From ea4b8c15797df12d81ea86125103d3cbe071c1f9 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 9 Jan 2025 12:52:04 +0100
Subject: [PATCH 01/30] adding vacuum test

---
 tests/unit_tests/dagmc/test_model.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 9fdfbcebc68..981237656d0 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -254,3 +254,28 @@ def test_dagmc_xml(model):
 
     for xml_mats, model_mats in zip(xml_dagmc_univ._material_overrides.values(), dag_univ._material_overrides.values()):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
+
+
+def test_dagmc_vacuum(model):
+    # Set the environment
+    mats = {}
+    mats["Vacuum"] = openmc.Material(1, name="Vacuum")
+    mats["Vacuum"].add_nuclide("U235", 0.03)
+    mats["Vacuum"].add_nuclide("U238", 0.97)
+    mats["Vacuum"].add_nuclide("O16", 2.0)
+    mats["Vacuum"].set_density("g/cm3", 10.0)
+
+    for univ in model.geometry.get_all_universes().values():
+        if isinstance(univ, openmc.DAGMCUniverse):
+            dag_univ = univ
+            break
+
+    for mat in dag_univ.material_names:
+        dag_univ.replace_material_assignment(mat, mats["Vacuum"])
+
+    model.export_to_xml()
+    # ensure that particles will be lost when cell intersections can't be found
+    # due to the removed triangles in this model
+    with pytest.raises(RuntimeError, match='Maximum number of lost particles has been reached.'):
+        openmc.run()
+  
\ No newline at end of file

From 4c4206880d837a9ca3bf25021458e88bddde7e7a Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 9 Jan 2025 15:48:01 +0100
Subject: [PATCH 02/30] testing vacuum keyword detection with DAGMC geometry

---
 tests/unit_tests/dagmc/test_model.py | 38 +++++++++++++++++++++-------
 1 file changed, 29 insertions(+), 9 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 981237656d0..fee655cbc42 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -257,25 +257,45 @@ def test_dagmc_xml(model):
 
 
 def test_dagmc_vacuum(model):
-    # Set the environment
-    mats = {}
-    mats["Vacuum"] = openmc.Material(1, name="Vacuum")
-    mats["Vacuum"].add_nuclide("U235", 0.03)
-    mats["Vacuum"].add_nuclide("U238", 0.97)
-    mats["Vacuum"].add_nuclide("O16", 2.0)
-    mats["Vacuum"].set_density("g/cm3", 10.0)
+
+    # Verify Not_A_Vacuum is not detected as a Vacuum
+    mat_not_a_vacuum = openmc.Material(1, name="Not_A_Vacuum")
+    mat_not_a_vacuum.add_nuclide("U235", 0.03)
+    mat_not_a_vacuum.add_nuclide("U238", 0.97)
+    mat_not_a_vacuum.add_nuclide("O16", 2.0)
+    mat_not_a_vacuum.set_density("g/cm3", 10.0)
+
+    for univ in model.geometry.get_all_universes().values():
+        if isinstance(univ, openmc.DAGMCUniverse):
+            dag_univ = univ
+            break
+
+    # Replacing all the materials with vacuum
+    for mat in dag_univ.material_names:
+        dag_univ.replace_material_assignment(mat, mat_not_a_vacuum)
+
+    model.export_to_xml()
+    # Ensure this run as expected.
+    openmc.run()
+
+    # Verify that the vacuum is detected as a Vacuum
+    mat_a_vacuum = openmc.Material(1, name="Vacuum")
+    mat_a_vacuum.add_nuclide("U235", 0.03)
+    mat_a_vacuum.add_nuclide("U238", 0.97)
+    mat_a_vacuum.add_nuclide("O16", 2.0)
+    mat_a_vacuum.set_density("g/cm3", 10.0)
 
     for univ in model.geometry.get_all_universes().values():
         if isinstance(univ, openmc.DAGMCUniverse):
             dag_univ = univ
             break
 
+    # Replacing all the materials with vacuum
     for mat in dag_univ.material_names:
-        dag_univ.replace_material_assignment(mat, mats["Vacuum"])
+        dag_univ.replace_material_assignment(mat, at_a_vacuum)
 
     model.export_to_xml()
     # ensure that particles will be lost when cell intersections can't be found
     # due to the removed triangles in this model
     with pytest.raises(RuntimeError, match='Maximum number of lost particles has been reached.'):
         openmc.run()
-  
\ No newline at end of file

From 6f303738b3927d9551b198931922223a6c0c1689 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 9 Jan 2025 17:45:17 +0100
Subject: [PATCH 03/30] does it run by default ?

---
 tests/unit_tests/dagmc/test_model.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index fee655cbc42..28a6eedc6fa 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -258,6 +258,8 @@ def test_dagmc_xml(model):
 
 def test_dagmc_vacuum(model):
 
+    openmc.run()
+
     # Verify Not_A_Vacuum is not detected as a Vacuum
     mat_not_a_vacuum = openmc.Material(1, name="Not_A_Vacuum")
     mat_not_a_vacuum.add_nuclide("U235", 0.03)

From ef6f0837d87060ec2c6d9fd3fc9fd05ae6266dda Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Fri, 10 Jan 2025 16:01:12 +0100
Subject: [PATCH 04/30] set my box boundary as vacuum

---
 tests/unit_tests/dagmc/test_model.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 28a6eedc6fa..0477a1bdb5c 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -41,6 +41,7 @@ def model(request):
         [daguniv, daguniv]]
 
     box = openmc.model.RectangularParallelepiped(-pitch, pitch, -pitch, pitch, -5, 5)
+    box.boundary_type = "vacuum"
 
     root = openmc.Universe(cells=[openmc.Cell(region=-box, fill=lattice)])
 

From ce1646a7015394995f2fbd9dbe1d924fd41e2a42 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Sun, 12 Jan 2025 11:18:14 +0100
Subject: [PATCH 05/30] typo

---
 tests/unit_tests/dagmc/test_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 0477a1bdb5c..b7dfa321c5a 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -295,7 +295,7 @@ def test_dagmc_vacuum(model):
 
     # Replacing all the materials with vacuum
     for mat in dag_univ.material_names:
-        dag_univ.replace_material_assignment(mat, at_a_vacuum)
+        dag_univ.replace_material_assignment(mat, mat_a_vacuum)
 
     model.export_to_xml()
     # ensure that particles will be lost when cell intersections can't be found

From af7726fcdba61d572728a52dd0664d5aea08bf46 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Mon, 13 Jan 2025 12:50:43 +0100
Subject: [PATCH 06/30] test tally

