From 3611479f7c1108137d92e11b453c30f899047fb3 Mon Sep 17 00:00:00 2001
From: Luigi Sbailo <luigi.sbailo@physik.hu-berlin.de>
Date: Sat, 2 Apr 2022 18:12:19 +0200
Subject: [PATCH] Upgrade nomad API
---
tetradymite_PRM2020.ipynb | 90 ++++++++++++++++++++++++++++-----------
1 file changed, 66 insertions(+), 24 deletions(-)
diff --git a/tetradymite_PRM2020.ipynb b/tetradymite_PRM2020.ipynb
index 0b63a42..21e0dd1 100644
--- a/tetradymite_PRM2020.ipynb
+++ b/tetradymite_PRM2020.ipynb
@@ -80,8 +80,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.333397Z",
- "start_time": "2022-02-03T15:17:02.326564Z"
+ "end_time": "2022-04-02T16:11:38.936835Z",
+ "start_time": "2022-04-02T16:11:38.929994Z"
},
"init_cell": true
},
@@ -113,8 +113,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.340869Z",
- "start_time": "2022-02-03T15:17:02.335388Z"
+ "end_time": "2022-04-02T16:11:38.944992Z",
+ "start_time": "2022-04-02T16:11:38.940335Z"
},
"init_cell": true
},
@@ -134,20 +134,48 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2021-06-21T15:58:13.011817Z",
- "start_time": "2021-06-21T15:58:01.884774Z"
+ "end_time": "2022-04-02T16:11:31.621762Z",
+ "start_time": "2022-04-02T16:11:30.061189Z"
}
},
"outputs": [],
"source": [
"# The dataset is stored in the NOMAD Archive and can be accessed with this query.\n",
"from nomad import client, config\n",
- "config.client.url = 'http://nomad-lab.eu/prod/rae/api'\n",
- "query = client.query_archive(query={\n",
- " 'dataset_id': ['BjT-NFK0QdOx81_z5TmyeQ']},\n",
- " per_page=100,\n",
- ")\n",
- "print(query)\n"
+ "from nomad.client.archive import ArchiveQuery\n",
+ "from nomad.metainfo import units\n",
+ "import nest_asyncio\n",
+ "nest_asyncio.apply()\n",
+ "\n",
+ "query_param={\n",
+ " \"datasets.dataset_id:any\": [\n",
+ " \"BjT-NFK0QdOx81_z5TmyeQ\"\n",
+ " ]\n",
+ " }\n",
+ "\n",
+ "required={\n",
+ " 'workflow':{\n",
+ " 'calculation_result_ref':{\n",
+ " 'energy':{\n",
+ " 'total':'*',\n",
+ " },\n",
+ " 'system_ref':{\n",
+ " 'chemical_composition_reduced': '*',\n",
+ " 'atoms': {\n",
+ " 'labels':'*', \n",
+ " 'positions':'*',\n",
+ " 'lattice_vectors':'*',\n",
+ " },\n",
+ " 'symmetry':{\n",
+ " 'space_group_number': '*', \n",
+ " }, \n",
+ " },\n",
+ " }, \n",
+ " } \n",
+ " }\n",
+ "max_entries=1000\n",
+ "query = ArchiveQuery(query=query_param, required=required, page_size=20, results_max=max_entries)\n",
+ "query.fetch()"
]
},
{
@@ -155,8 +183,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.357307Z",
- "start_time": "2022-02-03T15:17:02.341830Z"
+ "end_time": "2022-04-02T16:11:38.965829Z",
+ "start_time": "2022-04-02T16:11:38.946398Z"
},
"init_cell": true
},
@@ -165,6 +193,20 @@
"df_train = pd.read_pickle('./data/tetradymite_PRM2020/training_set')"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2022-04-02T16:09:31.283833Z",
+ "start_time": "2022-04-02T16:09:31.252040Z"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "df_train"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -227,8 +269,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.426971Z",
- "start_time": "2022-02-03T15:17:02.358431Z"
+ "end_time": "2022-04-02T16:11:39.006154Z",
+ "start_time": "2022-04-02T16:11:38.966910Z"
},
"init_cell": true
},
@@ -271,8 +313,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.435420Z",
- "start_time": "2022-02-03T15:17:02.428037Z"
+ "end_time": "2022-04-02T16:11:39.012351Z",
+ "start_time": "2022-04-02T16:11:39.007515Z"
},
"init_cell": true
},
@@ -335,8 +377,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.446436Z",
- "start_time": "2022-02-03T15:17:02.436346Z"
+ "end_time": "2022-04-02T16:11:39.060675Z",
+ "start_time": "2022-04-02T16:11:39.013346Z"
},
"init_cell": true
},
@@ -471,8 +513,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2022-02-03T15:17:02.597783Z",
- "start_time": "2022-02-03T15:17:02.447596Z"
+ "end_time": "2022-04-02T16:11:39.217140Z",
+ "start_time": "2022-04-02T16:11:39.061785Z"
},
"init_cell": true,
"scrolled": false
@@ -562,7 +604,7 @@
"metadata": {
"celltoolbar": "Initialization Cell",
"kernelspec": {
- "display_name": "Python 3 (ipykernel)",
+ "display_name": "Python 3",
"language": "python",
"name": "python3"
},
@@ -576,7 +618,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.9.7"
+ "version": "3.7.3"
}
},
"nbformat": 4,
--
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