From 687d43b0ab6e3e3ddfe867767c210f0a1cfb38a7 Mon Sep 17 00:00:00 2001
From: Patrick Myers <pmyers@anl.gov>
Date: Wed, 25 May 2022 09:06:53 -0500
Subject: [PATCH 001/119] added external xtensor within PhotonInteraction for
 all shell photoelectric xs to utilize contiguous memory in calculate_xs

---
 include/openmc/photon.h |  2 +-
 src/photon.cpp          | 26 +++++++++++---------------
 src/physics.cpp         |  6 +++---
 3 files changed, 15 insertions(+), 19 deletions(-)

diff --git a/include/openmc/photon.h b/include/openmc/photon.h
index e8ec82d10..50ee228c4 100644
--- a/include/openmc/photon.h
+++ b/include/openmc/photon.h
@@ -36,7 +36,6 @@ public:
   int threshold;
   double n_electrons;
   double binding_energy;
-  xt::xtensor<double, 1> cross_section;
   vector<Transition> transitions;
 };
 
@@ -82,6 +81,7 @@ public:
 
   // Photoionization and atomic relaxation data
   vector<ElectronSubshell> shells_;
+  xt::xtensor<double, 2> cross_sections_;
 
   // Compton profile data
   xt::xtensor<double, 2> profile_pdf_;
diff --git a/src/photon.cpp b/src/photon.cpp
index b0cd8aa87..3f9ff6dbf 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -16,6 +16,9 @@
 #include "xtensor/xbuilder.hpp"
 #include "xtensor/xoperation.hpp"
 #include "xtensor/xview.hpp"
+#include "xtensor/xmath.hpp"
+#include "xtensor/xslice.hpp"
+#include "xtensor/xtensor_forward.hpp"
 
 #include <cmath>
 #include <fmt/core.h>
@@ -125,6 +128,7 @@ PhotonInteraction::PhotonInteraction(hid_t group)
   }
 
   shells_.resize(n_shell);
+  cross_sections_.resize({energy_.size(), n_shell});
 
   // Create mapping from designator to index
   std::unordered_map<int, int> shell_map;
@@ -155,13 +159,14 @@ PhotonInteraction::PhotonInteraction(hid_t group)
     read_attribute(tgroup, "num_electrons", shell.n_electrons);
 
     // Read subshell cross section
+    xt::xtensor<double, 1> xs;
     dset = open_dataset(tgroup, "xs");
     read_attribute(dset, "threshold_idx", shell.threshold);
     close_dataset(dset);
-    read_dataset(tgroup, "xs", shell.cross_section);
+    read_dataset(tgroup, "xs", xs);
 
-    auto& xs = shell.cross_section;
-    xs = xt::where(xs > 0.0, xt::log(xs), -500.0);
+    auto cross_section = xt::view(cross_sections_, xt::range(shell.threshold, shell.threshold + xs.size()), i);
+    cross_section = xt::where(xs > 0.0, xt::log(xs), -500.0);
 
     if (object_exists(tgroup, "transitions")) {
       // Determine dimensions of transitions
@@ -565,19 +570,10 @@ void PhotonInteraction::calculate_xs(Particle& p) const
     incoherent_(i_grid) + f * (incoherent_(i_grid + 1) - incoherent_(i_grid)));
 
   // Calculate microscopic photoelectric cross section
-  xs.photoelectric = 0.0;
-  for (const auto& shell : shells_) {
-    // Check threshold of reaction
-    int i_start = shell.threshold;
-    if (i_grid < i_start)
-      continue;
+  const auto& xs_upper = xt::row(cross_sections_, i_grid);
+  const auto& xs_lower = xt::row(cross_sections_, i_grid + 1);
 
-    // Evaluation subshell photoionization cross section
-    xs.photoelectric +=
-      std::exp(shell.cross_section(i_grid - i_start) +
-               f * (shell.cross_section(i_grid + 1 - i_start) -
-                     shell.cross_section(i_grid - i_start)));
-  }
+  xs.photoelectric = xt::sum(xt::exp(xs_upper + f * (xs_upper - xs_lower)))[0];
 
   // Calculate microscopic pair production cross section
   xs.pair_production = std::exp(
diff --git a/src/physics.cpp b/src/physics.cpp
index 13dd063de..38d74dbed 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -358,9 +358,9 @@ void sample_photon_reaction(Particle& p)
         continue;
 
       // Evaluation subshell photoionization cross section
-      double xs = std::exp(shell.cross_section(i_grid - i_start) +
-                           f * (shell.cross_section(i_grid + 1 - i_start) -
-                                 shell.cross_section(i_grid - i_start)));
+      double xs = std::exp(element.cross_sections_(i_grid - i_start) +
+                           f * (element.cross_sections_(i_grid + 1 - i_start) -
+                                 element.cross_sections_(i_grid - i_start)));
 
       prob += xs;
       if (prob > cutoff) {

From 6df0286b2e20e39b4eff8d93b262821086a9304f Mon Sep 17 00:00:00 2001
From: Patrick Myers <pmyers@anl.gov>
Date: Wed, 25 May 2022 09:14:10 -0500
Subject: [PATCH 002/119] added clang-format

---
 src/photon.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/photon.cpp b/src/photon.cpp
index 3f9ff6dbf..1be515a62 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -14,11 +14,11 @@
 #include "openmc/settings.h"
 
 #include "xtensor/xbuilder.hpp"
-#include "xtensor/xoperation.hpp"
-#include "xtensor/xview.hpp"
 #include "xtensor/xmath.hpp"
+#include "xtensor/xoperation.hpp"
 #include "xtensor/xslice.hpp"
 #include "xtensor/xtensor_forward.hpp"
+#include "xtensor/xview.hpp"
 
 #include <cmath>
 #include <fmt/core.h>
@@ -165,7 +165,8 @@ PhotonInteraction::PhotonInteraction(hid_t group)
     close_dataset(dset);
     read_dataset(tgroup, "xs", xs);
 
-    auto cross_section = xt::view(cross_sections_, xt::range(shell.threshold, shell.threshold + xs.size()), i);
+    auto cross_section = xt::view(cross_sections_,
+      xt::range(shell.threshold, shell.threshold + xs.size()), i);
     cross_section = xt::where(xs > 0.0, xt::log(xs), -500.0);
 
     if (object_exists(tgroup, "transitions")) {

From 7484618c7c93d3bb75fe6decc0104e3201129ad6 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 5 Apr 2022 13:01:03 -0500
Subject: [PATCH 003/119] Adding sample methods to univariate distribution
 classes

---
 openmc/stats/univariate.py | 123 +++++++++++++++++++++++++++++++++++++
 1 file changed, 123 insertions(+)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index e4a9b8f92..ea8c9f943 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -60,6 +60,10 @@ class Univariate(EqualityMixin, ABC):
         elif distribution == 'mixture':
             return Mixture.from_xml_element(elem)
 
+    @abstractmethod
+    def sample(p, seed=None):
+        pass
+
 
 class Discrete(Univariate):
     """Distribution characterized by a probability mass function.
@@ -115,6 +119,26 @@ class Discrete(Univariate):
             cv.check_greater_than('discrete probability', pk, 0.0, True)
         self._p = p
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+
+        if len(self.x) == 1:
+            return np.full((n_samples), self.x[0])
+
+        out = np.zeros((n_samples,))
+        for i, xi in enumerate(np.random.rand(n_samples)):
+            c = 0.0
+            for j, prob in enumerate(self.p):
+                c += prob
+                if (xi < c):
+                    out[i] = self.x[j]
+                    break
+        return out
+
+    def normalize(self):
+        norm = sum(self.p)
+        self.p = [val / norm for val in self.p]
+
     def to_xml_element(self, element_name):
         """Return XML representation of the discrete distribution
 
@@ -240,6 +264,10 @@ class Uniform(Univariate):
         t.c = [0., 1.]
         return t
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        return np.random.uniform(self.a, self.b, n_samples)
+
     def to_xml_element(self, element_name):
         """Return XML representation of the uniform distribution
 
@@ -341,6 +369,14 @@ class PowerLaw(Univariate):
         cv.check_type('power law exponent', n, Real)
         self._n = n
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        xi = np.random.rand(n_samples)
+        pwr = self.n + 1
+        offset = self.a**pwr
+        span = self.b**pwr - offset
+        return np.power(offset + xi * span, (1/pwr))
+
     def to_xml_element(self, element_name):
         """Return XML representation of the power law distribution
 
@@ -414,6 +450,16 @@ class Maxwell(Univariate):
         cv.check_greater_than('Maxwell temperature', theta, 0.0)
         self._theta = theta
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        self.sample_maxwell(self.theta, n_samples)
+
+    @staticmethod
+    def sample_maxwell(t, n_samples):
+        r1, r2, r3 = np.random.rand(3, n_samples)
+        c = np.power(np.cos(0.5 * np.pi * r3), 2)
+        return t * (np.log(r1) + np.log(r2) * c)
+
     def to_xml_element(self, element_name):
         """Return XML representation of the Maxwellian distribution
 
@@ -502,6 +548,13 @@ class Watt(Univariate):
         cv.check_greater_than('Watt b', b, 0.0)
         self._b = b
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        w = Maxwell.sample_maxwell(self.a, n_samples)
+        u = np.random.uniform(-1., 1., n_samples)
+        aab = self.a * self.a * self.b
+        return w + 0.25*aab + u * np.sqrt(aab*w)
+
     def to_xml_element(self, element_name):
         """Return XML representation of the Watt distribution
 
@@ -588,6 +641,10 @@ class Normal(Univariate):
         cv.check_greater_than('Normal std_dev', std_dev, 0.0)
         self._std_dev = std_dev
 
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        return np.random.normal(self.mean_value, self.std_dev, n_samples)
+
     def to_xml_element(self, element_name):
         """Return XML representation of the Normal distribution
 
@@ -694,6 +751,12 @@ class Muir(Univariate):
         cv.check_greater_than('Muir kt', kt, 0.0)
         self._kt = kt
 
+    def sample(self, n_samples=1, seed=None):
+        # https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-05411-MS
+        np.random.seed(seed)
+        sigma = np.sqrt(4.*self.e0*self.kt/self.m_rat)
+        return np.random.normal(self.e0, sigma, n_samples)
+
     def to_xml_element(self, element_name):
         """Return XML representation of the Watt distribution
 
@@ -803,6 +866,63 @@ class Tabular(Univariate):
         cv.check_value('interpolation', interpolation, _INTERPOLATION_SCHEMES)
         self._interpolation = interpolation
 
+    def cdf(self):
+        if self.interpolation not in ('histogram', 'linear-linear'):
+            raise NotImplementedError('Can only generate CDFs for tabular '
+                                      'distributions using histogram or '
+                                      'linear-linear interpolation')
+        c = np.zeros_like((len(self.x),))
+        if self.interpolation == 'histogram':
+            c[1:] = self.p * np.diff(self.x)
+        elif self.interpolation == 'linear-linear':
+            c[1:] = 0.5 * np.diff(self.p) * np.diff(self.x)
+        return np.cumsum(c)
+
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        xi = np.random.rand(n_samples)
+        cdf = self.cdf()
+
+        # get CDF bins that are above the
+        # sampled values
+        c_i = np.full(n_samples, cdf[0])
+        cdf_idx = np.zeros_like(n_samples)
+        for i, val in enumerate(cdf):
+            mask = xi > val
+            c_i[mask] = val
+            cdf_idx[mask] = i
+
+        # get table values at each index where
+        # the random number is less than the next cdf
+        # entry
+        x_i = np.array([self.x[i] for i in cdf_idx])
+        p_i = np.array([self.p[i] for i in cdf_idx])
+
+        if self.interpolation == 'histogram':
+            # mask where probability
+            pos_mask = p_i > 0.0
+            p_i[pos_mask] = x_i[pos_mask] + (xi[pos_mask] - c_i[pos_mask]) \
+                           / p_i[pos_mask]
+            neg_mask = not pos_mask
+            p_i[neg_mask] = x_i[neg_mask]
+            return p_i
+        elif self.interpolation == 'linear-linear':
+            # get variable and probability values for the
+            # next entry
+            x_i1 = np.array([self.x[i+1] for i in cdf_idx])
+            p_i1 = np.array([self.p[i+1] for i in cdf_idx])
+            # compute slope between entries
+            m = (p_i1 - p_i) / (x_i1 - x_i)
+            # set values for zero slope
+            zero = m == 0.0
+            m[zero] = x_i[zero] + (xi[zero] - c_i[zero]) / p_i[zero]
+            # set values for non-zero slope
+            non_zero = not zero
+            quad = np.pow(p_i[non_zero]**2) + 2. * m[non_zero] * (xi[non_zero] - c_i[non_zero])
+            quad[quad < 0.0] = 0.0
+            m[non_zero] = x_i[non_zero] +  (np.sqrt(quad) - p_i) / m[non_zero]
+            return m
+
     def to_xml_element(self, element_name):
         """Return XML representation of the tabular distribution
 
@@ -890,6 +1010,9 @@ class Legendre(Univariate):
     def coefficients(self, coefficients):
         self._coefficients = np.asarray(coefficients)
 
+    def sample(self, n_samples=1, seed=None):
+        raise NotImplementedError
+
     def to_xml_element(self, element_name):
         raise NotImplementedError
 

From e856c6a27065eb9b2b64dd480f1200020937e276 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 5 Apr 2022 13:24:18 -0500
Subject: [PATCH 004/119] Correction to maxwell dist sampling

---
 openmc/stats/univariate.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index ea8c9f943..72a5568aa 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -452,13 +452,13 @@ class Maxwell(Univariate):
 
     def sample(self, n_samples=1, seed=None):
         np.random.seed(seed)
-        self.sample_maxwell(self.theta, n_samples)
+        return self.sample_maxwell(self.theta, n_samples)
 
     @staticmethod
     def sample_maxwell(t, n_samples):
         r1, r2, r3 = np.random.rand(3, n_samples)
         c = np.power(np.cos(0.5 * np.pi * r3), 2)
-        return t * (np.log(r1) + np.log(r2) * c)
+        return -t * (np.log(r1) + np.log(r2) * c)
 
     def to_xml_element(self, element_name):
         """Return XML representation of the Maxwellian distribution

From 136ff45cc56a4a552eea93b35aeaf792e9fad0e7 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 5 Apr 2022 13:52:50 -0500
Subject: [PATCH 005/119] Adding docstrings. Corrections to Tabular sampling

---
 openmc/stats/univariate.py | 34 +++++++++++++++++++++++++---------
 1 file changed, 25 insertions(+), 9 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 72a5568aa..3d99f8b8c 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -61,7 +61,21 @@ class Univariate(EqualityMixin, ABC):
             return Mixture.from_xml_element(elem)
 
     @abstractmethod
-    def sample(p, seed=None):
+    def sample(n_samples=1, seed=None):
+        """Sample the univariate distribution
+
+        Parameters
+        ----------
+        n_samples : int
+            Number of sampled values to generate
+        seed : int or None
+            Initial random number seed.
+
+        Returns
+        -------
+        numpy.ndarray
+            A 1-D array of sampled values
+        """
         pass
 
 
@@ -867,15 +881,17 @@ class Tabular(Univariate):
         self._interpolation = interpolation
 
     def cdf(self):
-        if self.interpolation not in ('histogram', 'linear-linear'):
+        if not self.interpolation in ('histogram', 'linear-linear'):
             raise NotImplementedError('Can only generate CDFs for tabular '
                                       'distributions using histogram or '
                                       'linear-linear interpolation')
-        c = np.zeros_like((len(self.x),))
+        c = np.zeros_like(self.x)
+        x = np.asarray(self.x)
+        p = np.asarray(self.p)
         if self.interpolation == 'histogram':
-            c[1:] = self.p * np.diff(self.x)
+            c[1:] = p * np.diff(x)
         elif self.interpolation == 'linear-linear':
-            c[1:] = 0.5 * np.diff(self.p) * np.diff(self.x)
+            c[1:] = 0.5 * (p[0:-1] + p[1:]) * np.diff(x)
         return np.cumsum(c)
 
     def sample(self, n_samples=1, seed=None):
@@ -886,7 +902,7 @@ class Tabular(Univariate):
         # get CDF bins that are above the
         # sampled values
         c_i = np.full(n_samples, cdf[0])
-        cdf_idx = np.zeros_like(n_samples)
+        cdf_idx = np.zeros((n_samples,), dtype=int)
         for i, val in enumerate(cdf):
             mask = xi > val
             c_i[mask] = val
@@ -903,7 +919,7 @@ class Tabular(Univariate):
             pos_mask = p_i > 0.0
             p_i[pos_mask] = x_i[pos_mask] + (xi[pos_mask] - c_i[pos_mask]) \
                            / p_i[pos_mask]
-            neg_mask = not pos_mask
+            neg_mask = np.invert(pos_mask)
             p_i[neg_mask] = x_i[neg_mask]
             return p_i
         elif self.interpolation == 'linear-linear':
@@ -917,8 +933,8 @@ class Tabular(Univariate):
             zero = m == 0.0
             m[zero] = x_i[zero] + (xi[zero] - c_i[zero]) / p_i[zero]
             # set values for non-zero slope
-            non_zero = not zero
-            quad = np.pow(p_i[non_zero]**2) + 2. * m[non_zero] * (xi[non_zero] - c_i[non_zero])
+            non_zero = np.invert(zero)
+            quad = np.power(p_i[non_zero], 2) + 2. * m[non_zero] * (xi[non_zero] - c_i[non_zero])
             quad[quad < 0.0] = 0.0
             m[non_zero] = x_i[non_zero] +  (np.sqrt(quad) - p_i) / m[non_zero]
             return m

From 17be0257a0ec05994ff6d2a2fea8edcd15b5dfc7 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 5 Apr 2022 14:05:35 -0500
Subject: [PATCH 006/119] Correction to histogram cdf method

---
 openmc/stats/univariate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 3d99f8b8c..7fc479e63 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -889,7 +889,7 @@ class Tabular(Univariate):
         x = np.asarray(self.x)
         p = np.asarray(self.p)
         if self.interpolation == 'histogram':
-            c[1:] = p * np.diff(x)
+            c[1:] = p[:-1] * np.diff(x)
         elif self.interpolation == 'linear-linear':
             c[1:] = 0.5 * (p[0:-1] + p[1:]) * np.diff(x)
         return np.cumsum(c)

