From 0af0d7c4ca89fef3c41e77ecd8dcd6918d20e62f Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 09:46:15 -0400
Subject: [PATCH 01/12] Support external-potential MBE reporting

---
 qcmanybody/core.py             |  7 +++++++
 qcmanybody/tests/test_utils.py | 24 ++++++++++++++++++++++++
 qcmanybody/utils.py            | 31 ++++++++++++++++++++++++-------
 3 files changed, 55 insertions(+), 7 deletions(-)

diff --git a/qcmanybody/core.py b/qcmanybody/core.py
index a89af67..30892f1 100644
--- a/qcmanybody/core.py
+++ b/qcmanybody/core.py
@@ -526,6 +526,8 @@ def _analyze(
     def analyze(
         self,
         component_results: Dict[str, Dict[str, Union[float, np.ndarray]]],
+        *,
+        external_potential: bool = False,
     ):
         """
 
@@ -548,6 +550,9 @@ def analyze(
                '["mp2", [2], [2]]': {'energy': -2.86, 'gradient': array([[0., 0., 0.]])},
                '["mp2", [1, 2], [1, 2]]': {'energy': -5.73, 'gradient': array([[ 0., 0., 0.0053], [ 0., 0., -0.0053]])},
               }
+        external_potential
+            Whether the component calculations use fragment-scoped external potentials. Interaction energies are
+            unavailable in the printed energy summary because the component Hamiltonians differ.
 
         """
 
@@ -602,6 +607,7 @@ def analyze(
                 is_embedded,
                 self.supersystem_ie_only,
                 self.max_nbody if self.has_supersystem else None,
+                external_potential=external_potential,
             )
 
         for property_label in available_properties:
@@ -615,6 +621,7 @@ def analyze(
                         is_embedded,
                         self.supersystem_ie_only,
                         self.has_supersystem,
+                        external_potential=external_potential,
                     )
                 )
 
diff --git a/qcmanybody/tests/test_utils.py b/qcmanybody/tests/test_utils.py
index 75cdd06..5003503 100644
--- a/qcmanybody/tests/test_utils.py
+++ b/qcmanybody/tests/test_utils.py
@@ -136,6 +136,30 @@ def test_resize_gradient(gin, bas, reverse, gans):
     assert compare_values(gans, gout, atol=1e-5, label="resize_gradient")
 
 
+def test_print_nbody_energy_external_potential_without_total_energy():
+    stdout = qcmb.utils.print_nbody_energy(
+        {1: 0.0, 2: 0.005150000059},
+        "Counterpoise Corrected (CP)",
+        2,
+        {1: ("model", "§A"), 2: ("model", "§A")},
+        embedding=False,
+        supersystem_ie_only=False,
+        supersystem_beyond=None,
+        external_potential=True,
+    )
+
+    rows = [line.split() for line in stdout.splitlines() if "§A" in line and "N/A" in line]
+    assert len(rows) == 2
+    assert all(row[-5:-2] == ["N/A", "N/A", "N/A"] for row in rows)
+    assert "nan" not in stdout.lower()
+
+    properties = qcmb.utils.collect_vars(
+        "cp", "energy", {1: 0.0, 2: 0.005150000059}, 2, external_potential=True
+    )
+    assert "cp_corrected_2_body_contribution_to_energy" in properties
+    assert not any("interaction" in name for name in properties)
+
+
 @pytest.mark.parametrize("hin,bas,reverse,hans", [
     pytest.param(f3hesses["full"], [1, 2, 3], False, f3hesses["full"]),  # idempotent
     pytest.param(f3hesses["full"], [1, 2, 3], True, f3hesses["full"]),  # idempotent
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index 41677f2..bb3ed41 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -322,6 +322,7 @@ def print_nbody_energy(
     embedding: bool,
     supersystem_ie_only: bool,
     supersystem_beyond: Optional[int],
+    external_potential: bool = False,
 ) -> str:
     """Format summary string for energies of a single bsse_type. Logs and returns output.
 