---
 tests/unit_tests/dagmc/test_model.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index b7dfa321c5a..14464e0b7fd 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -5,7 +5,7 @@
 import pytest
 import openmc
 from openmc.utility_funcs import change_directory
-
+import openmc.lib
 pytestmark = pytest.mark.skipif(
     not openmc.lib._dagmc_enabled(),
     reason="DAGMC CAD geometry is not enabled.")
@@ -259,8 +259,6 @@ def test_dagmc_xml(model):
 
 def test_dagmc_vacuum(model):
 
-    openmc.run()
-
     # Verify Not_A_Vacuum is not detected as a Vacuum
     mat_not_a_vacuum = openmc.Material(1, name="Not_A_Vacuum")
     mat_not_a_vacuum.add_nuclide("U235", 0.03)
@@ -277,6 +275,12 @@ def test_dagmc_vacuum(model):
     for mat in dag_univ.material_names:
         dag_univ.replace_material_assignment(mat, mat_not_a_vacuum)
 
+    current = openmc.Tally()
+    current.scores = ['current']
+    model._tallies.append(current)
+    src = openmc.IndependentSource(space=openmc.stats.Point())
+    model.settings.source = src
+
     model.export_to_xml()
     # Ensure this run as expected.
     openmc.run()

From 4a9b560cdfa1ee142a8f6fe98530443748c88c25 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Mon, 13 Jan 2025 16:26:09 +0100
Subject: [PATCH 07/30] new suf tally

---
 tests/unit_tests/dagmc/test_model.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 14464e0b7fd..eaaf9cf6055 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -275,9 +275,13 @@ def test_dagmc_vacuum(model):
     for mat in dag_univ.material_names:
         dag_univ.replace_material_assignment(mat, mat_not_a_vacuum)
 
+
+    pitch = 1.26
+    box = openmc.SurfaceFilter(openmc.Sphere(r=pitch))
     current = openmc.Tally()
     current.scores = ['current']
-    model._tallies.append(current)
+    current.filters = [box]
+    model.tallies.append(current)
     src = openmc.IndependentSource(space=openmc.stats.Point())
     model.settings.source = src
 

From 35830117f55b7047f8aa75ffee7b48cdf00d54cb Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Mon, 13 Jan 2025 18:45:31 +0100
Subject: [PATCH 08/30] printing tally content

---
 tests/unit_tests/dagmc/test_model.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index eaaf9cf6055..9cec4e1e256 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -288,7 +288,14 @@ def test_dagmc_vacuum(model):
     model.export_to_xml()
     # Ensure this run as expected.
     openmc.run()
-
+    # Read the statepoint file.
+    sp = openmc.StatePoint("statepoint.100.h5")
+
+    # Extract the tally data as a Pandas DataFrame.
+    tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]
+    df = pd.concat(tally_dfs, ignore_index=True)
+    print(df)
+    
     # Verify that the vacuum is detected as a Vacuum
     mat_a_vacuum = openmc.Material(1, name="Vacuum")
     mat_a_vacuum.add_nuclide("U235", 0.03)

From 8f6d1bdb4aa2dae9cfe360dcd3fad3794114a2fe Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Tue, 14 Jan 2025 17:13:14 +0100
Subject: [PATCH 09/30] add vacuum test

---
 tests/unit_tests/dagmc/test_model.py | 127 +++++++++++++++++++--------
 1 file changed, 89 insertions(+), 38 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 9cec4e1e256..4fa5b7cc7cf 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import pandas as pd
 import lxml.etree as ET
 import numpy as np
 import pytest
@@ -256,64 +257,114 @@ def test_dagmc_xml(model):
     for xml_mats, model_mats in zip(xml_dagmc_univ._material_overrides.values(), dag_univ._material_overrides.values()):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
+def test_dagmc_vacuum(request, run_in_tmpdir):
+    
+    import shutil
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m")
 
-def test_dagmc_vacuum(model):
-
-    # Verify Not_A_Vacuum is not detected as a Vacuum
-    mat_not_a_vacuum = openmc.Material(1, name="Not_A_Vacuum")
-    mat_not_a_vacuum.add_nuclide("U235", 0.03)
-    mat_not_a_vacuum.add_nuclide("U238", 0.97)
-    mat_not_a_vacuum.add_nuclide("O16", 2.0)
-    mat_not_a_vacuum.set_density("g/cm3", 10.0)
+    mats = {}
+    mats["not_a_vacuum"] = openmc.Material(1, name="not_a_vacuum")
+    mats["not_a_vacuum"].add_nuclide("U235", 0.03)
+    mats["not_a_vacuum"].add_nuclide("U238", 0.97)
+    mats["not_a_vacuum"].add_nuclide("O16", 2.0)
+    mats["not_a_vacuum"].set_density("g/cm3", 10.0)
+
+    mats["vacuum"] = openmc.Material(name="vacuum")
+    mats["vacuum"].add_nuclide("U235", 0.03)
+    mats["vacuum"].add_nuclide("U238", 0.97)
+    mats["vacuum"].add_nuclide("O16", 2.0)
+    mats["vacuum"].set_density("g/cm3", 10.0)
 
+    mats["41"] = openmc.Material(name="41")
+    mats["41"].add_nuclide("U235", 0.03)
+    mats["41"].add_nuclide("U238", 0.97)
+    mats["41"].add_nuclide("O16", 2.0)
+    mats["41"].set_density("g/cm3", 10.0)
+
+    import h5py
+    hf = h5py.File(Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m", 'r+')
+    new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
+    hf['/tstt/tags/NAME']['values'][1] = new_assignment
+    hf.close()
+    
+    p = Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m"
+    daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
+    settings = openmc.Settings()
+    settings.batches = 100
+    settings.inactive = 10
+    settings.particles = 1000
+    model = openmc.Model()
+    model.materials = openmc.Materials(mats.values())
+    model.geometry = openmc.Geometry(root=daguniv)
+    model.settings = settings
+    model.init_lib()
+    model.sync_dagmc_universes()
     for univ in model.geometry.get_all_universes().values():
         if isinstance(univ, openmc.DAGMCUniverse):
             dag_univ = univ
             break
 
-    # Replacing all the materials with vacuum
-    for mat in dag_univ.material_names:
-        dag_univ.replace_material_assignment(mat, mat_not_a_vacuum)
-
+    my_tally = openmc.Tally()
+    cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
 
