From 323bf0d9104a28d6924b430c0b30df19096c6fef Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 26 Mar 2024 17:03:26 -0700
Subject: [PATCH 1/6] update: move materials import to 3
---
...create_interface_with_min_strain_zsl.ipynb | 79 ++++++++++---------
1 file changed, 40 insertions(+), 39 deletions(-)
diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
index 7277ddfd..6d195872 100644
--- a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
+++ b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -10,8 +10,7 @@
"\n",
"Usage
\n",
"\n",
- "0. Make sure to select Input Materials\n",
- "1. Execute \"Run first: ...\" cell below to load Input Materials into the current kernel\n",
+ "1. Make sure to select Input Materials\n",
"2. Set Input Parameters (e.g. `MILLER_INDICES`, `THICKNESS`, `MAX_AREA`) below or use the default values\n",
"3. Click \"Run\" > \"Run All Cells\" to run all cells\n",
"4. Wait for the run to complete (depending on the area, it can take 1-2 min or more). Scroll down to view cell results.\n",
@@ -31,25 +30,6 @@
"3. When the strain matching is finished, the interface with the lowest strain (and the smallest number of atoms) is selected. We create the corresponding supercells and place them at a specified distance from each other (note no shift is performed currently).\n"
]
},
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Run first: load input materials in current kernel
\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "from jupyterlite.utils import get_data\n",
- "\n",
- "# Get the list of input materials and load them into `materials_in` variable\n",
- "get_data(\"materials_in\", globals())"
- ]
- },
{
"cell_type": "markdown",
"metadata": {},
@@ -143,12 +123,40 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 3. Create interfaces\n",
+ "## 3. Load and prepare input Materials\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "outputs": [],
+ "source": [
+ "from jupyterlite.utils import get_data\n",
+ "from src.utils import to_pymatgen\n",
+ "# Get the list of input materials and load them into `materials_in` variable\n",
+ "get_data(\"materials_in\", globals())\n",
+ "\n",
+ "if \"materials_in\" in globals():\n",
+ " pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
+ "for material in pymatgen_materials:\n",
+ " print(material, \"\\n\")"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "execution_count": null
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 4. Create interfaces\n",
"\n",
- "### 3.1. Extract Interfaces and Terminations\n",
+ "### 4.1. Extract Interfaces and Terminations\n",
"\n",
"Extract all possible layer/substrate supercell combinations within the maximum area including different terminations."
- ]
+ ],
+ "metadata": {
+ "collapsed": false
+ }
},
{
"cell_type": "code",
@@ -160,13 +168,6 @@
"outputs": [],
"source": [
"from src.pymatgen_coherent_interface_builder import CoherentInterfaceBuilder, ZSLGenerator\n",
- "from src.utils import to_pymatgen\n",
- "\n",
- "if \"materials_in\" in globals():\n",
- " pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
- "for material in pymatgen_materials:\n",
- " print(material, \"\\n\")\n",
- "\n",
"\n",
"def create_interfaces(settings):\n",
" print(\"Creating interfaces...\")\n",
@@ -221,7 +222,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 3.2. Print out the interfaces and terminations"
+ "### 5.2. Print out the interfaces and terminations"
]
},
{
@@ -239,9 +240,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 4. Sort interfaces by strain\n",
+ "## 5. Sort interfaces by strain\n",
"\n",
- "### 4.1. Sort all interfaces"
+ "### 5.1. Sort all interfaces"
]
},
{
@@ -271,7 +272,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 4.2. Print out interfaces with lowest strain for each termination"
+ "### 5.2. Print out interfaces with lowest strain for each termination"
]
},
{
@@ -291,7 +292,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 5. Plot the results\n",
+ "## 6. Plot the results\n",
"\n",
"Plot the number of atoms vs strain. Adjust the parameters as needed.\n"
]
@@ -367,9 +368,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 6. Select the interface to pass outside this kernel\n",
+ "## 7. Select the interface to pass outside this kernel\n",
"\n",
- "### 6.1. Select the interface with the desired termination and strain\n",
+ "### 7.1. Select the interface with the desired termination and strain\n",
"\n",
"The data in `sorted_interfaces` now contains an object with the following structure:\n",
"\n",
@@ -409,7 +410,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 6.2. Pass data to the outside runtime\n"
+ "### 7.2. Pass data to the outside runtime\n"
]
},
{
From 62428cc03992078cb04730f4b3a8288a72a5811f Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 26 Mar 2024 18:53:13 -0700
Subject: [PATCH 2/6] update: adjust notebook 2
---
