save changes to HPF2023 notebook

Author: tschaume

mpcontribs-portal/notebooks/contribs.materialsproject.org/HFP2023.ipynb

@@ -11,6 +11,7 @@
     "# pip install mpcontribs-client mp_api pandas flatten_dict\n",
     "import os\n",
     "import gzip\n",
+    "import json\n",
     "\n",
     "from pathlib import Path\n",
     "from mpcontribs.client import Client\n",
@@ -27,8 +28,28 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "client = Client(project=\"HFP2023\")\n",
-    "mpr = MPRester(api_key=os.environ[\"MPCONTRIBS_API_KEY\"])"
+    "# mpr = MPRester(api_key=os.environ[\"MPCONTRIBS_API_KEY\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7bf789df-1db1-4ff9-b7ca-0811a2ea840c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"/Users/patrick/Downloads/usf_formates_tasks.json\", \"r\") as f:\n",
+    "    tasks = json.load(f)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "824df967-358b-4399-b24f-18b31a42c864",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lookup = {doc[\"formula_pretty\"] + \"_\" + str(doc[\"symmetry\"][\"number\"]): doc[\"task_id\"] for doc in tasks}"
    ]
   },
   {
@@ -50,11 +71,11 @@
    "outputs": [],
    "source": [
     "# function to search MP via its summary API endpoint\n",
-    "def search(formula=None, spacegroup_number=None, chemsys=None):\n",
-    "    return mpr.summary.search(\n",
-    "        formula=formula, chemsys=chemsys, spacegroup_number=spacegroup_number,\n",
-    "        fields=[\"material_id\"], sort_fields=\"energy_above_hull\"\n",
-    "    )"
+    "# def search(formula=None, spacegroup_number=None, chemsys=None):\n",
+    "#     return mpr.summary.search(\n",
+    "#         formula=formula, chemsys=chemsys, spacegroup_number=spacegroup_number,\n",
+    "#         fields=[\"material_id\"], sort_fields=\"energy_above_hull\"\n",
+    "#     )"
    ]
   },
   {
@@ -120,33 +141,37 @@
     "        # assuming there's only one CIF per directory\n",
     "        structure = Structure.from_file(cifs[0])\n",
     "\n",
-    "        # try to match CIF against MP\n",
-    "        matching_mpids = mpr.find_structure(structure)\n",
+    "        # # try to match CIF against MP\n",
+    "        # matching_mpids = mpr.find_structure(structure)\n",
     "\n",
-    "        if matching_mpids:\n",
-    "            identifier = matching_mpids[0]\n",
-    "        else:\n",
-    "            # structure not in MP (yet)\n",
-    "            # get composition, formula, space group, and chemical system\n",
-    "            composition = structure.composition\n",
-    "            formula, _ = composition.get_reduced_formula_and_factor()\n",
-    "            _, spacegroup_number = structure.get_space_group_info()\n",
-    "            chemsys = composition.chemical_system\n",
+    "        # if matching_mpids:\n",
+    "        #     identifier = matching_mpids[0]\n",
+    "        # else:\n",
+    "        #     # structure not in MP (yet)\n",
+    "        #     # get composition, formula, space group, and chemical system\n",
+    "        #     composition = structure.composition\n",
+    "        #     formula, _ = composition.get_reduced_formula_and_factor()\n",
+    "        #     _, spacegroup_number = structure.get_space_group_info()\n",
+    "        #     chemsys = composition.chemical_system\n",
     "\n",
-    "            # 1) try formula and space group \n",
-    "            docs = search(formula=formula, spacegroup_number=spacegroup_number)\n",
-    "            if not docs:\n",
-    "                # 2) try formula\n",
-    "                docs = search(formula=formula)\n",
-    "                if not docs:\n",
-    "                    # 3) try chemical system\n",
-    "                    docs = search(chemsys=chemsys)\n",
+    "        #     # 1) try formula and space group \n",
+    "        #     docs = search(formula=formula, spacegroup_number=spacegroup_number)\n",
+    "        #     if not docs:\n",
+    "        #         # 2) try formula\n",
+    "        #         docs = search(formula=formula)\n",
+    "        #         if not docs:\n",
+    "        #             # 3) try chemical system\n",
+    "        #             docs = search(chemsys=chemsys)\n",
     "\n",
-    "            if docs:\n",
-    "                # always use material with lowest energy above hull\n",
-    "                identifier = docs[0].material_id\n",
-    "        \n",
-    "    print(identifier) # \"link to MP\"\n",
+    "        #     if docs:\n",
+    "        #         # always use material with lowest energy above hull\n",
+    "        #         identifier = docs[0].material_id\n",
+    "\n",
+    "        composition = structure.composition\n",
+    "        formula, _ = composition.get_reduced_formula_and_factor()\n",
+    "        _, spacegroup_number = structure.get_space_group_info()\n",
+    "        identifier = lookup[f\"{formula}_{spacegroup_number}\"]\n",
+    "        print(identifier) # \"link to MP\"\n",
     "    \n",
     "    # make sure everything's gzipped\n",
     "    for p in subdir.glob(\"*.*\"):\n",
@@ -155,7 +180,7 @@
     "    \n",
     "    # init contribution; add all files as attachments; add structure\n",
     "    contrib = {\n",
-    "        \"identifier\": identifier, \"data\": {},\n",
+    "        \"identifier\": identifier, \"formula\": formula, \"data\": {},\n",
     "        \"attachments\": list(subdir.glob(\"*.gz\"))\n",
     "    }\n",
     "    if identifier.startswith(\"mp-\"):\n",
@@ -182,6 +207,16 @@
     "    contributions.append(contrib)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "43104a49-3e15-4f27-a794-db2acfab11e0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "client = Client(project=\"HFP2023\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,