From 65bb47d6af370485dfc6df262f07e4b8961bcc1c Mon Sep 17 00:00:00 2001
From: Michael Hucka <mhucka@google.com>
Date: Wed, 14 Oct 2026 01:44:47 +0000
Subject: [PATCH] Save diatomic example data to working directory

Fixes #64.

In examples/generate_diatomic.py, MolecularData instances were created
without specifying data_directory, causing them to default to
openfermion.config.DATA_DIRECTORY (located within the installed
openfermion package). In read-only or system installations, running the
example raised PermissionError when run_pyscf and molecule.save()
attempted to write HDF5 data into the package directory.

This change:
- Sets data_directory = os.getcwd() in examples/generate_diatomic.py and
  passes it to MolecularData calls so output is written to the working
  directory.
- Removes redundant explicit molecule.save() calls since run_pyscf saves
  by default.
- Adds an integration test in openfermionpyscf/tests/_run_pyscf_test.py
  verifying generate_diatomic.py runs and saves files to the working
  directory even when DATA_DIRECTORY is read-only.
---
 examples/generate_diatomic.py             |  9 ++++---
 openfermionpyscf/tests/_run_pyscf_test.py | 33 +++++++++++++++++++++++
 2 files changed, 38 insertions(+), 4 deletions(-)

diff --git a/examples/generate_diatomic.py b/examples/generate_diatomic.py
index f81f45a..10e3f4c 100644
--- a/examples/generate_diatomic.py
+++ b/examples/generate_diatomic.py
@@ -39,6 +39,7 @@
     run_ccsd = 1
     run_fci = 1
     verbose = 1
+    data_directory = os.getcwd()
 
     # Run Diatomic Curve
     for spacing in spacings:
@@ -49,7 +50,8 @@
                                  basis,
                                  multiplicity,
                                  charge,
-                                 description)
+                                 description,
+                                 data_directory=data_directory)
 
         molecule = run_pyscf(molecule,
                              run_scf=run_scf,
@@ -58,7 +60,6 @@
                              run_ccsd=run_ccsd,
                              run_fci=run_fci,
                              verbose=verbose)
-        molecule.save()
 
     # Run Li H single point
     description = "1.45"
@@ -68,7 +69,8 @@
                              basis,
                              multiplicity,
                              charge,
-                             description)
+                             description,
+                             data_directory=data_directory)
 
     molecule = run_pyscf(molecule,
                          run_scf=run_scf,
@@ -77,4 +79,3 @@
                          run_ccsd=run_ccsd,
                          run_fci=run_fci,
                          verbose=verbose)
-    molecule.save()
diff --git a/openfermionpyscf/tests/_run_pyscf_test.py b/openfermionpyscf/tests/_run_pyscf_test.py
index a7083a7..004b322 100644
--- a/openfermionpyscf/tests/_run_pyscf_test.py
+++ b/openfermionpyscf/tests/_run_pyscf_test.py
@@ -14,8 +14,11 @@
 from __future__ import absolute_import
 
 import os
+import runpy
 
+import openfermion.chem.molecular_data
 from openfermion.chem import MolecularData
+import openfermion.config
 from openfermionpyscf import run_pyscf
 from openfermionpyscf import PyscfMolecularData
 
@@ -58,3 +61,33 @@ def test_run_pyscf_without_save(tmp_path):
                                run_scf=True)
     assert isinstance(new_mole_saved, PyscfMolecularData)
     assert os.path.exists(f'{new_mole_saved.filename}.hdf5')
+
+
+def test_generate_diatomic(tmp_path, monkeypatch):
+    """Verify generate_diatomic.py saves files to the working directory."""
+    readonly_dir = tmp_path / 'readonly_data'
+    readonly_dir.mkdir()
+    readonly_dir.chmod(0o555)
+
+    work_dir = tmp_path / 'work'
+    work_dir.mkdir()
+
+    example_path = os.path.abspath(
+        os.path.join(os.path.dirname(__file__), '..', '..', 'examples',
+                     'generate_diatomic.py'))
+
+    try:
+        monkeypatch.setattr(openfermion.chem.molecular_data, 'DATA_DIRECTORY',
+                            str(readonly_dir))
+        monkeypatch.setattr(openfermion.config, 'DATA_DIRECTORY',
+                            str(readonly_dir))
+        monkeypatch.chdir(work_dir)
+
+        runpy.run_path(example_path, run_name='__main__')
+
+        assert (work_dir / 'H2_sto-3g_singlet_0.7414.hdf5').exists()
+        assert (work_dir / 'H1-Li1_sto-3g_singlet_1.45.hdf5').exists()
+        assert len(list(work_dir.glob('*.hdf5'))) == 32
+        assert not list(readonly_dir.iterdir())
+    finally:
+        readonly_dir.chmod(0o755)