@@ -338,11 +339,13 @@ def print_nbody_energy(
         full model chemistry key and second element a short label. A suitable
         dictionary is `modelchem_labels(manybodycore_instance.nbodies_per_mc_level)`.
     embedding
-        Whether charge embedding present suppress printing, usually False
+        Whether charge embedding is present and suppresses interaction energies, usually False.
     supersystem_ie_only
         Whether only 1-body and nfragments-body levels are available, usually False.
     supersystem_beyond
         If not None, the number of nbody-levels computed by MBE explicitly. Beyond this gets supersystem SS label.
+    external_potential
+        Whether fragment-scoped external potentials are present and suppress interaction energies, usually False.
 
     Returns
     -------
@@ -385,7 +388,8 @@ def print_nbody_energy(
         if nb in nbody_range:
             delta_e = energy_body_dict[nb] - previous_e
             delta_e_kcal = delta_e * constants.hartree2kcalmol
-            if embedding:
+            interaction_data_unavailable = embedding or external_potential
+            if interaction_data_unavailable:
                 int_e = np.nan
                 int_e_kcal = np.nan
             else:
@@ -393,17 +397,26 @@ def print_nbody_energy(
                 int_e_kcal = int_e * constants.hartree2kcalmol
             if supersystem_ie_only and nb == nfragments:
                 if tot_e:
-                    info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}        {"N/A":20}  {"N/A":14}        {"N/A":20}  {"N/A":20}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
                 else:
-                    info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}        {"N/A":20}  {"N/A":14}        {"N/A":20}  {"N/A":20}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
             else:
                 if tot_e:
-                    if embedding:
+                    if interaction_data_unavailable:
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}        {"N/A":20}  {"N/A":14}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
                     else:
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
                 else:
-                    info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}        {"N/A":20}  {"N/A":14}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
             previous_e = energy_body_dict[nb]
         else:
             info += f"""  {lbl:>11} {"":2} {nb:2}        {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}\n"""
@@ -422,6 +435,7 @@ def collect_vars(
     embedding: bool = False,
     supersystem_ie_only: bool = False,
     has_supersystem: bool = False,
+    external_potential: bool = False,
 ) -> Dict:
     """From *body_dict*, construct data for ManyBodyResultProperties/ManyBodyProperties.
 
@@ -445,6 +459,9 @@ def collect_vars(
         By default False: data is available for consecutive levels, up to max_nbody-body.
     has_supersystem
         Whether contributions higher than max_nbody are a summary correction.
+    external_potential
+        Whether fragment-scoped external potentials are present. Interaction properties are unavailable because the
+        component Hamiltonians differ.
 
     Returns
     -------
@@ -495,7 +512,7 @@ def collect_vars(
             for nb in nbody_range:
                 res[f"{bsse}_corrected_total_{prop}_through_{nb}_body"] = body_dict[nb]
 
-    if embedding:
+    if embedding or external_potential:
         res = {k: v for k, v in res.items() if "interaction" not in k}
 
     return res

From 70fa81dee2568ce763ed889b456f76ee38dd50ce Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 10:14:14 -0400
Subject: [PATCH 02/12] Address external-potential review findings

---
 qcmanybody/core.py                        |  5 +--
 qcmanybody/tests/test_core_singlelevel.py | 20 +++++++++++
 qcmanybody/utils.py                       | 41 +++++++++--------------
 3 files changed, 38 insertions(+), 28 deletions(-)

diff --git a/qcmanybody/core.py b/qcmanybody/core.py
index 30892f1..91353b2 100644
--- a/qcmanybody/core.py
+++ b/qcmanybody/core.py
@@ -551,8 +551,9 @@ def analyze(
                '["mp2", [1, 2], [1, 2]]': {'energy': -5.73, 'gradient': array([[ 0., 0., 0.0053], [ 0., 0., -0.0053]])},
               }
         external_potential
-            Whether the component calculations use fragment-scoped external potentials. Interaction energies are
-            unavailable in the printed energy summary because the component Hamiltonians differ.
+            Whether the component calculations use fragment-scoped external potentials. Because the component
+            Hamiltonians differ, interaction energies are unavailable in the printed summary and interaction-energy
+            properties are omitted from the returned results. This classification is distinct from charge embedding.
 