...te_interface_with_relaxation_ase_emt.ipynb | 90 ++++++++++---------
1 file changed, 46 insertions(+), 44 deletions(-)
diff --git a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
index 5cdd03e4..f58e76cf 100644
--- a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
+++ b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
@@ -11,8 +11,7 @@
"\n",
"Usage
\n",
"\n",
- "0. Make sure to select Input Materials\n",
- "1. Execute \"Run first: ...\" cell below to load Input Materials into the current kernel\n",
+ "1. Make sure to select Input Materials\n",
"2. Set Input Parameters (e.g. `THICKNESS`, `MAX_AREA`, `FMAX`) below or use the default values\n",
"3. Click \"Run\" > \"Run All\" to run all cells\n",
"4. Wait for the run to complete (depending on the parameters it can take a few min or more). Scroll down to view cell results.\n",
@@ -29,25 +28,6 @@
"2. The interface with the lowest strain is selected and relaxed using the optimizer selected below (BFGS, by default). The EMT potential is used as an energy calculator.\n"
]
},
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Run first: load input materials in current kernel
\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "from jupyterlite.utils import get_data\n",
- "\n",
- "# Get the list of input materials and load them into `materials_in` variable\n",
- "get_data(\"materials_in\", globals())"
- ]
- },
{
"cell_type": "markdown",
"metadata": {},
@@ -147,13 +127,45 @@
"await install_packages(\"create_interface_with_min_strain_zsl.ipynb\")"
]
},
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 3. Load and prepare Input Materials"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "outputs": [],
+ "source": [
+ "from jupyterlite.utils import get_data\n",
+ "from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer\n",
+ "from src.utils import to_pymatgen\n",
+ "\n",
+ "# Get the list of input materials and load them into `materials_in` variable\n",
+ "get_data(\"materials_in\", globals())\n",
+ "\n",
+ "if \"materials_in\" in globals():\n",
+ " pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
+ " if USE_CONVENTIONAL_CELL: pymatgen_materials = [SpacegroupAnalyzer(item).get_conventional_standard_structure() for\n",
+ " item in pymatgen_materials]\n",
+ "\n",
+ " for material in pymatgen_materials:\n",
+ " print(material, \"\\n\")"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 3. Create interfaces\n",
+ "## 4. Create interfaces\n",
"\n",
- "### 3.1. Extract Interfaces and Terminations\n",
+ "### 4.1. Extract Interfaces and Terminations\n",
"\n",
"Extract all possible layer/substrate supercell combinations within the maximum area including different terminations.\n"
]
@@ -168,16 +180,6 @@
"outputs": [],
"source": [
"from src.pymatgen_coherent_interface_builder import CoherentInterfaceBuilder, ZSLGenerator\n",
- "from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer\n",
- "from src.utils import to_pymatgen\n",
- "\n",
- "if \"materials_in\" in globals():\n",
- " pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
- " if USE_CONVENTIONAL_CELL: pymatgen_materials = [SpacegroupAnalyzer(item).get_conventional_standard_structure() for\n",
- " item in pymatgen_materials]\n",
- "\n",
- " for material in pymatgen_materials:\n",
- " print(material, \"\\n\")\n",
"\n",
"\n",
"def create_interfaces(settings: dict):\n",
@@ -233,7 +235,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 3.2. Print out the interfaces and terminations\n"
+ "### 4.2. Print out the interfaces and terminations\n"
]
},
{
@@ -251,9 +253,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 4. Sort interfaces by strain\n",
+ "## 5. Sort interfaces by strain\n",
"\n",
- "### 4.1. Sort all interfaces\n"
+ "### 5.1. Sort all interfaces\n"
]
},
{
@@ -283,7 +285,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 4.2. Print out interfaces with lowest strain for each termination\n"
+ "### 5.2. Print out interfaces with lowest strain for each termination\n"
]
},
{
@@ -303,7 +305,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 5. Plot the results\n",
+ "## 6. Plot the results\n",
"\n",
"Plot the number of atoms vs strain. Adjust the parameters as needed.\n"
]
@@ -379,7 +381,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 6. Select the interface with the desired termination and strain\n",
+ "## 7. Select the interface with the desired termination and strain\n",
"\n",
"The data in `sorted_interfaces` now contains an object with the following structure:\n",
"\n",
@@ -421,9 +423,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## 7. Apply relaxation to the interface\n",
+ "## 8. Apply relaxation to the interface\n",
"\n",
- "### 7.1. Apply relaxation to the selected interface with ASE\n",
+ "### 8.1. Apply relaxation to the selected interface with ASE\n",
"\n",
"Optimizer is set from the available options in the settings and EMT is used as the energy calculator."
