diff --git a/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb b/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb index b535b478e..f5b7334b2 100644 --- a/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb +++ b/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb @@ -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." ] }, { @@ -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": [ @@ -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", @@ -217,7 +228,7 @@ { "cell_type": "code", "execution_count": null, - "id": "15", + "id": "16", "metadata": {}, "outputs": [], "source": [ @@ -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." @@ -260,7 +271,7 @@ { "cell_type": "code", "execution_count": null, - "id": "17", + "id": "18", "metadata": {}, "outputs": [], "source": [ @@ -286,7 +297,7 @@ }, { "cell_type": "markdown", - "id": "18", + "id": "19", "metadata": {}, "source": [ "## 5. Visualize the slabs" @@ -295,7 +306,7 @@ { "cell_type": "code", "execution_count": null, - "id": "19", + "id": "20", "metadata": {}, "outputs": [], "source": [ @@ -304,7 +315,7 @@ }, { "cell_type": "markdown", - "id": "20", + "id": "21", "metadata": {}, "source": [ "## 6. Download materials" @@ -313,7 +324,7 @@ { "cell_type": "code", "execution_count": null, - "id": "21", + "id": "22", "metadata": {}, "outputs": [], "source": [ diff --git a/other/materials_designer/specific_examples/slab_strontium_titanate_SIMULATION.ipynb b/other/materials_designer/specific_examples/slab_strontium_titanate_SIMULATION.ipynb index de9f72aea..3dbdfe3d5 100644 --- a/other/materials_designer/specific_examples/slab_strontium_titanate_SIMULATION.ipynb +++ b/other/materials_designer/specific_examples/slab_strontium_titanate_SIMULATION.ipynb @@ -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": [ @@ -230,7 +238,7 @@ }, { "cell_type": "markdown", - "id": "16", + "id": "17", "metadata": {}, "source": [ "### 2.4. Select project" @@ -239,7 +247,7 @@ { "cell_type": "code", "execution_count": null, - "id": "17", + "id": "18", "metadata": {}, "outputs": [], "source": [ @@ -250,7 +258,7 @@ }, { "cell_type": "markdown", - "id": "18", + "id": "19", "metadata": {}, "source": [ "## 3. Load the materials\n", @@ -260,7 +268,7 @@ { "cell_type": "code", "execution_count": null, - "id": "19", + "id": "20", "metadata": {}, "outputs": [], "source": [ @@ -278,7 +286,7 @@ }, { "cell_type": "markdown", - "id": "20", + "id": "21", "metadata": {}, "source": [ "### 3.2. Save the materials to the platform" @@ -287,7 +295,7 @@ { "cell_type": "code", "execution_count": null, - "id": "21", + "id": "22", "metadata": {}, "outputs": [], "source": [ @@ -299,7 +307,7 @@ }, { "cell_type": "markdown", - "id": "22", + "id": "23", "metadata": {}, "source": [ "## 4. Configure the shared DFT model and k-grid\n", @@ -309,7 +317,7 @@ { "cell_type": "code", "execution_count": null, - "id": "23", + "id": "24", "metadata": {}, "outputs": [], "source": [ @@ -329,7 +337,7 @@ }, { "cell_type": "markdown", - "id": "24", + "id": "25", "metadata": {}, "source": [ "### 4.2. k-grid per material" @@ -338,7 +346,7 @@ { "cell_type": "code", "execution_count": null, - "id": "25", + "id": "26", "metadata": {}, "outputs": [], "source": [ @@ -352,7 +360,7 @@ }, { "cell_type": "markdown", - "id": "26", + "id": "27", "metadata": {}, "source": [ "## 5. Create the compute configuration\n", @@ -362,7 +370,7 @@ { "cell_type": "code", "execution_count": null, - "id": "27", + "id": "28", "metadata": {}, "outputs": [], "source": [ @@ -372,7 +380,7 @@ }, { "cell_type": "markdown", - "id": "28", + "id": "29", "metadata": {}, "source": [ "### 5.2. Create the compute configuration for the jobs" @@ -381,7 +389,7 @@ { "cell_type": "code", "execution_count": null, - "id": "29", + "id": "30", "metadata": {}, "outputs": [], "source": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -476,7 +501,7 @@ }, { "cell_type": "markdown", - "id": "34", + "id": "37", "metadata": {}, "source": [ "## 7. Relax the slabs (optional)\n", @@ -487,7 +512,7 @@ { "cell_type": "code", "execution_count": null, - "id": "35", + "id": "38", "metadata": {}, "outputs": [], "source": [ @@ -513,7 +538,7 @@ }, { "cell_type": "markdown", - "id": "36", + "id": "39", "metadata": {}, "source": [ "## 8. Retrieve the results\n", @@ -523,7 +548,7 @@ { "cell_type": "code", "execution_count": null, - "id": "37", + "id": "40", "metadata": {}, "outputs": [], "source": [ @@ -544,7 +569,7 @@ }, { "cell_type": "markdown", - "id": "38", + "id": "41", "metadata": {}, "source": [ "### 8.2. Cleavage, relaxation and surface energies\n", @@ -564,7 +589,7 @@ { "cell_type": "code", "execution_count": null, - "id": "39", + "id": "42", "metadata": {}, "outputs": [], "source": [ @@ -591,7 +616,7 @@ }, { "cell_type": "markdown", - "id": "40", + "id": "43", "metadata": {}, "source": [ "## 9. Comparison with Eglitis & Vanderbilt (2008)\n", @@ -602,7 +627,7 @@ { "cell_type": "code", "execution_count": null, - "id": "41", + "id": "44", "metadata": {}, "outputs": [], "source": [ @@ -627,7 +652,7 @@ }, { "cell_type": "markdown", - "id": "42", + "id": "45", "metadata": {}, "source": [ "## References\n",