From 8070ccaf52abb93eca2e3ee99784284d5b730a26 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Tue, 5 Apr 2022 15:32:38 -0500
Subject: [PATCH 007/119] Adding sampling for Mixture. Improving performance of
 Discrete sampling

---
 openmc/stats/univariate.py | 36 ++++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 7fc479e63..0e6b4ae61 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -133,20 +133,19 @@ class Discrete(Univariate):
             cv.check_greater_than('discrete probability', pk, 0.0, True)
         self._p = p
 
+    def cdf(self):
+        return np.insert(np.cumsum(self.p), 0, 0.0)
+
     def sample(self, n_samples=1, seed=None):
         np.random.seed(seed)
 
         if len(self.x) == 1:
             return np.full((n_samples), self.x[0])
 
-        out = np.zeros((n_samples,))
-        for i, xi in enumerate(np.random.rand(n_samples)):
-            c = 0.0
-            for j, prob in enumerate(self.p):
-                c += prob
-                if (xi < c):
-                    out[i] = self.x[j]
-                    break
+        xi = np.random.rand(n_samples)
+        out = np.zeros_like(xi)
+        for i, c in enumerate(self.cdf()[:-1]):
+            out[xi >= c] = self.x[i]
         return out
 
     def normalize(self):
@@ -1086,6 +1085,27 @@ class Mixture(Univariate):
                       Iterable, Univariate)
         self._distribution = distribution
 
+    def cdf(self):
+        return np.insert(np.cumsum(self.probability), 0, 0.0)
+
+    def sample(self, n_samples=1, seed=None):
+        np.random.seed(seed)
+        xi = np.random.rand(n_samples)
+        idx = np.zeros_like(xi, dtype=int)
+        for i, c in enumerate(self.cdf()[:-1]):
+            idx[xi >= c] = i
+
+        out = np.zeros_like(xi)
+        for i in np.unique(idx):
+            n_dist_samples = np.count_nonzero(idx == i)
+            samples = self.distribution[i].sample(n_dist_samples)
+            out[idx == i] = samples
+        return out
+
+    def normalize(self):
+        norm = sum(self.probability)
+        self.probability = [val / norm for val in self.probability]
+
     def to_xml_element(self, element_name):
         """Return XML representation of the mixture distribution
 

From 2f22474aea252d2bdff2fecd5ef7e17aa31bba8f Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Wed, 6 Apr 2022 10:32:39 -0500
Subject: [PATCH 008/119] Adding simple test for normal distribution

---
 tests/unit_tests/test_stats.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index 51a561bd3..7bf67c1fa 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -65,6 +65,7 @@ def test_uniform():
     assert t.p == [1/(b-a), 1/(b-a)]
     assert t.interpolation == 'histogram'
 
+
 def test_powerlaw():
     a, b, n = 10.0, 20.0, 2.0
     d = openmc.stats.PowerLaw(a, b, n)
@@ -76,6 +77,7 @@ def test_powerlaw():
     assert d.n == n
     assert len(d) == 3
 
+
 def test_maxwell():
     theta = 1.2895e6
     d = openmc.stats.Maxwell(theta)
@@ -264,6 +266,18 @@ def test_normal():
     assert d.std_dev == pytest.approx(std_dev)
     assert len(d) == 2
 
+    # sample normal distribution
+    n_samples = 10000
+    samples = d.sample(n_samples, seed=100)
+    samples = np.abs(samples - mean)
+    within_1_sigma = np.count_nonzero(samples < std_dev)
+    assert within_1_sigma / n_samples >= 0.68
+    within_2_sigma = np.count_nonzero(samples < 2*std_dev)
+    assert within_2_sigma / n_samples >= 0.95
+    within_3_sigma = np.count_nonzero(samples < 3*std_dev)
+    assert within_3_sigma / n_samples >= 0.99
+
+
 def test_muir():
     mean = 10.0
     mass = 5.0

From 2c74dcf336f135a11649391616bb9741aa139ee3 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Wed, 6 Apr 2022 10:35:46 -0500
Subject: [PATCH 009/119] Adding similar test for Muir distribution

---
 openmc/stats/univariate.py     |  7 +++++--
 tests/unit_tests/test_stats.py | 11 +++++++++++
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 0e6b4ae61..4f2fbf66c 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -764,11 +764,14 @@ class Muir(Univariate):
         cv.check_greater_than('Muir kt', kt, 0.0)
         self._kt = kt
 
+    @property
+    def std_dev(self):
+        return np.sqrt(4.*self.e0*self.kt/self.m_rat)
+
     def sample(self, n_samples=1, seed=None):
         # https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-05411-MS
         np.random.seed(seed)
-        sigma = np.sqrt(4.*self.e0*self.kt/self.m_rat)
-        return np.random.normal(self.e0, sigma, n_samples)
+        return np.random.normal(self.e0, self.std_dev, n_samples)
 
     def to_xml_element(self, element_name):
         """Return XML representation of the Watt distribution
diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index 7bf67c1fa..532936e42 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -292,3 +292,14 @@ def test_muir():
     assert d.m_rat == pytest.approx(mass)
     assert d.kt == pytest.approx(temp)
     assert len(d) == 3
+
+    # sample normal distribution
+    n_samples = 10000
+    samples = d.sample(n_samples, seed=100)
+    samples = np.abs(samples - mean)
+    within_1_sigma = np.count_nonzero(samples < d.std_dev)
+    assert within_1_sigma / n_samples >= 0.68
+    within_2_sigma = np.count_nonzero(samples < 2*d.std_dev)
+    assert within_2_sigma / n_samples >= 0.95
+    within_3_sigma = np.count_nonzero(samples < 3*d.std_dev)
+    assert within_3_sigma / n_samples >= 0.99

From 12b8a0802f7579ca1da24a7d2a0ba6bebdad6b3f Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 2 Jun 2022 23:42:06 -0500
Subject: [PATCH 010/119] Updating masks and adding some comments for clarity

---
 openmc/stats/univariate.py | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 4f2fbf66c..120dc62b6 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -897,6 +897,10 @@ class Tabular(Univariate):
         return np.cumsum(c)
 
     def sample(self, n_samples=1, seed=None):
+        if not self.interpolation in ('histogram', 'linear-linear'):
+            raise NotImplementedError('Can only sample tabular distributions '
+                                      'using histogram or '
+                                      'linear-linear interpolation')
         np.random.seed(seed)
         xi = np.random.rand(n_samples)
         cdf = self.cdf()
@@ -905,7 +909,7 @@ class Tabular(Univariate):
         # sampled values
         c_i = np.full(n_samples, cdf[0])
         cdf_idx = np.zeros((n_samples,), dtype=int)
-        for i, val in enumerate(cdf):
+        for i, val in enumerate(cdf[:-1]):
             mask = xi > val
             c_i[mask] = val
             cdf_idx[mask] = i
@@ -916,13 +920,17 @@ class Tabular(Univariate):
         x_i = np.array([self.x[i] for i in cdf_idx])
         p_i = np.array([self.p[i] for i in cdf_idx])
 
+        # TODO: check that probability doesn't exceed the last value
+
         if self.interpolation == 'histogram':
-            # mask where probability
+            # mask where probability is greater than zero
             pos_mask = p_i > 0.0
+            # probabilities greater than zero are set proportional to the
+            # position of the random numebers in relation to the cdf value
             p_i[pos_mask] = x_i[pos_mask] + (xi[pos_mask] - c_i[pos_mask]) \
                            / p_i[pos_mask]
-            neg_mask = np.invert(pos_mask)
-            p_i[neg_mask] = x_i[neg_mask]
+            # probabilities smaller than zero are set to the random number value
+            p_i[~pos_mask] = x_i[~pos_mask]
             return p_i
         elif self.interpolation == 'linear-linear':
             # get variable and probability values for the
@@ -935,10 +943,10 @@ class Tabular(Univariate):
             zero = m == 0.0
             m[zero] = x_i[zero] + (xi[zero] - c_i[zero]) / p_i[zero]
             # set values for non-zero slope
-            non_zero = np.invert(zero)
+            non_zero = ~zero
             quad = np.power(p_i[non_zero], 2) + 2. * m[non_zero] * (xi[non_zero] - c_i[non_zero])
             quad[quad < 0.0] = 0.0
-            m[non_zero] = x_i[non_zero] +  (np.sqrt(quad) - p_i) / m[non_zero]
+            m[non_zero] = x_i[non_zero] +  (np.sqrt(quad) - p_i[non_zero]) / m[non_zero]
             return m
 
     def to_xml_element(self, element_name):

From 94c91cc6593fa6f61816e06b169dd6c82995bb19 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 2 Jun 2022 23:42:24 -0500
Subject: [PATCH 011/119] Adding more mean value tests for sampling
 distributions

---
 tests/unit_tests/test_stats.py | 84 +++++++++++++++++++++++++++++++++-
 1 file changed, 83 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index 532936e42..a3b5cfafb 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -253,6 +253,88 @@ def test_point():
     d = openmc.stats.Point.from_xml_element(elem)
     assert d.xyz == pytest.approx(p)
 
+
+def test_discrete():
+
+    vals = np.array([1.0, 2.0, 3.0])
+    probs = np.array([0.1, 0.7, 0.2])
+
+    exp_mean = (vals * probs).sum()
+
+    d = openmc.stats.Discrete(vals, probs)
+
+    # sample discrete distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    # check that the mean of the samples is close to the true mean
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
+def test_uniform():
+
+    lower = 1.1
+    upper = 23.3
+
+    exp_mean = 0.5 * (lower + upper)
+
+    d = openmc.stats.Uniform(lower, upper)
+
+    # sample the uniform distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
+def test_power_law():
+
+    lower = 0.0
+    upper = 1.0
+    exponent = 2.0
+
+    d = openmc.stats.PowerLaw(lower, upper, exponent)
+
+    exp_mean = (exponent + 1) / (exponent + 2)
+
+    # sample power law distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
+def test_maxwell():
+    theta = 1000
+
+    exp_mean = 0
+
+    d = openmc.stats.Maxwell(theta)
+
+    exp_mean = 3/2 * theta
+
+    # sample maxwell distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+def test_watt():
+
+    a = 10
+    b = 20
+
+    d = openmc.stats.Watt(a, b)
+
+    # mean value form adapted from
+    # "Prompt-fission-neutron average energy for 238U(n, f ) from
+    # threshold to 200 MeV" Ethvignot et. al.
+    # https://doi.org/10.1016/j.physletb.2003.09.048
+    exp_mean = 3/2 * a + a**2 * b / 4
+
+    # sample Watt distribution
+    n_samples = 100_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
+
 def test_normal():
     mean = 10.0
     std_dev = 2.0
@@ -293,7 +375,7 @@ def test_muir():
     assert d.kt == pytest.approx(temp)
     assert len(d) == 3
 
-    # sample normal distribution
+    # sample muir distribution
     n_samples = 10000
     samples = d.sample(n_samples, seed=100)
     samples = np.abs(samples - mean)

From e030b748360c833f63fe38a760f89b3ce03e396e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Jun 2022 17:28:33 +0100
Subject: [PATCH 012/119] add get_activity

---
 openmc/data/data.py | 3565 +++++++++++++++++++++++++++++++++++++++++++
 openmc/material.py  |   16 +
 2 files changed, 3581 insertions(+)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index a1d0ee1dc..48a98dedd 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -177,6 +177,3571 @@ ATOMIC_SYMBOL = {0: 'n', 1: 'H', 2: 'He', 3: 'Li', 4: 'Be', 5: 'B', 6: 'C',
                  118: 'Og'}
 ATOMIC_NUMBER = {value: key for key, value in ATOMIC_SYMBOL.items()}
 