]
@@ -516,7 +518,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 7.2. View structure before and after relaxation\n"
+ "### 8.2. View structure before and after relaxation\n"
]
},
{
@@ -579,7 +581,7 @@
"collapsed": false
},
"source": [
- "### 7.3. Calculate the energy metrics\n",
+ "### 8.3. Calculate the energy metrics\n",
"Calculate the energy metrics for the relaxed interface.\n",
"The effective delta energy per area calculation accounts for the energy contribution of each component (substrate and layer) relative to their proportion in the overall interface. \n"
]
@@ -675,7 +677,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### 8. Pass relaxed interface to Materials Designer"
+ "## 9. Pass relaxed interface to Materials Designer"
]
},
{
From 2a4a4482148d384d84dd2564f386520371f86ed1 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 26 Mar 2024 18:53:27 -0700
Subject: [PATCH 3/6] update: adjust notebook 1
---
.../create_interface_with_min_strain_zsl.ipynb | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
index 6d195872..d1113eb6 100644
--- a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
+++ b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -55,7 +55,9 @@
" \"MATERIAL_INDEX\": 1, # the index of the material in the materials_in list\n",
" \"MILLER_INDICES\": (0, 0, 1), # the miller indices of the interfacial plane\n",
" \"THICKNESS\": 1, # in layers\n",
- "}"
+ "}\n",
+ "\n",
+ "USE_CONVENTIONAL_CELL = True # if True, the surface plane is constructed using miller indices of the conventional cell"
]
},
{
@@ -131,14 +133,19 @@
"outputs": [],
"source": [
"from jupyterlite.utils import get_data\n",
+ "from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer\n",
"from src.utils import to_pymatgen\n",
+ "\n",
"# Get the list of input materials and load them into `materials_in` variable\n",
"get_data(\"materials_in\", globals())\n",
"\n",
"if \"materials_in\" in globals():\n",
" pymatgen_materials = [to_pymatgen(item) for item in materials_in]\n",
- "for material in pymatgen_materials:\n",
- " print(material, \"\\n\")"
+ " if USE_CONVENTIONAL_CELL: pymatgen_materials = [SpacegroupAnalyzer(item).get_conventional_standard_structure() for\n",
+ " item in pymatgen_materials]\n",
+ "\n",
+ " for material in pymatgen_materials:\n",
+ " print(material, \"\\n\")"
],
"metadata": {
"collapsed": false
From 040c6207c770873300c962441b781c2d1e597522 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 27 Mar 2024 16:51:31 -0700
Subject: [PATCH 4/6] update: fix order of dependencies
---
other/jupyterlite/utils.py | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/other/jupyterlite/utils.py b/other/jupyterlite/utils.py
index 238eead0..e133816b 100644
--- a/other/jupyterlite/utils.py
+++ b/other/jupyterlite/utils.py
@@ -69,22 +69,28 @@ async def install_packages(notebook_name, requirements_path="config.yml", verbos
requirements_hash = str(hash(json.dumps(requirements)))
if os.environ.get("requirements_hash") != requirements_hash:
packages_default_common = requirements.get("default", {}).get("packages_common", []) or []
- packages_default_environment_specific = requirements.get("default", {}).get(f"packages_{ENVIRONMENT.value}", []) or []
+ packages_default_environment_specific = (
+ requirements.get("default", {}).get(f"packages_{ENVIRONMENT.value}", []) or []
+ )
notebook_requirements = next(
(cfg for cfg in requirements.get("notebooks", []) if cfg.get("name") == notebook_name), None
)
if notebook_requirements:
packages_notebook_common = notebook_requirements.get("packages_common", []) or []
- packages_notebook_environment_specific= notebook_requirements.get(f"packages_{ENVIRONMENT.value}", []) or []
+ packages_notebook_environment_specific = (
+ notebook_requirements.get(f"packages_{ENVIRONMENT.value}", []) or []
+ )
else:
raise ValueError(f"No packages found for notebook {notebook_name}")
+ # Note: environment specific packages have to be installed first,
+ # because in Pyodide common packages might depend on them
packages = [
- *packages_default_common,
*packages_default_environment_specific,
- *packages_notebook_common,
*packages_notebook_environment_specific,
+ *packages_default_common,
+ *packages_notebook_common,
]
for pkg in packages:
From 04648fb3c5b93a9d8d39b68ba2c3a6c60ad60368 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 27 Mar 2024 17:44:11 -0700
Subject: [PATCH 5/6] update: trnaslate to bottom to allow for multiple layers
---
...create_interface_with_min_strain_zsl.ipynb | 4 +
...te_interface_with_relaxation_ase_emt.ipynb | 250 +++++++++++++++++-
other/materials_designer/src/utils.py | 17 ++
3 files changed, 268 insertions(+), 3 deletions(-)
diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
index d1113eb6..c02b225b 100644
--- a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
+++ b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -175,7 +175,11 @@
"outputs": [],
"source": [