-    pitch = 1.26
-    box = openmc.SurfaceFilter(openmc.Sphere(r=pitch))
-    current = openmc.Tally()
-    current.scores = ['current']
-    current.filters = [box]
-    model.tallies.append(current)
+    my_tally.scores = ['nu-fission']
+    my_tally.filters = [cell_filter]
+    model.tallies.append(my_tally)
     src = openmc.IndependentSource(space=openmc.stats.Point())
     model.settings.source = src
 
-    model.export_to_xml()
-    # Ensure this run as expected.
-    openmc.run()
+    model.export_to_model_xml('sub_dir_not_a_vacuum/model.xml',)
+    openmc.run(cwd='sub_dir_not_a_vacuum')
     # Read the statepoint file.
-    sp = openmc.StatePoint("statepoint.100.h5")
+    sp = openmc.StatePoint("sub_dir_not_a_vacuum/statepoint.100.h5")
 
     # Extract the tally data as a Pandas DataFrame.
     tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]
     df = pd.concat(tally_dfs, ignore_index=True)
-    print(df)
-    
-    # Verify that the vacuum is detected as a Vacuum
-    mat_a_vacuum = openmc.Material(1, name="Vacuum")
-    mat_a_vacuum.add_nuclide("U235", 0.03)
-    mat_a_vacuum.add_nuclide("U238", 0.97)
-    mat_a_vacuum.add_nuclide("O16", 2.0)
-    mat_a_vacuum.set_density("g/cm3", 10.0)
+    # not detected as vacuum so tally should be non-zero
+    assert df['mean'].loc[0] > 0
+
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", Path(request.fspath).parent / "dagmc_a_vacuum.h5m")
+    hf = h5py.File(Path(request.fspath).parent / "dagmc_a_vacuum.h5m", 'r+')
+    new_assignment = 'mat:vacuum'.encode('utf-8')
+    hf['/tstt/tags/NAME']['values'][1] = new_assignment
+    hf.close()
+
+    p = Path(request.fspath).parent / "dagmc_a_vacuum.h5m"
 
+    daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
+    settings = openmc.Settings()
+    settings.batches = 100
+    settings.inactive = 10
+    settings.particles = 1000
+    model = openmc.Model()
+    model.materials = openmc.Materials(mats.values())
+    model.geometry = openmc.Geometry(root=daguniv)
+    model.settings = settings
+    model.init_lib()
+    model.sync_dagmc_universes()
     for univ in model.geometry.get_all_universes().values():
         if isinstance(univ, openmc.DAGMCUniverse):
             dag_univ = univ
             break
 
-    # Replacing all the materials with vacuum
-    for mat in dag_univ.material_names:
-        dag_univ.replace_material_assignment(mat, mat_a_vacuum)
+    my_tally = openmc.Tally()
+    cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
+
+    my_tally.scores = ['nu-fission']
+    my_tally.filters = [cell_filter]
+    model.tallies.append(my_tally)
+    src = openmc.IndependentSource(space=openmc.stats.Point())
+    model.settings.source = src
+
+    model.export_to_model_xml('sub_dir_vacuum/model.xml',)
+    openmc.run(cwd='sub_dir_vacuum')
+    # Read the statepoint file.
+    sp = openmc.StatePoint("sub_dir_vacuum/statepoint.100.h5")
 
-    model.export_to_xml()
-    # ensure that particles will be lost when cell intersections can't be found
-    # due to the removed triangles in this model
-    with pytest.raises(RuntimeError, match='Maximum number of lost particles has been reached.'):
-        openmc.run()
+    # Extract the tally data as a Pandas DataFrame.
+    tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]
+    df = pd.concat(tally_dfs, ignore_index=True)
+    # detected as vacuum so tally should be zero
+    assert df['mean'].loc[0] == 0
+    

From f2aded519e49f4a59d04a64454b61338ca51d150 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Tue, 14 Jan 2025 17:23:09 +0100
Subject: [PATCH 10/30] now all run in tmp

---
 tests/unit_tests/dagmc/test_model.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 4fa5b7cc7cf..36acbc4f4c8 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -257,10 +257,10 @@ def test_dagmc_xml(model):
     for xml_mats, model_mats in zip(xml_dagmc_univ._material_overrides.values(), dag_univ._material_overrides.values()):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
-def test_dagmc_vacuum(request, run_in_tmpdir):
+def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     
     import shutil
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m")
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", tmpdir/"dagmc_not_a_vacuum.h5m")
 
     mats = {}
     mats["not_a_vacuum"] = openmc.Material(1, name="not_a_vacuum")
@@ -282,12 +282,12 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     mats["41"].set_density("g/cm3", 10.0)
 
     import h5py
-    hf = h5py.File(Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m", 'r+')
+    hf = h5py.File(tmpdir/ "dagmc_not_a_vacuum.h5m", 'r+')
     new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
     
-    p = Path(request.fspath).parent / "dagmc_not_a_vacuum.h5m"
+    p = tmpdir/"dagmc_not_a_vacuum.h5m"
     daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
     settings.batches = 100
@@ -324,14 +324,13 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     # not detected as vacuum so tally should be non-zero
     assert df['mean'].loc[0] > 0
 
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", Path(request.fspath).parent / "dagmc_a_vacuum.h5m")
-    hf = h5py.File(Path(request.fspath).parent / "dagmc_a_vacuum.h5m", 'r+')
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", tmpdir/"dagmc_a_vacuum.h5m")
+    hf = h5py.File(tmpdir/ "dagmc_a_vacuum.h5m", 'r+')
     new_assignment = 'mat:vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
 
-    p = Path(request.fspath).parent / "dagmc_a_vacuum.h5m"
-
+    p = tmpdir/"dagmc_a_vacuum.h5m"
     daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
     settings.batches = 100

From 16169d34f8ee4cb7f0f76e27a9d4473295ab9564 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
Date: Tue, 14 Jan 2025 17:38:56 +0100
Subject: [PATCH 11/30] Apply suggestions from code review

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 tests/unit_tests/dagmc/test_model.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 36acbc4f4c8..21dff3d24ff 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -1,5 +1,7 @@
 from pathlib import Path
 
+import h5py
+import shutil
 import pandas as pd
 import lxml.etree as ET
 import numpy as np
@@ -259,7 +261,6 @@ def test_dagmc_xml(model):
 
 def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     
-    import shutil
     shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", tmpdir/"dagmc_not_a_vacuum.h5m")
 
     mats = {}
@@ -281,7 +282,6 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     mats["41"].add_nuclide("O16", 2.0)
     mats["41"].set_density("g/cm3", 10.0)
 
