new version based on materials toolkit (with convex hulls)

download-and-process.py

@@ -20,7 +20,7 @@ from ase.io import read
 import numpy as np
 import torch
 import h5py
-from materials_toolkit.data import HDF5Dataset, StructureData
+from materials_toolkit.data import HDF5Dataset
 from materials_toolkit.data.datasets import MaterialsProjectData
 
 zip_file = "mp.2019.04.01.json.zip"
@@ -123,22 +123,24 @@ def parse_structure(json_str: str) -> MaterialsProjectData:
 
 def process(path: Optional[str] = "."):
     mp_dir = os.path.join(path, "materials-project")
+    processed_dir = os.path.join(mp_dir, "processed")
 
-    os.makedirs(mp_dir, exist_ok=True)
+    os.makedirs(processed_dir, exist_ok=True)
 
-    if os.path.exists(os.path.join(mp_dir, "batching.json")) and os.path.exists(
-        os.path.join(mp_dir, "data.hdf5")
+    if (not os.path.exists(os.path.join(processed_dir, "batching.json"))) or not (
+        os.path.exists(os.path.join(processed_dir, "data.hdf5"))
     ):
-        return
+        results = [
+            parse_structure(elem)
+            for elem in gen_structure_from_json(
+                os.path.join(path, "unzipped/mp.2019.04.01.json")
+            )
+        ]
 
-    results = [
-        parse_structure(elem)
-        for elem in gen_structure_from_json(
-            os.path.join(path, "unzipped/mp.2019.04.01.json")
-        )
-    ]
+        HDF5Dataset.create_dataset(processed_dir, results)
 
-    HDF5Dataset.create_dataset(mp_dir, results)
+    dataset = HDF5Dataset(mp_dir)
+    dataset.compute_convex_hulls()
 
 
 def compress(path: Optional[str] = "."):
@@ -149,8 +151,13 @@ def compress(path: Optional[str] = "."):
 
     print("compress into materials-project.tar.gz")
     with tarfile.open(output_file, "w:gz") as tar:
-        tar.add(os.path.join(path, "materials-project/batching.json"),"batching.json")
-        tar.add(os.path.join(path, "materials-project/data.hdf5"),"data.hdf5")
+        tar.add(
+            os.path.join(path, "materials-project/processed/batching.json"),
+            "batching.json",
+        )
+        tar.add(
+            os.path.join(path, "materials-project/processed/data.hdf5"), "data.hdf5"
+        )
 
 
 download_raw_mp()

materials-project.tar.gz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:14a727400bfa71c8ca2c41ba3a331f479019f494f1bb78602d31981a79c570b9
-size 38793462
+oid sha256:5372c6da7fdfe8212b19bb985a6c6718672751f6554c659b052f3d1b80e0dbbb
+size 38735048