Initial commit

.gitignore

+.ipynb_checkpoints/
+simulation_venv/
+__pycache__
+/.jupyter_ystore.db
+/.virtual_documents/

ML4QDM.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "136f209c-91a7-4a11-8386-ef5535eeba9a",
+   "metadata": {},
+   "source": [
+    "# Data generation\n",
+    "\n",
+    "Create a virtual environment with the correct \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "e18e2f2d-e0da-43eb-b378-2b617dbb73fa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import simulation\n",
+    "import numpy as np\n",
+    "\n",
+    "materials = ['Au', 'Ag', 'Al', 'Cu', 'Ni']\n",
+    "lattice_constants = np.linspace(3.0, 4.5, 100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "eaa1b986-1329-491d-850f-4d5edefe5b14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "emt_data = simulation.simulate_multi(\n",
+    "    materials = materials,\n",
+    "    lattice_constants = lattice_constants,  # Ångstroms\n",
+    "    calculator='EMT',\n",
+    "    pool_size=None,\n",
+    ")\n",
+    "emt_data.to_netcdf('emt_data.ndf')\n",
+    "emt_df = emt_data.to_dataframe()\n",
+    "emt_df.to_csv('emt_data.csv')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "36aac675-21f5-4c7b-b225-416c3681b0b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lj_data = simulation.simulate_multi(\n",
+    "    materials = materials,\n",
+    "    lattice_constants = lattice_constants,  # Ångstroms\n",
+    "    calculator='LennardJones',\n",
+    ")\n",
+    "lj_data.to_netcdf('lj_data.ndf')\n",
+    "lj_df = lj_data.to_dataframe()\n",
+    "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",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Project (ml4q DM workshop Simulation)",
+   "language": "python",
+   "name": "simulation_venv"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

simulation.py

+from multiprocessing import Pool as ProcessPool
+import itertools
+from typing import Literal
+
+import numpy as np
+import xarray as xr
+from ase.build import bulk
+from ase.calculators.emt import EMT
+from ase.calculators.lj import LennardJones
+
+CALCULATORS = {
+    # Effective Medium Theory
+    'EMT': EMT,
+    # LennardJones potential
+    'LennardJones': LennardJones,
+}
+
+def simulate_properties(material, lattice_constant, calculator: Literal['EMT', 'EAM']):
+    atoms = bulk(material, a=lattice_constant)
+    atoms.calc = CALCULATORS[calculator]()
+
+    return {
+        'Energy': atoms.get_potential_energy(),
+        'Volume': atoms.get_volume(),
+    }
+
+def simulate_multi(materials, lattice_constants, calculator: Literal['EMT', 'EAM'] = 'EMT', pool_size=None):
+    arg_iter = ((material, lattice_constant, calculator) for (material, lattice_constant) in itertools.product(materials, lattice_constants))
+    
+    with ProcessPool(pool_size) as pool:
+        results = pool.starmap(simulate_properties, arg_iter, chunksize=10)
+
+    shape = len(materials), len(lattice_constants)
+    energies, volumes = zip(*((result['Energy'], result['Volume']) for result in results))
+
+    return xr.Dataset(
+        {
+            "Energy": (("material", "lattice_constant"), np.array(energies).reshape(shape)),
+            "Volume": (("material", "lattice_constant"), np.array(volumes).reshape(shape)),
+        },
+        coords={
+            "lattice_constant": lattice_constants,
+            "material": materials,        
+        }
+    )
+