Merge pull request #1820 from paulromano/translational-periodic-fix

Fix for translational periodic boundary conditions

.github/actions/fix-etc-hosts/action.yml

@@ -1,18 +0,0 @@
-name: Fix /etc/hosts
-description: |
-  Workaround for
-  "Reverse name lookup is broken for current hostname in ubuntu-latest VMs",
-  reported as https://github.com/actions/virtual-environments/issues/3185
-runs:
-  using: composite
-  steps:
-    - run: |
-        if [[ "$OSTYPE" == "linux-gnu"* ]]; then
-            # Ensure that reverse lookups for current hostname are handled properly
-            # Add the current IP address, long hostname and short hostname record to /etc/hosts file
-            eth0_ip_addr=$(ip addr show eth0 | grep "inet\b" | awk '{print $2}' | cut -d/ -f1)
-            hostname_fqdn=$(hostname -f)
-            hostname_short=$(hostname -s)
-            echo -e "${eth0_ip_addr}\t${hostname_fqdn} ${hostname_short}" | sudo tee -a /etc/hosts
-        fi
-      shell: bash

.github/workflows/ci.yml

@@ -78,8 +78,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: ./.github/actions/fix-etc-hosts
-
       -
         name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
@@ -97,12 +95,11 @@ jobs:
         shell: bash
         run: |
           sudo apt -y update
-          sudo apt install -y mpich \
-                              libmpich-dev \
+          sudo apt install -y libopenmpi-dev \
                               libnetcdf-dev \
                               libpnetcdf-dev \
                               libhdf5-serial-dev \
-                              libhdf5-mpich-dev \
+                              libhdf5-openmpi-dev \
                               libeigen3-dev
       -
         name: install

src/surface.cpp

@@ -1168,6 +1168,8 @@ void read_surfaces(pugi::xml_node node)
     // Compute the dot product of the surface normals
     Direction norm1 = surf1.normal({0, 0, 0});
     Direction norm2 = surf2.normal({0, 0, 0});
+    norm1 /= norm1.norm();
+    norm2 /= norm2.norm();
     double dot_prod = norm1.dot(norm2);
 
     // If the dot product is 1 (to within floating point precision) then the

tests/regression_tests/cpp_driver/driver.cpp

@@ -1,6 +1,10 @@
+#ifdef OPENMC_MPI
+#include <mpi.h>
+#endif
 
 #include "openmc/capi.h"
 #include "openmc/cell.h"
+#include "openmc/error.h"
 #include "openmc/geometry.h"
 #include "openmc/message_passing.h"
 #include "openmc/summary.h"
@@ -11,7 +15,13 @@
 using namespace openmc;
 
 int main(int argc, char** argv) {
-  openmc_init(argc, argv, nullptr);
+#ifdef OPENMC_MPI
+  MPI_Comm world {MPI_COMM_WORLD};
+  int err = openmc_init(argc, argv, &world);
+#else
+  int err = openmc_init(argc, argv, nullptr);
+#endif
+  if (err) fatal_error(openmc_err_msg);
 
   // create a new cell filter
   auto cell_filter = Filter::create<CellFilter>();
@@ -57,5 +67,10 @@ int main(int argc, char** argv) {
 
   openmc_run();
   openmc_finalize();
+
+#ifdef OPENMC_MPI
+  MPI_Finalize();
+#endif
+
   return 0;
 }

tests/regression_tests/periodic/test.py

@@ -1,58 +1,53 @@
 import openmc
+import pytest
 
 from tests.testing_harness import PyAPITestHarness
 
 
-class PeriodicTest(PyAPITestHarness):
-    def _build_inputs(self):
-        # Define materials
-        water = openmc.Material(1)
-        water.add_nuclide('H1', 2.0)
-        water.add_nuclide('O16', 1.0)
-        water.add_s_alpha_beta('c_H_in_H2O')
-        water.set_density('g/cc', 1.0)
+@pytest.fixture
+def box_model():
+    model = openmc.model.Model()
+    # Define materials
+    water = openmc.Material()
+    water.add_nuclide('H1', 2.0)
+    water.add_nuclide('O16', 1.0)
+    water.add_s_alpha_beta('c_H_in_H2O')
+    water.set_density('g/cc', 1.0)
 
-        fuel = openmc.Material(2)
-        fuel.add_nuclide('U235', 1.0)
-        fuel.set_density('g/cc', 4.5)
+    fuel = openmc.Material()
+    fuel.add_nuclide('U235', 1.0)
+    fuel.set_density('g/cc', 4.5)
 
