lanl · AstroBarker · Oct 17, 2024 · Oct 17, 2024 · Oct 17, 2024 · Oct 17, 2024
diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
@@ -18,6 +18,11 @@ jobs:
           run: export DEBIAN_FRONTEND=noninteractive
         - name: install dependencies
           run: |
-            sudo apt-get install -y --force-yes -qq git clang-format-12
+            sudo apt-get install -y --force-yes -qq git
+        - name: Install pip, clang-format
+          uses: BSFishy/pip-action@v1
+          with:
+            packages: |
+               clang-format==12.0.1
         - name: check formatting
-          run: find . -regex '.*\.\(cpp\|hpp\)' | xargs clang-format-12 -style=file -i && git diff --exit-code --ignore-submodules
+          run: find . -regex '.*\.\(cpp\|hpp\)' | xargs clang-format -style=file -i && git diff --exit-code --ignore-submodules
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -32,22 +32,22 @@ jobs:
             cd tst/regression
             mkdir build_minkowski_release
             cd build_minkowski_release
-            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON ../../../
+            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON -DPHOEBUS_DO_NU_ELECTRON_ANTI=Off -DPHOEBUS_DO_NU_HEAVY=Off ../../../
             cmake --build . --parallel 8
             cd ..
             mkdir build_fmks_release
             cd build_fmks_release
-            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=FMKS -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON ../../../
+            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=FMKS -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON -DPHOEBUS_DO_NU_ELECTRON_ANTI=Off -DPHOEBUS_DO_NU_HEAVY=Off ../../../
             cmake --build . --parallel 8
             cd ..
             mkdir build_minkowski_debug
             cd build_minkowski_debug
-            cmake -DCMAKE_BUILD_TYPE=Debug -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON ../../../
+            cmake -DCMAKE_BUILD_TYPE=Debug -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON -DPHOEBUS_DO_NU_ELECTRON_ANTI=Off -DPHOEBUS_DO_NU_HEAVY=Off ../../../
             cmake --build . --parallel 8
             cd ..
             mkdir build_fmks_debug
             cd build_fmks_debug
-            cmake -DCMAKE_BUILD_TYPE=Debug -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=FMKS -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON ../../../
+            cmake -DCMAKE_BUILD_TYPE=Debug -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=FMKS -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON -DPHOEBUS_DO_NU_ELECTRON_ANTI=Off -DPHOEBUS_DO_NU_HEAVY=Off ../../../
             cmake --build . --parallel 8
             cd ..
             # is there a run directory that shouldn't be here?
@@ -79,7 +79,7 @@ jobs:
           run: |
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON ../
+            cmake -DCMAKE_BUILD_TYPE=Release -DPHOEBUS_ENABLE_UNIT_TESTS=ON -DMAX_NUMBER_CONSERVED_VARS=10 -DPHOEBUS_GEOMETRY=Minkowski -DPHOEBUS_CACHE_GEOMETRY=ON -DPARTHENON_DISABLE_HDF5_COMPRESSION=ON .-DPHOEBUS_DO_NU_ELECTRON_ANTI=Off -DPHOEBUS_DO_NU_HEAVY=Off ../
             cmake --build . --parallel 4
         - name: Run unit tests
           run: |

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -166,6 +166,7 @@ set(SINGULARITY_USE_FORTRAN OFF CACHE BOOL "" FORCE)
 set(SINGULARITY_FORCE_SUBMODULE_MODE ON CACHE BOOL "" FORCE)
 set(SINGULARITY_USE_KOKKOSKERNELS OFF CACHE BOOL "" FORCE)
 set(SINGULARITY_BUILD_CLOSURE OFF CACHE BOOL "" FORCE)
+set(SINGULARITY_USE_TRUE_LOG_GRIDDING ON CACHE BOOL "" FORCE)
 
 # Kill cmake's package registry because it can interfere
 set(CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ON CACHE BOOL "" FORCE)
@@ -184,6 +185,9 @@ include(cmake/Geometry.cmake)
 # Fluid
 include(cmake/Fluid.cmake)
 