-    import h5py
     hf = h5py.File(tmpdir/ "dagmc_not_a_vacuum.h5m", 'r+')
     new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
@@ -291,7 +291,6 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
     settings.batches = 100
-    settings.inactive = 10
     settings.particles = 1000
     model = openmc.Model()
     model.materials = openmc.Materials(mats.values())

From 30ca476a838dbb04ce00a66e303dd62338d998ea Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Tue, 14 Jan 2025 17:39:40 +0100
Subject: [PATCH 12/30] revert 2 change

---
 tests/unit_tests/dagmc/test_model.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 21dff3d24ff..01386b4ad6a 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -8,7 +8,6 @@
 import pytest
 import openmc
 from openmc.utility_funcs import change_directory
-import openmc.lib
 pytestmark = pytest.mark.skipif(
     not openmc.lib._dagmc_enabled(),
     reason="DAGMC CAD geometry is not enabled.")
@@ -44,7 +43,6 @@ def model(request):
         [daguniv, daguniv]]
 
     box = openmc.model.RectangularParallelepiped(-pitch, pitch, -pitch, pitch, -5, 5)
-    box.boundary_type = "vacuum"
 
     root = openmc.Universe(cells=[openmc.Cell(region=-box, fill=lattice)])
 

From 5fb1640f56948945919ac9cc92d71e5272d06349 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
Date: Tue, 14 Jan 2025 18:07:39 +0100
Subject: [PATCH 13/30] Update tests/unit_tests/dagmc/test_model.py

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 tests/unit_tests/dagmc/test_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 01386b4ad6a..63c159561be 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -354,9 +354,9 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     model.settings.source = src
 
     model.export_to_model_xml('sub_dir_vacuum/model.xml',)
-    openmc.run(cwd='sub_dir_vacuum')
+    sp_filename = openmc.run(cwd='sub_dir_vacuum')
     # Read the statepoint file.
-    sp = openmc.StatePoint("sub_dir_vacuum/statepoint.100.h5")
+    sp = openmc.StatePoint(sp_filename)
 
     # Extract the tally data as a Pandas DataFrame.
     tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]

From a483ab18d2c13ef6cceb34e2d44d72441a1d1189 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
Date: Wed, 15 Jan 2025 08:50:39 +0100
Subject: [PATCH 14/30] Update tests/unit_tests/dagmc/test_model.py

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 tests/unit_tests/dagmc/test_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 63c159561be..d2f4511ce4a 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -330,7 +330,7 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     p = tmpdir/"dagmc_a_vacuum.h5m"
     daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
-    settings.batches = 100
+    settings.batches = 2
     settings.inactive = 10
     settings.particles = 1000
     model = openmc.Model()

From bc7fa45412550e21fc9329194fdebf6083dd1059 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
Date: Wed, 15 Jan 2025 08:50:50 +0100
Subject: [PATCH 15/30] Update tests/unit_tests/dagmc/test_model.py

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 tests/unit_tests/dagmc/test_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index d2f4511ce4a..38ce92c45cb 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -332,7 +332,7 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     settings = openmc.Settings()
     settings.batches = 2
     settings.inactive = 10
-    settings.particles = 1000
+    settings.particles = 100
     model = openmc.Model()
     model.materials = openmc.Materials(mats.values())
     model.geometry = openmc.Geometry(root=daguniv)

From 63ccfe04682bca5360c4bde4ac4e7ca438b822b3 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 10:34:21 +0100
Subject: [PATCH 16/30] This look good

---
 tests/unit_tests/dagmc/test_model.py | 115 +++++++++++++++------------
 1 file changed, 64 insertions(+), 51 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 38ce92c45cb..30ee8f58e2f 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -8,6 +8,7 @@
 import pytest
 import openmc
 from openmc.utility_funcs import change_directory
+import openmc.lib
 pytestmark = pytest.mark.skipif(
     not openmc.lib._dagmc_enabled(),
     reason="DAGMC CAD geometry is not enabled.")
@@ -259,20 +260,8 @@ def test_dagmc_xml(model):
 
 def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", tmpdir/"dagmc_not_a_vacuum.h5m")
-
+    # Required initial mats.
     mats = {}
-    mats["not_a_vacuum"] = openmc.Material(1, name="not_a_vacuum")
-    mats["not_a_vacuum"].add_nuclide("U235", 0.03)
-    mats["not_a_vacuum"].add_nuclide("U238", 0.97)
-    mats["not_a_vacuum"].add_nuclide("O16", 2.0)
-    mats["not_a_vacuum"].set_density("g/cm3", 10.0)
-
-    mats["vacuum"] = openmc.Material(name="vacuum")
-    mats["vacuum"].add_nuclide("U235", 0.03)
-    mats["vacuum"].add_nuclide("U238", 0.97)
-    mats["vacuum"].add_nuclide("O16", 2.0)
-    mats["vacuum"].set_density("g/cm3", 10.0)
 
     mats["41"] = openmc.Material(name="41")
     mats["41"].add_nuclide("U235", 0.03)
@@ -280,87 +269,111 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     mats["41"].add_nuclide("O16", 2.0)
     mats["41"].set_density("g/cm3", 10.0)
 
-    hf = h5py.File(tmpdir/ "dagmc_not_a_vacuum.h5m", 'r+')
+    # Not a vacuum material
+    na_vacuum_str = "not_a_vacuum"
+    mats[na_vacuum_str] = openmc.Material(name=na_vacuum_str)
+    mats[na_vacuum_str].add_nuclide("U235", 0.03)
+    mats[na_vacuum_str].add_nuclide("U238", 0.97)
+    mats[na_vacuum_str].add_nuclide("O16", 2.0)
+    mats[na_vacuum_str].set_density("g/cm3", 10.0)
+
+    # Tweaking the h5m file to change the material assignment
+    na_vacuum_h5 = tmpdir / f"dagmc_{na_vacuum_str}.h5m"
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m",
+                    na_vacuum_h5)
+    hf = h5py.File(na_vacuum_h5, 'r+')
     new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
-    
-    p = tmpdir/"dagmc_not_a_vacuum.h5m"
-    daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
+
+    # Set the Model
+    daguniv = openmc.DAGMCUniverse(na_vacuum_h5,
+                                   auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
-    settings.batches = 100
-    settings.particles = 1000
+    settings.batches = 10
+    settings.particles = 100
     model = openmc.Model()
     model.materials = openmc.Materials(mats.values())
     model.geometry = openmc.Geometry(root=daguniv)
     model.settings = settings
+
+    # Set the Tally
     model.init_lib()
     model.sync_dagmc_universes()
     for univ in model.geometry.get_all_universes().values():
         if isinstance(univ, openmc.DAGMCUniverse):
             dag_univ = univ
             break
-
     my_tally = openmc.Tally()
     cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
-
     my_tally.scores = ['nu-fission']
     my_tally.filters = [cell_filter]
     model.tallies.append(my_tally)
+
+    # Only a confined point source
     src = openmc.IndependentSource(space=openmc.stats.Point())
     model.settings.source = src
 