+# Half life values are from ENDF/B VII.1 and have units of seconds
+HALF_LIFE = {
+    "H3": 388789600.0,
+    "H4": 9.90652e-23,
+    "H5": 7.99473e-23,
+    "H6": 2.84812e-22,
+    "H7": 2.3e-23,
+    "He5": 7.595e-22,
+    "He6": 0.8067,
+    "He7": 3.038e-21,
+    "He8": 0.1191,
+    "He9": 7e-21,
+    "He10": 1.519e-21,
+    "Li4": 7.55721e-23,
+    "Li5": 3.06868e-22,
+    "Li8": 0.838,
+    "Li9": 0.1783,
+    "Li10": 2e-21,
+    "Li11": 0.00859,
+    "Li12": 1e-08,
+    "Be5": 1e-09,
+    "Be6": 4.95326e-21,
+    "Be8": 8.18132e-17,
+    "Be10": 47652000000000.0,
+    "Be11": 13.81,
+    "Be12": 0.0213,
+    "Be13": 2.7e-21,
+    "Be14": 0.00435,
+    "Be15": 2e-07,
+    "Be16": 2e-07,
+    "B6": 1e-09,
+    "B7": 3.255e-22,
+    "B8": 0.77,
+    "B9": 8.43888e-19,
+    "B12": 0.0202,
+    "B13": 0.01736,
+    "B14": 0.0125,
+    "B15": 0.00993,
+    "B16": 1.9e-10,
+    "B17": 0.00508,
+    "B18": 2.6e-08,
+    "B19": 0.00292,
+    "C8": 1.9813e-21,
+    "C9": 0.1265,
+    "C10": 19.29,
+    "C11": 1223.1,
+    "C14": 179878000000.0,
+    "C15": 2.449,
+    "C16": 0.747,
+    "C17": 0.193,
+    "C18": 0.092,
+    "C19": 0.049,
+    "C20": 0.0145,
+    "C21": 3e-08,
+    "C22": 0.0062,
+    "N10": 2e-22,
+    "N11": 3.12742e-22,
+    "N12": 0.011,
+    "N13": 597.9,
+    "N16": 7.13,
+    "N17": 4.171,
+    "N18": 0.624,
+    "N19": 0.271,
+    "N20": 0.13,
+    "N21": 0.085,
+    "N22": 0.024,
+    "N23": 0.0145,
+    "N24": 5.2e-08,
+    "N25": 2.6e-07,
+    "O12": 1.13925e-21,
+    "O13": 0.00858,
+    "O14": 70.606,
+    "O15": 122.24,
+    "O19": 26.88,
+    "O20": 13.51,
+    "O21": 3.42,
+    "O22": 2.25,
+    "O23": 0.0905,
+    "O24": 0.065,
+    "O25": 5e-08,
+    "O26": 4e-08,
+    "O27": 2.6e-07,
+    "O28": 1e-07,
+    "F14": 5.0007e-22,
+    "F15": 4.557e-22,
+    "F16": 1.13925e-20,
+    "F17": 64.49,
+    "F18": 6586.2,
+    "F20": 11.163,
+    "F21": 4.158,
+    "F22": 4.23,
+    "F23": 2.23,
+    "F24": 0.39,
+    "F25": 0.05,
+    "F26": 0.0096,
+    "F27": 0.005,
+    "F28": 4e-08,
+    "F29": 0.0025,
+    "F30": 2.6e-07,
+    "F31": 2.5e-07,
+    "Ne16": 3.73524e-21,
+    "Ne17": 0.1092,
+    "Ne18": 1.672,
+    "Ne19": 17.22,
+    "Ne23": 37.24,
+    "Ne24": 202.8,
+    "Ne25": 0.602,
+    "Ne26": 0.197,
+    "Ne27": 0.032,
+    "Ne28": 0.0189,
+    "Ne29": 0.0148,
+    "Ne30": 0.0073,
+    "Ne31": 0.0034,
+    "Ne32": 0.0035,
+    "Ne33": 1.8e-07,
+    "Ne34": 6e-08,
+    "Na18": 1.3e-21,
+    "Na19": 4e-08,
+    "Na20": 0.4479,
+    "Na21": 22.49,
+    "Na22": 82134970.0,
+    "Na24": 53989.2,
+    "Na24_m1": 0.02018,
+    "Na25": 59.1,
+    "Na26": 1.077,
+    "Na27": 0.301,
+    "Na28": 0.0305,
+    "Na29": 0.0449,
+    "Na30": 0.048,
+    "Na31": 0.017,
+    "Na32": 0.0132,
+    "Na33": 0.008,
+    "Na34": 0.0055,
+    "Na35": 0.0015,
+    "Na36": 1.8e-07,
+    "Na37": 6e-08,
+    "Mg19": 4e-12,
+    "Mg20": 0.0908,
+    "Mg21": 0.122,
+    "Mg22": 3.8755,
+    "Mg23": 11.317,
+    "Mg27": 567.48,
+    "Mg28": 75294.0,
+    "Mg29": 1.3,
+    "Mg30": 0.335,
+    "Mg31": 0.232,
+    "Mg32": 0.086,
+    "Mg33": 0.0905,
+    "Mg34": 0.02,
+    "Mg35": 0.07,
+    "Mg36": 0.0039,
+    "Mg37": 2.6e-07,
+    "Mg38": 2.6e-07,
+    "Mg39": 1.8e-07,
+    "Mg40": 1.7e-07,
+    "Al21": 3.5e-08,
+    "Al22": 0.059,
+    "Al23": 0.47,
+    "Al24": 2.053,
+    "Al24_m1": 0.13,
+    "Al25": 7.183,
+    "Al26": 22626800000000.0,
+    "Al26_m1": 6.3452,
+    "Al28": 134.484,
+    "Al29": 393.6,
+    "Al30": 3.62,
+    "Al31": 0.644,
+    "Al32": 0.033,
+    "Al33": 0.0417,
+    "Al34": 0.042,
+    "Al35": 0.0386,
+    "Al36": 0.09,
+    "Al37": 0.0107,
+    "Al38": 0.0076,
+    "Al39": 7.6e-06,
+    "Al40": 2.6e-07,
+    "Al41": 2.6e-07,
+    "Al42": 1.7e-07,
+    "Si22": 0.029,
+    "Si23": 0.0423,
+    "Si24": 0.14,
+    "Si25": 0.22,
+    "Si26": 2.234,
+    "Si27": 4.16,
+    "Si31": 9438.0,
+    "Si32": 4828310000.0,
+    "Si33": 6.11,
+    "Si34": 2.77,
+    "Si35": 0.78,
+    "Si36": 0.45,
+    "Si37": 0.09,
+    "Si38": 1e-06,
+    "Si39": 0.0475,
+    "Si40": 0.033,
+    "Si41": 0.02,
+    "Si42": 0.0125,
+    "Si43": 6e-08,
+    "Si44": 3.6e-07,
+    "P24": 0.0074,
+    "P25": 3e-08,
+    "P26": 0.0437,
+    "P27": 0.26,
+    "P28": 0.2703,
+    "P29": 4.142,
+    "P30": 149.88,
+    "P32": 1232323.0,
+    "P33": 2189376.0,
+    "P34": 12.43,
+    "P35": 47.3,
+    "P36": 5.6,
+    "P37": 2.31,
+    "P38": 0.64,
+    "P39": 0.28,
+    "P40": 0.125,
+    "P41": 0.1,
+    "P42": 0.0485,
+    "P43": 0.0365,
+    "P44": 0.0185,
+    "P45": 2e-07,
+    "P46": 2e-07,
+    "S26": 0.01,
+    "S27": 0.0155,
+    "S28": 0.125,
+    "S29": 0.187,
+    "S30": 1.178,
+    "S31": 2.572,
+    "S35": 7560864.0,
+    "S37": 303.0,
+    "S38": 10218.0,
+    "S39": 11.5,
+    "S40": 8.8,
+    "S41": 1.99,
+    "S42": 1.013,
+    "S43": 0.28,
+    "S44": 0.1,
+    "S45": 0.068,
+    "S46": 0.05,
+    "S48": 2e-07,
+    "S49": 2e-07,
+    "Cl28": 0.0017,
+    "Cl29": 2e-08,
+    "Cl30": 3e-08,
+    "Cl31": 0.15,
+    "Cl32": 0.298,
+    "Cl33": 2.511,
+    "Cl34": 1.5264,
+    "Cl34_m1": 1920.0,
+    "Cl36": 9498840000000.0,
+    "Cl38": 2233.8,
+    "Cl38_m1": 0.715,
+    "Cl39": 3336.0,
+    "Cl40": 81.0,
+    "Cl41": 38.4,
+    "Cl42": 6.8,
+    "Cl43": 3.13,
+    "Cl44": 0.56,
+    "Cl45": 0.413,
+    "Cl46": 0.232,
+    "Cl47": 0.101,
+    "Cl48": 2e-07,
+    "Cl49": 1.7e-07,
+    "Cl50": 0.02,
+    "Cl51": 2e-07,
+    "Ar30": 2e-08,
+    "Ar31": 0.0151,
+    "Ar32": 0.098,
+    "Ar33": 0.173,
+    "Ar34": 0.8445,
+    "Ar35": 1.775,
+    "Ar37": 3027456.0,
+    "Ar39": 8488990000.0,
+    "Ar41": 6576.6,
+    "Ar42": 1038250000.0,
+    "Ar43": 322.2,
+    "Ar44": 712.2,
+    "Ar45": 21.48,
+    "Ar46": 8.4,
+    "Ar47": 1.23,
+    "Ar48": 0.475,
+    "Ar49": 0.17,
+    "Ar50": 0.085,
+    "Ar51": 2e-07,
+    "Ar52": 0.01,
+    "Ar53": 0.003,
+    "K32": 0.0033,
+    "K33": 2.5e-08,
+    "K34": 2.5e-08,
+    "K35": 0.178,
+    "K36": 0.342,
+    "K37": 1.226,
+    "K38": 458.16,
+    "K38_m1": 0.924,
+    "K40": 3.93839e16,
+    "K42": 44496.0,
+    "K43": 80280.0,
+    "K44": 1327.8,
+    "K45": 1068.6,
+    "K46": 105.0,
+    "K47": 17.5,
+    "K48": 6.8,
+    "K49": 1.26,
+    "K50": 0.472,
+    "K51": 0.365,
+    "K52": 0.105,
+    "K53": 0.03,
+    "K54": 0.01,
+    "K55": 0.003,
+    "Ca34": 3.5e-08,
+    "Ca35": 0.0257,
+    "Ca36": 0.102,
+    "Ca37": 0.1811,
+    "Ca38": 0.44,
+    "Ca39": 0.8596,
+    "Ca41": 3218880000000.0,
+    "Ca45": 14049500.0,
+    "Ca47": 391910.4,
+    "Ca48": 7.25824e26,
+    "Ca49": 523.08,
+    "Ca50": 13.9,
+    "Ca51": 10.0,
+    "Ca52": 4.6,
+    "Ca53": 0.09,
+    "Ca54": 0.086,
+    "Ca55": 0.022,
+    "Ca56": 0.01,
+    "Ca57": 0.005,
+    "Sc36": 0.0088,
+    "Sc37": 0.056,
+    "Sc38": 0.0423,
+    "Sc39": 3e-07,
+    "Sc40": 0.1823,
+    "Sc41": 0.5963,
+    "Sc42": 0.6808,
+    "Sc42_m1": 62.0,
+    "Sc43": 14007.6,
+    "Sc44": 14292.0,
+    "Sc44_m1": 210996.0,
+    "Sc45_m1": 0.318,
+    "Sc46": 7239456.0,
+    "Sc46_m1": 18.75,
+    "Sc47": 289370.9,
+    "Sc48": 157212.0,
+    "Sc49": 3430.8,
+    "Sc50": 102.5,
+    "Sc50_m1": 0.35,
+    "Sc51": 12.4,
+    "Sc52": 8.2,
+    "Sc53": 3.0,
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+    "Cf245": 2700.0,
+    "Cf246": 128520.0,
+    "Cf247": 11196.0,
+    "Cf248": 28814400.0,
+    "Cf249": 11076700000.0,
+    "Cf250": 412773400.0,
+    "Cf251": 28338700000.0,
+    "Cf252": 83468070.0,
+    "Cf253": 1538784.0,
+    "Cf254": 5227200.0,
+    "Cf255": 5100.0,
+    "Cf256": 738.0,
+    "Es240": 1.0,
+    "Es241": 8.5,
+    "Es242": 13.5,
+    "Es243": 21.0,
+    "Es244": 37.0,
+    "Es245": 66.0,
+    "Es246": 462.0,
+    "Es247": 273.0,
+    "Es247_m1": 54000000.0,
+    "Es248": 1620.0,
+    "Es249": 6132.0,
+    "Es250": 30960.0,
+    "Es250_m1": 7992.0,
+    "Es251": 118800.0,
+    "Es252": 40754880.0,
+    "Es253": 1768608.0,
+    "Es254": 23820480.0,
+    "Es254_m1": 141479.9,
+    "Es255": 3438720.0,
+    "Es256": 1524.0,
+    "Es256_m1": 27360.0,
+    "Es257": 665280.0,
+    "Es258": 180.0,
+    "Fm242": 0.0008,
+    "Fm243": 0.2,
+    "Fm244": 0.0033,
+    "Fm245": 4.2,
+    "Fm246": 1.1,
+    "Fm247": 29.0,
+    "Fm248": 36.0,
+    "Fm249": 156.0,
+    "Fm250": 1800.0,
+    "Fm250_m1": 1.8,
+    "Fm251": 19080.0,
+    "Fm252": 91404.0,
+    "Fm253": 259200.0,
+    "Fm254": 11664.0,
+    "Fm255": 72252.0,
+    "Fm256": 9456.0,
+    "Fm257": 8683200.0,
+    "Fm258": 0.00037,
+    "Fm259": 1.5,
+    "Fm260": 0.004,
+    "Md245": 0.0009,
+    "Md245_m1": 0.39,
+    "Md246": 0.9,
+    "Md247": 1.12,
+    "Md247_m1": 0.26,
+    "Md248": 7.0,
+    "Md249": 24.0,
+    "Md249_m1": 1.9,
+    "Md250": 27.5,
+    "Md251": 240.0,
+    "Md252": 138.0,
+    "Md253": 630.0,
+    "Md254": 1680.0,
+    "Md254_m1": 1680.0,
+    "Md255": 1620.0,
+    "Md256": 4620.0,
+    "Md257": 19872.0,
+    "Md258": 4449600.0,
+    "Md258_m1": 3420.0,
+    "Md259": 5760.0,
+    "Md260": 2747520.0,
+    "Md261": 2400.0,
+    "No250": 4.35e-06,
+    "No251": 0.8,
+    "No251_m1": 1.02,
+    "No252": 2.44,
+    "No253": 97.2,
+    "No254": 51.0,
+    "No254_m1": 0.28,
+    "No255": 186.0,
+    "No256": 2.91,
+    "No257": 25.0,
+    "No258": 0.0012,
+    "No259": 3480.0,
+    "No260": 0.106,
+    "No261": 160000.0,
+    "No262": 0.005,
+    "Lr251": 1.341,
+    "Lr252": 0.38,
+    "Lr253": 0.575,
+    "Lr253_m1": 1.535,
+    "Lr254": 13.0,
+    "Lr255": 22.0,
+    "Lr255_m1": 2.53,
+    "Lr256": 27.0,
+    "Lr257": 0.646,
+    "Lr258": 4.1,
+    "Lr259": 6.2,
+    "Lr260": 180.0,
+    "Lr261": 2340.0,
+    "Lr262": 14400.0,
+    "Lr263": 18000.0,
+    "Rf253": 5.15e-05,
+    "Rf254": 2.3e-05,
+    "Rf255": 1.68,
+    "Rf256": 0.0064,
+    "Rf257": 4.7,
+    "Rf257_m1": 3.9,
+    "Rf258": 0.012,
+    "Rf259": 3.2,
+    "Rf260": 0.021,
+    "Rf261": 65.0,
+    "Rf261_m1": 81.0,
+    "Rf262": 2.3,
+    "Rf263": 600.0,
+    "Rf264": 3600.0,
+    "Rf265": 1.0,
+    "Db255": 1.7,
+    "Db256": 1.7,
+    "Db257": 1.52,
+    "Db257_m1": 0.78,
+    "Db258": 4.0,
+    "Db258_m1": 20.0,
+    "Db259": 0.51,
+    "Db260": 1.52,
+    "Db261": 1.8,
+    "Db262": 35.0,
+    "Db263": 28.5,
+    "Db264": 180.0,
+    "Db265": 900.0,
+    "Sg258": 0.0032,
+    "Sg259": 0.555,
+    "Sg260": 0.0036,
+    "Sg261": 0.23,
+    "Sg262": 0.0079,
+    "Sg263": 1.0,
+    "Sg263_m1": 0.12,
+    "Sg264": 0.045,
+    "Sg265": 8.0,
+    "Sg266": 25.0,
+    "Sg269": 50.0,
+    "Bh260": 0.0003,
+    "Bh261": 0.013,
+    "Bh262": 0.102,
+    "Bh262_m1": 0.022,
+    "Bh263": 0.0002,
+    "Bh264": 0.66,
+    "Bh265": 1.1,
+    "Bh266": 5.4,
+    "Bh267": 21.0,
+    "Bh269": 50.0,
+    "Hs263": 0.00355,
+    "Hs264": 0.0008,
+    "Hs265": 0.00205,
+    "Hs265_m1": 0.0003,
+    "Hs266": 0.00265,
+    "Hs267": 0.0545,
+    "Hs268": 1.2,
+    "Hs269": 12.9,
+    "Hs273": 50.0,
+    "Mt265": 120.0,
+    "Mt266": 0.0018,
+    "Mt266_m1": 0.0017,
+    "Mt267": 0.01,
+    "Mt268": 0.0225,
+    "Mt269": 0.05,
+    "Mt270": 0.00605,
+    "Mt271": 5.0,
+    "Mt273": 20.0,
+    "Ds267": 2.8e-06,
+    "Ds268": 0.0001,
+    "Ds269": 0.000268,
+    "Ds270": 0.00015,
+    "Ds270_m1": 0.009,
+    "Ds271": 0.001705,
+    "Ds271_m1": 0.0865,
+    "Ds272": 1.0,
+    "Ds273": 0.000225,
+    "Ds279_m1": 0.19,
+    "Rg272": 0.0041,
+}
+
+
 # Values here are from the Committee on Data for Science and Technology
 # (CODATA) 2018 recommendation (https://physics.nist.gov/cuu/Constants/).
 
diff --git a/openmc/material.py b/openmc/material.py
index e5c3f8e4b..5952162f6 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,6 +3,7 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
+import math
 import re
 import warnings
 from xml.etree import ElementTree as ET
@@ -705,6 +706,21 @@ class Material(IDManagerMixin):
     def make_isotropic_in_lab(self):
         self.isotropic = [x.name for x in self._nuclides]
 
+
+    def get_activity(self):
+        """Returns the total activity of the material in Becquerels."""
+
+        atoms_per_barn_cm2 = self.get_nuclide_atom_densities()
+        total_activity = 0
+        for key, value in atoms_per_barn_cm2.items():
+            if key in openmc.data.HALF_LIFE.keys():
+                atoms = value[1] * self.volume * 1e24
+                activity = 0.693 * atoms / openmc.data.HALF_LIFE[key]
+                print('activity', activity)
+                total_activity += activity
+
+        return total_activity
+
     def get_elements(self):
         """Returns all elements in the material
 

From 5bf60560afa3f7036a928395fd26bded949bfffb Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Jun 2022 17:31:30 +0100
Subject: [PATCH 013/119] removed import math

---
 openmc/material.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openmc/material.py b/openmc/material.py
index 5952162f6..fc1fd1646 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,7 +3,6 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
-import math
 import re
 import warnings
 from xml.etree import ElementTree as ET

From 47e242551d23a2285e3353b8a91b1efd91c66740 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 8 Jun 2022 17:34:10 +0100
Subject: [PATCH 014/119] using math to get ln(2)

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

diff --git a/openmc/material.py b/openmc/material.py
index fc1fd1646..b62ba4142 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,6 +3,7 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
+import math
 import re
 import warnings
 from xml.etree import ElementTree as ET
@@ -714,7 +715,7 @@ class Material(IDManagerMixin):
         for key, value in atoms_per_barn_cm2.items():
             if key in openmc.data.HALF_LIFE.keys():
                 atoms = value[1] * self.volume * 1e24
-                activity = 0.693 * atoms / openmc.data.HALF_LIFE[key]
+                activity = math.log(2) * atoms / openmc.data.HALF_LIFE[key]
                 print('activity', activity)
                 total_activity += activity
 

From a4661fdca84807af15e19f125f4db30bcbeaca98 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Wed, 8 Jun 2022 17:39:40 +0100
Subject: [PATCH 015/119] [skip ci] removed print statement

---
 openmc/material.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openmc/material.py b/openmc/material.py
index b62ba4142..a9f5afac8 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -716,7 +716,6 @@ class Material(IDManagerMixin):
             if key in openmc.data.HALF_LIFE.keys():
                 atoms = value[1] * self.volume * 1e24
                 activity = math.log(2) * atoms / openmc.data.HALF_LIFE[key]
-                print('activity', activity)
                 total_activity += activity
 
         return total_activity

From 9dc84fdb1859c73886b1f7596f30d3f6b9fa2cc9 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 9 Jun 2022 01:17:46 -0500
Subject: [PATCH 016/119] Always normalize distributions when sampling. Adding
 normalization method for tabular.

---
 openmc/stats/univariate.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 120dc62b6..df1a72150 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -890,12 +890,17 @@ class Tabular(Univariate):
         c = np.zeros_like(self.x)
         x = np.asarray(self.x)
         p = np.asarray(self.p)
+
         if self.interpolation == 'histogram':
             c[1:] = p[:-1] * np.diff(x)
         elif self.interpolation == 'linear-linear':
             c[1:] = 0.5 * (p[0:-1] + p[1:]) * np.diff(x)
+
         return np.cumsum(c)
 
+    def normalize(self):
+        self.p = self.p / self.cdf().max()
+
     def sample(self, n_samples=1, seed=None):
         if not self.interpolation in ('histogram', 'linear-linear'):
             raise NotImplementedError('Can only sample tabular distributions '
@@ -904,6 +909,9 @@ class Tabular(Univariate):
         np.random.seed(seed)
         xi = np.random.rand(n_samples)
         cdf = self.cdf()
+        cdf /= cdf.max()
+        # always use normalized probabilities when sampling
+        p = self.p / cdf.max()
 
         # get CDF bins that are above the
         # sampled values
@@ -918,7 +926,7 @@ class Tabular(Univariate):
         # the random number is less than the next cdf
         # entry
         x_i = np.array([self.x[i] for i in cdf_idx])
-        p_i = np.array([self.p[i] for i in cdf_idx])
+        p_i = np.array([p[i] for i in cdf_idx])
 
         # TODO: check that probability doesn't exceed the last value
 
@@ -936,7 +944,7 @@ class Tabular(Univariate):
             # get variable and probability values for the
             # next entry
             x_i1 = np.array([self.x[i+1] for i in cdf_idx])
-            p_i1 = np.array([self.p[i+1] for i in cdf_idx])
+            p_i1 = np.array([p[i+1] for i in cdf_idx])
             # compute slope between entries
             m = (p_i1 - p_i) / (x_i1 - x_i)
             # set values for zero slope
@@ -944,9 +952,9 @@ class Tabular(Univariate):
             m[zero] = x_i[zero] + (xi[zero] - c_i[zero]) / p_i[zero]
             # set values for non-zero slope
             non_zero = ~zero
-            quad = np.power(p_i[non_zero], 2) + 2. * m[non_zero] * (xi[non_zero] - c_i[non_zero])
+            quad = np.power(p_i[non_zero], 2) + 2.0 * m[non_zero] * (xi[non_zero] - c_i[non_zero])
             quad[quad < 0.0] = 0.0
-            m[non_zero] = x_i[non_zero] +  (np.sqrt(quad) - p_i[non_zero]) / m[non_zero]
+            m[non_zero] = x_i[non_zero] + (np.sqrt(quad) - p_i[non_zero]) / m[non_zero]
             return m
 
     def to_xml_element(self, element_name):

From 85b6566fd74c9c082ee943dd8d64a8138a119259 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 9 Jun 2022 01:18:17 -0500
Subject: [PATCH 017/119] Updating tabular means. Removing re-defined functions

