From 9bbd63dd8114161f5ae1f5b85029c600fd76fe58 Mon Sep 17 00:00:00 2001
From: Johannes Steinmetzer <johannes.steinmetzer@uni-jena.de>
Date: Fri, 10 Nov 2023 09:02:43 +0100
Subject: [PATCH] fix: added missing file

---
 pysisyphus/io/molcas.py | 57 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 pysisyphus/io/molcas.py

diff --git a/pysisyphus/io/molcas.py b/pysisyphus/io/molcas.py
new file mode 100644
index 000000000..9bf0b4fde
--- /dev/null
+++ b/pysisyphus/io/molcas.py
@@ -0,0 +1,57 @@
+import h5py
+import numpy as np
+
+from pysisyphus.wavefunction.shells import Shell, MolcasShells
+
+
+def shells_from_molcas_h5(h5_fn, **kwargs):
+    with h5py.File(h5_fn) as handle:
+        # shape (nprims, 2); (exponent, contr. coeff) in every row
+        primitives = handle["PRIMITIVES"][:]
+        # shape (nprims, 3); (center_ind, L, shell_id) in every row
+        primitive_ids = handle["PRIMITIVE_IDS"][:]
+        # shape (ncenters, )
+        atnums = handle["CENTER_ATNUMS"][:]
+        # shape (ncenters, ); unused but checked to be the same as 'atnums'
+        charges = handle["CENTER_CHARGES"][:]
+        # shape (ncenters, 3); center coordinates in Bohr
+        coords3d = handle["CENTER_COORDINATES"][:]
+
+    # As I never thought about cases where these two arrays aren't the same
+    # we check that they are the same! So we can deal with such cases when they
+    # actually appear.
+    np.testing.assert_allclose(atnums.astype(float), charges)
+
+    shells = list()
+    exps = list()
+    coeffs = list()
+    nprims = len(primitives)
+    last_index = nprims - 1
+    for i, prim_id in enumerate(primitive_ids):
+        prim_id = tuple(prim_id)
+        center_ind, L, _ = prim_id
+        exponent, coeff = primitives[i]
+        exps.append(exponent)
+        coeffs.append(coeff)
+
+        # Look ahead to see if we are at the end or if a new shell will begin.
+        # In either case we create a new Shell object from the stored data and insert
+        # it into the shells list. Then we reset the 'exps' and 'coeffs' list and starting
+        # filling the next shell.
+        if (i == last_index) or (prim_id != tuple(primitive_ids[i + 1])):
+            ind0 = center_ind - 1
+            shell = Shell(
+                L,
+                coords3d[ind0],
+                coeffs,
+                exps,
+                ind0,
+                atnums[ind0],
+            )
+            shells.append(shell)
+            # Reset exponent & contraction coefficient lists
+            exps = list()
+            coeffs = list()
+    # Outside of loop over primitives
+
+    return MolcasShells(shells, **kwargs)