         """
 
diff --git a/qcmanybody/tests/test_core_singlelevel.py b/qcmanybody/tests/test_core_singlelevel.py
index b5a93a2..b6d4299 100644
--- a/qcmanybody/tests/test_core_singlelevel.py
+++ b/qcmanybody/tests/test_core_singlelevel.py
@@ -33,6 +33,26 @@ def test_h2o_trimer_single(levels, component_file, ref_file):
     compare_results(nbody_results, ref_data, levels)
 
 
+def test_external_potential_reporting():
+    levels = {1: "e_scf", 2: "e_scf", 3: "e_scf"}
+    component_results = load_component_data("h2o_trimer_single_energy_1")
+    mc = ManyBodyCore(
+        mol_h2o_3_dict,
+        [BsseEnum.cp],
+        levels,
+        embedding_charges=None,
+        supersystem_ie_only=False,
+        return_total_data=True,
+    )
+
+    nbody_results = mc.analyze(component_results, external_potential=True)
+
+    assert "cp_corrected_2_body_contribution_to_energy" in nbody_results["results"]
+    assert not any("interaction" in name for name in nbody_results["results"])
+    assert "N/A" in nbody_results["stdout"]
+    assert "nan" not in nbody_results["stdout"].lower()
+
+
 def test_core_mol_error():
     # check sensible error from internal Molecule construction
     odd_mol = mol_h2o_3_dict.copy()
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index bb3ed41..e1d92ca 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -369,6 +369,7 @@ def print_nbody_energy(
     info += f"""                         [Eh]                    [Eh]                  [kcal/mol]            [Eh]                  [kcal/mol]\n"""
     previous_e = energy_body_dict[1]
     tot_e = previous_e != 0.0
+    interaction_data_unavailable = embedding or external_potential
     nbody_range = list(energy_body_dict)
     if supersystem_ie_only:
         nbody_range = [1, nfragments]
@@ -387,36 +388,24 @@ def print_nbody_energy(
 
         if nb in nbody_range:
             delta_e = energy_body_dict[nb] - previous_e
-            delta_e_kcal = delta_e * constants.hartree2kcalmol
-            interaction_data_unavailable = embedding or external_potential
+            total_e = f"{energy_body_dict[nb]:20.12f}" if tot_e else f'{"N/A":>20}'
+
             if interaction_data_unavailable:
-                int_e = np.nan
-                int_e_kcal = np.nan
+                int_e = f'{"N/A":>20}'
+                int_e_kcal = f'{"N/A":>20}'
             else:
-                int_e = energy_body_dict[nb] - energy_body_dict[1]
-                int_e_kcal = int_e * constants.hartree2kcalmol
+                interaction_energy = energy_body_dict[nb] - energy_body_dict[1]
+                int_e = f"{interaction_energy:20.12f}"
+                int_e_kcal = f"{interaction_energy * constants.hartree2kcalmol:20.12f}"
+
             if supersystem_ie_only and nb == nfragments:
-                if tot_e:
-                    if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}        {"N/A":20}  {"N/A":14}        {"N/A":20}  {"N/A":20}\n"""
-                    else:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
-                else:
-                    if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}        {"N/A":20}  {"N/A":14}        {"N/A":20}  {"N/A":20}\n"""
-                    else:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
+                delta_e = f'{"N/A":>20}'
+                delta_e_kcal = f'{"N/A":>20}'
             else:
-                if tot_e:
-                    if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}        {"N/A":20}  {"N/A":14}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
-                    else:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
-                else:
-                    if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}        {"N/A":20}  {"N/A":14}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
-                    else:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                delta_e_kcal = f"{delta_e * constants.hartree2kcalmol:20.12f}"
+                delta_e = f"{delta_e:20.12f}"
+
+            info += f"  {lbl:>11} {mclbl:2} {nb:2}  {total_e}  {int_e}  {int_e_kcal}  {delta_e}  {delta_e_kcal}\n"
             previous_e = energy_body_dict[nb]
         else:
             info += f"""  {lbl:>11} {"":2} {nb:2}        {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}\n"""