---
 tests/unit_tests/test_stats.py | 174 +++++++++++++++++----------------
 1 file changed, 88 insertions(+), 86 deletions(-)

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index a3b5cfafb..f847970c0 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -26,6 +26,20 @@ def test_discrete():
     assert d2.p == [1.0]
     assert len(d2) == 1
 
+    vals = np.array([1.0, 2.0, 3.0])
+    probs = np.array([0.1, 0.7, 0.2])
+
+    exp_mean = (vals * probs).sum()
+
+    d3 = openmc.stats.Discrete(vals, probs)
+
+    # sample discrete distribution
+    n_samples = 1_000_000
+    samples = d3.sample(n_samples, seed=100)
+    # check that the mean of the samples is close to the true mean
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
 
 def test_merge_discrete():
     x1 = [0.0, 1.0, 10.0]
@@ -65,9 +79,14 @@ def test_uniform():
     assert t.p == [1/(b-a), 1/(b-a)]
     assert t.interpolation == 'histogram'
 
+    exp_mean = 0.5 * (a + b)
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
 
 def test_powerlaw():
-    a, b, n = 10.0, 20.0, 2.0
+    a, b, n = 10.0, 100.0, 2.0
     d = openmc.stats.PowerLaw(a, b, n)
     elem = d.to_xml_element('distribution')
 
@@ -77,6 +96,13 @@ def test_powerlaw():
     assert d.n == n
     assert len(d) == 3
 
+    exp_mean = 100.0 * (n+1) / (n+2)
+
+    # sample power law distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
 
 def test_maxwell():
     theta = 1.2895e6
@@ -87,6 +113,14 @@ def test_maxwell():
     assert d.theta == theta
     assert len(d) == 1
 
+    exp_mean = 3/2 * theta
+
+    # sample maxwell distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+
+
 
 def test_watt():
     a, b = 0.965e6, 2.29e-6
@@ -98,19 +132,68 @@ def test_watt():
     assert d.b == b
     assert len(d) == 2
 
+    d = openmc.stats.Watt(a, b)
+
+    # mean value form adapted from
+    # "Prompt-fission-neutron average energy for 238U(n, f ) from
+    # threshold to 200 MeV" Ethvignot et. al.
+    # https://doi.org/10.1016/j.physletb.2003.09.048
+    exp_mean = 3/2 * a + a**2 * b / 4
+
+    # sample Watt distribution
+    n_samples = 1_000_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(exp_mean, rel=1e-03)
+
 
 def test_tabular():
-    x = [0.0, 5.0, 7.0]
-    p = [0.1, 0.2, 0.05]
+    x = np.array([0.0, 5.0, 7.0])
+    p = np.array([0.1, 0.2, 0.05])
     d = openmc.stats.Tabular(x, p, 'linear-linear')
     elem = d.to_xml_element('distribution')
 
     d = openmc.stats.Tabular.from_xml_element(elem)
-    assert d.x == x
-    assert d.p == p
+    assert all(d.x == x)
+    assert all(d.p == p)
     assert d.interpolation == 'linear-linear'
     assert len(d) == len(x)
 
+    # test linear-lienar sampling
+    d = openmc.stats.Tabular(x, p)
+
+    # compute the expected value (mean) of the
+    # piecewise pdf
+    mean = 0.0
+    d.normalize()
+    for i in range(1, len(x)):
+        y_min = d.p[i-1]
+        y_max = d.p[i]
+        x_min = d.x[i-1]
+        x_max = d.x[i]
+
+        m = (y_max - y_min) / (x_max - x_min)
+
+        exp_val = (1./3.) * m * (x_max**3 - x_min**3)
+        exp_val += 0.5 * m * x_min * (x_min**2 - x_max**2)
+        exp_val += 0.5 * y_min * (x_max**2 - x_min**2)
+
+        mean += exp_val
+
+    n_samples = 100_000
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(mean, rel=1e-03)
+
+    # test histogram sampling
+    d = openmc.stats.Tabular(x, p, interpolation='histogram')
+    d.normalize()
+
+    mean = 0.5 * (x[:-1] + x[1:])
+    mean *= np.diff(d.cdf())
+    mean = sum(mean)
+
+    samples = d.sample(n_samples, seed=100)
+    assert samples.mean() == pytest.approx(mean, rel=1e-03)
+
 
 def test_legendre():
     # Pu239 elastic scattering at 100 keV
@@ -254,87 +337,6 @@ def test_point():
     assert d.xyz == pytest.approx(p)
 
 
-def test_discrete():
-
-    vals = np.array([1.0, 2.0, 3.0])
-    probs = np.array([0.1, 0.7, 0.2])
-
-    exp_mean = (vals * probs).sum()
-
-    d = openmc.stats.Discrete(vals, probs)
-
-    # sample discrete distribution
-    n_samples = 1_000_000
-    samples = d.sample(n_samples, seed=100)
-    # check that the mean of the samples is close to the true mean
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
-
-
-def test_uniform():
-
-    lower = 1.1
-    upper = 23.3
-
-    exp_mean = 0.5 * (lower + upper)
-
-    d = openmc.stats.Uniform(lower, upper)
-
-    # sample the uniform distribution
-    n_samples = 1_000_000
-    samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
-
-
-def test_power_law():
-
-    lower = 0.0
-    upper = 1.0
-    exponent = 2.0
-
-    d = openmc.stats.PowerLaw(lower, upper, exponent)
-
-    exp_mean = (exponent + 1) / (exponent + 2)
-
-    # sample power law distribution
-    n_samples = 1_000_000
-    samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
-
-
-def test_maxwell():
-    theta = 1000
-
-    exp_mean = 0
-
-    d = openmc.stats.Maxwell(theta)
-
-    exp_mean = 3/2 * theta
-
-    # sample maxwell distribution
-    n_samples = 1_000_000
-    samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
-
-def test_watt():
-
-    a = 10
-    b = 20
-
-    d = openmc.stats.Watt(a, b)
-
-    # mean value form adapted from
-    # "Prompt-fission-neutron average energy for 238U(n, f ) from
-    # threshold to 200 MeV" Ethvignot et. al.
-    # https://doi.org/10.1016/j.physletb.2003.09.048
-    exp_mean = 3/2 * a + a**2 * b / 4
-
-    # sample Watt distribution
-    n_samples = 100_000
-    samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
-
-
-
 def test_normal():
     mean = 10.0
     std_dev = 2.0

From 1e83df9dc1d6709cfcb181fb818f6e7e28bb85d0 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 9 Jun 2022 01:20:30 -0500
Subject: [PATCH 018/119] Removing re-defined distribution

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

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index f847970c0..8e38a7b48 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -132,8 +132,6 @@ def test_watt():
     assert d.b == b
     assert len(d) == 2
 
-    d = openmc.stats.Watt(a, b)
-
     # mean value form adapted from
     # "Prompt-fission-neutron average energy for 238U(n, f ) from
     # threshold to 200 MeV" Ethvignot et. al.

From e1fd9959bc3aeb9d69005d5e5e971d11b441850f Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Thu, 9 Jun 2022 08:00:17 -0500
Subject: [PATCH 019/119] A little cleanup

---
 openmc/stats/univariate.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index df1a72150..d733b6193 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -566,7 +566,7 @@ class Watt(Univariate):
         w = Maxwell.sample_maxwell(self.a, n_samples)
         u = np.random.uniform(-1., 1., n_samples)
         aab = self.a * self.a * self.b
-        return w + 0.25*aab + u * np.sqrt(aab*w)
+        return w + 0.25*aab + u*np.sqrt(aab*w)
 
     def to_xml_element(self, element_name):
         """Return XML representation of the Watt distribution
@@ -769,7 +769,7 @@ class Muir(Univariate):
         return np.sqrt(4.*self.e0*self.kt/self.m_rat)
 
     def sample(self, n_samples=1, seed=None):
-        # https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-05411-MS
+        # Based on LANL report LA-05411-MS
         np.random.seed(seed)
         return np.random.normal(self.e0, self.std_dev, n_samples)
 
@@ -899,7 +899,7 @@ class Tabular(Univariate):
         return np.cumsum(c)
 
     def normalize(self):
-        self.p = self.p / self.cdf().max()
+        self.p = np.asarray(self.p) / self.cdf().max()
 
     def sample(self, n_samples=1, seed=None):
         if not self.interpolation in ('histogram', 'linear-linear'):

From 1234e0b17c4443b5602eda59125945fab610412b Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Jun 2022 14:59:28 +0100
Subject: [PATCH 020/119] review suggestions from @PaulRomano

---
 openmc/data/data.py               | 3602 +----------------------------
 openmc/data/half_life.json        | 3563 ++++++++++++++++++++++++++++
 openmc/material.py                |   36 +-
 tests/unit_tests/test_material.py |   18 +
 4 files changed, 3636 insertions(+), 3583 deletions(-)
 create mode 100644 openmc/data/half_life.json

diff --git a/openmc/data/data.py b/openmc/data/data.py
index 48a98dedd..65702f7a5 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -1,10 +1,10 @@
 import itertools
-from math import sqrt
+import json
 import os
 import re
+from math import sqrt
 from warnings import warn
 
-
 # Isotopic abundances from Meija J, Coplen T B, et al, "Isotopic compositions
 # of the elements 2013 (IUPAC Technical Report)", Pure. Appl. Chem. 88 (3),
 # pp. 293-306 (2013). The "representative isotopic abundance" values from
@@ -177,3571 +177,6 @@ ATOMIC_SYMBOL = {0: 'n', 1: 'H', 2: 'He', 3: 'Li', 4: 'Be', 5: 'B', 6: 'C',
                  118: 'Og'}
 ATOMIC_NUMBER = {value: key for key, value in ATOMIC_SYMBOL.items()}
 