-    model.export_to_model_xml('sub_dir_not_a_vacuum/model.xml',)
-    openmc.run(cwd='sub_dir_not_a_vacuum')
-    # Read the statepoint file.
-    sp = openmc.StatePoint("sub_dir_not_a_vacuum/statepoint.100.h5")
-
-    # Extract the tally data as a Pandas DataFrame.
-    tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]
-    df = pd.concat(tally_dfs, ignore_index=True)
-    # not detected as vacuum so tally should be non-zero
-    assert df['mean'].loc[0] > 0
-
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", tmpdir/"dagmc_a_vacuum.h5m")
-    hf = h5py.File(tmpdir/ "dagmc_a_vacuum.h5m", 'r+')
+    # Run and check the results
+    sub_dir = f"sub_dir_{na_vacuum_str}"
+    model.export_to_model_xml(f'{sub_dir}/model.xml',)
+    openmc.run(cwd=sub_dir)
+    # If cell are not vacuum, fission site should not spread to other cells
+    with openmc.StatePoint(f"{sub_dir}/statepoint.{settings.batches}.h5") as sp:
+        tally = list(sp.tallies.values())[0]
+        non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
+        assert len(non_zero_tal) > 1
+
+    # Not a vacuum material
+    vacuum_str = "vacuum"
+    mats[vacuum_str] = openmc.Material(name=vacuum_str)
+    mats[vacuum_str].add_nuclide("U235", 0.03)
+    mats[vacuum_str].add_nuclide("U238", 0.97)
+    mats[vacuum_str].add_nuclide("O16", 2.0)
+    mats[vacuum_str].set_density("g/cm3", 10.0)
+
+    # Tweaking the h5m file to change the material assignment
+    vacuum_h5 = tmpdir / f"dagmc_{vacuum_str}.h5m"
+    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", vacuum_h5)
+    hf = h5py.File(vacuum_h5, 'r+')
     new_assignment = 'mat:vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
 
-    p = tmpdir/"dagmc_a_vacuum.h5m"
-    daguniv = openmc.DAGMCUniverse(p, auto_geom_ids=True).bounded_universe()
+    # Set the Model
+    daguniv = openmc.DAGMCUniverse(vacuum_h5,
+                                   auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
-    settings.batches = 2
-    settings.inactive = 10
+    settings.batches = 10
     settings.particles = 100
     model = openmc.Model()
     model.materials = openmc.Materials(mats.values())
     model.geometry = openmc.Geometry(root=daguniv)
     model.settings = settings
+
+    # Set the Tally
     model.init_lib()
     model.sync_dagmc_universes()
     for univ in model.geometry.get_all_universes().values():
         if isinstance(univ, openmc.DAGMCUniverse):
             dag_univ = univ
             break
-
     my_tally = openmc.Tally()
     cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
-
     my_tally.scores = ['nu-fission']
     my_tally.filters = [cell_filter]
     model.tallies.append(my_tally)
+
+    # Only a confined point source
     src = openmc.IndependentSource(space=openmc.stats.Point())
     model.settings.source = src
 
-    model.export_to_model_xml('sub_dir_vacuum/model.xml',)
-    sp_filename = openmc.run(cwd='sub_dir_vacuum')
-    # Read the statepoint file.
-    sp = openmc.StatePoint(sp_filename)
-
-    # Extract the tally data as a Pandas DataFrame.
-    tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()]
-    df = pd.concat(tally_dfs, ignore_index=True)
-    # detected as vacuum so tally should be zero
-    assert df['mean'].loc[0] == 0
-    
+    # Run and check the results
+    sub_dir = f"sub_dir_{vacuum_str}"
+    model.export_to_model_xml(f'{sub_dir}/model.xml',)
+    openmc.run(cwd=sub_dir)
+    # If cell are not vacuum, fission site should not spread to other cells
+    with openmc.StatePoint(f"{sub_dir}/statepoint.{settings.batches}.h5") as sp:
+        tally = list(sp.tallies.values())[0]
+        non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
+        assert len(non_zero_tal) == 1

From b36da05bb3ddd4b9c0f3ec34f8d94ff54bf449d4 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 10:35:14 +0100
Subject: [PATCH 17/30] fixing comments

---
 tests/unit_tests/dagmc/test_model.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 30ee8f58e2f..423941864a7 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -259,10 +259,8 @@ def test_dagmc_xml(model):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
 def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
-    
     # Required initial mats.
     mats = {}
-
     mats["41"] = openmc.Material(name="41")
     mats["41"].add_nuclide("U235", 0.03)
     mats["41"].add_nuclide("U238", 0.97)
@@ -324,7 +322,7 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
         non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
         assert len(non_zero_tal) > 1
 
-    # Not a vacuum material
+    # Vacuum material
     vacuum_str = "vacuum"
     mats[vacuum_str] = openmc.Material(name=vacuum_str)
     mats[vacuum_str].add_nuclide("U235", 0.03)

From ea29f54e93c01d2c4c8d2fd5174a1129a8acfa19 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
Date: Wed, 15 Jan 2025 10:41:21 +0100
Subject: [PATCH 18/30] Apply suggestions from code review

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 tests/unit_tests/dagmc/test_model.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 423941864a7..18a35e22e75 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -2,7 +2,6 @@
 
 import h5py
 import shutil
-import pandas as pd
 import lxml.etree as ET
 import numpy as np
 import pytest
@@ -262,18 +261,14 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     # Required initial mats.
     mats = {}
     mats["41"] = openmc.Material(name="41")
-    mats["41"].add_nuclide("U235", 0.03)
-    mats["41"].add_nuclide("U238", 0.97)
-    mats["41"].add_nuclide("O16", 2.0)
-    mats["41"].set_density("g/cm3", 10.0)
+    mats["41"].add_nuclide("U235", 1)
+    mats["41"].set_density("g/cm3", 0.03)
 
     # Not a vacuum material
     na_vacuum_str = "not_a_vacuum"
     mats[na_vacuum_str] = openmc.Material(name=na_vacuum_str)
-    mats[na_vacuum_str].add_nuclide("U235", 0.03)
-    mats[na_vacuum_str].add_nuclide("U238", 0.97)
-    mats[na_vacuum_str].add_nuclide("O16", 2.0)
-    mats[na_vacuum_str].set_density("g/cm3", 10.0)
+    mats[na_vacuum_str].add_nuclide("U235", 1)
+    mats[na_vacuum_str].set_density("g/cm3", 0.03)
 