From 35a329e3a1824215ccd1de6c651814c27673aef0 Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 10:36:11 -0400
Subject: [PATCH 03/12] no-mistakes(document): Correct collect_vars result
 documentation

---
 qcmanybody/utils.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index e1d92ca..0957146 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -455,7 +455,8 @@ def collect_vars(
     Returns
     -------
     dict
-        _description_. Empty return if *embedding* enabled.
+        Many-body result properties. Interaction properties are omitted when *embedding* or *external_potential* is
+        enabled; valid total and n-body contribution properties remain.
     """
     bsse = bsse.lower()
     prop = prop.lower()

From 070b8978ca62a07609a2c876c8a66561e132129a Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 10:41:20 -0400
Subject: [PATCH 04/12] no-mistakes: apply CI fixes

---
 qcmanybody/tests/test_utils.py | 10 +++++++---
 qcmanybody/utils.py            |  5 +++--
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/qcmanybody/tests/test_utils.py b/qcmanybody/tests/test_utils.py
index 5003503..6a8a6aa 100644
--- a/qcmanybody/tests/test_utils.py
+++ b/qcmanybody/tests/test_utils.py
@@ -148,9 +148,13 @@ def test_print_nbody_energy_external_potential_without_total_energy():
         external_potential=True,
     )
 
-    rows = [line.split() for line in stdout.splitlines() if "§A" in line and "N/A" in line]
-    assert len(rows) == 2
-    assert all(row[-5:-2] == ["N/A", "N/A", "N/A"] for row in rows)
+    rows = [line for line in stdout.splitlines() if "§A" in line and "N/A" in line]
+    assert rows == [
+        "              §A  1                   N/A        N/A                         N/A"
+        "                   0.000000000000        0.000000000000",
+        "     FULL/RTN §A  2                   N/A        N/A                         N/A"
+        "                   0.005150000059        3.231673826977",
+    ]
     assert "nan" not in stdout.lower()
 
     properties = qcmb.utils.collect_vars(
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index 0957146..006a2dd 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -391,8 +391,9 @@ def print_nbody_energy(
             total_e = f"{energy_body_dict[nb]:20.12f}" if tot_e else f'{"N/A":>20}'
 
             if interaction_data_unavailable:
-                int_e = f'{"N/A":>20}'
-                int_e_kcal = f'{"N/A":>20}'
+                # Retain the established table alignment for unavailable interaction energies.
+                int_e = f'      {"N/A":<20}'
+                int_e_kcal = f'      {"N/A":<14}'
             else:
                 interaction_energy = energy_body_dict[nb] - energy_body_dict[1]
                 int_e = f"{interaction_energy:20.12f}"

From 3fe722388d9d2aeb4ff70793dd50ff9147908a5a Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 10:47:07 -0400
Subject: [PATCH 05/12] no-mistakes: apply CI fixes

---
 qcmanybody/tests/test_utils.py | 4 ++--
 qcmanybody/utils.py            | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/qcmanybody/tests/test_utils.py b/qcmanybody/tests/test_utils.py
index 6a8a6aa..e8744b5 100644
--- a/qcmanybody/tests/test_utils.py
+++ b/qcmanybody/tests/test_utils.py
@@ -150,9 +150,9 @@ def test_print_nbody_energy_external_potential_without_total_energy():
 
     rows = [line for line in stdout.splitlines() if "§A" in line and "N/A" in line]
     assert rows == [
-        "              §A  1                   N/A        N/A                         N/A"
+        "              §A  1                   N/A        N/A                   N/A"
         "                   0.000000000000        0.000000000000",
-        "     FULL/RTN §A  2                   N/A        N/A                         N/A"
+        "     FULL/RTN §A  2                   N/A        N/A                   N/A"
         "                   0.005150000059        3.231673826977",
     ]
     assert "nan" not in stdout.lower()
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index 006a2dd..c4945a8 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -393,7 +393,7 @@ def print_nbody_energy(
             if interaction_data_unavailable:
                 # Retain the established table alignment for unavailable interaction energies.
                 int_e = f'      {"N/A":<20}'
-                int_e_kcal = f'      {"N/A":<14}'
+                int_e_kcal = f'{"N/A":<14}'
             else:
                 interaction_energy = energy_body_dict[nb] - energy_body_dict[1]
                 int_e = f"{interaction_energy:20.12f}"

