From 10abd43bb93524d5f0e25750d5a35e90b13c21c4 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 18 May 2026 13:03:58 -0500
Subject: [PATCH 1/5] Reproduce thread safety issue

---
 openff/packmol/_tests/test_issues.py |    34 +
 pixi.lock                            | 13688 +++++++++++++------------
 pyproject.toml                       |     6 +-
 3 files changed, 7421 insertions(+), 6307 deletions(-)
 create mode 100644 openff/packmol/_tests/test_issues.py

diff --git a/openff/packmol/_tests/test_issues.py b/openff/packmol/_tests/test_issues.py
new file mode 100644
index 0000000..36fe3a8
--- /dev/null
+++ b/openff/packmol/_tests/test_issues.py
@@ -0,0 +1,34 @@
+import threading
+
+import pytest
+from openff.toolkit import Molecule, Quantity
+
+from openff.packmol import pack_box
+
+
+@pytest.fixture
+def water():
+    return Molecule.from_smiles("O")
+
+
+@pytest.mark.filterwarnings("error::pytest.PytestUnhandledThreadExceptionWarning")
+def test_thread_safety(water):
+    """See https://github.com/openforcefield/openff-packmol/issues/10."""
+    threads = []
+    for i in range(3):
+        t = threading.Thread(
+            target=pack_box,
+            args=(
+                [water],
+                [i],
+                None,
+                Quantity(0.2, "nanometer"),
+                None,
+                Quantity(0.5, "g/mL"),
+            ),
+        )
+        threads.append(t)
+        t.start()
+
+    for t in threads:
+        t.join()
diff --git a/pixi.lock b/pixi.lock
index bf4920a..ecdce98 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,335 +1,551 @@
-version: 6
+version: 7
+platforms:
+- name: linux-64
+- name: osx-arm64
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   default:
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     packages:
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+  md5: a9d9010d246205c63f824b0bcf050acd
   depends:
   - __osx >=11.0
   - python >=3.11,<3.12.0a0
@@ -9036,11 +10304,11 @@ packages:
   license_family: Apache
   purls:
   - pkg:pypi/unicodedata2?source=hash-mapping
-  size: 416311
-  timestamp: 1763055361431
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/unicodedata2-17.0.0-py312h4409184_1.conda
-  sha256: 567cebbb3a1a5c76e5ec43508e01ccbe98923ad0003eafd87acbbc546fcd588c
-  md5: b0b0c7ea4888b6f4009afa7001e6adaa
+  size: 416024
+  timestamp: 1770909604661
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/unicodedata2-17.0.1-py312h2bbb03f_0.conda
+  sha256: e935d0c11581e31e89ce4899a28b16f924d1a3c1af89f18f8a2c5f5728b3107f
+  md5: 45b836f333fd3e282c16fff7dc82994e
   depends:
   - __osx >=11.0
   - python >=3.12,<3.13.0a0
@@ -9050,58 +10318,8 @@ packages:
   license_family: Apache
   purls:
   - pkg:pypi/unicodedata2?source=hash-mapping
-  size: 416271
-  timestamp: 1763055285615
-- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda
-  sha256: fa0a21fdcd0a8e6cf64cc8cd349ed6ceb373f09854fd3c4365f0bc4586dccf9a
-  md5: 6b0259cea8ffa6b66b35bae0ca01c447
-  depends:
-  - distlib >=0.3.7,<1
-  - filelock >=3.20.1,<4
-  - platformdirs >=3.9.1,<5
-  - python >=3.10
-  - typing_extensions >=4.13.2
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/virtualenv?source=hash-mapping
-  size: 4404318
-  timestamp: 1768069793682
-- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
-  sha256: d6cf2f0ebd5e09120c28ecba450556ce553752652d91795442f0e70f837126ae
-  md5: bdbd7385b4a67025ac2dba4ef8cb6a8f
-  depends:
-  - packaging >=24.0
-  - python >=3.10
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/wheel?source=hash-mapping
-  size: 31858
-  timestamp: 1769139207397
-- conda: https://conda.anaconda.org/conda-forge/noarch/xmltodict-1.0.2-pyhcf101f3_0.conda
-  sha256: 5001a8b0a26810f5b8e20a05bca8cd458b0f6dcfbe00bf648aec017b1fd341f1
-  md5: e91301ac8b2ad640df6165db24914332
-  depends:
-  - python >=3.10
-  - python
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/xmltodict?source=hash-mapping
-  size: 20026
-  timestamp: 1758191083015
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
-  sha256: c12396aabb21244c212e488bbdc4abcdef0b7404b15761d9329f5a4a39113c4b
