Split notebook in genmeration and analysis

1392064c · Simon Sebastian Humpohl · e1d20b83 · 1392064c · 1392064c · 1392064c
Commit 1392064c authored 1 year ago by Simon Sebastian Humpohl
--- a/DataAnalysis.ipynb
+++ b/DataAnalysis.ipynb
+{
+ "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
+}
+%% Cell type:markdown id:b115b402-4588-49a0-b984-e8983488aebc tags:
+
+# Data analysis
+
+%% Cell type:code id:3df6f25e-a136-4524-8081-96524ed88848 tags:
+
+``` python
+import xarray as xr
+
+lj_data = xr.load_dataset('lj_data.ndf')
+emt_data = xr.load_dataset('emt_data.ndf')
+all_data = xr.concat([lj_data, emt_data], xr.Variable('Method', ['LennardJones', 'EMT']))
+```
+
+%% Cell type:code id:d9a52cce-24aa-4286-9732-6c772389425a tags:
+
+``` python
+all_data
+```
+
+%% Cell type:code id:c5c696be-1713-4cd0-8cdf-bf890af3156b tags:
+
+``` python
+lj_data['Energy'].loc[..., 'Al', :].plot.line(x='lattice_constant')
+```
+
+%% Cell type:code id:4a51b954-c2ed-4f94-a7a6-35a45254f8c3 tags:
+
+``` python
+```
--- a/ML4QDM.ipynb
+++ b/ML4QDM.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,

-%% Cell type:markdown id:136f209c-91a7-4a11-8386-ef5535eeba9a tags:
+%% Cell type:markdown id:524f1ba2-39ab-40a9-9cab-dd170c39bf16 tags:

 # Data generation

 Create a virtual environment with the correct

 %% Cell type:code id:e18e2f2d-e0da-43eb-b378-2b617dbb73fa tags:

 ``` python
 import simulation
 import numpy as np

 materials = ['Au', 'Ag', 'Al', 'Cu', 'Ni']
 lattice_constants = np.linspace(3.0, 4.5, 100)
 ```

 %% Cell type:code id:eaa1b986-1329-491d-850f-4d5edefe5b14 tags:

 ``` python
 emt_data = simulation.simulate_multi(
    materials = materials,
    lattice_constants = lattice_constants,  # Ångstroms
    calculator='EMT',
    pool_size=None,
 )
 emt_data.to_netcdf('emt_data.ndf')
 emt_df = emt_data.to_dataframe()
 emt_df.to_csv('emt_data.csv')
 ```

 %% Cell type:code id:36aac675-21f5-4c7b-b225-416c3681b0b8 tags:

 ``` python
 lj_data = simulation.simulate_multi(
    materials = materials,
    lattice_constants = lattice_constants,  # Ångstroms
    calculator='LennardJones',
 )
 lj_data.to_netcdf('lj_data.ndf')
 lj_df = lj_data.to_dataframe()
 lj_df.to_csv('lj_data.csv')
 ```

-%% Cell type:markdown id:f7a5a554-26ce-4695-aa37-c787df57268d tags:
-
-# Data analysis
-
-%% Cell type:code id:941fe208-519d-4c9f-ab6d-1d973181c66f tags:
-
-``` python
-```
-
-%% Cell type:code id:028e3710-8ab2-44c6-809b-f7b1ae1a3e98 tags:
+%% Cell type:code id:54f57a76-f131-459f-98d0-f16b5b59b297 tags:

 ``` python
 ```

--- a/requirements.txt
+++ b/requirements.txt
 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
--- 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']):