File size: 2,369 Bytes
39ea985 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | """Write a flat per-calculation index for a store: one row per calculation with its shard, row
number and the handful of columns most queries filter on. Lets a consumer find a calculation
without opening every shard.
python build_index.py --store $PSCRATCH/omol_100k
writes <store>/index.tsv
"""
from __future__ import annotations
import argparse, glob, os
import numpy as np
import zarr
def p2_shards(store):
out = []
for depth in ("*", "*/*/*"):
out += glob.glob(os.path.join(store, "p2", depth, "*.zarr"))
return sorted(set(out))
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--store", required=True)
args = ap.parse_args()
shards = p2_shards(args.store)
out = os.path.join(args.store, "index.tsv")
n = 0
cols = ["calc_id", "dataset", "shard", "row", "n_atoms", "nbas", "nelec", "charge", "mult",
"is_uhf", "has_fock", "scf_converged", "mo_ok", "e_total", "conv_diiserr", "rel_path"]
with open(out, "w") as fh:
fh.write("\t".join(cols) + "\n")
for sp in shards:
g = zarr.open_group(sp, mode="r")
rel = os.path.relpath(sp, os.path.join(args.store, "p2"))
ids, rels, ds = g.attrs["calc_id"], g.attrs["rel_path"], g.attrs["dataset"]
si = np.asarray(g["scalar_i"]); ic = {k: j for j, k in enumerate(g.attrs["scalar_i_cols"])}
sf = np.asarray(g["scalar_f8"]); fc_ = {k: j for j, k in enumerate(g.attrs["scalar_f8_cols"])}
fl = np.asarray(g["flags"]); fc = {k: j for j, k in enumerate(g.attrs["flag_cols"])}
if g.attrs.get("has_mo"):
cf = np.asarray(g["mo_flags"])[:, g.attrs["mo_flag_cols"].index("mo_ok")]
else:
cf = np.full(len(ids), -1)
for i in range(len(ids)):
fh.write("\t".join(map(str, [
ids[i], ds, rel, i, si[i, ic["n_atoms"]], si[i, ic["nbas"]], si[i, ic["nelec"]],
si[i, ic["charge"]], si[i, ic["mult"]], int(fl[i, fc["is_uhf"]]),
int(fl[i, fc["has_fock"]]), int(fl[i, fc["scf_converged"]]), int(cf[i]),
f"{sf[i, fc_['e_total']]:.10f}", f"{sf[i, fc_['conv_diiserr']]:.3e}", rels[i]])) + "\n")
n += 1
print(f"wrote {out}: {n:,} rows from {len(shards)} shards")
if __name__ == "__main__":
main()
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