +652,7 @@
},
{
"cell_type": "markdown",
"id": "42",
"id": "45",
"metadata": {},
"source": [
"## References\n",
Expand Down
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