"from src.pymatgen_coherent_interface_builder import CoherentInterfaceBuilder, ZSLGenerator\n",
+ "from src.utils import translate_to_bottom\n",
"\n",
+ "# Translate the materials to the bottom of the cell to allow for multilayer heterostructures creation\n",
+ "pymatgen_materials = [translate_to_bottom(item) for item in pymatgen_materials]\n",
+ " \n",
"def create_interfaces(settings):\n",
" print(\"Creating interfaces...\")\n",
" zsl = ZSLGenerator(\n",
diff --git a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
index f58e76cf..5f36e7df 100644
--- a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
+++ b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
@@ -118,9 +118,250 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
+ "execution_count": 1,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-03-28T00:00:14.528456Z",
+ "start_time": "2024-03-27T23:59:51.381151Z"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Requirement already satisfied: pymatgen==2023.9.10 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (2023.9.10)\n",
+ "Requirement already satisfied: matplotlib>=1.5 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.8.3)\n",
+ "Requirement already satisfied: monty>=3.0.2 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (2024.2.2)\n",
+ "Requirement already satisfied: mp-api>=0.27.3 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (0.38.0)\n",
+ "Requirement already satisfied: networkx>=2.2 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.2.1)\n",
+ "Requirement already satisfied: numpy>=1.20.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.26.4)\n",
+ "Requirement already satisfied: palettable>=3.1.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.3.3)\n",
+ "Requirement already satisfied: pandas in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.5.3)\n",
+ "Requirement already satisfied: plotly>=4.5.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (5.18.0)\n",
+ "Requirement already satisfied: pybtex in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (0.24.0)\n",
+ "Requirement already satisfied: requests in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (2.31.0)\n",
+ "Requirement already satisfied: ruamel.yaml>=0.17.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (0.17.40)\n",
+ "Requirement already satisfied: scipy>=1.5.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.12.0)\n",
+ "Requirement already satisfied: spglib>=2.0.2 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (2.0.2)\n",
+ "Requirement already satisfied: sympy in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.12)\n",
+ "Requirement already satisfied: tabulate in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (0.9.0)\n",
+ "Requirement already satisfied: tqdm in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (4.66.2)\n",
+ "Requirement already satisfied: uncertainties>=3.1.4 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.1.7)\n",
+ "Requirement already satisfied: joblib in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.3.2)\n",
+ "Requirement already satisfied: contourpy>=1.0.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from matplotlib>=1.5->pymatgen==2023.9.10) (1.2.0)\n",
+ "Requirement already satisfied: cycler>=0.10 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from matplotlib>=1.5->pymatgen==2023.9.10) (0.12.1)\n",
+ "Requirement already satisfied: fonttools>=4.22.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from matplotlib>=1.5->pymatgen==2023.9.10) (4.49.0)\n",
+ "Requirement already satisfied: kiwisolver>=1.3.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from matplotlib>=1.5->pymatgen==2023.9.10) (1.4.5)\n",
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+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed pymatgen==2023.9.10\n",
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+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
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+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ },
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+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed ase==3.22.1\n",
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+ ]
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+ "text": [
+ "\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed pandas==1.5.3\n",
+ "Requirement already satisfied: ipywidgets in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (8.1.2)\n",
+ "Requirement already satisfied: comm>=0.1.3 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipywidgets) (0.2.1)\n",
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+ "Requirement already satisfied: traitlets>=4.3.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipywidgets) (5.14.1)\n",
+ "Requirement already satisfied: widgetsnbextension~=4.0.10 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipywidgets) (4.0.10)\n",