+# Transport
+include(cmake/Transport.cmake)
+
 # Phoebus src
 message("\nConfiguring src")
 add_subdirectory(src)

diff --git a/cmake/Transport.cmake b/cmake/Transport.cmake
@@ -0,0 +1,33 @@
+# © 2021-2025. Triad National Security, LLC. All rights reserved.  This
+# program was produced under U.S. Government contract 89233218CNA000001
+# for Los Alamos National Laboratory (LANL), which is operated by Triad
+# National Security, LLC for the U.S.  Department of Energy/National
+# Nuclear Security Administration. All rights in the program are
+# reserved by Triad National Security, LLC, and the U.S. Department of
+# Energy/National Nuclear Security Administration. The Government is
+# granted for itself and others acting on its behalf a nonexclusive,
+# paid-up, irrevocable worldwide license in this material to reproduce,
+# prepare derivative works, distribute copies to the public, perform
+# publicly and display publicly, and to permit others to do so.
+
+option(PHOEBUS_DO_NU_ELECTRON "Evolve electron neutrinos" ON)
+option(PHOEBUS_DO_NU_ELECTRON_ANTI "Evolve electron antineutrinos" ON)
+option(PHOEBUS_DO_NU_HEAVY "Evolve heavy composite type neutrinos" ON)
+
+if(PHOEBUS_DO_NU_ELECTRON)
+  set(DO_NU_ELECTRON 1 CACHE BOOL "Electron neutrinos enabled")
+else()
+  set(DO_NU_ELECTRON 0 CACHE BOOL "Electron neutrinos disabled")
+endif()
+
+if(PHOEBUS_DO_NU_ELECTRON_ANTI)
+  set(DO_NU_ELECTRON_ANTI 1 CACHE BOOL "Electron antineutrinos enabled")
+else()
+  set(DO_NU_ELECTRON_ANTI 0 CACHE BOOL "Electron antineutrinos disabled")
+endif()
+
+if(PHOEBUS_DO_NU_HEAVY)
+  set(DO_NU_HEAVY 1 CACHE BOOL "Heavy neutrinos enabled")
+else()
+  set(DO_NU_HEAVY 0 CACHE BOOL "Heavy neutrinos disabled")
+endif()
diff --git a/external/parthenon b/external/parthenon
diff --git a/external/singularity-eos b/external/singularity-eos
diff --git a/external/singularity-opac b/external/singularity-opac
diff --git a/inputs/blandford_mckee.pin b/inputs/blandford_mckee.pin
@@ -15,6 +15,12 @@
 
 <phoebus>
 problem = blandford_mckee
+ix1_bc = reflect 
+ox1_bc = gr_outflow
+ix2_bc = reflect 
+ox2_bc = reflect 
+ix3_bc = periodic
+ox3_bc = periodic
 
 <parthenon/job>
 problem_id  = blast # problem ID: basename of output filenames
@@ -50,14 +56,14 @@ nghost = 4
 nx1         = 512         # Number of zones in X1-direction
 x1min       = 0        # minimum value of X1
 x1max       = 1         # maximum value of X1
-ix1_bc      = user        # Inner-X1 boundary condition flag
-ox1_bc      = user        # Outer-X1 boundary condition flag
+ix1_bc      = reflect # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow        # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 3.14159265359 # maximum value of X2. Pi
-ix2_bc      = reflecting    # Inner-X2 boundary condition flag
-ox2_bc      = reflecting    # Outer-X2 boundary condition flag
+ix2_bc      = reflect    # Inner-X2 boundary condition flag
+ox2_bc      = reflect    # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3

diff --git a/inputs/blast_wave.pin b/inputs/blast_wave.pin
@@ -18,6 +18,8 @@
 
 <phoebus>
 problem = sedov
+ix1_bc = reflect
+ox1_bc = gr_outflow
 ix2_bc = reflect
 ox2_bc = reflect
 