-# Half life values are from ENDF/B VII.1 and have units of seconds
-HALF_LIFE = {
-    "H3": 388789600.0,
-    "H4": 9.90652e-23,
-    "H5": 7.99473e-23,
-    "H6": 2.84812e-22,
-    "H7": 2.3e-23,
-    "He5": 7.595e-22,
-    "He6": 0.8067,
-    "He7": 3.038e-21,
-    "He8": 0.1191,
-    "He9": 7e-21,
-    "He10": 1.519e-21,
-    "Li4": 7.55721e-23,
-    "Li5": 3.06868e-22,
-    "Li8": 0.838,
-    "Li9": 0.1783,
-    "Li10": 2e-21,
-    "Li11": 0.00859,
-    "Li12": 1e-08,
-    "Be5": 1e-09,
-    "Be6": 4.95326e-21,
-    "Be8": 8.18132e-17,
-    "Be10": 47652000000000.0,
-    "Be11": 13.81,
-    "Be12": 0.0213,
-    "Be13": 2.7e-21,
-    "Be14": 0.00435,
-    "Be15": 2e-07,
-    "Be16": 2e-07,
-    "B6": 1e-09,
-    "B7": 3.255e-22,
-    "B8": 0.77,
-    "B9": 8.43888e-19,
-    "B12": 0.0202,
-    "B13": 0.01736,
-    "B14": 0.0125,
-    "B15": 0.00993,
-    "B16": 1.9e-10,
-    "B17": 0.00508,
-    "B18": 2.6e-08,
-    "B19": 0.00292,
-    "C8": 1.9813e-21,
-    "C9": 0.1265,
-    "C10": 19.29,
-    "C11": 1223.1,
-    "C14": 179878000000.0,
-    "C15": 2.449,
-    "C16": 0.747,
-    "C17": 0.193,
-    "C18": 0.092,
-    "C19": 0.049,
-    "C20": 0.0145,
-    "C21": 3e-08,
-    "C22": 0.0062,
-    "N10": 2e-22,
-    "N11": 3.12742e-22,
-    "N12": 0.011,
-    "N13": 597.9,
-    "N16": 7.13,
-    "N17": 4.171,
-    "N18": 0.624,
-    "N19": 0.271,
-    "N20": 0.13,
-    "N21": 0.085,
-    "N22": 0.024,
-    "N23": 0.0145,
-    "N24": 5.2e-08,
-    "N25": 2.6e-07,
-    "O12": 1.13925e-21,
-    "O13": 0.00858,
-    "O14": 70.606,
-    "O15": 122.24,
-    "O19": 26.88,
-    "O20": 13.51,
-    "O21": 3.42,
-    "O22": 2.25,
-    "O23": 0.0905,
-    "O24": 0.065,
-    "O25": 5e-08,
-    "O26": 4e-08,
-    "O27": 2.6e-07,
-    "O28": 1e-07,
-    "F14": 5.0007e-22,
-    "F15": 4.557e-22,
-    "F16": 1.13925e-20,
-    "F17": 64.49,
-    "F18": 6586.2,
-    "F20": 11.163,
-    "F21": 4.158,
-    "F22": 4.23,
-    "F23": 2.23,
-    "F24": 0.39,
-    "F25": 0.05,
-    "F26": 0.0096,
-    "F27": 0.005,
-    "F28": 4e-08,
-    "F29": 0.0025,
-    "F30": 2.6e-07,
-    "F31": 2.5e-07,
-    "Ne16": 3.73524e-21,
-    "Ne17": 0.1092,
-    "Ne18": 1.672,
-    "Ne19": 17.22,
-    "Ne23": 37.24,
-    "Ne24": 202.8,
-    "Ne25": 0.602,
-    "Ne26": 0.197,
-    "Ne27": 0.032,
-    "Ne28": 0.0189,
-    "Ne29": 0.0148,
-    "Ne30": 0.0073,
-    "Ne31": 0.0034,
-    "Ne32": 0.0035,
-    "Ne33": 1.8e-07,
-    "Ne34": 6e-08,
-    "Na18": 1.3e-21,
-    "Na19": 4e-08,
-    "Na20": 0.4479,
-    "Na21": 22.49,
-    "Na22": 82134970.0,
-    "Na24": 53989.2,
-    "Na24_m1": 0.02018,
-    "Na25": 59.1,
-    "Na26": 1.077,
-    "Na27": 0.301,
-    "Na28": 0.0305,
-    "Na29": 0.0449,
-    "Na30": 0.048,
-    "Na31": 0.017,
-    "Na32": 0.0132,
-    "Na33": 0.008,
-    "Na34": 0.0055,
-    "Na35": 0.0015,
-    "Na36": 1.8e-07,
-    "Na37": 6e-08,
-    "Mg19": 4e-12,
-    "Mg20": 0.0908,
-    "Mg21": 0.122,
-    "Mg22": 3.8755,
-    "Mg23": 11.317,
-    "Mg27": 567.48,
-    "Mg28": 75294.0,
-    "Mg29": 1.3,
-    "Mg30": 0.335,
-    "Mg31": 0.232,
-    "Mg32": 0.086,
-    "Mg33": 0.0905,
-    "Mg34": 0.02,
-    "Mg35": 0.07,
-    "Mg36": 0.0039,
-    "Mg37": 2.6e-07,
-    "Mg38": 2.6e-07,
-    "Mg39": 1.8e-07,
-    "Mg40": 1.7e-07,
-    "Al21": 3.5e-08,
-    "Al22": 0.059,
-    "Al23": 0.47,
-    "Al24": 2.053,
-    "Al24_m1": 0.13,
-    "Al25": 7.183,
-    "Al26": 22626800000000.0,
-    "Al26_m1": 6.3452,
-    "Al28": 134.484,
-    "Al29": 393.6,
-    "Al30": 3.62,
-    "Al31": 0.644,
-    "Al32": 0.033,
-    "Al33": 0.0417,
-    "Al34": 0.042,
-    "Al35": 0.0386,
-    "Al36": 0.09,
-    "Al37": 0.0107,
-    "Al38": 0.0076,
-    "Al39": 7.6e-06,
-    "Al40": 2.6e-07,
-    "Al41": 2.6e-07,
-    "Al42": 1.7e-07,
-    "Si22": 0.029,
-    "Si23": 0.0423,
-    "Si24": 0.14,
-    "Si25": 0.22,
-    "Si26": 2.234,
-    "Si27": 4.16,
-    "Si31": 9438.0,
-    "Si32": 4828310000.0,
-    "Si33": 6.11,
-    "Si34": 2.77,
-    "Si35": 0.78,
-    "Si36": 0.45,
-    "Si37": 0.09,
-    "Si38": 1e-06,
-    "Si39": 0.0475,
-    "Si40": 0.033,
-    "Si41": 0.02,
-    "Si42": 0.0125,
-    "Si43": 6e-08,
-    "Si44": 3.6e-07,
-    "P24": 0.0074,
-    "P25": 3e-08,
-    "P26": 0.0437,
-    "P27": 0.26,
-    "P28": 0.2703,
-    "P29": 4.142,
-    "P30": 149.88,
-    "P32": 1232323.0,
-    "P33": 2189376.0,
-    "P34": 12.43,
-    "P35": 47.3,
-    "P36": 5.6,
-    "P37": 2.31,
-    "P38": 0.64,
-    "P39": 0.28,
-    "P40": 0.125,
-    "P41": 0.1,
-    "P42": 0.0485,
-    "P43": 0.0365,
-    "P44": 0.0185,
-    "P45": 2e-07,
-    "P46": 2e-07,
-    "S26": 0.01,
-    "S27": 0.0155,
-    "S28": 0.125,
-    "S29": 0.187,
-    "S30": 1.178,
-    "S31": 2.572,
-    "S35": 7560864.0,
-    "S37": 303.0,
-    "S38": 10218.0,
-    "S39": 11.5,
-    "S40": 8.8,
-    "S41": 1.99,
-    "S42": 1.013,
-    "S43": 0.28,
-    "S44": 0.1,
-    "S45": 0.068,
-    "S46": 0.05,
-    "S48": 2e-07,
-    "S49": 2e-07,
-    "Cl28": 0.0017,
-    "Cl29": 2e-08,
-    "Cl30": 3e-08,
-    "Cl31": 0.15,
-    "Cl32": 0.298,
-    "Cl33": 2.511,
-    "Cl34": 1.5264,
-    "Cl34_m1": 1920.0,
-    "Cl36": 9498840000000.0,
-    "Cl38": 2233.8,
-    "Cl38_m1": 0.715,
-    "Cl39": 3336.0,
-    "Cl40": 81.0,
-    "Cl41": 38.4,
-    "Cl42": 6.8,
-    "Cl43": 3.13,
-    "Cl44": 0.56,
-    "Cl45": 0.413,
-    "Cl46": 0.232,
-    "Cl47": 0.101,
-    "Cl48": 2e-07,
-    "Cl49": 1.7e-07,
-    "Cl50": 0.02,
-    "Cl51": 2e-07,
-    "Ar30": 2e-08,
-    "Ar31": 0.0151,
-    "Ar32": 0.098,
-    "Ar33": 0.173,
-    "Ar34": 0.8445,
-    "Ar35": 1.775,
-    "Ar37": 3027456.0,
-    "Ar39": 8488990000.0,
-    "Ar41": 6576.6,
-    "Ar42": 1038250000.0,
-    "Ar43": 322.2,
-    "Ar44": 712.2,
-    "Ar45": 21.48,
-    "Ar46": 8.4,
-    "Ar47": 1.23,
-    "Ar48": 0.475,
-    "Ar49": 0.17,
-    "Ar50": 0.085,
-    "Ar51": 2e-07,
-    "Ar52": 0.01,
-    "Ar53": 0.003,
-    "K32": 0.0033,
-    "K33": 2.5e-08,
-    "K34": 2.5e-08,
-    "K35": 0.178,
-    "K36": 0.342,
-    "K37": 1.226,
-    "K38": 458.16,
-    "K38_m1": 0.924,
-    "K40": 3.93839e16,
-    "K42": 44496.0,
-    "K43": 80280.0,
-    "K44": 1327.8,
-    "K45": 1068.6,
-    "K46": 105.0,
-    "K47": 17.5,
-    "K48": 6.8,
-    "K49": 1.26,
-    "K50": 0.472,
-    "K51": 0.365,
-    "K52": 0.105,
-    "K53": 0.03,
-    "K54": 0.01,
-    "K55": 0.003,
-    "Ca34": 3.5e-08,
-    "Ca35": 0.0257,
-    "Ca36": 0.102,
-    "Ca37": 0.1811,
-    "Ca38": 0.44,
-    "Ca39": 0.8596,
-    "Ca41": 3218880000000.0,
-    "Ca45": 14049500.0,
-    "Ca47": 391910.4,
-    "Ca48": 7.25824e26,
-    "Ca49": 523.08,
-    "Ca50": 13.9,
-    "Ca51": 10.0,
-    "Ca52": 4.6,
-    "Ca53": 0.09,
-    "Ca54": 0.086,
-    "Ca55": 0.022,
-    "Ca56": 0.01,
-    "Ca57": 0.005,
-    "Sc36": 0.0088,
-    "Sc37": 0.056,
-    "Sc38": 0.0423,
-    "Sc39": 3e-07,
-    "Sc40": 0.1823,
-    "Sc41": 0.5963,
-    "Sc42": 0.6808,
-    "Sc42_m1": 62.0,
-    "Sc43": 14007.6,
-    "Sc44": 14292.0,
-    "Sc44_m1": 210996.0,
-    "Sc45_m1": 0.318,
-    "Sc46": 7239456.0,
-    "Sc46_m1": 18.75,
-    "Sc47": 289370.9,
-    "Sc48": 157212.0,
-    "Sc49": 3430.8,
-    "Sc50": 102.5,
-    "Sc50_m1": 0.35,
-    "Sc51": 12.4,
-    "Sc52": 8.2,
-    "Sc53": 3.0,
-    "Sc54": 0.36,
-    "Sc55": 0.105,
-    "Sc56": 0.06,
-    "Sc57": 0.013,
-    "Sc58": 0.012,
-    "Sc59": 0.01,
-    "Sc60": 0.003,
-    "Ti38": 1.2e-07,
-    "Ti39": 0.032,
-    "Ti40": 0.0533,
-    "Ti41": 0.0804,
-    "Ti42": 0.199,
-    "Ti43": 0.509,
-    "Ti44": 1893460000.0,
-    "Ti45": 11088.0,
-    "Ti51": 345.6,
-    "Ti52": 102.0,
-    "Ti53": 32.7,
-    "Ti54": 1.5,
-    "Ti55": 1.3,
-    "Ti56": 0.2,
-    "Ti57": 0.06,
-    "Ti58": 0.059,
-    "Ti59": 0.03,
-    "Ti60": 0.022,
-    "Ti61": 3e-07,
-    "Ti62": 0.01,
-    "Ti63": 0.003,
-    "V40": 0.0077,
-    "V41": 0.0244,
-    "V42": 5.5e-08,
-    "V43": 0.8,
-    "V44": 0.111,
-    "V44_m1": 0.15,
-    "V45": 0.547,
-    "V46": 0.4225,
-    "V46_m1": 0.00102,
-    "V47": 1956.0,
-    "V48": 1380110.0,
-    "V49": 28512000.0,
-    "V50": 4.41806e24,
-    "V52": 224.58,
-    "V53": 92.58,
-    "V54": 49.8,
-    "V55": 6.54,
-    "V56": 0.216,
-    "V57": 0.35,
-    "V58": 0.185,
-    "V59": 0.075,
-    "V60": 0.068,
-    "V61": 0.047,
-    "V62": 1.5e-07,
-    "V63": 0.017,
-    "V64": 0.019,
-    "V65": 0.01,
-    "Cr42": 0.014,
-    "Cr43": 0.0216,
-    "Cr44": 0.0535,
-    "Cr45": 0.0609,
-    "Cr46": 0.26,
-    "Cr47": 0.5,
-    "Cr48": 77616.0,
-    "Cr49": 2538.0,
-    "Cr51": 2393366.0,
-    "Cr55": 209.82,
-    "Cr56": 356.4,
-    "Cr57": 21.1,
-    "Cr58": 7.0,
-    "Cr59": 0.46,
-    "Cr60": 0.49,
-    "Cr61": 0.27,
-    "Cr62": 0.19,
-    "Cr63": 0.129,
-    "Cr64": 0.043,
-    "Cr65": 0.027,
-    "Cr66": 0.01,
-    "Cr67": 0.05,
-    "Mn44": 1.05e-07,
-    "Mn45": 7e-08,
-    "Mn46": 0.0345,
-    "Mn47": 0.1,
-    "Mn48": 0.1581,
-    "Mn49": 0.382,
-    "Mn50": 0.28319,
-    "Mn50_m1": 105.0,
-    "Mn51": 2772.0,
-    "Mn52": 483062.4,
-    "Mn52_m1": 1266.0,
-    "Mn53": 116763000000000.0,
-    "Mn54": 26961120.0,
-    "Mn56": 9284.04,
-    "Mn57": 85.4,
-    "Mn58": 3.0,
-    "Mn58_m1": 65.4,
-    "Mn59": 4.59,
-    "Mn60": 51.0,
-    "Mn60_m1": 1.77,
-    "Mn61": 0.67,
-    "Mn62": 0.671,
-    "Mn62_m1": 0.092,
-    "Mn63": 0.29,
-    "Mn64": 0.09,
-    "Mn65": 0.092,
-    "Mn66": 0.064,
-    "Mn67": 0.047,
-    "Mn68": 0.028,
-    "Mn69": 0.014,
-    "Fe45": 0.00203,
-    "Fe46": 0.013,
-    "Fe47": 0.0219,
-    "Fe48": 0.044,
-    "Fe49": 0.0647,
-    "Fe50": 0.155,
-    "Fe51": 0.305,
-    "Fe52": 29790.0,
-    "Fe52_m1": 45.9,
-    "Fe53": 510.6,
-    "Fe53_m1": 152.4,
-    "Fe55": 86594050.0,
-    "Fe59": 3844368.0,
-    "Fe60": 47336400000000.0,
-    "Fe61": 358.8,
-    "Fe62": 68.0,
-    "Fe63": 6.1,
-    "Fe64": 2.0,
-    "Fe65": 0.81,
-    "Fe65_m1": 1.12,
-    "Fe66": 0.44,
-    "Fe67": 0.416,
-    "Fe68": 0.187,
-    "Fe69": 0.109,
-    "Fe70": 0.094,
-    "Fe71": 0.028,
-    "Fe72": 1.5e-07,
-    "Co49": 3.5e-08,
-    "Co50": 0.044,
-    "Co51": 2e-07,
-    "Co52": 0.115,
-    "Co53": 0.24,
-    "Co53_m1": 0.247,
-    "Co54": 0.19328,
-    "Co54_m1": 88.8,
-    "Co55": 63108.0,
-    "Co56": 6672931.0,
-    "Co57": 23478340.0,
-    "Co58": 6122304.0,
-    "Co58_m1": 32760.0,
-    "Co60": 166344200.0,
-    "Co60_m1": 628.02,
-    "Co61": 5940.0,
-    "Co62": 90.0,
-    "Co62_m1": 834.6,
-    "Co63": 27.4,
-    "Co64": 0.3,
-    "Co65": 1.16,
-    "Co66": 0.2,
-    "Co67": 0.425,
-    "Co68": 0.199,
-    "Co68_m1": 1.6,
-    "Co69": 0.22,
-    "Co70": 0.119,
-    "Co70_m1": 0.5,
-    "Co71": 0.079,
-    "Co72": 0.0599,
-    "Co73": 0.041,
-    "Co74": 0.03,
-    "Co75": 0.034,
-    "Ni48": 0.0021,
-    "Ni49": 0.0075,
-    "Ni50": 0.012,
-    "Ni51": 2e-07,
-    "Ni52": 0.038,
-    "Ni53": 0.045,
-    "Ni54": 0.104,
-    "Ni55": 0.2047,
-    "Ni56": 524880.0,
-    "Ni57": 128160.0,
-    "Ni59": 2398380000000.0,
-    "Ni63": 3193630000.0,
-    "Ni65": 9061.884,
-    "Ni66": 196560.0,
-    "Ni67": 21.0,
-    "Ni68": 29.0,
-    "Ni69": 11.4,
-    "Ni69_m1": 3.5,
-    "Ni70": 6.0,
-    "Ni71": 2.56,
-    "Ni72": 1.57,
-    "Ni73": 0.84,
-    "Ni74": 0.68,
-    "Ni75": 0.6,
-    "Ni76": 0.238,
-    "Ni77": 0.061,
-    "Ni78": 0.11,
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-    "Rg272": 0.0041,
-}
-
-
 # Values here are from the Committee on Data for Science and Technology
 # (CODATA) 2018 recommendation (https://physics.nist.gov/cuu/Constants/).
 
@@ -3764,6 +199,9 @@ _ATOMIC_MASS = {}
 # Regex for GND nuclide names (used in zam function)
 _GND_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)')
 
+# Used in half_life function as a cache
+_HALF_LIFE = {}
+
 
 def atomic_mass(isotope):
     """Return atomic mass of isotope in atomic mass units.
@@ -3838,6 +276,36 @@ def atomic_weight(element):
                          .format(element))
 
 
+def half_life(isotope):
+    """Return half-life of isotope in seconds. Returns None if isotope is stable
+
+    Half-life values are from `ENDF/B VIII.0 Decay Reaction Sublibrary
+    <https://www.nndc.bnl.gov/endf-b8.0/download.html>`_.
+
+    Parameters
+    ----------
+    isotope : str
+        Name of isotope, e.g., 'Pu239'
+
+    Returns
+    -------
+    float
+        Half-life of isotope in [seconds]
+
+    """
+    global _HALF_LIFE
+    if not _HALF_LIFE:
+        print('reading json file')
+        # Load data from AME2016 file
+        half_life_filename = os.path.join(os.path.dirname(__file__), 'half_life.json')
+        with open(half_life_filename, 'r') as f:
+            _HALF_LIFE = json.load(f)
+
+    if isotope.title() not in _HALF_LIFE.keys():
+        return None
+
+    return _HALF_LIFE[isotope.title()]
+
 def water_density(temperature, pressure=0.1013):
     """Return the density of liquid water at a given temperature and pressure.
 
diff --git a/openmc/data/half_life.json b/openmc/data/half_life.json
new file mode 100644
index 000000000..bb67da75d
--- /dev/null
+++ b/openmc/data/half_life.json
@@ -0,0 +1,3563 @@
+{
+    "H3": 388789600.0,
+    "H4": 9.90652e-23,
+    "H5": 7.99473e-23,
+    "H6": 2.84812e-22,
+    "H7": 2.3e-23,
+    "He5": 7.595e-22,
+    "He6": 0.8067,
+    "He7": 3.038e-21,
+    "He8": 0.1191,
+    "He9": 7e-21,
+    "He10": 1.519e-21,
+    "Li4": 7.55721e-23,
+    "Li5": 3.06868e-22,
+    "Li8": 0.838,
+    "Li9": 0.1783,
+    "Li10": 2e-21,
+    "Li11": 0.00859,
+    "Li12": 1e-08,
+    "Be5": 1e-09,
+    "Be6": 4.95326e-21,
+    "Be7": 4598208.0,
+    "Be8": 8.18132e-17,
+    "Be10": 47652000000000.0,
+    "Be11": 13.81,
+    "Be12": 0.0213,
+    "Be13": 2.7e-21,
+    "Be14": 0.00435,
+    "Be15": 2e-07,
+    "Be16": 2e-07,
+    "B6": 1e-09,
+    "B7": 3.255e-22,
+    "B8": 0.77,
+    "B9": 8.43888e-19,
+    "B12": 0.0202,
+    "B13": 0.01736,
+    "B14": 0.0125,
+    "B15": 0.00993,
+    "B16": 1.9e-10,
+    "B17": 0.00508,
+    "B18": 2.6e-08,
+    "B19": 0.00292,
+    "C8": 1.9813e-21,
+    "C9": 0.1265,
+    "C10": 19.29,
+    "C11": 1223.1,
+    "C14": 179878000000.0,
+    "C15": 2.449,
+    "C16": 0.747,
+    "C17": 0.193,
+    "C18": 0.092,
+    "C19": 0.049,
+    "C20": 0.0145,
+    "C21": 3e-08,
+    "C22": 0.0062,
+    "N10": 2e-22,
+    "N11": 3.12742e-22,
+    "N12": 0.011,
+    "N13": 597.9,
+    "N16": 7.13,
+    "N17": 4.171,
+    "N18": 0.624,
+    "N19": 0.271,
+    "N20": 0.13,
+    "N21": 0.085,
+    "N22": 0.024,
+    "N23": 0.0145,
+    "N24": 5.2e-08,
+    "N25": 2.6e-07,
+    "O12": 1.13925e-21,
+    "O13": 0.00858,
+    "O14": 70.606,
+    "O15": 122.24,
+    "O19": 26.88,
+    "O20": 13.51,
+    "O21": 3.42,
+    "O22": 2.25,
+    "O23": 0.0905,
+    "O24": 0.065,
+    "O25": 5e-08,
+    "O26": 4e-08,
+    "O27": 2.6e-07,
+    "O28": 1e-07,
+    "F14": 5.0007e-22,
+    "F15": 4.557e-22,
+    "F16": 1.13925e-20,
+    "F17": 64.49,
+    "F18": 6586.2,
+    "F20": 11.163,
+    "F21": 4.158,
+    "F22": 4.23,
+    "F23": 2.23,
+    "F24": 0.39,
+    "F25": 0.05,
+    "F26": 0.0096,
+    "F27": 0.005,
+    "F28": 4e-08,
+    "F29": 0.0025,
+    "F30": 2.6e-07,
+    "F31": 2.5e-07,
+    "Ne16": 3.73524e-21,
+    "Ne17": 0.1092,
+    "Ne18": 1.672,
+    "Ne19": 17.22,
+    "Ne23": 37.24,
+    "Ne24": 202.8,
+    "Ne25": 0.602,
+    "Ne26": 0.197,
+    "Ne27": 0.032,
+    "Ne28": 0.0189,
+    "Ne29": 0.0148,
+    "Ne30": 0.0073,
+    "Ne31": 0.0034,
+    "Ne32": 0.0035,
+    "Ne33": 1.8e-07,
+    "Ne34": 6e-08,
+    "Na18": 1.3e-21,
+    "Na19": 4e-08,
+    "Na20": 0.4479,
+    "Na21": 22.49,
+    "Na22": 82134970.0,
+    "Na24": 53989.2,
+    "Na24_m1": 0.02018,
+    "Na25": 59.1,
+    "Na26": 1.077,
+    "Na27": 0.301,
+    "Na28": 0.0305,
+    "Na29": 0.0449,
+    "Na30": 0.048,
+    "Na31": 0.017,
+    "Na32": 0.0132,
+    "Na33": 0.008,
+    "Na34": 0.0055,
+    "Na35": 0.0015,
+    "Na36": 1.8e-07,
+    "Na37": 6e-08,
+    "Mg19": 4e-12,
+    "Mg20": 0.0908,
+    "Mg21": 0.122,
+    "Mg22": 3.8755,
+    "Mg23": 11.317,
+    "Mg27": 567.48,
+    "Mg28": 75294.0,
+    "Mg29": 1.3,
+    "Mg30": 0.335,
+    "Mg31": 0.232,
+    "Mg32": 0.086,
+    "Mg33": 0.0905,
+    "Mg34": 0.02,
+    "Mg35": 0.07,
+    "Mg36": 0.0039,
+    "Mg37": 2.6e-07,
+    "Mg38": 2.6e-07,
+    "Mg39": 1.8e-07,
+    "Mg40": 1.7e-07,
+    "Al21": 3.5e-08,
+    "Al22": 0.059,
+    "Al23": 0.47,
+    "Al24": 2.053,
+    "Al24_m1": 0.13,
+    "Al25": 7.183,
+    "Al26": 22626800000000.0,
+    "Al26_m1": 6.3452,
+    "Al28": 134.484,
+    "Al29": 393.6,
+    "Al30": 3.62,
+    "Al31": 0.644,
+    "Al32": 0.033,
+    "Al33": 0.0417,
+    "Al34": 0.042,
+    "Al35": 0.0386,
+    "Al36": 0.09,
+    "Al37": 0.0107,
+    "Al38": 0.0076,
+    "Al39": 7.6e-06,
+    "Al40": 2.6e-07,
+    "Al41": 2.6e-07,
+    "Al42": 1.7e-07,
+    "Si22": 0.029,
+    "Si23": 0.0423,
+    "Si24": 0.14,
+    "Si25": 0.22,
+    "Si26": 2.234,
+    "Si27": 4.16,
+    "Si31": 9438.0,
+    "Si32": 4828310000.0,
+    "Si33": 6.11,
+    "Si34": 2.77,
+    "Si35": 0.78,
+    "Si36": 0.45,
+    "Si37": 0.09,
+    "Si38": 1e-06,
+    "Si39": 0.0475,
+    "Si40": 0.033,
+    "Si41": 0.02,
+    "Si42": 0.0125,
+    "Si43": 6e-08,
+    "Si44": 3.6e-07,
+    "P24": 0.0074,
+    "P25": 3e-08,
+    "P26": 0.0437,
+    "P27": 0.26,
+    "P28": 0.2703,
+    "P29": 4.142,
+    "P30": 149.88,
+    "P32": 1232323.0,
+    "P33": 2189376.0,
+    "P34": 12.43,
+    "P35": 47.3,
+    "P36": 5.6,
+    "P37": 2.31,
+    "P38": 0.64,
+    "P39": 0.28,
+    "P40": 0.125,
+    "P41": 0.1,
+    "P42": 0.0485,
+    "P43": 0.0365,
+    "P44": 0.0185,
+    "P45": 2e-07,
+    "P46": 2e-07,
+    "S26": 0.01,
+    "S27": 0.0155,
+    "S28": 0.125,
+    "S29": 0.187,
+    "S30": 1.178,
+    "S31": 2.572,
+    "S35": 7560864.0,
+    "S37": 303.0,
+    "S38": 10218.0,
+    "S39": 11.5,
+    "S40": 8.8,
+    "S41": 1.99,
+    "S42": 1.013,
+    "S43": 0.28,
+    "S44": 0.1,
+    "S45": 0.068,
+    "S46": 0.05,
+    "S48": 2e-07,
+    "S49": 2e-07,
+    "Cl28": 0.0017,
+    "Cl29": 2e-08,
+    "Cl30": 3e-08,
+    "Cl31": 0.15,
+    "Cl32": 0.298,
+    "Cl33": 2.511,
+    "Cl34": 1.5264,
+    "Cl34_m1": 1920.0,
+    "Cl36": 9498840000000.0,
+    "Cl38": 2233.8,
+    "Cl38_m1": 0.715,
+    "Cl39": 3336.0,
+    "Cl40": 81.0,
+    "Cl41": 38.4,
+    "Cl42": 6.8,
+    "Cl43": 3.13,
+    "Cl44": 0.56,
+    "Cl45": 0.413,
+    "Cl46": 0.232,
+    "Cl47": 0.101,
+    "Cl48": 2e-07,
+    "Cl49": 1.7e-07,
+    "Cl50": 0.02,
+    "Cl51": 2e-07,
+    "Ar30": 2e-08,
+    "Ar31": 0.0151,
+    "Ar32": 0.098,
+    "Ar33": 0.173,
+    "Ar34": 0.8445,
+    "Ar35": 1.775,
+    "Ar37": 3027456.0,
+    "Ar39": 8488990000.0,
+    "Ar41": 6576.6,
+    "Ar42": 1038250000.0,
+    "Ar43": 322.2,
+    "Ar44": 712.2,
+    "Ar45": 21.48,
+    "Ar46": 8.4,
+    "Ar47": 1.23,
+    "Ar48": 0.475,
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+    "Ar50": 0.085,
+    "Ar51": 2e-07,
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+    "K32": 0.0033,
+    "K33": 2.5e-08,
+    "K34": 2.5e-08,
+    "K35": 0.178,
+    "K36": 0.342,
+    "K37": 1.226,
+    "K38": 458.16,
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+    "Ca34": 3.5e-08,
+    "Ca35": 0.0257,
+    "Ca36": 0.102,
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+    "Ca38": 0.44,
+    "Ca39": 0.8596,
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+    "Ca47": 391910.4,
+    "Ca48": 7.25824e26,
+    "Ca49": 523.08,
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+    "Sc39": 3e-07,
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+    "Sc41": 0.5963,
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+    "Mn52_m1": 1266.0,
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+    "Db262": 35.0,
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+    "Sg263_m1": 0.12,
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+    "Sg266": 25.0,
+    "Sg269": 50.0,
+    "Bh260": 0.0003,
+    "Bh261": 0.013,
+    "Bh262": 0.102,
+    "Bh262_m1": 0.022,
+    "Bh263": 0.0002,
+    "Bh264": 0.66,
+    "Bh265": 1.1,
+    "Bh266": 5.4,
+    "Bh267": 21.0,
+    "Bh269": 50.0,
+    "Hs263": 0.00355,
+    "Hs264": 0.0008,
+    "Hs265": 0.00205,
+    "Hs265_m1": 0.0003,
+    "Hs266": 0.00265,
+    "Hs267": 0.0545,
+    "Hs268": 1.2,
+    "Hs269": 12.9,
+    "Hs273": 50.0,
+    "Mt265": 120.0,
+    "Mt266": 0.0018,
+    "Mt266_m1": 0.0017,
+    "Mt267": 0.01,
+    "Mt268": 0.0225,
+    "Mt269": 0.05,
+    "Mt270": 0.00605,
+    "Mt271": 5.0,
+    "Mt273": 20.0,
+    "Ds267": 2.8e-06,
+    "Ds268": 0.0001,
+    "Ds269": 0.000268,
+    "Ds270": 0.00015,
+    "Ds270_m1": 0.009,
+    "Ds271": 0.001705,
+    "Ds271_m1": 0.0865,
+    "Ds272": 1.0,
+    "Ds273": 0.000225,
+    "Ds279_m1": 0.19,
+    "Rg272": 0.0041
+}
diff --git a/openmc/material.py b/openmc/material.py
index a9f5afac8..9706ffe78 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -30,9 +30,9 @@ class Material(IDManagerMixin):
 
