Merge pull request #2 from ICAMS/docs

add docs and tutorials, gracemaker -t and grace_models

.readthedocs.yaml

@@ -16,4 +16,4 @@ mkdocs:
 # Optionally declare the Python requirements required to build your docs
 python:
   install:
-  - requirements: doc/requirements.txt
+  - requirements: docs/requirements.txt

bin/extxyz2df

@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+import os
+import pandas as pd
+import argparse
+import sys
+from ase.io import read
+
+import logging
+
+LOG_FMT = "%(asctime)s %(levelname).1s - %(message)s"
+logging.basicConfig(level=logging.INFO, format=LOG_FMT, datefmt="%Y/%m/%d %H:%M:%S")
+logger = logging.getLogger()
+
+
+def sizeof_fmt(file_name_or_size, suffix="B"):
+    if isinstance(file_name_or_size, str):
+        file_name_or_size = os.path.getsize(file_name_or_size)
+    for unit in ["", "Ki", "Mi", "Gi", "Ti", "Pi", "Ei", "Zi"]:
+        if abs(file_name_or_size) < 1024.0:
+            return "%3.1f%s%s" % (file_name_or_size, unit, suffix)
+        file_name_or_size /= 1024.0
+    return "%.1f%s%s" % (file_name_or_size, "Yi", suffix)
+
+
+def main(args):
+    ##############################################################################################
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument(
+        "extxyz_filename",
+        help="Name of extxyz file",
+        type=str,
+    )
+
+    parser.add_argument(
+        "--output-dataset-filename",
+        help="pickle filename, default is inferenced from extxyz_filename",
+        type=str,
+        default=None,
+    )
+
+    args_parse = parser.parse_args(args)
+    extxyz_filename = os.path.abspath(args_parse.extxyz_filename)
+    output_dataset_filename = args_parse.output_dataset_filename
+    if output_dataset_filename is None:
+        output_dataset_filename = extxyz_filename.replace(".extxyz", ".pkl.gz")
+        output_dataset_filename = extxyz_filename.replace(".xyz", ".pkl.gz")
+
+    logging.info(f"Input filename: {extxyz_filename}")
+    logging.info(f"Output filename: {output_dataset_filename}")
+
+    logging.info(
+        f"Reading extxyz file: {extxyz_filename} ({sizeof_fmt(extxyz_filename)})"
+    )
+    data = read(extxyz_filename, format="extxyz", index=":")
+    logging.info(f"{len(data)} structures read from {extxyz_filename}")
+    logging.info("Converting to dataframe")
+    df = pd.DataFrame({"ase_atoms": data})
+    logging.info("Extracting energy")
+    df["energy"] = df["ase_atoms"].map(
+        lambda at: at.get_potential_energy(force_consistent=True)
+    )
+    logging.info("Extracting forces")
+    df["forces"] = df["ase_atoms"].map(lambda at: at.get_forces())
+
+    try:
+        logging.info("Trying to extract stresses")
+        df["stress"] = df["ase_atoms"].map(lambda at: at.get_stress())
+    except Exception as e:
+        logger.error(f"Error while trying to extract stress: {e}, ignoring")
+
+    logging.info("Extracting info")
+    df["info"] = df["ase_atoms"].map(lambda at: at.info)
+
+    logging.info(f"Saving dataframe")
+    df.to_pickle(output_dataset_filename, compression="gzip")
+    logging.info(
+        f"Saved dataframe to {output_dataset_filename} ({sizeof_fmt(output_dataset_filename)})"
+    )
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])