-  md5: fb901ff28063514abb6046c9ec2c4a45
-  depends:
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-  - libgcc >=13
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 58628
-  timestamp: 1734227592886
+  size: 415828
+  timestamp: 1770909782683
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libice-1.1.2-h5505292_0.conda
   sha256: 0e68b75a51901294ab21c031dcc1e485a65770a4893f98943b0908c4217b14e1
   md5: daf3b34253eea046c9ab94e0c3b2f83d
@@ -9112,19 +10330,6 @@ packages:
   purls: []
   size: 48418
   timestamp: 1734227712919
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
-  sha256: 277841c43a39f738927145930ff963c5ce4c4dacf66637a3d95d802a64173250
-  md5: 1c74ff8c35dcadf952a16f752ca5aa49
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libuuid >=2.38.1,<3.0a0
-  - xorg-libice >=1.1.2,<2.0a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 27590
-  timestamp: 1741896361728
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libsm-1.2.6-h5505292_0.conda
   sha256: 9bd3cb47ad7bb6c2d0b3b39d76c0e0a7b1d39fc76524fe76a7ff014073467bf5
   md5: a01171a0aee17fc4e74a50971a87755d
@@ -9136,40 +10341,17 @@ packages:
   purls: []
   size: 24419
   timestamp: 1741896544082
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.12-h4f16b4b_0.conda
-  sha256: 51909270b1a6c5474ed3978628b341b4d4472cd22610e5f22b506855a5e20f67
-  md5: db038ce880f100acc74dba10302b5630
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libxcb >=1.17.0,<2.0a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 835896
-  timestamp: 1741901112627
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libx11-1.8.12-h6a5fb8c_0.conda
-  sha256: 3ba39f182ecb6bf0bfb2dbbc08b1fc80a0a97e5c07cad06a03e71baf1fe7ac9d
-  md5: 89b59aaa3c35257dba0b7c2d980f35f0
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libx11-1.8.13-hf948f5a_0.conda
+  sha256: e8889281828ee19afb2fdd7b5d7a4b7c2e013b2ae38af4529040de542f92b065
+  md5: 85b1ce864f9a18468db4c583c7778c7d
   depends:
   - __osx >=11.0
   - libxcb >=1.17.0,<2.0a0
   license: MIT
   license_family: MIT
   purls: []
-  size: 761938
-  timestamp: 1741901455497
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda
-  sha256: 6bc6ab7a90a5d8ac94c7e300cc10beb0500eeba4b99822768ca2f2ef356f731b
-  md5: b2895afaf55bf96a8c8282a2e47a5de0
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 15321
-  timestamp: 1762976464266
+  size: 756862
+  timestamp: 1770819743113
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxau-1.0.12-hc919400_1.conda
   sha256: adae11db0f66f86156569415ed79cda75b2dbf4bea48d1577831db701438164f
   md5: 78b548eed8227a689f93775d5d23ae09
@@ -9180,17 +10362,6 @@ packages:
   purls: []
   size: 14105
   timestamp: 1762976976084
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda
-  sha256: 25d255fb2eef929d21ff660a0c687d38a6d2ccfbcbf0cc6aa738b12af6e9d142
-  md5: 1dafce8548e38671bea82e3f5c6ce22f
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 20591
-  timestamp: 1762976546182
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxdmcp-1.1.5-hc919400_1.conda
   sha256: f7fa0de519d8da589995a1fe78ef74556bb8bc4172079ae3a8d20c3c81354906
   md5: 9d1299ace1924aa8f4e0bc8e71dd0cf7
@@ -9201,18 +10372,6 @@ packages:
   purls: []
   size: 19156
   timestamp: 1762977035194
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.7-hb03c661_0.conda
-  sha256: 79c60fc6acfd3d713d6340d3b4e296836a0f8c51602327b32794625826bd052f
-  md5: 34e54f03dfea3e7a2dcf1453a85f1085
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - xorg-libx11 >=1.8.12,<2.0a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 50326
-  timestamp: 1769445253162
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxext-1.3.7-h84a0fba_0.conda
   sha256: 18bbf20b4da142b368e1ae8c2124a3fd7148e2003480ad8b1acdcaa3e6454b07
   md5: 72851739795cdef9bb7124114c630df9
@@ -9224,32 +10383,6 @@ packages:
   purls: []
   size: 42748
   timestamp: 1769445838425
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.12-hb9d3cd8_0.conda
-  sha256: 044c7b3153c224c6cedd4484dd91b389d2d7fd9c776ad0f4a34f099b3389f4a1
-  md5: 96d57aba173e878a2089d5638016dc5e