@@ -55,14 +57,14 @@ nghost = 4
 nx1         = 512         # Number of zones in X1-direction
 x1min       = 0.0         # minimum value of X1
 x1max       = 0.3         # maximum value of X1
-ix1_bc      = user        # Inner-X1 boundary condition flag
-ox1_bc      = user        # Outer-X1 boundary condition flag
+ix1_bc      = reflect  # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow  # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 3.14159265359 # maximum value of X2. Pi
-ix2_bc      = user          # Inner-X2 boundary condition flag
-ox2_bc      = user          # Outer-X2 boundary condition flag
+ix2_bc      = reflect       # Inner-X2 boundary condition flag
+ox2_bc      = reflect       # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3

diff --git a/inputs/blast_wave_2d.pin b/inputs/blast_wave_2d.pin
@@ -74,8 +74,8 @@ num_threads = 1         # maximum number of OMP threads
 bc_vars = conserved
 
 <parthenon/meshblock>
-nx1 = 32
-nx2 = 32
+nx1 = 64
+nx2 = 64
 nx3 = 1
 
 <parthenon/refinement0>

diff --git a/inputs/bondi.pin b/inputs/bondi.pin
@@ -12,10 +12,12 @@
 
 <phoebus>
 problem = bondi
-ix1_bc = outflow
-ox1_bc = outflow
+ix1_bc = gr_outflow
+ox1_bc = gr_outflow
 ix2_bc = reflect
 ox2_bc = reflect
+ix3_bc = periodic
+ox3_bc = periodic
 
 <parthenon/job>
 problem_id  = bondi       # problem ID: basename of output filenames
@@ -51,14 +53,14 @@ nghost = 4
 nx1         = 256           # Number of zones in X1-direction
 x1min       = 0.59          # minimum value of X1
 x1max       = 5             # maximum value of X1
-ix1_bc      = user          # Inner-X1 boundary condition flag
-ox1_bc      = user          # Outer-X1 boundary condition flag
+ix1_bc      = gr_outflow    # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow    # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 1 #3.14159265359 #1 # maximum value of X2. Pi
-ix2_bc      = user          # Inner-X2 boundary condition flag
-ox2_bc      = user          # Outer-X2 boundary condition flag
+ix2_bc      = reflect       # Inner-X2 boundary condition flag
+ox2_bc      = reflect       # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3

diff --git a/inputs/homogeneous_sphere.pin b/inputs/homogeneous_sphere.pin
@@ -13,7 +13,7 @@
 <phoebus>
 problem = homogeneous_sphere
 ix1_bc = reflect
-ox1_bc = outflow
+ox1_bc = gr_outflow
 
 <parthenon/job>
 problem_id  = hom_sph   # problem ID: basename of output filenames
@@ -39,17 +39,17 @@ nghost = 4
 #refinement = adaptive
 #numlevel = 3
 
-nx1         = 128      # Number of zones in X1-direction
-x1min       = 0        # minimum value of X1
-x1max       = 5        # maximum value of X1
-ix1_bc      = user     # Inner-X1 boundary condition flag
-ox1_bc      = user     # Outer-X1 boundary condition flag
+nx1         = 128        # Number of zones in X1-direction
+x1min       = 0          # minimum value of X1
+x1max       = 5          # maximum value of X1
+ix1_bc      = reflect    # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow # Outer-X1 boundary condition flag
 
-nx2         = 1         # Number of zones in X2-direction
-x2min       = 0         # minimum value of X2
-x2max       = 3.14159265359   # maximum value of X2
-ix2_bc      = periodic  # Inner-X2 boundary condition flag
-ox2_bc      = periodic  # Outer-X2 boundary condition flag
+nx2         = 1             # Number of zones in X2-direction
+x2min       = 0             # minimum value of X2
+x2max       = 3.14159265359 # maximum value of X2
+ix2_bc      = periodic      # Inner-X2 boundary condition flag
+ox2_bc      = periodic      # Outer-X2 boundary condition flag
 
 nx3         = 1         # Number of zones in X3-direction
 x3min       = -1        # minimum value of X3
@@ -98,10 +98,7 @@ nu_min = 1.e15
 nu_max = 1.e22
 nu_bins = 200
 absorption = true
-do_nu_electron = true
-do_nu_electron_anti = false
-do_nu_heavy = false
-
+:x
 B_fake = 1.0
 use_B_fake = true
 