     To create a material, one should create an instance of this class, add
     nuclides or elements with :meth:`Material.add_nuclide` or
-    `Material.add_element`, respectively, and set the total material density
-    with `Material.set_density()`. The material can then be assigned to a cell
-    using the :attr:`Cell.fill` attribute.
+    :meth:`Material.add_element`, respectively, and set the total material
+    density with :meth:`Material.set_density()`. The material can then be
+    assigned to a cell using the :attr:`Cell.fill` attribute.
 
     Parameters
     ----------
@@ -142,6 +142,23 @@ class Material(IDManagerMixin):
 
         return string
 
+
+    @property
+    def activity(self):
+        """Returns the total activity of the material in Becquerels."""
+
+        atoms_per_barn_cm2 = self.get_nuclide_atom_densities()
+        total_activity = 0
+        for key, value in atoms_per_barn_cm2.items():
+            half_life = openmc.data.half_life(key)
+            print('half_life', half_life)
+            if half_life:
+                atoms = value[1] * self.volume * 1e24
+                activity = math.log(2) * atoms / half_life
+                total_activity += activity
+
+        return total_activity
+
     @property
     def name(self):
         return self._name
@@ -707,19 +724,6 @@ class Material(IDManagerMixin):
         self.isotropic = [x.name for x in self._nuclides]
 
 
-    def get_activity(self):
-        """Returns the total activity of the material in Becquerels."""
-
-        atoms_per_barn_cm2 = self.get_nuclide_atom_densities()
-        total_activity = 0
-        for key, value in atoms_per_barn_cm2.items():
-            if key in openmc.data.HALF_LIFE.keys():
-                atoms = value[1] * self.volume * 1e24
-                activity = math.log(2) * atoms / openmc.data.HALF_LIFE[key]
-                total_activity += activity
-
-        return total_activity
-
     def get_elements(self):
         """Returns all elements in the material
 
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index 02e53a28d..baef3f9ef 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -404,3 +404,21 @@ def test_mix_materials():
     assert m3.density == pytest.approx(dens3)
     assert m4.density == pytest.approx(dens4)
     assert m5.density == pytest.approx(dens5)
+
+
+def test_activity_of_stable():
+    """Creates a material with stable isotopes to checks the activity is 0"""
+    m1 = openmc.Material()
+    m1.add_element("Fe", 1)
+    m1.set_density('g/cm3', 1)
+    m1.volume = 1
+    assert m1.activity == 0
+
+
+def test_activity_of_tritium():
+    """Checks that 1g of tritium has the correct activity"""
+    m1 = openmc.Material()
+    m1.add_nuclide("H3", 1)
+    m1.set_density('g/cm3', 1)
+    m1.volume = 1
+    assert pytest.approx(m1.activity) == 3.559778e14 

From e5e1daf23fcf0f332ac2e79542dff36424d863e0 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Thu, 9 Jun 2022 15:02:10 +0100
Subject: [PATCH 021/119] [skip ci] removed diagnostic prints

---
 openmc/data/data.py               | 1 -
 openmc/material.py                | 2 --
 tests/unit_tests/test_material.py | 1 +
 3 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index 65702f7a5..5aadfac87 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -295,7 +295,6 @@ def half_life(isotope):
     """
     global _HALF_LIFE
     if not _HALF_LIFE:
-        print('reading json file')
         # Load data from AME2016 file
         half_life_filename = os.path.join(os.path.dirname(__file__), 'half_life.json')
         with open(half_life_filename, 'r') as f:
diff --git a/openmc/material.py b/openmc/material.py
index 9706ffe78..e49696706 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -151,7 +151,6 @@ class Material(IDManagerMixin):
         total_activity = 0
         for key, value in atoms_per_barn_cm2.items():
             half_life = openmc.data.half_life(key)
-            print('half_life', half_life)
             if half_life:
                 atoms = value[1] * self.volume * 1e24
                 activity = math.log(2) * atoms / half_life
@@ -723,7 +722,6 @@ class Material(IDManagerMixin):
     def make_isotropic_in_lab(self):
         self.isotropic = [x.name for x in self._nuclides]
 
-
     def get_elements(self):
         """Returns all elements in the material
 
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index baef3f9ef..c5d3276a0 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -422,3 +422,4 @@ def test_activity_of_tritium():
     m1.set_density('g/cm3', 1)
     m1.volume = 1
     assert pytest.approx(m1.activity) == 3.559778e14 
+

From 61db44f40e33d132d895974852c448beeacc6770 Mon Sep 17 00:00:00 2001
From: myerspat <myerspat@umich.edu>
Date: Thu, 9 Jun 2022 09:52:50 -0500
Subject: [PATCH 022/119] Xtensor for photoelectric cross sections matches the
 flux spectrum for uranium of the previous iteration of OpenMC

---
 src/photon.cpp  | 15 +++++++++------
 src/physics.cpp | 22 +++++++++++-----------
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/src/photon.cpp b/src/photon.cpp
index 1be515a62..bb715cdea 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -128,7 +128,7 @@ PhotonInteraction::PhotonInteraction(hid_t group)
   }
 
   shells_.resize(n_shell);
-  cross_sections_.resize({energy_.size(), n_shell});
+  cross_sections_ = xt::zeros<double>({energy_.size(), n_shell});
 
   // Create mapping from designator to index
   std::unordered_map<int, int> shell_map;
@@ -166,8 +166,8 @@ PhotonInteraction::PhotonInteraction(hid_t group)
     read_dataset(tgroup, "xs", xs);
 
     auto cross_section = xt::view(cross_sections_,
-      xt::range(shell.threshold, shell.threshold + xs.size()), i);
-    cross_section = xt::where(xs > 0.0, xt::log(xs), -500.0);
+      xt::range(shell.threshold, xt::placeholders::_), i);
+    cross_section = xt::where(xs > 0, xt::log(xs), 0);
 
     if (object_exists(tgroup, "transitions")) {
       // Determine dimensions of transitions
@@ -571,10 +571,13 @@ void PhotonInteraction::calculate_xs(Particle& p) const
     incoherent_(i_grid) + f * (incoherent_(i_grid + 1) - incoherent_(i_grid)));
 
   // Calculate microscopic photoelectric cross section
-  const auto& xs_upper = xt::row(cross_sections_, i_grid);
-  const auto& xs_lower = xt::row(cross_sections_, i_grid + 1);
+  xs.photoelectric = 0.0;
+  const auto& xs_lower = xt::row(cross_sections_, i_grid);
+  const auto& xs_upper = xt::row(cross_sections_, i_grid + 1);
 
-  xs.photoelectric = xt::sum(xt::exp(xs_upper + f * (xs_upper - xs_lower)))[0];
+  for (int i = 0; i < xs_upper.size(); ++i)
+    if (xs_lower(i) != 0)
+      xs.photoelectric += std::exp(xs_lower(i) + f * (xs_upper(i) - xs_lower(i)));
 
   // Calculate microscopic pair production cross section
   xs.pair_production = std::exp(
diff --git a/src/physics.cpp b/src/physics.cpp
index 38d74dbed..26b3a3520 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -29,6 +29,7 @@
 
 #include <algorithm> // for max, min, max_element
 #include <cmath>     // for sqrt, exp, log, abs, copysign
+#include <xtensor/xview.hpp>
 
 namespace openmc {
 
@@ -344,25 +345,24 @@ void sample_photon_reaction(Particle& p)
 
   // Photoelectric effect
   double prob_after = prob + micro.photoelectric;
+  int i_grid = micro.index_grid;
+  double f = micro.interp_factor;
+  const auto& xs_lower = xt::row(element.cross_sections_, i_grid);
+  const auto& xs_upper = xt::row(element.cross_sections_, i_grid + 1);
+
   if (prob_after > cutoff) {
     for (int i_shell = 0; i_shell < element.shells_.size(); ++i_shell) {
       const auto& shell {element.shells_[i_shell]};
 
-      // Get grid index and interpolation factor
-      int i_grid = micro.index_grid;
-      double f = micro.interp_factor;
-
       // Check threshold of reaction
-      int i_start = shell.threshold;
-      if (i_grid < i_start)
+      if (xs_lower(i_shell) == 0)
         continue;
 
-      // Evaluation subshell photoionization cross section
-      double xs = std::exp(element.cross_sections_(i_grid - i_start) +
-                           f * (element.cross_sections_(i_grid + 1 - i_start) -
-                                 element.cross_sections_(i_grid - i_start)));
+      //  Evaluation subshell photoionization cross section
+      prob += std::exp(xs_lower(i_shell) +
+                       f * (xs_upper(i_shell) -
+                             xs_lower(i_shell)));
 
-      prob += xs;
       if (prob > cutoff) {
         double E_electron = p.E() - shell.binding_energy;
 

From 70b1706460166ff6d0a05744ad804ef9fd0671ef Mon Sep 17 00:00:00 2001
From: myerspat <myerspat@umich.edu>
Date: Thu, 9 Jun 2022 10:39:46 -0500
Subject: [PATCH 023/119] Moved initialized variables into if statement

---
 src/physics.cpp | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/physics.cpp b/src/physics.cpp
index 26b3a3520..0df8e63c0 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -345,12 +345,14 @@ void sample_photon_reaction(Particle& p)
 
   // Photoelectric effect
   double prob_after = prob + micro.photoelectric;
-  int i_grid = micro.index_grid;
-  double f = micro.interp_factor;
-  const auto& xs_lower = xt::row(element.cross_sections_, i_grid);
-  const auto& xs_upper = xt::row(element.cross_sections_, i_grid + 1);
 
   if (prob_after > cutoff) {
+
+    int i_grid = micro.index_grid;
+    double f = micro.interp_factor;
+    const auto& xs_lower = xt::row(element.cross_sections_, i_grid);
+    const auto& xs_upper = xt::row(element.cross_sections_, i_grid + 1);
+
     for (int i_shell = 0; i_shell < element.shells_.size(); ++i_shell) {
       const auto& shell {element.shells_[i_shell]};
 

From aba235e0b46a33cd6dbbb388d52a27f56e149cba Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Fri, 10 Jun 2022 08:50:52 -0500
Subject: [PATCH 024/119] Update tests/unit_tests/test_stats.py

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

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index 8e38a7b48..c2578ea8b 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -120,6 +120,11 @@ def test_maxwell():
     samples = d.sample(n_samples, seed=100)
     assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
 
+    # A second sample with a different seed
+    samples_2 = d.sample(n_samples, seed=200)
+    assert samples_2.mean() == pytest.approx(exp_mean, rel=1e-02)
+    assert samples_2.mean() != samples.mean()
+
 
 
 def test_watt():

From 98a7d5eabc972a986a64307bc709dda7ecadaf3d Mon Sep 17 00:00:00 2001
From: myerspat <myerspat@umich.edu>
Date: Fri, 10 Jun 2022 11:57:35 -0500
Subject: [PATCH 025/119] added clang format

---
 src/photon.cpp  | 7 ++++---
 src/physics.cpp | 5 ++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/photon.cpp b/src/photon.cpp
index bb715cdea..85bd435c9 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -165,8 +165,8 @@ PhotonInteraction::PhotonInteraction(hid_t group)
     close_dataset(dset);
     read_dataset(tgroup, "xs", xs);
 
-    auto cross_section = xt::view(cross_sections_,
-      xt::range(shell.threshold, xt::placeholders::_), i);
+    auto cross_section = xt::view(
+      cross_sections_, xt::range(shell.threshold, xt::placeholders::_), i);
     cross_section = xt::where(xs > 0, xt::log(xs), 0);
 
     if (object_exists(tgroup, "transitions")) {
@@ -577,7 +577,8 @@ void PhotonInteraction::calculate_xs(Particle& p) const
 
   for (int i = 0; i < xs_upper.size(); ++i)
     if (xs_lower(i) != 0)
-      xs.photoelectric += std::exp(xs_lower(i) + f * (xs_upper(i) - xs_lower(i)));
+      xs.photoelectric +=
+        std::exp(xs_lower(i) + f * (xs_upper(i) - xs_lower(i)));
 
   // Calculate microscopic pair production cross section
   xs.pair_production = std::exp(
diff --git a/src/physics.cpp b/src/physics.cpp
index 0df8e63c0..cc712affd 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -361,9 +361,8 @@ void sample_photon_reaction(Particle& p)
         continue;
 