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - xorg-libx11 >=1.8.10,<2.0a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 33005
-  timestamp: 1734229037766
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.1-hb9d3cd8_0.conda
-  sha256: a8afba4a55b7b530eb5c8ad89737d60d60bc151a03fbef7a2182461256953f0e
-  md5: 279b0de5f6ba95457190a1c459a64e31
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - xorg-libice >=1.1.1,<2.0a0
-  - xorg-libsm >=1.2.4,<2.0a0
-  - xorg-libx11 >=1.8.10,<2.0a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 379686
-  timestamp: 1731860547604
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxt-1.3.1-h5505292_0.conda
   sha256: c32235891d65e49e97babe649c45ec2e40a148b4e6ca4cae4ed84811238e0aae
   md5: a5c47d582f31083353559dc9aff907c3
@@ -9263,17 +10396,6 @@ packages:
   purls: []
   size: 185960
   timestamp: 1731860774152
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
-  sha256: 6d9ea2f731e284e9316d95fa61869fe7bbba33df7929f82693c121022810f4ad
-  md5: a77f85f77be52ff59391544bfe73390a
-  depends:
-  - libgcc >=14
-  - __glibc >=2.17,<3.0.a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 85189
-  timestamp: 1753484064210
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h925e9cb_3.conda
   sha256: b03433b13d89f5567e828ea9f1a7d5c5d697bf374c28a4168d71e9464f5dafac
   md5: 78a0fe9e9c50d2c381e8ee47e3ea437d
@@ -9284,53 +10406,17 @@ packages:
   purls: []
   size: 83386
   timestamp: 1753484079473
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
-  sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae
-  md5: 30cd29cb87d819caead4d55184c1d115
-  depends:
-  - python >=3.10
-  - python
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/zipp?source=hash-mapping
-  size: 24194
-  timestamp: 1764460141901
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
-  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
-  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libzlib 1.3.1 hb9d3cd8_2
-  license: Zlib
-  license_family: Other
-  purls: []
-  size: 92286
-  timestamp: 1727963153079
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.1-h8359307_2.conda
-  sha256: 58f8860756680a4831c1bf4f294e2354d187f2e999791d53b1941834c4b37430
-  md5: e3170d898ca6cb48f1bb567afb92f775
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.2-h8088a28_2.conda
+  sha256: 8dd2ac25f0ba714263aac5832d46985648f4bfb9b305b5021d702079badc08d2
+  md5: f1c0bce276210bed45a04949cfe8dc20
   depends:
   - __osx >=11.0
-  - libzlib 1.3.1 h8359307_2
-  license: Zlib
-  license_family: Other
-  purls: []
-  size: 77606
-  timestamp: 1727963209370
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
-  sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f
-  md5: 2aadb0d17215603a82a2a6b0afd9a4cb
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - libstdcxx >=14
+  - libzlib 1.3.2 h8088a28_2
   license: Zlib
   license_family: Other
   purls: []
-  size: 122618
-  timestamp: 1770167931827
+  size: 81123
+  timestamp: 1774072974535
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.3.3-hed4e4f5_1.conda
   sha256: a339606a6b224bb230ff3d711e801934f3b3844271df9720165e0353716580d4
   md5: d99c2a23a31b0172e90f456f580b695e
@@ -9342,17 +10428,6 @@ packages:
   purls: []
   size: 94375
   timestamp: 1770168363685
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
-  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
-  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libzlib >=1.3.1,<2.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  purls: []
-  size: 601375
-  timestamp: 1764777111296
 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
   sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
   md5: ab136e4c34e97f34fb621d2592a393d8
@@ -9364,3 +10439,6 @@ packages:
   purls: []
   size: 433413
   timestamp: 1764777166076
+- pypi: .
+  name: openff-packmol
+  requires_python: '>=3.11'
diff --git a/pyproject.toml b/pyproject.toml
index 3d925ad..3e5ca71 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,7 +35,7 @@ namespace-packages = [ "openff/packmol/" ]
 lint.select = [ "E", "F", "I", "NPY", "RUF", "UP", "W" ]
 