@@ -110,7 +107,7 @@ type = gray
 gray_kappa = 1.e1
 
 <homogeneous_sphere>
-J = 0.01
+J = 0.1
 Hx = 0.01
 Hy = 0.0
 Hz = 0.0

diff --git a/inputs/homologous.pin b/inputs/homologous.pin
@@ -64,14 +64,14 @@ numlevel = 3
 nx1         = 10000        # Number of zones in X1-direction
 x1min       = 0       # minimum value of X1
 x1max       =  0.10086475522209183         # maximum value of X1
-ix1_bc      = user        # Inner-X1 boundary condition flag
-ox1_bc      = user        # Outer-X1 boundary condition flag
+ix1_bc      = reflect        # Inner-X1 boundary condition flag
+ox1_bc      = reflect        # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 3.14159265359 # maximum value of X2. Pi
-ix2_bc      = user          # Inner-X2 boundary condition flag
-ox2_bc      = user          # Outer-X2 boundary condition flag
+ix2_bc      = reflect          # Inner-X2 boundary condition flag
+ox2_bc      = reflect          # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3

diff --git a/inputs/mhd_shocktube.pin b/inputs/mhd_shocktube.pin
@@ -12,8 +12,8 @@
 
 <phoebus>
 problem   = shock_tube
-ix1_bc = outflow
-ox1_bc = outflow
+ix1_bc = gr_outflow
+ox1_bc = gr_outflow
 
 <parthenon/job>
 problem_id  = sod       # problem ID: basename of output filenames
@@ -43,13 +43,13 @@ dt_init_fact = 1.e-6
 #numlevel = 3
 nghost = 4
 
-nx1         = 256       # Number of zones in X1-direction
-x1min       = 0        # minimum value of X1
-x1max       = 1         # maximum value of X1
-ix1_bc      = user     # Inner-X1 boundary condition flag
-ox1_bc      = user     # Outer-X1 boundary condition flag
+nx1         = 256        # Number of zones in X1-direction
+x1min       = 0          # minimum value of X1
+x1max       = 1          # maximum value of X1
+ix1_bc      = gr_outflow # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow # Outer-X1 boundary condition flag
 
-nx2         = 1       # Number of zones in X2-direction
+nx2         = 1		# Number of zones in X2-direction
 x2min       = -1        # minimum value of X2
 x2max       = 1         # maximum value of X2
 ix2_bc      = periodic  # Inner-X2 boundary condition flag

diff --git a/inputs/progenitor.pin b/inputs/progenitor.pin
@@ -73,14 +73,14 @@ bc_vars = conserved
 nx1         = 8000        # Number of zones in X1-direction
 x1min       = 0       # minimum value of X1
 x1max       = 1.         # maximum value of X1
-ix1_bc      = user        # Inner-X1 boundary condition flag
-ox1_bc      = user        # Outer-X1 boundary condition flag
+ix1_bc      = reflect        # Inner-X1 boundary condition flag
+ox1_bc      = reflect        # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 3.14159265359 # maximum value of X2. Pi
-ix2_bc      = user          # Inner-X2 boundary condition flag
-ox2_bc      = user          # Outer-X2 boundary condition flag
+ix2_bc      = reflect          # Inner-X2 boundary condition flag
+ox2_bc      = reflect          # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3

diff --git a/inputs/radiation_advection.pin b/inputs/radiation_advection.pin
@@ -108,9 +108,6 @@ nu_min = 1.e-2
 nu_max = 1.e2
 nu_bins = 10
 absorption = true
-do_nu_electron = true
-do_nu_electron_anti = false
-do_nu_heavy = false
 src_solver = oned
 
 <radiation/mocmc>

diff --git a/inputs/radiation_equilibration.pin b/inputs/radiation_equilibration.pin
@@ -101,9 +101,6 @@ nu_min = 1.e-2
 nu_max = 1.e2
 nu_bins = 10
 absorption = true
-do_nu_electron = true
-do_nu_electron_anti = false
-do_nu_heavy = false
 