-        materials = openmc.Materials((water, fuel))
-        materials.default_temperature = '294K'
-        materials.export_to_xml()
+    # Define geometry
+    x_min = openmc.XPlane(surface_id=1, x0=0., boundary_type='periodic')
+    x_max = openmc.XPlane(surface_id=2, x0=5., boundary_type='reflective')
 
-        # Define geometry
-        x_min = openmc.XPlane(surface_id=1, x0=0., boundary_type='periodic')
-        x_max = openmc.XPlane(surface_id=2, x0=5., boundary_type='reflective')
+    y_min = openmc.YPlane(surface_id=3, y0=0., boundary_type='periodic')
+    y_max = openmc.YPlane(surface_id=4, y0=5., boundary_type='reflective')
+    y_min.periodic_surface = x_min
 
-        y_min = openmc.YPlane(surface_id=3, y0=0., boundary_type='periodic')
-        y_max = openmc.YPlane(surface_id=4, y0=5., boundary_type='reflective')
-        y_min.periodic_surface = x_min
+    z_min = openmc.ZPlane(surface_id=5, z0=-5., boundary_type='periodic')
+    z_max = openmc.Plane(surface_id=6, a=0, b=0, c=1, d=5.,
+                         boundary_type='periodic')
+    z_cyl = openmc.ZCylinder(surface_id=7, x0=2.5, y0=0., r=2.0)
 
-        z_min = openmc.ZPlane(surface_id=5, z0=-5., boundary_type='periodic')
-        z_max = openmc.Plane(surface_id=6, a=0, b=0, c=1, d=5.,
-                             boundary_type='periodic')
-        z_cyl = openmc.ZCylinder(surface_id=7, x0=2.5, y0=0., r=2.0)
+    outside_cyl = openmc.Cell(1, fill=water, region=(
+        +x_min & -x_max & +y_min & -y_max & +z_min & -z_max & +z_cyl))
+    inside_cyl = openmc.Cell(2, fill=fuel, region=(
+        +y_min & +z_min & -z_max & -z_cyl))
+    root_universe = openmc.Universe(0, cells=(outside_cyl, inside_cyl))
+    model.geometry = openmc.Geometry(root_universe)
 
-        outside_cyl = openmc.Cell(1, fill=water, region=(
-            +x_min & -x_max & +y_min & -y_max & +z_min & -z_max & +z_cyl))
-        inside_cyl = openmc.Cell(2, fill=fuel, region=(
-            +y_min & +z_min & -z_max & -z_cyl))
-        root_universe = openmc.Universe(0, cells=(outside_cyl, inside_cyl))
-
-        geometry = openmc.Geometry()
-        geometry.root_universe = root_universe
-        geometry.export_to_xml()
-
-        # Define settings
-        settings = openmc.Settings()
-        settings.particles = 1000
-        settings.batches = 4
-        settings.inactive = 0
-        settings.source = openmc.Source(space=openmc.stats.Box(
-            (0, 0, 0), (5, 5, 0)))
-        settings.export_to_xml()
+    # Define settings
+    model.settings.particles = 1000
+    model.settings.batches = 4
+    model.settings.inactive = 0
+    model.settings.source = openmc.Source(space=openmc.stats.Box(
+        (0, 0, 0), (5, 5, 0))
+    )
+    return model
 
 
-def test_periodic():
-    harness = PeriodicTest('statepoint.4.h5')
+def test_periodic(box_model):
+    harness = PyAPITestHarness('statepoint.4.h5', box_model)
     harness.main()