     # Tweaking the h5m file to change the material assignment
     na_vacuum_h5 = tmpdir / f"dagmc_{na_vacuum_str}.h5m"

From 6915706ff90fd085291ef536e77a1d24b2dcce81 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 10:43:16 +0100
Subject: [PATCH 19/30] increasing density a bit

---
 tests/unit_tests/dagmc/test_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 18a35e22e75..308dd271545 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -262,13 +262,13 @@ def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
     mats = {}
     mats["41"] = openmc.Material(name="41")
     mats["41"].add_nuclide("U235", 1)
-    mats["41"].set_density("g/cm3", 0.03)
+    mats["41"].set_density("g/cm3", 1)
 
     # Not a vacuum material
     na_vacuum_str = "not_a_vacuum"
     mats[na_vacuum_str] = openmc.Material(name=na_vacuum_str)
     mats[na_vacuum_str].add_nuclide("U235", 1)
-    mats[na_vacuum_str].set_density("g/cm3", 0.03)
+    mats[na_vacuum_str].set_density("g/cm3", 1)
 
     # Tweaking the h5m file to change the material assignment
     na_vacuum_h5 = tmpdir / f"dagmc_{na_vacuum_str}.h5m"

From d4c45f8121a132ceefe891974565e08b3e3cea7b Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 10:43:34 +0100
Subject: [PATCH 20/30] Revmoving locally required import

---
 tests/unit_tests/dagmc/test_model.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 308dd271545..e2e1e8d771a 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -7,7 +7,6 @@
 import pytest
 import openmc
 from openmc.utility_funcs import change_directory
-import openmc.lib
 pytestmark = pytest.mark.skipif(
     not openmc.lib._dagmc_enabled(),
     reason="DAGMC CAD geometry is not enabled.")

From de6d8ba53802ab639042a3504c5f8786b74c6267 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 14:18:28 +0100
Subject: [PATCH 21/30] working

---
 tests/unit_tests/dagmc/test_model.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index e2e1e8d771a..308dd271545 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -7,6 +7,7 @@
 import pytest
 import openmc
 from openmc.utility_funcs import change_directory
+import openmc.lib
 pytestmark = pytest.mark.skipif(
     not openmc.lib._dagmc_enabled(),
     reason="DAGMC CAD geometry is not enabled.")

From 85802f58e29cd3a589bec2dab7529a5261d468a5 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 14:57:51 +0100
Subject: [PATCH 22/30] trying to tweak tempdir

---
 tests/unit_tests/dagmc/test_model.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 308dd271545..7645251deca 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import os
 import h5py
 import shutil
 import lxml.etree as ET
@@ -257,7 +258,8 @@ def test_dagmc_xml(model):
     for xml_mats, model_mats in zip(xml_dagmc_univ._material_overrides.values(), dag_univ._material_overrides.values()):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
-def test_dagmc_vacuum(request, run_in_tmpdir, tmpdir):
+def test_dagmc_vacuum(request, run_in_tmpdir):
+    tmpdir = Path(os.getcwd())
     # Required initial mats.
     mats = {}
     mats["41"] = openmc.Material(name="41")

From ae2812504ed2aa500317f5a5924c7d5964da8002 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Wed, 15 Jan 2025 19:03:21 +0100
Subject: [PATCH 23/30] update path management

---
 tests/unit_tests/dagmc/test_model.py | 37 +++++++++++++++-------------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 7645251deca..bcd8bb1a3b3 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -258,8 +258,9 @@ def test_dagmc_xml(model):
     for xml_mats, model_mats in zip(xml_dagmc_univ._material_overrides.values(), dag_univ._material_overrides.values()):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
-def test_dagmc_vacuum(request, run_in_tmpdir):
-    tmpdir = Path(os.getcwd())
+def test_dagmc_vacuum(run_in_tmpdir, request):
+    h5m = Path(request.fspath).parent / "dagmc.h5m"
+
     # Required initial mats.
     mats = {}
     mats["41"] = openmc.Material(name="41")
@@ -273,16 +274,17 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     mats[na_vacuum_str].set_density("g/cm3", 1)
 
     # Tweaking the h5m file to change the material assignment
-    na_vacuum_h5 = tmpdir / f"dagmc_{na_vacuum_str}.h5m"
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m",
-                    na_vacuum_h5)
+    subdir = Path(na_vacuum_str)
+    subdir.mkdir()
+    na_vacuum_h5 = subdir / f"dagmc_{na_vacuum_str}.h5m"
+    shutil.copy(h5m, na_vacuum_h5)
     hf = h5py.File(na_vacuum_h5, 'r+')
     new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
 
     # Set the Model
-    daguniv = openmc.DAGMCUniverse(na_vacuum_h5,
+    daguniv = openmc.DAGMCUniverse(na_vacuum_h5.absolute(),
                                    auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
     settings.batches = 10
@@ -310,11 +312,10 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     model.settings.source = src
 
     # Run and check the results
-    sub_dir = f"sub_dir_{na_vacuum_str}"
-    model.export_to_model_xml(f'{sub_dir}/model.xml',)
-    openmc.run(cwd=sub_dir)
+    model.export_to_model_xml((subdir / 'model.xml').absolute())
+    openmc.run(cwd=subdir.absolute())
     # If cell are not vacuum, fission site should not spread to other cells
-    with openmc.StatePoint(f"{sub_dir}/statepoint.{settings.batches}.h5") as sp:
+    with openmc.StatePoint(subdir / f"statepoint.{settings.batches}.h5") as sp:
         tally = list(sp.tallies.values())[0]
         non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
         assert len(non_zero_tal) > 1
@@ -328,15 +329,18 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     mats[vacuum_str].set_density("g/cm3", 10.0)
 
     # Tweaking the h5m file to change the material assignment
-    vacuum_h5 = tmpdir / f"dagmc_{vacuum_str}.h5m"
-    shutil.copyfile(Path(request.fspath).parent / "dagmc.h5m", vacuum_h5)
+    subdir = Path(vacuum_str)
+    subdir.mkdir()
+    vacuum_h5 = subdir / f"dagmc_{vacuum_str}.h5m"
+    shutil.copy(h5m, vacuum_h5)
+    hf = h5py.File(vacuum_h5, 'r+')
     hf = h5py.File(vacuum_h5, 'r+')
     new_assignment = 'mat:vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
 