From cce0220e34b60b41081c0dc59f67f20ad0a6f2dc Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 10:52:10 -0400
Subject: [PATCH 06/12] no-mistakes: apply CI fixes

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9c05dec..6e41924 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,7 +89,7 @@ pythonpath = [
     "tests",
 ]
 testpaths = [
-    "tests",
+    "qcmanybody/tests",
 ]
 markers = [
     "addon: tests require external non-required software",

From e6dad35cdd1aa9553dba10f7934f060a07dcd8ac Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:17:08 -0400
Subject: [PATCH 07/12] no-mistakes: apply CI fixes

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 518a445..937503d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -156,7 +156,7 @@ jobs:
 
     - name: PyTest
       run: |
-        pytest -rws -v ${{ matrix.cfg.pytest }} \
+        python -m pytest qcmanybody/tests -rws -v ${{ matrix.cfg.pytest }} \
             --cov=qcmanybody --cov-report=xml \
             --color=yes --durations 50 --durations-min 20
 

From feea7706675de689c7a80bb4f0233d5eb9251070 Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:21:39 -0400
Subject: [PATCH 08/12] no-mistakes: apply CI fixes

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 937503d..518a445 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -156,7 +156,7 @@ jobs:
 
     - name: PyTest
       run: |
-        python -m pytest qcmanybody/tests -rws -v ${{ matrix.cfg.pytest }} \
+        pytest -rws -v ${{ matrix.cfg.pytest }} \
             --cov=qcmanybody --cov-report=xml \
             --color=yes --durations 50 --durations-min 20
 

From b18d5319c2a65052ee25a380cc92165081cd860a Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:26:12 -0400
Subject: [PATCH 09/12] Preserve legacy energy table spacing

---
 pyproject.toml                 |  2 +-
 qcmanybody/tests/test_utils.py | 46 +++++++++++++++++++++++++++++++---
 qcmanybody/utils.py            | 41 +++++++++++++++++-------------
 3 files changed, 67 insertions(+), 22 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6e41924..9c05dec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,7 +89,7 @@ pythonpath = [
     "tests",
 ]
 testpaths = [
-    "qcmanybody/tests",
+    "tests",
 ]
 markers = [
     "addon: tests require external non-required software",
diff --git a/qcmanybody/tests/test_utils.py b/qcmanybody/tests/test_utils.py
index e8744b5..9b093e2 100644
--- a/qcmanybody/tests/test_utils.py
+++ b/qcmanybody/tests/test_utils.py
@@ -150,10 +150,10 @@ def test_print_nbody_energy_external_potential_without_total_energy():
 
     rows = [line for line in stdout.splitlines() if "§A" in line and "N/A" in line]
     assert rows == [
-        "              §A  1                   N/A        N/A                   N/A"
-        "                   0.000000000000        0.000000000000",
-        "     FULL/RTN §A  2                   N/A        N/A                   N/A"
-        "                   0.005150000059        3.231673826977",
+        "              §A  1        N/A                              N/A                   N/A"
+        "        0.000000000000        0.000000000000",
+        "     FULL/RTN §A  2        N/A                              N/A                   N/A"
+        "        0.005150000059        3.231673826977",
     ]
     assert "nan" not in stdout.lower()
 
@@ -164,6 +164,44 @@ def test_print_nbody_energy_external_potential_without_total_energy():
     assert not any("interaction" in name for name in properties)
 