+ "Requirement already satisfied: jupyterlab-widgets~=3.0.10 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipywidgets) (3.0.10)\n",
+ "Requirement already satisfied: decorator in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (5.1.1)\n",
+ "Requirement already satisfied: jedi>=0.16 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (0.19.1)\n",
+ "Requirement already satisfied: matplotlib-inline in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (0.1.6)\n",
+ "Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.41 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (3.0.43)\n",
+ "Requirement already satisfied: pygments>=2.4.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (2.17.2)\n",
+ "Requirement already satisfied: stack-data in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (0.6.3)\n",
+ "Requirement already satisfied: pexpect>4.3 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets) (4.9.0)\n",
+ "Requirement already satisfied: parso<0.9.0,>=0.8.3 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jedi>=0.16->ipython>=6.1.0->ipywidgets) (0.8.3)\n",
+ "Requirement already satisfied: ptyprocess>=0.5 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pexpect>4.3->ipython>=6.1.0->ipywidgets) (0.7.0)\n",
+ "Requirement already satisfied: wcwidth in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=6.1.0->ipywidgets) (0.2.13)\n",
+ "Requirement already satisfied: executing>=1.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from stack-data->ipython>=6.1.0->ipywidgets) (2.0.1)\n",
+ "Requirement already satisfied: asttokens>=2.1.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from stack-data->ipython>=6.1.0->ipywidgets) (2.4.1)\n",
+ "Requirement already satisfied: pure-eval in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from stack-data->ipython>=6.1.0->ipywidgets) (0.2.2)\n",
+ "Requirement already satisfied: six>=1.12.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from asttokens>=2.1.0->stack-data->ipython>=6.1.0->ipywidgets) (1.16.0)\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed ipywidgets\n",
+ "Requirement already satisfied: plotly==5.18 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (5.18.0)\n",
+ "Requirement already satisfied: tenacity>=6.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from plotly==5.18) (8.2.3)\n",
+ "Requirement already satisfied: packaging in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from plotly==5.18) (23.2)\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Installed plotly==5.18\n",
+ "Requirement already satisfied: nbformat>=4.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (5.9.2)\n",
+ "Requirement already satisfied: fastjsonschema in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (2.19.1)\n",
+ "Requirement already satisfied: jsonschema>=2.6 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (4.21.1)\n",
+ "Requirement already satisfied: jupyter-core in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (5.7.1)\n",
+ "Requirement already satisfied: traitlets>=5.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (5.14.1)\n",
+ "Requirement already satisfied: attrs>=22.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (23.2.0)\n",
+ "Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (2023.12.1)\n",
+ "Requirement already satisfied: referencing>=0.28.4 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (0.33.0)\n",
+ "Requirement already satisfied: rpds-py>=0.7.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (0.18.0)\n",
+ "Requirement already satisfied: platformdirs>=2.5 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jupyter-core->nbformat>=4.2.0) (4.2.0)\n",
+ "Installed nbformat>=4.2.0\n",
+ "Packages installed successfully.\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
+ "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
+ ]
+ }
+ ],
"source": [
"from jupyterlite.utils import install_packages\n",
"\n",
@@ -180,7 +421,10 @@
"outputs": [],
"source": [
"from src.pymatgen_coherent_interface_builder import CoherentInterfaceBuilder, ZSLGenerator\n",
+ "from src.utils import translate_to_bottom\n",
"\n",
+ "# Translate the materials to the bottom of the cell to allow for multilayer heterostructures creation\n",
+ "pymatgen_materials = [translate_to_bottom(item) for item in pymatgen_materials]\n",
"\n",
"def create_interfaces(settings: dict):\n",
" print(\"Creating interfaces...\")\n",
diff --git a/other/materials_designer/src/utils.py b/other/materials_designer/src/utils.py
index 13973502..5bef131e 100644
--- a/other/materials_designer/src/utils.py
+++ b/other/materials_designer/src/utils.py
@@ -348,3 +348,20 @@ def from_ase(atoms: Atoms):
structure = ase_to_pymatgen(atoms)
material = from_pymatgen(structure)
return material
+
+
+def translate_to_bottom(structure):
+ """
+ Translate the structure to the bottom of the cell.