     # Set the Model
-    daguniv = openmc.DAGMCUniverse(vacuum_h5,
+    daguniv = openmc.DAGMCUniverse(vacuum_h5.absolute(),
                                    auto_geom_ids=True).bounded_universe()
     settings = openmc.Settings()
     settings.batches = 10
@@ -364,11 +368,10 @@ def test_dagmc_vacuum(request, run_in_tmpdir):
     model.settings.source = src
 
     # Run and check the results
-    sub_dir = f"sub_dir_{vacuum_str}"
-    model.export_to_model_xml(f'{sub_dir}/model.xml',)
-    openmc.run(cwd=sub_dir)
+    model.export_to_model_xml((subdir / 'model.xml').absolute())
+    openmc.run(cwd=subdir.absolute())
     # If cell are not vacuum, fission site should not spread to other cells
-    with openmc.StatePoint(f"{sub_dir}/statepoint.{settings.batches}.h5") as sp:
+    with openmc.StatePoint(subdir / f"statepoint.{settings.batches}.h5") as sp:
         tally = list(sp.tallies.values())[0]
         non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
         assert len(non_zero_tal) == 1

From 761d22c51b522d1b55ea93708a035129d3505e5e Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 09:49:47 +0100
Subject: [PATCH 24/30] enabling ssh

---
 .github/workflows/ci.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c5051b8d0bb..37d8a2d2c49 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -153,6 +153,11 @@ jobs:
           CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
           $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
+      - name: Setup tmate debug session
+          continue-on-error: true
+          uses: mxschmitt/action-tmate@v3
+          timeout-minutes: 60
+
       - name: after_success
         shell: bash
         run: |

From ef989df57a211da2dab7e9427307b500e809fa8a Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 09:50:47 +0100
Subject: [PATCH 25/30] fixing formating

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 37d8a2d2c49..b97c3544263 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -154,9 +154,9 @@ jobs:
           $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: Setup tmate debug session
-          continue-on-error: true
-          uses: mxschmitt/action-tmate@v3
-          timeout-minutes: 60
+        continue-on-error: true
+        uses: mxschmitt/action-tmate@v3
+        timeout-minutes: 60
 
       - name: after_success
         shell: bash

From d2c48820713990d7058eb4674251087886f19781 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 11:11:47 +0100
Subject: [PATCH 26/30] putting ssh session at the right place

---
 .github/workflows/ci.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b97c3544263..31336ea6823 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -146,6 +146,11 @@ jobs:
       - name: before
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
+        
+      - name: Setup tmate debug session
+        continue-on-error: true
+        uses: mxschmitt/action-tmate@v3
+        timeout-minutes: 60
 
       - name: test
         shell: bash
@@ -153,10 +158,7 @@ jobs:
           CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
           $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
-      - name: Setup tmate debug session
-        continue-on-error: true
-        uses: mxschmitt/action-tmate@v3
-        timeout-minutes: 60
+
 
       - name: after_success
         shell: bash

From 9958ac050aa42204a81abcecada96dc17f2e195b Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 12:08:20 +0100
Subject: [PATCH 27/30] tweaking mat composition

---
 .github/workflows/ci.yml             |  5 -----
 tests/unit_tests/dagmc/test_model.py | 12 ++++++++----
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 31336ea6823..fa8cdab9c61 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -146,11 +146,6 @@ jobs:
       - name: before
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
-        
-      - name: Setup tmate debug session
-        continue-on-error: true
-        uses: mxschmitt/action-tmate@v3
-        timeout-minutes: 60
 
       - name: test
         shell: bash
diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index bcd8bb1a3b3..f681993ecca 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -264,14 +264,18 @@ def test_dagmc_vacuum(run_in_tmpdir, request):
     # Required initial mats.
     mats = {}
     mats["41"] = openmc.Material(name="41")
-    mats["41"].add_nuclide("U235", 1)
-    mats["41"].set_density("g/cm3", 1)
+    mats["41"].add_nuclide("U235", 0.03)
+    mats["41"].add_nuclide("U238", 0.97)
+    mats["41"].add_nuclide("O16", 2.0)
+    mats["41"].set_density("g/cm3", 10.0)
 
     # Not a vacuum material
     na_vacuum_str = "not_a_vacuum"
     mats[na_vacuum_str] = openmc.Material(name=na_vacuum_str)
-    mats[na_vacuum_str].add_nuclide("U235", 1)
-    mats[na_vacuum_str].set_density("g/cm3", 1)
+    mats[na_vacuum_str].add_nuclide("U235", 0.03)
+    mats[na_vacuum_str].add_nuclide("U238", 0.97)
+    mats[na_vacuum_str].add_nuclide("O16", 2.0)
+    mats[na_vacuum_str].set_density("g/cm3", 10.0)
 
     # Tweaking the h5m file to change the material assignment
     subdir = Path(na_vacuum_str)

From ee84c13cfe63526cc0c6526b562c1bd0b5a8668a Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 12:13:29 +0100
Subject: [PATCH 28/30] restoring the exact ci.yml

---
 .github/workflows/ci.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fa8cdab9c61..c5051b8d0bb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -153,8 +153,6 @@ jobs:
           CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
           $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
-
-
       - name: after_success
         shell: bash
         run: |

From ffe27fddc7a184afc29214b9e0b1a5805d6e37c8 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <bam.git.no.reply@gmail.com>
Date: Thu, 16 Jan 2025 16:09:12 +0100
Subject: [PATCH 29/30] woudl a finalize() help ?

---
 tests/unit_tests/dagmc/test_model.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index f681993ecca..8c91ad36d4f 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -379,3 +379,4 @@ def test_dagmc_vacuum(run_in_tmpdir, request):
         tally = list(sp.tallies.values())[0]
         non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
         assert len(non_zero_tal) == 1
+    openmc.lib.finalize()

From d806829b256954eaae4d1a41abb3d7a11a1ebd62 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 21 Jan 2025 14:17:05 -0600
Subject: [PATCH 30/30] Simplifying vacuum assignment test