 <opacity>
 type = gray

diff --git a/inputs/rhs_tester.pin b/inputs/rhs_tester.pin
@@ -15,7 +15,7 @@
 <phoebus>
 problem = rhs_tester
 ix1_bc = reflect
-ox1_bc = outflow
+ox1_bc = gr_outflow
 ix2_bc = reflect
 ox2_bc = reflect
 
@@ -50,17 +50,17 @@ nghost = 4
 #refinement = adaptive
 #numlevel = 3
 
-nx1         = 64         # Number of zones in X1-direction
-x1min       = 0           # minimum value of X1
-x1max       = 1           # maximum value of X1
-ix1_bc      = user        # Inner-X1 boundary condition flag
-ox1_bc      = user        # Outer-X1 boundary condition flag
+nx1         = 64            # Number of zones in X1-direction
+x1min       = 0             # minimum value of X1
+x1max       = 1             # maximum value of X1
+ix1_bc      = reflect       # Inner-X1 boundary condition flag
+ox1_bc      = gr_outflow    # Outer-X1 boundary condition flag
 
 nx2         = 1             # Number of zones in X2-direction
 x2min       = 0             # minimum value of X2
 x2max       = 3.14159265359 # maximum value of X2. Pi
-ix2_bc      = user          # Inner-X2 boundary condition flag
-ox2_bc      = user          # Outer-X2 boundary condition flag
+ix2_bc      = reflect       # Inner-X2 boundary condition flag
+ox2_bc      = reflect       # Outer-X2 boundary condition flag
 
 nx3         = 1             # Number of zones in X3-direction
 x3min       = 0             # minimum value of X3
+1 −1		CMakeLists.txt
+103 −13		README.md
+19 −10		cmake/SetupDeps.cmake
+10 −3		cmake/SetupOptions.cmake
+64 −18		singularity-opac/constants/constants.hpp
+8 −1		singularity-opac/neutrinos/brt_neutrinos.hpp
+8 −1		singularity-opac/neutrinos/gray_opacity_neutrinos.hpp
+13 −1		singularity-opac/neutrinos/mean_neutrino_variant.hpp
+19 −8		singularity-opac/neutrinos/mean_opacity_neutrinos.hpp
+7 −1		singularity-opac/neutrinos/neutrino_variant.hpp
+29 −5		singularity-opac/neutrinos/non_cgs_neutrinos.hpp
+186 −23		singularity-opac/neutrinos/spiner_opac_neutrinos.hpp
+2 −2		singularity-opac/neutrinos/thermal_distributions_neutrinos.hpp
+11 −3		singularity-opac/neutrinos/tophat_emissivity_neutrinos.hpp
+14 −3		singularity-opac/photons/epbremsstrahlung_opacity_photons.hpp
+19 −0		singularity-opac/photons/example_ascii/kap_plaw.txt
+103 −0		singularity-opac/photons/example_ascii/preproc_ascii_opac.py
+10 −5		singularity-opac/photons/gray_opacity_photons.hpp
+172 −39		singularity-opac/photons/mean_opacity_photons.hpp
+31 −0		singularity-opac/photons/mean_photon_types.hpp
+35 −1		singularity-opac/photons/mean_photon_variant.hpp
+46 −5		singularity-opac/photons/non_cgs_photons.hpp
+6 −2		singularity-opac/photons/opac_photons.hpp
+7 −1		singularity-opac/photons/photon_variant.hpp
+190 −0		singularity-opac/photons/powerlaw_opacity_photons.hpp
+2 −2		singularity-opac/photons/thermal_distributions_photons.hpp
+8 −2		test/CMakeLists.txt
+100 −4		test/test_gray_opacities.cpp
+172 −16		test/test_mean_opacities.cpp
+198 −0		test/test_powerlaw_opacities.cpp
+5 −1		utils/fast-math/logs.hpp
+1 −1		utils/kokkos
+1 −1		utils/ports-of-call
+1 −1		utils/spiner
+1 −1		utils/variant