tests/regression_tests/periodic_6fold/inputs_true.dat

@@ -1,11 +1,11 @@
 <?xml version='1.0' encoding='utf-8'?>
 <geometry>
-  <cell id="1" material="1" region="9 10 -11 12" universe="0" />
-  <cell id="2" material="2" region="9 10 -12" universe="0" />
-  <surface boundary="periodic" coeffs="0.4999999999999999 0.8660254037844387 0.0 0.0" id="9" type="plane" />
-  <surface boundary="periodic" coeffs="0.4999999999999999 -0.8660254037844387 0.0 0.0" id="10" type="plane" />
-  <surface boundary="reflective" coeffs="5.0" id="11" type="x-plane" />
-  <surface coeffs="2.598076211353316 1.4999999999999998 2.0" id="12" type="z-cylinder" />
+  <cell id="1" material="1" region="1 2 -3 4" universe="0" />
+  <cell id="2" material="2" region="1 2 -4" universe="0" />
+  <surface boundary="periodic" coeffs="0.4999999999999999 0.8660254037844387 0.0 0.0" id="1" type="plane" />
+  <surface boundary="periodic" coeffs="0.4999999999999999 -0.8660254037844387 0.0 0.0" id="2" type="plane" />
+  <surface boundary="reflective" coeffs="5.0" id="3" type="x-plane" />
+  <surface coeffs="2.598076211353316 1.4999999999999998 2.0" id="4" type="z-cylinder" />
 </geometry>
 <?xml version='1.0' encoding='utf-8'?>
 <materials>

tests/regression_tests/periodic_6fold/test.py

@@ -1,62 +1,59 @@
 import openmc
 import numpy as np
+import pytest
 
 from tests.testing_harness import PyAPITestHarness
 
 
-class Periodic6FoldTest(PyAPITestHarness):
-    def _build_inputs(self):
-        # Define materials
-        water = openmc.Material(1)
-        water.add_nuclide('H1', 2.0)
-        water.add_nuclide('O16', 1.0)
-        water.add_s_alpha_beta('c_H_in_H2O')
-        water.set_density('g/cc', 1.0)
+@pytest.fixture
+def model():
+    model = openmc.model.Model()
 
-        fuel = openmc.Material(2)
-        fuel.add_nuclide('U235', 1.0)
-        fuel.set_density('g/cc', 4.5)
+    # Define materials
+    water = openmc.Material()
+    water.add_nuclide('H1', 2.0)
+    water.add_nuclide('O16', 1.0)
+    water.add_s_alpha_beta('c_H_in_H2O')
+    water.set_density('g/cc', 1.0)
 
-        materials = openmc.Materials((water, fuel))
-        materials.default_temperature = '294K'
-        materials.export_to_xml()
+    fuel = openmc.Material()
+    fuel.add_nuclide('U235', 1.0)
+    fuel.set_density('g/cc', 4.5)
 
-        # Define the geometry.  Note that this geometry is somewhat non-sensical
-        # (it essentially defines a circle of half-cylinders), but it is
-        # designed so that periodic and reflective BCs will give different
-        # answers.
-        theta1 = (-1/6 + 1/2) * np.pi
-        theta2 = (1/6 - 1/2) * np.pi
-        plane1 = openmc.Plane(a=np.cos(theta1), b=np.sin(theta1),
-                              boundary_type='periodic')
-        plane2 = openmc.Plane(a=np.cos(theta2), b=np.sin(theta2),
-                              boundary_type='periodic')
+    # Define the geometry.  Note that this geometry is somewhat non-sensical
+    # (it essentially defines a circle of half-cylinders), but it is
+    # designed so that periodic and reflective BCs will give different
+    # answers.
+    theta1 = (-1/6 + 1/2) * np.pi
+    theta2 = (1/6 - 1/2) * np.pi
+    plane1 = openmc.Plane(a=np.cos(theta1), b=np.sin(theta1),
+                            boundary_type='periodic')
+    plane2 = openmc.Plane(a=np.cos(theta2), b=np.sin(theta2),
+                            boundary_type='periodic')
 
-        x_max = openmc.XPlane(x0=5., boundary_type='reflective')
+    x_max = openmc.XPlane(x0=5., boundary_type='reflective')
 
-        z_cyl = openmc.ZCylinder(x0=3*np.cos(np.pi/6), y0=3*np.sin(np.pi/6),
-                                 r=2.0)
+    z_cyl = openmc.ZCylinder(x0=3*np.cos(np.pi/6), y0=3*np.sin(np.pi/6),
+                                r=2.0)
 
-        outside_cyl = openmc.Cell(1, fill=water, region=(
-            +plane1 & +plane2 & -x_max & +z_cyl))
-        inside_cyl = openmc.Cell(2, fill=fuel, region=(
-            +plane1 & +plane2 & -z_cyl))
-        root_universe = openmc.Universe(0, cells=(outside_cyl, inside_cyl))
+    outside_cyl = openmc.Cell(1, fill=water, region=(
+        +plane1 & +plane2 & -x_max & +z_cyl))
+    inside_cyl = openmc.Cell(2, fill=fuel, region=(
+        +plane1 & +plane2 & -z_cyl))
+    root_universe = openmc.Universe(0, cells=(outside_cyl, inside_cyl))
+    model.geometry = openmc.Geometry(root_universe)
 