       //  Evaluation subshell photoionization cross section
-      prob += std::exp(xs_lower(i_shell) +
-                       f * (xs_upper(i_shell) -
-                             xs_lower(i_shell)));
+      prob += std::exp(
+        xs_lower(i_shell) + f * (xs_upper(i_shell) - xs_lower(i_shell)));
 
       if (prob > cutoff) {
         double E_electron = p.E() - shell.binding_energy;

From 0c3d30e6d1ebf373c7d79de1aeacfce88504609e Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 19 Jun 2022 09:31:38 -0500
Subject: [PATCH 026/119] Update openmc/stats/univariate.py

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/stats/univariate.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index d733b6193..e4c53c559 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -139,14 +139,7 @@ class Discrete(Univariate):
     def sample(self, n_samples=1, seed=None):
         np.random.seed(seed)
 
-        if len(self.x) == 1:
-            return np.full((n_samples), self.x[0])
-
-        xi = np.random.rand(n_samples)
-        out = np.zeros_like(xi)
-        for i, c in enumerate(self.cdf()[:-1]):
-            out[xi >= c] = self.x[i]
-        return out
+        return np.random.choice(self.x, n_samples, p=self.p)
 
     def normalize(self):
         norm = sum(self.p)

From f52865854ba41746d58b6621215bb5c223c896f2 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 19 Jun 2022 09:39:53 -0500
Subject: [PATCH 027/119] Apply suggestions from @paulromano

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/stats/univariate.py     | 18 +++++++++---------
 tests/unit_tests/test_stats.py |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index e4c53c559..6875f4e4f 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -381,7 +381,7 @@ class PowerLaw(Univariate):
         pwr = self.n + 1
         offset = self.a**pwr
         span = self.b**pwr - offset
-        return np.power(offset + xi * span, (1/pwr))
+        return np.power(offset + xi * span, 1/pwr)
 
     def to_xml_element(self, element_name):
         """Return XML representation of the power law distribution
@@ -463,8 +463,8 @@ class Maxwell(Univariate):
     @staticmethod
     def sample_maxwell(t, n_samples):
         r1, r2, r3 = np.random.rand(3, n_samples)
-        c = np.power(np.cos(0.5 * np.pi * r3), 2)
-        return -t * (np.log(r1) + np.log(r2) * c)
+        c = np.cos(0.5 * np.pi * r3)
+        return -t * (np.log(r1) + np.log(r2) * c * c)
 
     def to_xml_element(self, element_name):
         """Return XML representation of the Maxwellian distribution
@@ -887,7 +887,7 @@ class Tabular(Univariate):
         if self.interpolation == 'histogram':
             c[1:] = p[:-1] * np.diff(x)
         elif self.interpolation == 'linear-linear':
-            c[1:] = 0.5 * (p[0:-1] + p[1:]) * np.diff(x)
+            c[1:] = 0.5 * (p[:-1] + p[1:]) * np.diff(x)
 
         return np.cumsum(c)
 
@@ -909,7 +909,7 @@ class Tabular(Univariate):
         # get CDF bins that are above the
         # sampled values
         c_i = np.full(n_samples, cdf[0])
-        cdf_idx = np.zeros((n_samples,), dtype=int)
+        cdf_idx = np.zeros(n_samples, dtype=int)
         for i, val in enumerate(cdf[:-1]):
             mask = xi > val
             c_i[mask] = val
@@ -918,8 +918,8 @@ class Tabular(Univariate):
         # get table values at each index where
         # the random number is less than the next cdf
         # entry
-        x_i = np.array([self.x[i] for i in cdf_idx])
-        p_i = np.array([p[i] for i in cdf_idx])
+        x_i = self.x[cdf_idx]
+        p_i = self.p[cdf_idx]
 
         # TODO: check that probability doesn't exceed the last value
 
@@ -936,8 +936,8 @@ class Tabular(Univariate):
         elif self.interpolation == 'linear-linear':
             # get variable and probability values for the
             # next entry
-            x_i1 = np.array([self.x[i+1] for i in cdf_idx])
-            p_i1 = np.array([p[i+1] for i in cdf_idx])
+            x_i1 = self.x[cdf_idx + 1]
+            p_i1 = self.p[cdf_idx + 1]
             # compute slope between entries
             m = (p_i1 - p_i) / (x_i1 - x_i)
             # set values for zero slope
diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index c2578ea8b..f62f2157b 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -161,7 +161,7 @@ def test_tabular():
     assert d.interpolation == 'linear-linear'
     assert len(d) == len(x)
 
-    # test linear-lienar sampling
+    # test linear-linear sampling
     d = openmc.stats.Tabular(x, p)
 
     # compute the expected value (mean) of the

From f46402fd87f33daf2da4050010973bd00b6c5bae Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 19 Jun 2022 09:36:31 -0500
Subject: [PATCH 028/119] Adding docstrings to normalize methods

---
 openmc/stats/univariate.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 6875f4e4f..bbac4c030 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -142,6 +142,7 @@ class Discrete(Univariate):
         return np.random.choice(self.x, n_samples, p=self.p)
 
     def normalize(self):
+        """Normalize the probabilities stored on the distribution"""
         norm = sum(self.p)
         self.p = [val / norm for val in self.p]
 
@@ -892,6 +893,7 @@ class Tabular(Univariate):
         return np.cumsum(c)
 
     def normalize(self):
+        """Normalize the probabilities stored on the distribution"""
         self.p = np.asarray(self.p) / self.cdf().max()
 
     def sample(self, n_samples=1, seed=None):
@@ -1115,6 +1117,7 @@ class Mixture(Univariate):
         return out
 
     def normalize(self):
+        """Normalize the probabilities stored on the distribution"""
         norm = sum(self.probability)
         self.probability = [val / norm for val in self.probability]
 

From 862189985b42253cebe12bcd6fc2888c954f6c09 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 19 Jun 2022 09:51:45 -0500
Subject: [PATCH 029/119] Check that output values do not exceed values in
 tabulated dist

---
 openmc/stats/univariate.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index bbac4c030..630bb665b 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -923,8 +923,6 @@ class Tabular(Univariate):
         x_i = self.x[cdf_idx]
         p_i = self.p[cdf_idx]
 
-        # TODO: check that probability doesn't exceed the last value
-
         if self.interpolation == 'histogram':
             # mask where probability is greater than zero
             pos_mask = p_i > 0.0
@@ -934,7 +932,9 @@ class Tabular(Univariate):
                            / p_i[pos_mask]
             # probabilities smaller than zero are set to the random number value
             p_i[~pos_mask] = x_i[~pos_mask]
-            return p_i
+
+            samples_out = p_i
+
         elif self.interpolation == 'linear-linear':
             # get variable and probability values for the
             # next entry
@@ -950,7 +950,10 @@ class Tabular(Univariate):
             quad = np.power(p_i[non_zero], 2) + 2.0 * m[non_zero] * (xi[non_zero] - c_i[non_zero])
             quad[quad < 0.0] = 0.0
             m[non_zero] = x_i[non_zero] + (np.sqrt(quad) - p_i[non_zero]) / m[non_zero]
-            return m
+            samples_out = m
+
+        assert all(samples_out < self.x[-1])
+        return samples_out
 
     def to_xml_element(self, element_name):
         """Return XML representation of the tabular distribution

From 967fc9f88bd7b22373505253eec7d5d6af3f7a4a Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 19 Jun 2022 10:00:27 -0500
Subject: [PATCH 030/119] Adding a 'mean' method to tabular dist

---
 openmc/stats/univariate.py     | 30 +++++++++++++++++++++++++++++-
 tests/unit_tests/test_stats.py | 27 ++-------------------------
 2 files changed, 31 insertions(+), 26 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index 630bb665b..ae89cb79f 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -138,7 +138,6 @@ class Discrete(Univariate):
 
     def sample(self, n_samples=1, seed=None):
         np.random.seed(seed)
-
         return np.random.choice(self.x, n_samples, p=self.p)
 
     def normalize(self):
@@ -892,6 +891,35 @@ class Tabular(Univariate):
 
         return np.cumsum(c)
 
+    def mean(self):
+        """Compute the mean of the tabular distribution"""
+        if not self.interpolation in ('histogram', 'linear-linear'):
+            raise NotImplementedError('Can only compute mean for tabular '
+                                      'distributions using histogram '
+                                      'or linear-linear interpolation.')
+        if self.interpolation == 'linear-linear':
+            mean = 0.0
+            self.normalize()
+            for i in range(1, len(self.x)):
+                y_min = self.p[i-1]
+                y_max = self.p[i]
+                x_min = self.x[i-1]
+                x_max = self.x[i]
+
+                m = (y_max - y_min) / (x_max - x_min)
+
+                exp_val = (1./3.) * m * (x_max**3 - x_min**3)
+                exp_val += 0.5 * m * x_min * (x_min**2 - x_max**2)
+                exp_val += 0.5 * y_min * (x_max**2 - x_min**2)
+                mean += exp_val
+
+        elif self.interpolation == 'histogram':
+            mean = 0.5 * (self.x[:-1] + self.x[1:])
+            mean *= np.diff(self.cdf())
+            mean = sum(mean)
+
+        return mean
+
     def normalize(self):
         """Normalize the probabilities stored on the distribution"""
         self.p = np.asarray(self.p) / self.cdf().max()
diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index f62f2157b..f789a0dca 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -40,7 +40,6 @@ def test_discrete():
     assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
 
 
-
 def test_merge_discrete():
     x1 = [0.0, 1.0, 10.0]
     p1 = [0.3, 0.2, 0.5]
@@ -164,38 +163,16 @@ def test_tabular():
     # test linear-linear sampling
     d = openmc.stats.Tabular(x, p)
 
-    # compute the expected value (mean) of the
-    # piecewise pdf
-    mean = 0.0
-    d.normalize()
-    for i in range(1, len(x)):
-        y_min = d.p[i-1]
-        y_max = d.p[i]
-        x_min = d.x[i-1]
-        x_max = d.x[i]
-
-        m = (y_max - y_min) / (x_max - x_min)
-
-        exp_val = (1./3.) * m * (x_max**3 - x_min**3)
-        exp_val += 0.5 * m * x_min * (x_min**2 - x_max**2)
-        exp_val += 0.5 * y_min * (x_max**2 - x_min**2)
-
-        mean += exp_val
-
     n_samples = 100_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(mean, rel=1e-03)
+    assert samples.mean() == pytest.approx(d.mean(), rel=1e-03)
 
     # test histogram sampling
     d = openmc.stats.Tabular(x, p, interpolation='histogram')
     d.normalize()
 
-    mean = 0.5 * (x[:-1] + x[1:])
-    mean *= np.diff(d.cdf())
-    mean = sum(mean)
-
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(mean, rel=1e-03)
+    assert samples.mean() == pytest.approx(d.mean(), rel=1e-03)
 
 
 def test_legendre():

From f92ea393f23a602ef56227e057091fd4a6f811d3 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Mon, 20 Jun 2022 06:39:55 -0500
Subject: [PATCH 031/119] Using np.random.choice in Mixture class

---
 openmc/stats/univariate.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/openmc/stats/univariate.py b/openmc/stats/univariate.py
index ae89cb79f..5528bdb30 100644
--- a/openmc/stats/univariate.py
+++ b/openmc/stats/univariate.py
@@ -1135,12 +1135,9 @@ class Mixture(Univariate):
 
     def sample(self, n_samples=1, seed=None):
         np.random.seed(seed)
-        xi = np.random.rand(n_samples)
-        idx = np.zeros_like(xi, dtype=int)
-        for i, c in enumerate(self.cdf()[:-1]):
-            idx[xi >= c] = i
+        idx = np.random.choice(self.distribution, n_samples, p=self.probability)
 
-        out = np.zeros_like(xi)
+        out = np.zeros_like(idx)
         for i in np.unique(idx):
             n_dist_samples = np.count_nonzero(idx == i)
             samples = self.distribution[i].sample(n_dist_samples)

From acd6c567c3e44b3cdee15278728f0d1f8e8918ea Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Tue, 21 Jun 2022 14:19:45 +0000
Subject: [PATCH 032/119] added test for remove eleemnt

---
 tests/unit_tests/test_material.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index 02e53a28d..3a976da99 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -38,6 +38,17 @@ def test_remove_nuclide():
     assert m.nuclides[1].percent == 2.0
 
 
+def test_remove_elements():
+    """Test removing elements."""
+    m = openmc.Material()
+    for elem, percent in [('Li', 1.0), ('Be', 1.0)]:
+        m.add_element(elem, percent)
+    m.remove_nuclide('Li')
+    assert len(m.nuclides) == 1
+    assert m.nuclides == ['Be9']
+    assert m.nuclides[0].percent == 1.0
+
+
 def test_elements():
     """Test adding elements."""
     m = openmc.Material()

From 8fe6c8244cd4e3988d39558d3069b2770099d395 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 21 Jun 2022 14:58:39 -0500
Subject: [PATCH 033/119] Set CMP0128 to NEW for recent versions of CMake

---
 CMakeLists.txt | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3cf72db20..85dcd7084 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -17,10 +17,15 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
 
 # Allow user to specify <project>_ROOT variables
-if (NOT (CMAKE_VERSION VERSION_LESS 3.12))
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
   cmake_policy(SET CMP0074 NEW)
 endif()
 
+# Enable correct usage of CXX_EXTENSIONS
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
+  cmake_policy(SET CMP0128 NEW)
+endif()
+
 #===============================================================================
 # Command line options
 #===============================================================================
@@ -118,7 +123,7 @@ endif()
 # Version 1.12 of HDF5 deprecates the H5Oget_info_by_idx() interface.
 # Thus, we give these flags to allow usage of the old interface in newer
 # versions of HDF5.
-if(NOT (${HDF5_VERSION} VERSION_LESS 1.12.0))
+if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0)
   list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1)
 endif()
 
@@ -205,7 +210,7 @@ endif()
 #===============================================================================
 
 # CMake 3.13+ will complain about policy CMP0079 unless it is set explicitly
-if (NOT (CMAKE_VERSION VERSION_LESS 3.13))
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
   cmake_policy(SET CMP0079 NEW)
 endif()
 

From 7bbc778fd7bb56dcb98eb787c14f711cae78711f Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Tue, 21 Jun 2022 23:27:44 +0100
Subject: [PATCH 034/119] [skip ci] review suggestions from @paulromano

---
 openmc/data/data.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index 5aadfac87..914c6c622 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -2,6 +2,7 @@ import itertools
 import json
 import os
 import re
+from pathlib import Path
 from math import sqrt
 from warnings import warn
 

From 87dafd1e3167a814f4e5b148e82242817cbf02e1 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Tue, 21 Jun 2022 23:14:49 +0000
Subject: [PATCH 035/119] review comments from @paulromano

---
 docs/source/pythonapi/data.rst | 1 +
 openmc/material.py             | 5 +++--
 setup.py                       | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/docs/source/pythonapi/data.rst b/docs/source/pythonapi/data.rst
index 95fdfeca9..6f5c006c2 100644
--- a/docs/source/pythonapi/data.rst
+++ b/docs/source/pythonapi/data.rst
@@ -63,6 +63,7 @@ Core Functions
     atomic_weight
     dose_coefficients
     gnd_name
+    half_life
     isotopes
     linearize
     thin
diff --git a/openmc/material.py b/openmc/material.py
index e49696706..70cfa7ade 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -152,9 +152,10 @@ class Material(IDManagerMixin):
         for key, value in atoms_per_barn_cm2.items():
             half_life = openmc.data.half_life(key)
             if half_life:
-                atoms = value[1] * self.volume * 1e24
-                activity = math.log(2) * atoms / half_life
+                atoms = value[1] * self.volume
+                activity = atoms / half_life
                 total_activity += activity
+        total_activity = math.log(2) * total_activity * 1e24
 
         return total_activity
 
diff --git a/setup.py b/setup.py
index b2e3f160a..477f29dec 100755
--- a/setup.py
+++ b/setup.py
@@ -32,7 +32,7 @@ kwargs = {
     # Data files and libraries
     'package_data': {
         'openmc.lib': ['libopenmc.{}'.format(suffix)],
-        'openmc.data': ['mass16.txt', 'BREMX.DAT', '*.h5'],
+        'openmc.data': ['mass16.txt', 'BREMX.DAT', 'half_life.json', '*.h5'],
         'openmc.data.effective_dose': ['*.txt']
     },
 

From 53b5cce209a9777368da90a53e29b7658b40295c Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Wed, 22 Jun 2022 08:01:07 +0100
Subject: [PATCH 036/119] Applying missed suggestions

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/data/data.py | 13 ++++++-------
 openmc/material.py  |  4 ++--
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index 914c6c622..d50afecc2 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -278,9 +278,9 @@ def atomic_weight(element):
 
 
 def half_life(isotope):
-    """Return half-life of isotope in seconds. Returns None if isotope is stable
+    """Return half-life of isotope in seconds or None if isotope is stable
 
-    Half-life values are from `ENDF/B VIII.0 Decay Reaction Sublibrary
+    Half-life values are from the `ENDF/B-VIII.0 decay sublibrary
     <https://www.nndc.bnl.gov/endf-b8.0/download.html>`_.
 
     Parameters
@@ -291,15 +291,14 @@ def half_life(isotope):
     Returns
     -------
     float
-        Half-life of isotope in [seconds]
+        Half-life of isotope in [s]
 
     """
     global _HALF_LIFE
     if not _HALF_LIFE:
-        # Load data from AME2016 file
-        half_life_filename = os.path.join(os.path.dirname(__file__), 'half_life.json')
-        with open(half_life_filename, 'r') as f:
-            _HALF_LIFE = json.load(f)
+        # Load ENDF/B-VIII.0 data from JSON file
+        half_life_path = Path(__file__).with_name('half_life.json')
+        _HALF_LIFE = json.load(half_life_path.read_text())
 
     if isotope.title() not in _HALF_LIFE.keys():
         return None
diff --git a/openmc/material.py b/openmc/material.py
index 70cfa7ade..95fd7aaf7 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -147,9 +147,9 @@ class Material(IDManagerMixin):
     def activity(self):
         """Returns the total activity of the material in Becquerels."""
 
