From 1392064cce1f12ae6786a79720e809e008dca5af Mon Sep 17 00:00:00 2001
From: Simon Humpohl <simon.humpohl@rwth-aachen.de>
Date: Tue, 9 Apr 2024 10:41:17 +0200
Subject: [PATCH] Split notebook in genmeration and analysis
---
DataAnalysis.ipynb | 75 ++++++++++++++++++++++++++++
ML4QDM.ipynb => DataGeneration.ipynb | 32 +++---------
requirements.txt | 2 +
simulation.py | 2 +
4 files changed, 87 insertions(+), 24 deletions(-)
create mode 100644 DataAnalysis.ipynb
rename ML4QDM.ipynb => DataGeneration.ipynb (77%)
diff --git a/DataAnalysis.ipynb b/DataAnalysis.ipynb
new file mode 100644
index 0000000..348b669
--- /dev/null
+++ b/DataAnalysis.ipynb
@@ -0,0 +1,75 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "b115b402-4588-49a0-b984-e8983488aebc",
+ "metadata": {},
+ "source": [
+ "# Data analysis"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "3df6f25e-a136-4524-8081-96524ed88848",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import xarray as xr\n",
+ "\n",
+ "lj_data = xr.load_dataset('lj_data.ndf')\n",
+ "emt_data = xr.load_dataset('emt_data.ndf')\n",
+ "all_data = xr.concat([lj_data, emt_data], xr.Variable('Method', ['LennardJones', 'EMT']))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "d9a52cce-24aa-4286-9732-6c772389425a",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "all_data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c5c696be-1713-4cd0-8cdf-bf890af3156b",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "lj_data['Energy'].loc[..., 'Al', :].plot.line(x='lattice_constant')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "4a51b954-c2ed-4f94-a7a6-35a45254f8c3",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.2"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/ML4QDM.ipynb b/DataGeneration.ipynb
similarity index 77%
rename from ML4QDM.ipynb
rename to DataGeneration.ipynb
index 7cc68d5..dab1dc1 100644
--- a/ML4QDM.ipynb
+++ b/DataGeneration.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
- "id": "136f209c-91a7-4a11-8386-ef5535eeba9a",
+ "id": "524f1ba2-39ab-40a9-9cab-dd170c39bf16",
"metadata": {},
"source": [
"# Data generation\n",
@@ -12,7 +12,7 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"id": "e18e2f2d-e0da-43eb-b378-2b617dbb73fa",
"metadata": {},
"outputs": [],
@@ -26,7 +26,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"id": "eaa1b986-1329-491d-850f-4d5edefe5b14",
"metadata": {},
"outputs": [],
@@ -44,7 +44,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"id": "36aac675-21f5-4c7b-b225-416c3681b0b8",
"metadata": {},
"outputs": [],
@@ -59,26 +59,10 @@
"lj_df.to_csv('lj_data.csv')"
]
},
- {
- "cell_type": "markdown",
- "id": "f7a5a554-26ce-4695-aa37-c787df57268d",
- "metadata": {},
- "source": [
- "# Data analysis"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "941fe208-519d-4c9f-ab6d-1d973181c66f",
- "metadata": {},
- "outputs": [],
- "source": []
- },
{
"cell_type": "code",
"execution_count": null,
- "id": "028e3710-8ab2-44c6-809b-f7b1ae1a3e98",
+ "id": "54f57a76-f131-459f-98d0-f16b5b59b297",
"metadata": {},
"outputs": [],
"source": []
@@ -86,9 +70,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Project (ml4q DM workshop Simulation)",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
- "name": "simulation_venv"
+ "name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -100,7 +84,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.11"
+ "version": "3.11.2"
}
},
"nbformat": 4,
diff --git a/requirements.txt b/requirements.txt
index d22d5d0..81e611f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,5 @@
numpy==1.25
ase==3.22.1
xarray==2024.2.0
+ipympl==0.9.3
+h5netcdf==1.3.0
\ No newline at end of file
diff --git a/simulation.py b/simulation.py
index 11292dc..9957a1f 100644
--- a/simulation.py
+++ b/simulation.py
@@ -7,12 +7,14 @@ import xarray as xr
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.calculators.lj import LennardJones
+from ase.calculators.eam import EAM
CALCULATORS = {
# Effective Medium Theory
'EMT': EMT,
# LennardJones potential
'LennardJones': LennardJones,
+ 'EAM': EAM,
}
def simulate_properties(material, lattice_constant, calculator: Literal['EMT', 'EAM']):
--
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