 
+def test_print_nbody_energy_preserves_legacy_spacing():
+    labels = {1: ("model", "§A"), 2: ("model", "§A")}
+
+    interaction_only = qcmb.utils.print_nbody_energy(
+        {1: 0.0, 2: 0.005150000059},
+        "Counterpoise Corrected (CP)",
+        2,
+        labels,
+        embedding=False,
+        supersystem_ie_only=False,
+        supersystem_beyond=None,
+    )
+    interaction_rows = [line for line in interaction_only.splitlines() if "§A" in line and "Legend" not in line]
+    assert interaction_rows == [
+        "              §A  1        N/A                   0.000000000000        0.000000000000"
+        "        0.000000000000        0.000000000000",
+        "     FULL/RTN §A  2        N/A                   0.005150000059        3.231673826977"
+        "        0.005150000059        3.231673826977",
+    ]
+
+    supersystem = qcmb.utils.print_nbody_energy(
+        {1: -1.0, 2: -0.9},
+        "Counterpoise Corrected (CP)",
+        2,
+        labels,
+        embedding=False,
+        supersystem_ie_only=True,
+        supersystem_beyond=None,
+    )
+    supersystem_rows = [line for line in supersystem.splitlines() if "§A" in line and "Legend" not in line]
+    assert supersystem_rows == [
+        "              §A  1       -1.000000000000        0.000000000000        0.000000000000"
+        "        0.000000000000        0.000000000000",
+        "     FULL/RTN §A  2       -0.900000000000        0.100000000000       62.750947377754"
+        "        N/A                   N/A                 ",
+    ]
+
+
 @pytest.mark.parametrize("hin,bas,reverse,hans", [
     pytest.param(f3hesses["full"], [1, 2, 3], False, f3hesses["full"]),  # idempotent
     pytest.param(f3hesses["full"], [1, 2, 3], True, f3hesses["full"]),  # idempotent
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index c4945a8..ccbcf64 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -388,25 +388,32 @@ def print_nbody_energy(
 
         if nb in nbody_range:
             delta_e = energy_body_dict[nb] - previous_e
-            total_e = f"{energy_body_dict[nb]:20.12f}" if tot_e else f'{"N/A":>20}'
-
-            if interaction_data_unavailable:
-                # Retain the established table alignment for unavailable interaction energies.
-                int_e = f'      {"N/A":<20}'
-                int_e_kcal = f'{"N/A":<14}'
-            else:
-                interaction_energy = energy_body_dict[nb] - energy_body_dict[1]
-                int_e = f"{interaction_energy:20.12f}"
-                int_e_kcal = f"{interaction_energy * constants.hartree2kcalmol:20.12f}"
-
+            delta_e_kcal = delta_e * constants.hartree2kcalmol
+            if not interaction_data_unavailable:
+                int_e = energy_body_dict[nb] - energy_body_dict[1]
+                int_e_kcal = int_e * constants.hartree2kcalmol
             if supersystem_ie_only and nb == nfragments:
-                delta_e = f'{"N/A":>20}'
-                delta_e_kcal = f'{"N/A":>20}'
+                if tot_e:
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {"N/A":>20}  {"N/A":>20}        {"N/A":20}  {"N/A":20}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
+                else:
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {"N/A":>20}  {"N/A":>20}        {"N/A":20}  {"N/A":20}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
             else:
-                delta_e_kcal = f"{delta_e * constants.hartree2kcalmol:20.12f}"
-                delta_e = f"{delta_e:20.12f}"
-
-            info += f"  {lbl:>11} {mclbl:2} {nb:2}  {total_e}  {int_e}  {int_e_kcal}  {delta_e}  {delta_e_kcal}\n"
+                if tot_e:
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}        {"N/A":20}  {"N/A":14}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                else:
+                    if interaction_data_unavailable:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {"N/A":>20}  {"N/A":>20}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                    else:
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
             previous_e = energy_body_dict[nb]
         else:
             info += f"""  {lbl:>11} {"":2} {nb:2}        {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}  {"N/A":20}\n"""

From 495d2485856464510f4e28423f16f80bb7268fa9 Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:39:33 -0400
Subject: [PATCH 10/12] no-mistakes: apply CI fixes

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9c05dec..6e41924 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,7 +89,7 @@ pythonpath = [
     "tests",
 ]
 testpaths = [
-    "tests",
+    "qcmanybody/tests",
 ]
 markers = [
     "addon: tests require external non-required software",

From 7e05e0a9eb0e67e9e66148cc506f08c2132407e5 Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:43:53 -0400
Subject: [PATCH 11/12] no-mistakes: apply CI fixes

