Merge pull request #50 from pyscal/query_building

Query building
pyscal · Nov 28, 2023 · 44e8585 · 44e8585
2 parents ceea7d3 + 4c9b981
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diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb
diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
diff --git a/examples/02_using_databases.ipynb b/examples/02_using_databases.ipynb
diff --git a/notebooks/create_onto.ipynb b/notebooks/create_onto.ipynb
@@ -0,0 +1,120 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "0480f3cb-a9df-4dff-89b6-95747572fb39",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from owlready2 import *"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "cdab09a3-b991-4c6f-ab11-3d630293e2a9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "onto = get_ontology(\"http://purls.helmholtz-metadaten.de/msmo/\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "8f470001-3a9c-4cd0-817f-57fa06a10da0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "class Calculation(Thing):\n",
+    "    namespace = onto\n",
+    "\n",
+    "class hasMethod(Calculation >> ComputationalMethod):\n",
+    "    pass\n",
+    "    \n",
+    "class ComputationalMethod(Thing):\n",
+    "    namespace = onto\n",
+    "\n",
+    "#Atomistic Method\n",
+    "class AtomisticMethod(ComputationalMethod):\n",
+    "    pass\n",
+    "\n",
+    "class DensityFunctionalTheory(AtomisticMethod):\n",
+    "    pass\n",
+    "\n",
+    "class MolecularDynamics(AtomisticMethod):\n",
+    "    pass\n",
+    "\n",
+    "class MolecularDynamicsMinimization(MolecularDynamics):\n",
+    "    pass\n",
+    "\n",
+    "class MolecularDynamicsNPT(MolecularDynamics):\n",
+    "    pass\n",
+    "\n",
+    "class MolecularDynamicsNVT(MolecularDynamics):\n",
+    "    pass\n",
+    "\n",
+    "#data properties\n",
+    "class hasPressure(MolecularDynamics >> float):\n",
+    "    pass\n",
+    "\n",
+    "class hasTemperature(MolecularDynamics >> float):\n",
+    "    pass\n",
+    "\n",
+    "class usesPotential(MolecularDynamics >> str):\n",
+    "    pass\n",
+    "\n",
+    "class AbinitioMolecularDynamics(AtomisticMethod):\n",
+    "    pass\n",
+    "\n",
+    "\n",
+    "#Monte Carlo\n",
+    "class MonteCarloMethod(ComputationalMethod):\n",
+    "    pass\n",
+    "\n",
+    "class KineticMonteCarloMethod(MonteCarloMethod):\n",
+    "    pass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "677852fc-e05a-4922-a808-47761f25ffcb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "onto.save(file = \"msmo.owl\", format = \"rdfxml\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22b6e284-2b54-4851-a379-1a8df26f4705",
+   "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/notebooks/data_read.ipynb b/notebooks/data_read.ipynb
@@ -0,0 +1,142 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "bec4e0e1-2e16-4241-89e0-a7bbf8a53d8c",
+   "metadata": {},
+   "source": [
+    "# DC3 dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "df95f07a-00a8-42f9-9a18-ba8532a5a512",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from pyscal3.core import System\n",
+    "import pyscal3.crystal_structures as pcs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "00abae5c-4123-4456-8144-cf6362ea2bfd",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "sys = System('datasets/T_0.04Tm_snapshot_1')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2be601e0-9ea5-4c63-9cd6-67e99fa95306",
+   "metadata": {},
+   "source": [
+    "Lacks all information about the underlying structure:\n",
+    "\n",
+    "- species (LAMMPS)\n",
+    "- lattice constant \n",
+    "- Crystal structure name\n",
+    "- Bravais lattice\n",
+    "- Basis positions\n",
+    "- Basis occupancy\n",
+    "- Lattice vectors\n",
+    "- Space group symbol (?)\n",
+    "- Space group name (?)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5ba58cff-3b6b-44b9-ad5b-92e14e61d517",
+   "metadata": {},
+   "source": [
+    "How we do currently"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "dd472cdf-ef2c-4ad4-9852-39370c715f5a",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Al\n"
+     ]
+    }
+   ],
+   "source": [
+    "atoms, box, sdict = pcs.make_crystal('fcc', lattice_constant=1,\n",
+    "     element='Al', return_structure_dict=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "aed4d624-b25a-48b3-8bbe-6140acc5e711",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'natoms': 4,\n",
+       " 'species': [1, 1, 1, 1],\n",
+       " 'scaling_factors': [1.0, 1.0, 1.0],\n",
+       " 'positions': [[0.0, 0.0, 0.0],\n",
+       "  [0.5, 0.0, 0.5],\n",
+       "  [0.0, 0.5, 0.5],\n",
+       "  [0.5, 0.5, 0.0]]}"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "sdict"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "712b32c7-1d6b-4fbb-ae65-64dbebc5a3b2",
+   "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": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}