 [tool.pytest.ini_options]
-addopts = "-n logical -x --cov=openff/packmol --cov-report=xml"
+addopts = "-n logical -x --cov=openff/packmol/ --cov-report=xml"
 
 [tool.coverage.run]
 omit = [
@@ -105,6 +105,8 @@ numpy = "2.2.*"       # ParmEd bugs
 
 [tool.pixi.feature.dev.dependencies]
 pre-commit = "*"
+ipython = "*"
+ipdb = "*"
 
 [tool.pixi.feature.py311.dependencies]
 python = "3.11.*"
@@ -120,5 +122,5 @@ py313-standalone = [ "py313", "test", "standalone" ]
 py311-ambertools = [ "py311", "test", "ambertools" ]
 py312-ambertools = [ "py312", "test", "ambertools" ]
 py313-ambertools = [ "py313", "test", "ambertools" ]
-dev = [ "py313", "dev" ]
+dev = [ "py313", "test", "dev" ]
 typing = [ "py313", "typing" ]

From 07774c216804747053344221a3ee113a4a8a7a10 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 18 May 2026 13:50:00 -0500
Subject: [PATCH 2/5] Trigger failure case we care about

---
 openff/packmol/_tests/test_issues.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openff/packmol/_tests/test_issues.py b/openff/packmol/_tests/test_issues.py
index 36fe3a8..fb18a3b 100644
--- a/openff/packmol/_tests/test_issues.py
+++ b/openff/packmol/_tests/test_issues.py
@@ -20,7 +20,7 @@ def test_thread_safety(water):
             target=pack_box,
             args=(
                 [water],
-                [i],
+                [100 + i],
                 None,
                 Quantity(0.2, "nanometer"),
                 None,

From 3a030be065e4cb4cb1194a636d42f6858995ea19 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 18 May 2026 16:06:44 -0500
Subject: [PATCH 3/5] Slight refactor

---
 openff/packmol/_packmol.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/openff/packmol/_packmol.py b/openff/packmol/_packmol.py
index 3d977ca..71e0a46 100644
--- a/openff/packmol/_packmol.py
+++ b/openff/packmol/_packmol.py
@@ -3,9 +3,11 @@
 """
 
 import os
+import pathlib
 import shutil
 import subprocess
 import tempfile
+import uuid
 from collections.abc import Callable
 from copy import deepcopy
 from typing import Literal
@@ -67,6 +69,10 @@
 """
 
 
+def get_uuid():
+    return uuid.uuid4().hex
+
+
 def _find_packmol() -> str | None:
     """
     Attempt to find the path to the `packmol` binary.
@@ -407,7 +413,7 @@ def _create_solute_pdb(
         ),
     )
     # Write to pdb
-    solute_pdb_filename = "_PACKING_SOLUTE.pdb"
+    solute_pdb_filename = f"_PACKING_SOLUTE_{get_uuid()}.pdb"
     topology.to_file(
         solute_pdb_filename,
         file_format="PDB",
@@ -511,7 +517,7 @@ def _build_input_file(
     tolerance = tolerance.m_as("angstrom")
 