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6e41924..ea6f23c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -86,7 +86,7 @@ default-tag = "0.0.99" # useful for CI/shallow clones
 minversion = "7.0"
 addopts = "--import-mode=importlib"
 pythonpath = [
-    "tests",
+    "qcmanybody/tests",
 ]
 testpaths = [
     "qcmanybody/tests",

From eeb5b4959287bd6b5d4a96df4b04b728408e44ee Mon Sep 17 00:00:00 2001
From: "Wallace, Austin" <awallace43@gatech.edu>
Date: Mon, 31 Aug 2026 11:51:25 -0400
Subject: [PATCH 12/12] no-mistakes: apply CI fixes

---
 qcmanybody/tests/test_utils.py | 20 ++++++++++++++++++++
 qcmanybody/utils.py            |  9 ++++++---
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/qcmanybody/tests/test_utils.py b/qcmanybody/tests/test_utils.py
index 9b093e2..5d1e1b3 100644
--- a/qcmanybody/tests/test_utils.py
+++ b/qcmanybody/tests/test_utils.py
@@ -201,6 +201,26 @@ def test_print_nbody_energy_preserves_legacy_spacing():
         "        N/A                   N/A                 ",
     ]
 
+    external_supersystem = qcmb.utils.print_nbody_energy(
+        {1: -1.0, 2: -0.9},
+        "Counterpoise Corrected (CP)",
+        2,
+        labels,
+        embedding=False,
+        supersystem_ie_only=True,
+        supersystem_beyond=None,
+        external_potential=True,
+    )
+    external_supersystem_rows = [
+        line for line in external_supersystem.splitlines() if "§A" in line and "Legend" not in line
+    ]
+    assert external_supersystem_rows == [
+        "              §A  1       -1.000000000000        N/A                   N/A"
+        "                   0.000000000000        0.000000000000",
+        "     FULL/RTN §A  2       -0.900000000000                   N/A                   N/A"
+        "        N/A                   N/A                 ",
+    ]
+
 
 @pytest.mark.parametrize("hin,bas,reverse,hans", [
     pytest.param(f3hesses["full"], [1, 2, 3], False, f3hesses["full"]),  # idempotent
diff --git a/qcmanybody/utils.py b/qcmanybody/utils.py
index ccbcf64..18afd93 100644
--- a/qcmanybody/utils.py
+++ b/qcmanybody/utils.py
@@ -370,6 +370,9 @@ def print_nbody_energy(
     previous_e = energy_body_dict[1]
     tot_e = previous_e != 0.0
     interaction_data_unavailable = embedding or external_potential
+    # Preserve the historical numeric-field offsets while replacing only the
+    # literal unavailable ``nan`` token with ``N/A``.
+    unavailable_interaction = f"{np.nan:20.12f}".replace("nan", "N/A")
     nbody_range = list(energy_body_dict)
     if supersystem_ie_only:
         nbody_range = [1, nfragments]
@@ -395,12 +398,12 @@ def print_nbody_energy(
             if supersystem_ie_only and nb == nfragments:
                 if tot_e:
                     if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {"N/A":>20}  {"N/A":>20}        {"N/A":20}  {"N/A":20}\n"""
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {unavailable_interaction}  {unavailable_interaction}        {"N/A":20}  {"N/A":20}\n"""
                     else:
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
                 else:
                     if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {"N/A":>20}  {"N/A":>20}        {"N/A":20}  {"N/A":20}\n"""
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {unavailable_interaction}  {unavailable_interaction}        {"N/A":20}  {"N/A":20}\n"""
                     else:
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}        {"N/A":20}  {"N/A":20}\n"""
             else:
@@ -411,7 +414,7 @@ def print_nbody_energy(
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}  {energy_body_dict[nb]:20.12f}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
                 else:
                     if interaction_data_unavailable:
-                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {"N/A":>20}  {"N/A":>20}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
+                        info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {unavailable_interaction}  {unavailable_interaction}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
                     else:
                         info += f"""  {lbl:>11} {mclbl:2} {nb:2}        {"N/A":14}  {int_e:20.12f}  {int_e_kcal:20.12f}  {delta_e:20.12f}  {delta_e_kcal:20.12f}\n"""
             previous_e = energy_body_dict[nb]