-        geometry = openmc.Geometry()
-        geometry.root_universe = root_universe
-        geometry.export_to_xml()
-
-        # Define settings
-        settings = openmc.Settings()
-        settings.particles = 1000
-        settings.batches = 4
-        settings.inactive = 0
-        settings.source = openmc.Source(space=openmc.stats.Box(
-            (0, 0, 0), (5, 5, 0)))
-        settings.export_to_xml()
+    # Define settings
+    model.settings = openmc.Settings()
+    model.settings.particles = 1000
+    model.settings.batches = 4
+    model.settings.inactive = 0
+    model.settings.source = openmc.Source(space=openmc.stats.Box(
+        (0, 0, 0), (5, 5, 0))
+    )
+    return model
 
 
-def test_periodic():
-    harness = Periodic6FoldTest('statepoint.4.h5')
+def test_periodic(model):
+    harness = PyAPITestHarness('statepoint.4.h5', model)
     harness.main()

tests/regression_tests/periodic_hex/inputs_true.dat

@@ -0,0 +1,24 @@
+<?xml version='1.0' encoding='utf-8'?>
+<geometry>
+  <cell id="1" material="1" region="-1 2 -3 -4 5 6" universe="1" />
+  <surface boundary="periodic" coeffs="8.660254037844386" id="1" periodic_surface_id="2" type="x-plane" />
+  <surface boundary="periodic" coeffs="-8.660254037844386" id="2" periodic_surface_id="1" type="x-plane" />
+  <surface boundary="periodic" coeffs="0.5773502691896257 1.0 0.0 10.0" id="3" periodic_surface_id="6" type="plane" />
+  <surface boundary="periodic" coeffs="-0.5773502691896257 1.0 0.0 10.0" id="4" periodic_surface_id="5" type="plane" />
+  <surface boundary="periodic" coeffs="-0.5773502691896257 1.0 0.0 -10.0" id="5" periodic_surface_id="4" type="plane" />
+  <surface boundary="periodic" coeffs="0.5773502691896257 1.0 0.0 -10.0" id="6" periodic_surface_id="3" type="plane" />
+</geometry>
+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+  <material depletable="true" id="1">
+    <density units="g/cc" value="4.5" />
+    <nuclide ao="1.0" name="U235" />
+  </material>
+</materials>
+<?xml version='1.0' encoding='utf-8'?>
+<settings>
+  <run_mode>eigenvalue</run_mode>
+  <particles>1000</particles>
+  <batches>5</batches>
+  <inactive>0</inactive>
+</settings>

tests/regression_tests/periodic_hex/results_true.dat

@@ -0,0 +1,2 @@
+k-combined:
+2.276564E+00 7.905769E-04

tests/regression_tests/periodic_hex/test.py

@@ -0,0 +1,28 @@
+import openmc
+import pytest
+
+from tests.testing_harness import PyAPITestHarness
+
+
+@pytest.fixture
+def hex_model():
+    model = openmc.model.Model()
+
+    fuel = openmc.Material()
+    fuel.add_nuclide('U235', 1.0)
+    fuel.set_density('g/cc', 4.5)
+
+    hex_region = openmc.model.hexagonal_prism(10.0, boundary_type='periodic')
+    cell = openmc.Cell(fill=fuel, region=hex_region)
+    model.geometry = openmc.Geometry([cell])
+
+    # Define settings
+    model.settings.particles = 1000
+    model.settings.batches = 5
+    model.settings.inactive = 0
+    return model
+
+
+def test_periodic_hex(hex_model):
+    harness = PyAPITestHarness('statepoint.5.h5', hex_model)
+    harness.main()

tools/ci/gha-install.sh

@@ -24,9 +24,15 @@ if [[ $LIBMESH = 'y' ]]; then
     ./tools/ci/gha-install-libmesh.sh
 fi
 
-# Install mpi4py for MPI configurations
+# For MPI configurations, make sure mpi4py and h5py are built against the
+# correct version of MPI
 if [[ $MPI == 'y' ]]; then
     pip install --no-binary=mpi4py mpi4py
+
+    export CC=mpicc
+    export HDF5_MPI=ON
+    export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+    pip install --no-binary=h5py h5py
 fi
 
 # Build and install OpenMC executable