     # Add the global header options.
-    output_file_path = "packmol_output.pdb"
+    output_file_path = f"OUT_{get_uuid()}.pdb"
     input_lines = [
         f"tolerance {tolerance:f}",
         "filetype pdb",

From 96686ac4116a77ceb1a75c17d840a5b3d0012f60 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 May 2026 21:08:16 +0000
Subject: [PATCH 4/5] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openff/packmol/_packmol.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openff/packmol/_packmol.py b/openff/packmol/_packmol.py
index 71e0a46..552a7d8 100644
--- a/openff/packmol/_packmol.py
+++ b/openff/packmol/_packmol.py
@@ -3,7 +3,6 @@
 """
 
 import os
-import pathlib
 import shutil
 import subprocess
 import tempfile

From 433a6eac3baa9681b8e6cb65979eff0e4c6f0bc5 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Wed, 27 May 2026 11:02:50 -0500
Subject: [PATCH 5/5] Debug

---
 openff/packmol/_packmol.py | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/openff/packmol/_packmol.py b/openff/packmol/_packmol.py
index 71e0a46..bce0797 100644
--- a/openff/packmol/_packmol.py
+++ b/openff/packmol/_packmol.py
@@ -516,8 +516,9 @@ def _build_input_file(
     box_size = box_size.m_as("angstrom") if PACKMOL_USE_PBC else (box_size - tolerance).m_as("angstrom")
     tolerance = tolerance.m_as("angstrom")
 
+    this_id = get_uuid()
     # Add the global header options.
-    output_file_path = f"OUT_{get_uuid()}.pdb"
+    output_file_path = f"OUT_{this_id}.pdb"
     input_lines = [
         f"tolerance {tolerance:f}",
         "filetype pdb",
@@ -555,10 +556,11 @@ def _build_input_file(
             ],
         )
 
+    print(f"{input_lines=}")
     packmol_input = "\n".join(input_lines)
 
     # Write packmol input
-    packmol_file_name = "packmol_input.txt"
+    packmol_file_name = f"packmol_input_{this_id}.txt"
 
     with open(packmol_file_name, "w") as file_handle:
         file_handle.write(packmol_input)
@@ -754,6 +756,12 @@ def pack_box(
         os.makedirs(working_directory, exist_ok=True)
 
     with temporary_cd(working_directory):
+        path = pathlib.Path(".")
+
+        # List only items that are files
+        files = [f for f in path.iterdir() if f.is_file()]
+        print(f"Working directory: {path.resolve()}")
+        print(f"{files=}")
         solute_pdb_filename = _create_solute_pdb(
             solute,
             box_vectors,
@@ -787,7 +795,9 @@ def pack_box(
                 raise PACKMOLRuntimeError(
                     f"PACKMOL failed with error code {error.returncode}. Wrote file packmol_error.log in working "
                     "directory, which might be a temporary directory. Set the argument `working_directory` to "
-                    "point this to a persistent path.",
+                    "point this to a persistent path. "
+                    + f"\nPackmol input was:\n{open(input_file_path).read()}\n"
+                    + f"\nPackmol output was:\n{error.stdout.decode('utf-8')}",
                 ) from error
 
             packmol_succeeded = result.decode("utf-8").find("Success!") > 0
@@ -798,6 +808,10 @@ def pack_box(
                 "Please raise an issue showing how you arrived at this error.",
             )
 
+        assert pathlib.Path(output_file_path).exists(), (
+            f"PACKMOL reported success but output file ({output_file_path}) not found. "
+            f"Files in this directory are: {list(pathlib.Path('.').iterdir())}. "
+        )
         positions = _load_positions(output_file_path)
 
     # TODO: This currently does not run if we encountered an error in the