+ Args:
+ structure (Structure): The pymatgen Structure object to translate.
+
+ Returns:
+ Structure: The translated pymatgen Structure object.
+ """
+ min_c = min(site.c for site in structure)
+ translation_vector = [0, 0, -min_c]
+ translated_structure = structure.copy()
+ for site in translated_structure:
+ site.coords += translation_vector
+ return translated_structure
From f68e612d4182d2997d359fe7e23fe2ccb4e22f85 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 27 Mar 2024 17:44:57 -0700
Subject: [PATCH 6/6] chore: clear outputs
---
...te_interface_with_relaxation_ase_emt.ipynb | 247 +-----------------
1 file changed, 3 insertions(+), 244 deletions(-)
diff --git a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
index 5f36e7df..8f8f5474 100644
--- a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
+++ b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
@@ -118,250 +118,9 @@
},
{
"cell_type": "code",
- "execution_count": 1,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2024-03-28T00:00:14.528456Z",
- "start_time": "2024-03-27T23:59:51.381151Z"
- }
- },
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Requirement already satisfied: pymatgen==2023.9.10 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (2023.9.10)\n",
- "Requirement already satisfied: matplotlib>=1.5 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.8.3)\n",
- "Requirement already satisfied: monty>=3.0.2 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (2024.2.2)\n",
- "Requirement already satisfied: mp-api>=0.27.3 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (0.38.0)\n",
- "Requirement already satisfied: networkx>=2.2 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.2.1)\n",
- "Requirement already satisfied: numpy>=1.20.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.26.4)\n",
- "Requirement already satisfied: palettable>=3.1.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (3.3.3)\n",
- "Requirement already satisfied: pandas in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (1.5.3)\n",
- "Requirement already satisfied: plotly>=4.5.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from pymatgen==2023.9.10) (5.18.0)\n",
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- "Requirement already satisfied: tenacity>=6.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from plotly==5.18) (8.2.3)\n",
- "Requirement already satisfied: packaging in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from plotly==5.18) (23.2)\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "\n",
- "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
- "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Installed plotly==5.18\n",
- "Requirement already satisfied: nbformat>=4.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (5.9.2)\n",
- "Requirement already satisfied: fastjsonschema in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (2.19.1)\n",
- "Requirement already satisfied: jsonschema>=2.6 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (4.21.1)\n",
- "Requirement already satisfied: jupyter-core in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (5.7.1)\n",
- "Requirement already satisfied: traitlets>=5.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from nbformat>=4.2.0) (5.14.1)\n",
- "Requirement already satisfied: attrs>=22.2.0 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (23.2.0)\n",
- "Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (2023.12.1)\n",
- "Requirement already satisfied: referencing>=0.28.4 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (0.33.0)\n",
- "Requirement already satisfied: rpds-py>=0.7.1 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0) (0.18.0)\n",
- "Requirement already satisfied: platformdirs>=2.5 in /Users/mat3ra/code/GREEN/api-examples/.venv/lib/python3.11/site-packages (from jupyter-core->nbformat>=4.2.0) (4.2.0)\n",
- "Installed nbformat>=4.2.0\n",
- "Packages installed successfully.\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "\n",
- "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.3.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.0\u001B[0m\n",
- "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\n"
- ]
- }
- ],
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"from jupyterlite.utils import install_packages\n",
"\n",