---
 tests/unit_tests/dagmc/test_model.py | 110 ++++++---------------------
 1 file changed, 22 insertions(+), 88 deletions(-)

diff --git a/tests/unit_tests/dagmc/test_model.py b/tests/unit_tests/dagmc/test_model.py
index 8c91ad36d4f..9016d918d05 100644
--- a/tests/unit_tests/dagmc/test_model.py
+++ b/tests/unit_tests/dagmc/test_model.py
@@ -259,29 +259,29 @@ def test_dagmc_xml(model):
         assert all([xml_mat.id == orig_mat.id for xml_mat, orig_mat in zip(xml_mats, model_mats)])
 
 def test_dagmc_vacuum(run_in_tmpdir, request):
-    h5m = Path(request.fspath).parent / "dagmc.h5m"
-
-    # Required initial mats.
+    # Required initial mats
     mats = {}
     mats["41"] = openmc.Material(name="41")
-    mats["41"].add_nuclide("U235", 0.03)
-    mats["41"].add_nuclide("U238", 0.97)
-    mats["41"].add_nuclide("O16", 2.0)
-    mats["41"].set_density("g/cm3", 10.0)
+    mats["41"].add_nuclide("H1", 1.0)
+    mats["41"].set_density("g/cm3", 1.0)
 
     # Not a vacuum material
     na_vacuum_str = "not_a_vacuum"
     mats[na_vacuum_str] = openmc.Material(name=na_vacuum_str)
-    mats[na_vacuum_str].add_nuclide("U235", 0.03)
-    mats[na_vacuum_str].add_nuclide("U238", 0.97)
-    mats[na_vacuum_str].add_nuclide("O16", 2.0)
+    mats[na_vacuum_str].add_nuclide("U238", 1.0)
     mats[na_vacuum_str].set_density("g/cm3", 10.0)
 
+    model = openmc.Model()
+    model.settings = openmc.Settings()
+    model.settings.batches = 10
+    model.settings.particles = 100
+    model.materials = openmc.Materials(mats.values())
+
+    orig_h5m = Path(request.fspath).parent / "dagmc.h5m"
+
     # Tweaking the h5m file to change the material assignment
-    subdir = Path(na_vacuum_str)
-    subdir.mkdir()
-    na_vacuum_h5 = subdir / f"dagmc_{na_vacuum_str}.h5m"
-    shutil.copy(h5m, na_vacuum_h5)
+    na_vacuum_h5 = Path(f"dagmc_{na_vacuum_str}.h5m")
+    shutil.copy(orig_h5m, na_vacuum_h5)
     hf = h5py.File(na_vacuum_h5, 'r+')
     new_assignment = 'mat:not_a_vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
@@ -290,93 +290,27 @@ def test_dagmc_vacuum(run_in_tmpdir, request):
     # Set the Model
     daguniv = openmc.DAGMCUniverse(na_vacuum_h5.absolute(),
                                    auto_geom_ids=True).bounded_universe()
-    settings = openmc.Settings()
-    settings.batches = 10
-    settings.particles = 100
-    model = openmc.Model()
-    model.materials = openmc.Materials(mats.values())
     model.geometry = openmc.Geometry(root=daguniv)
-    model.settings = settings
-
-    # Set the Tally
-    model.init_lib()
-    model.sync_dagmc_universes()
-    for univ in model.geometry.get_all_universes().values():
-        if isinstance(univ, openmc.DAGMCUniverse):
-            dag_univ = univ
-            break
-    my_tally = openmc.Tally()
-    cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
-    my_tally.scores = ['nu-fission']
-    my_tally.filters = [cell_filter]
-    model.tallies.append(my_tally)
-
-    # Only a confined point source
-    src = openmc.IndependentSource(space=openmc.stats.Point())
-    model.settings.source = src
-
-    # Run and check the results
-    model.export_to_model_xml((subdir / 'model.xml').absolute())
-    openmc.run(cwd=subdir.absolute())
-    # If cell are not vacuum, fission site should not spread to other cells
-    with openmc.StatePoint(subdir / f"statepoint.{settings.batches}.h5") as sp:
-        tally = list(sp.tallies.values())[0]
-        non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
-        assert len(non_zero_tal) > 1
 
     # Vacuum material
     vacuum_str = "vacuum"
-    mats[vacuum_str] = openmc.Material(name=vacuum_str)
-    mats[vacuum_str].add_nuclide("U235", 0.03)
-    mats[vacuum_str].add_nuclide("U238", 0.97)
-    mats[vacuum_str].add_nuclide("O16", 2.0)
-    mats[vacuum_str].set_density("g/cm3", 10.0)
 
     # Tweaking the h5m file to change the material assignment
-    subdir = Path(vacuum_str)
-    subdir.mkdir()
-    vacuum_h5 = subdir / f"dagmc_{vacuum_str}.h5m"
-    shutil.copy(h5m, vacuum_h5)
+    vacuum_h5 = Path(f"dagmc_{vacuum_str}.h5m")
+    shutil.copy(orig_h5m, vacuum_h5)
     hf = h5py.File(vacuum_h5, 'r+')
     hf = h5py.File(vacuum_h5, 'r+')
     new_assignment = 'mat:vacuum'.encode('utf-8')
     hf['/tstt/tags/NAME']['values'][1] = new_assignment
     hf.close()
 
-    # Set the Model
+    # Create a new DAGMC unvierse
     daguniv = openmc.DAGMCUniverse(vacuum_h5.absolute(),
                                    auto_geom_ids=True).bounded_universe()
-    settings = openmc.Settings()
-    settings.batches = 10
-    settings.particles = 100
-    model = openmc.Model()
-    model.materials = openmc.Materials(mats.values())
+    # Update the model geometry
     model.geometry = openmc.Geometry(root=daguniv)
-    model.settings = settings
 
-    # Set the Tally
-    model.init_lib()
-    model.sync_dagmc_universes()
-    for univ in model.geometry.get_all_universes().values():
-        if isinstance(univ, openmc.DAGMCUniverse):
-            dag_univ = univ
-            break
-    my_tally = openmc.Tally()
-    cell_filter = openmc.CellFilter([x.id for x in dag_univ.get_all_cells().values()])
-    my_tally.scores = ['nu-fission']
-    my_tally.filters = [cell_filter]
-    model.tallies.append(my_tally)
-
-    # Only a confined point source
-    src = openmc.IndependentSource(space=openmc.stats.Point())
-    model.settings.source = src
-
-    # Run and check the results
-    model.export_to_model_xml((subdir / 'model.xml').absolute())
-    openmc.run(cwd=subdir.absolute())
-    # If cell are not vacuum, fission site should not spread to other cells
-    with openmc.StatePoint(subdir / f"statepoint.{settings.batches}.h5") as sp:
-        tally = list(sp.tallies.values())[0]
-        non_zero_tal = [x for x in tally.mean.flatten() if x > 0]
-        assert len(non_zero_tal) == 1
-    openmc.lib.finalize()
+    model.export_to_model_xml()
+    with openmc.lib.run_in_memory():
+        material = openmc.lib.find_material((0, 0, 0))
+        assert material is None
\ No newline at end of file