-        atoms_per_barn_cm2 = self.get_nuclide_atom_densities()
+        atoms_per_barn_cm = self.get_nuclide_atom_densities()
         total_activity = 0
-        for key, value in atoms_per_barn_cm2.items():
+        for key, value in atoms_per_barn_cm.items():
             half_life = openmc.data.half_life(key)
             if half_life:
                 atoms = value[1] * self.volume

From 9b36424e1632aa69716f8f07a51fc8c68d6ad3bf Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 08:19:00 +0100
Subject: [PATCH 037/119] added remove element to material

---
 openmc/material.py                | 17 +++++++++++++++++
 tests/unit_tests/test_material.py |  2 +-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/openmc/material.py b/openmc/material.py
index de1b2187b..188ec2d47 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -407,6 +407,23 @@ class Material(IDManagerMixin):
             if nuclide == nuc.name:
                 self.nuclides.remove(nuc)
 
+    def remove_element(self, element):
+        """Remove an element from the material
+
+        Parameters
+        ----------
+        element : str
+            Element to remove
+
+        """
+        cv.check_type('element', element, str)
+
+        # If the Material contains the element, delete it
+        for nuc in reversed(self.nuclides):
+            element_name = re.split(r'(\d+)', nuc)
+            if nuc == element_name:
+                self.nuclides.remove(nuc)
+
     def add_macroscopic(self, macroscopic):
         """Add a macroscopic to the material.  This will also set the
         density of the material to 1.0, unless it has been otherwise set,
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index 3a976da99..dda75c88b 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -43,7 +43,7 @@ def test_remove_elements():
     m = openmc.Material()
     for elem, percent in [('Li', 1.0), ('Be', 1.0)]:
         m.add_element(elem, percent)
-    m.remove_nuclide('Li')
+    m.remove_element('Li')
     assert len(m.nuclides) == 1
     assert m.nuclides == ['Be9']
     assert m.nuclides[0].percent == 1.0

From 839c0fe81b1b65d205429f79dab317b3251b606a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 08:32:37 +0100
Subject: [PATCH 038/119] refined remove element

---
 openmc/material.py                | 5 +++--
 tests/unit_tests/test_material.py | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/openmc/material.py b/openmc/material.py
index 188ec2d47..d8fd1859f 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -420,8 +420,9 @@ class Material(IDManagerMixin):
 
         # If the Material contains the element, delete it
         for nuc in reversed(self.nuclides):
-            element_name = re.split(r'(\d+)', nuc)
-            if nuc == element_name:
+            element_name = re.split(r'(\d+)', nuc.name)[0]
+            print(element_name, element)
+            if element_name == element:
                 self.nuclides.remove(nuc)
 
     def add_macroscopic(self, macroscopic):
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index dda75c88b..bfa40bb21 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -45,7 +45,7 @@ def test_remove_elements():
         m.add_element(elem, percent)
     m.remove_element('Li')
     assert len(m.nuclides) == 1
-    assert m.nuclides == ['Be9']
+    assert m.nuclides[0].name == 'Be9'
     assert m.nuclides[0].percent == 1.0
 
 

From 649f4a28f260574725d9ae847a22d59ad42b69e3 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Wed, 22 Jun 2022 14:21:02 +0200
Subject: [PATCH 039/119] Apply suggestions from code review

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/data/data.py | 7 ++-----
 openmc/material.py  | 6 ++----
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index d50afecc2..108b3c63a 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -298,12 +298,9 @@ def half_life(isotope):
     if not _HALF_LIFE:
         # Load ENDF/B-VIII.0 data from JSON file
         half_life_path = Path(__file__).with_name('half_life.json')
-        _HALF_LIFE = json.load(half_life_path.read_text())
+        _HALF_LIFE = json.loads(half_life_path.read_text())
 
-    if isotope.title() not in _HALF_LIFE.keys():
-        return None
-
-    return _HALF_LIFE[isotope.title()]
+    return _HALF_LIFE.get(isotope.title())
 
 def water_density(temperature, pressure=0.1013):
     """Return the density of liquid water at a given temperature and pressure.
diff --git a/openmc/material.py b/openmc/material.py
index 95fd7aaf7..47f39b990 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -152,10 +152,8 @@ class Material(IDManagerMixin):
         for key, value in atoms_per_barn_cm.items():
             half_life = openmc.data.half_life(key)
             if half_life:
-                atoms = value[1] * self.volume
-                activity = atoms / half_life
-                total_activity += activity
-        total_activity = math.log(2) * total_activity * 1e24
+                total_activity += value[1] / half_life
+        total_activity *= math.log(2) * 1e24 * self.volume
 
         return total_activity
 

From a003c5850a9dba44355c1af50ce5661ec74d742f Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 14:59:21 +0100
Subject: [PATCH 040/119] added type hints to match doc strings

---
 openmc/material.py | 69 ++++++++++++++++++++++++++--------------------
 1 file changed, 39 insertions(+), 30 deletions(-)

diff --git a/openmc/material.py b/openmc/material.py
index de1b2187b..31e674611 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,8 +3,11 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
+import os
 import re
+import typing  # imported separately as py3.8 requires typing.Iterable
 import warnings
+from typing import Optional, Union
 from xml.etree import ElementTree as ET
 
 import numpy as np
@@ -206,7 +209,7 @@ class Material(IDManagerMixin):
         return self._volume
 
     @name.setter
-    def name(self, name):
+    def name(self, name: Optional[str]):
         if name is not None:
             cv.check_type(f'name for Material ID="{self._id}"',
                           name, str)
@@ -215,25 +218,25 @@ class Material(IDManagerMixin):
             self._name = ''
 
     @temperature.setter
-    def temperature(self, temperature):
+    def temperature(self, temperature: Optional[Real]):
         cv.check_type(f'Temperature for Material ID="{self._id}"',
                       temperature, (Real, type(None)))
         self._temperature = temperature
 
     @depletable.setter
-    def depletable(self, depletable):
+    def depletable(self, depletable: bool):
         cv.check_type(f'Depletable flag for Material ID="{self._id}"',
                       depletable, bool)
         self._depletable = depletable
 
     @volume.setter
-    def volume(self, volume):
+    def volume(self, volume: Real):
         if volume is not None:
             cv.check_type('material volume', volume, Real)
         self._volume = volume
 
     @isotropic.setter
-    def isotropic(self, isotropic):
+    def isotropic(self, isotropic: typing.Iterable[str]):
         cv.check_iterable_type('Isotropic scattering nuclides', isotropic,
                                str)
         self._isotropic = list(isotropic)
@@ -251,7 +254,7 @@ class Material(IDManagerMixin):
         return density*self.volume
 
     @classmethod
-    def from_hdf5(cls, group):
+    def from_hdf5(cls, group: str):
         """Create material from HDF5 group
 
         Parameters
@@ -305,7 +308,7 @@ class Material(IDManagerMixin):
 
         return material
 
-    def add_volume_information(self, volume_calc):
+    def add_volume_information(self, volume_calc: openmc.VolumeCalculation):
         """Add volume information to a material.
 
         Parameters
@@ -325,7 +328,7 @@ class Material(IDManagerMixin):
             raise ValueError('No volume information found for material ID={}.'
                 .format(self.id))
 
-    def set_density(self, units, density=None):
+    def set_density(self, units: str, density:Optional[float]=None):
         """Set the density of the material
 
         Parameters
@@ -357,7 +360,7 @@ class Material(IDManagerMixin):
                           density, Real)
             self._density = density
 
-    def add_nuclide(self, nuclide, percent, percent_type='ao'):
+    def add_nuclide(self, nuclide: str, percent: float, percent_type: str='ao'):
         """Add a nuclide to the material
 
         Parameters
@@ -391,7 +394,7 @@ class Material(IDManagerMixin):
 
         self._nuclides.append(NuclideTuple(nuclide, percent, percent_type))
 
-    def remove_nuclide(self, nuclide):
+    def remove_nuclide(self, nuclide: str):
         """Remove a nuclide from the material
 
         Parameters
@@ -407,7 +410,7 @@ class Material(IDManagerMixin):
             if nuclide == nuc.name:
                 self.nuclides.remove(nuc)
 
-    def add_macroscopic(self, macroscopic):
+    def add_macroscopic(self, macroscopic: str):
         """Add a macroscopic to the material.  This will also set the
         density of the material to 1.0, unless it has been otherwise set,
         as a default for Macroscopic cross sections.
@@ -449,7 +452,7 @@ class Material(IDManagerMixin):
         if self._density is None:
             self.set_density('macro', 1.0)
 
-    def remove_macroscopic(self, macroscopic):
+    def remove_macroscopic(self, macroscopic: str):
         """Remove a macroscopic from the material
 
         Parameters
@@ -468,8 +471,10 @@ class Material(IDManagerMixin):
         if macroscopic == self._macroscopic:
             self._macroscopic = None
 
-    def add_element(self, element, percent, percent_type='ao', enrichment=None,
-                    enrichment_target=None, enrichment_type=None):
+    def add_element(self, element: str, percent: float, percent_type: str='ao',
+                   enrichment: Optional[float]=None,
+                   enrichment_target: Optional[str]=None,
+                   enrichment_type: Optional[str]=None):
         """Add a natural element to the material
 
         Parameters
@@ -574,8 +579,10 @@ class Material(IDManagerMixin):
                                       enrichment_type):
             self.add_nuclide(*nuclide)
 
-    def add_elements_from_formula(self, formula, percent_type='ao', enrichment=None,
-                                  enrichment_target=None, enrichment_type=None):
+    def add_elements_from_formula(self, formula: str, percent_type: str='ao',
+                                  enrichment: Optional[float]=None,
+                                  enrichment_target: Optional[float]=None,
+                                  enrichment_type: Optional[str]=None):
         """Add a elements from a chemical formula to the material.
 
         .. versionadded:: 0.12
@@ -672,7 +679,7 @@ class Material(IDManagerMixin):
             else:
                 self.add_element(element, percent, percent_type)
 
-    def add_s_alpha_beta(self, name, fraction=1.0):
+    def add_s_alpha_beta(self, name: str, fraction: float=1.0):
         r"""Add an :math:`S(\alpha,\beta)` table to the material
 
         Parameters
@@ -821,7 +828,7 @@ class Material(IDManagerMixin):
 
         return nuclides
 
-    def get_mass_density(self, nuclide=None):
+    def get_mass_density(self, nuclide: Optional[str]=None):
         """Return mass density of one or all nuclides
 
         Parameters
@@ -844,7 +851,7 @@ class Material(IDManagerMixin):
                 mass_density += density_i
         return mass_density
 
-    def get_mass(self, nuclide=None):
+    def get_mass(self, nuclide: Optional[str]=None):
         """Return mass of one or all nuclides.
 
         Note that this method requires that the :attr:`Material.volume` has
@@ -866,7 +873,7 @@ class Material(IDManagerMixin):
             raise ValueError("Volume must be set in order to determine mass.")
         return self.volume*self.get_mass_density(nuclide)
 
-    def clone(self, memo=None):
+    def clone(self, memo: Optional[dict]=None):
         """Create a copy of this material with a new unique ID.
 
         Parameters
@@ -905,7 +912,7 @@ class Material(IDManagerMixin):
 
         return memo[self]
 
-    def _get_nuclide_xml(self, nuclide):
+    def _get_nuclide_xml(self, nuclide: str):
         xml_element = ET.Element("nuclide")
         xml_element.set("name", nuclide.name)
 
@@ -916,13 +923,13 @@ class Material(IDManagerMixin):
 
         return xml_element
 
-    def _get_macroscopic_xml(self, macroscopic):
+    def _get_macroscopic_xml(self, macroscopic: str):
         xml_element = ET.Element("macroscopic")
         xml_element.set("name", macroscopic)
 
         return xml_element
 
-    def _get_nuclides_xml(self, nuclides):
+    def _get_nuclides_xml(self, nuclides: typing.Iterable[str]):
         xml_elements = []
         for nuclide in nuclides:
             xml_elements.append(self._get_nuclide_xml(nuclide))
@@ -989,7 +996,9 @@ class Material(IDManagerMixin):
         return element
 
     @classmethod
-    def mix_materials(cls, materials, fracs, percent_type='ao', name=None):
+    def mix_materials(cls, materials: typing.Iterable[openmc.Material],
+                      fracs: typing.Iterable[float], percent_type: str='ao',
+                      name: Optional[str]=None):
         """Mix materials together based on atom, weight, or volume fractions
 
         .. versionadded:: 0.12
@@ -1087,7 +1096,7 @@ class Material(IDManagerMixin):
         return new_mat
 
     @classmethod
-    def from_xml_element(cls, elem):
+    def from_xml_element(cls, elem: ET.Element):
         """Generate material from an XML element
 
         Parameters
@@ -1190,7 +1199,7 @@ class Materials(cv.CheckedList):
         if cross_sections is not None:
             self._cross_sections = Path(cross_sections)
 
-    def append(self, material):
+    def append(self, material: openmc.Material):
         """Append material to collection
 
         Parameters
@@ -1201,7 +1210,7 @@ class Materials(cv.CheckedList):
         """
         super().append(material)
 
-    def insert(self, index, material):
+    def insert(self, index: int, material: openmc.Material):
         """Insert material before index
 
         Parameters
@@ -1218,7 +1227,7 @@ class Materials(cv.CheckedList):
         for material in self:
             material.make_isotropic_in_lab()
 
-    def export_to_xml(self, path='materials.xml'):
+    def export_to_xml(self, path: Union[str, os.PathLike]='materials.xml'):
         """Export material collection to an XML file.
 
         Parameters
@@ -1265,12 +1274,12 @@ class Materials(cv.CheckedList):
             fh.write('</materials>\n')
 
     @classmethod
-    def from_xml(cls, path='materials.xml'):
+    def from_xml(cls, path: Union[str, os.PathLike]='materials.xml'):
         """Generate materials collection from XML file
 
         Parameters
         ----------
-        path : str, optional
+        path : str
             Path to materials XML file
 
         Returns

From c2018c41fdc87d069e00cbe4e87cc07b87d8fc52 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Wed, 22 Jun 2022 22:45:37 +0200
Subject: [PATCH 041/119] More efficient regex usage

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/material.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/openmc/material.py b/openmc/material.py
index d8fd1859f..7e142f09a 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -420,8 +420,7 @@ class Material(IDManagerMixin):
 
         # If the Material contains the element, delete it
         for nuc in reversed(self.nuclides):
-            element_name = re.split(r'(\d+)', nuc.name)[0]
-            print(element_name, element)
+            element_name = re.split(r'\d+', nuc.name)[0]
             if element_name == element:
                 self.nuclides.remove(nuc)
 

From bebf729ad0872b48504243326e06c3a0dd587790 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 22:41:01 +0100
Subject: [PATCH 042/119] removed circular import types

---
 openmc/material.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/openmc/material.py b/openmc/material.py
index 31e674611..78655007f 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -308,7 +308,7 @@ class Material(IDManagerMixin):
 
         return material
 
-    def add_volume_information(self, volume_calc: openmc.VolumeCalculation):
+    def add_volume_information(self, volume_calc):
         """Add volume information to a material.
 
         Parameters
@@ -472,9 +472,9 @@ class Material(IDManagerMixin):
             self._macroscopic = None
 
     def add_element(self, element: str, percent: float, percent_type: str='ao',
-                   enrichment: Optional[float]=None,
-                   enrichment_target: Optional[str]=None,
-                   enrichment_type: Optional[str]=None):
+                    enrichment: Optional[float]=None,
+                    enrichment_target: Optional[str]=None,
+                    enrichment_type: Optional[str]=None):
         """Add a natural element to the material
 
         Parameters
@@ -996,9 +996,8 @@ class Material(IDManagerMixin):
         return element
 
     @classmethod
-    def mix_materials(cls, materials: typing.Iterable[openmc.Material],
-                      fracs: typing.Iterable[float], percent_type: str='ao',
-                      name: Optional[str]=None):
+    def mix_materials(cls, materials, fracs: typing.Iterable[float],
+                      percent_type: str='ao', name: Optional[str]=None):
         """Mix materials together based on atom, weight, or volume fractions
 
         .. versionadded:: 0.12
@@ -1199,7 +1198,7 @@ class Materials(cv.CheckedList):
         if cross_sections is not None:
             self._cross_sections = Path(cross_sections)
 
-    def append(self, material: openmc.Material):
+    def append(self, material):
         """Append material to collection
 
         Parameters
@@ -1210,7 +1209,7 @@ class Materials(cv.CheckedList):
         """
         super().append(material)
 
-    def insert(self, index: int, material: openmc.Material):
+    def insert(self, index: int, material):
         """Insert material before index
 
         Parameters

From 270ef8346ceadf03c1724db355f4ec06768e1f07 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 23:18:14 +0100
Subject: [PATCH 043/119] added metastable activity test

---
 tests/unit_tests/test_material.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index c5d3276a0..c56c350b0 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -423,3 +423,11 @@ def test_activity_of_tritium():
     m1.volume = 1
     assert pytest.approx(m1.activity) == 3.559778e14 
 
+
+def test_activity_of_metastable():
+    """Checks that 1 mol of a Tc99_m1 nuclides has the correct activity"""
+    m1 = openmc.Material()
+    m1.add_nuclide("Tc99_m1", 1)
+    m1.set_density('g/cm3', 1)
+    m1.volume = 98.9
+    assert pytest.approx(m1.activity, rel=0.001) == 1.93e19

From 344c2a46404cdc74a114efd2f78fb8bc86dc46e2 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Wed, 22 Jun 2022 23:27:41 +0100
Subject: [PATCH 044/119] lower case nucs in half-life

---
 openmc/data/data.py        |    2 +-
 openmc/data/half_life.json | 7122 ++++++++++++++++++------------------
 2 files changed, 3562 insertions(+), 3562 deletions(-)

diff --git a/openmc/data/data.py b/openmc/data/data.py
index 108b3c63a..3a3cf5826 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -300,7 +300,7 @@ def half_life(isotope):
         half_life_path = Path(__file__).with_name('half_life.json')
         _HALF_LIFE = json.loads(half_life_path.read_text())
 
-    return _HALF_LIFE.get(isotope.title())
+    return _HALF_LIFE.get(isotope.lower())
 
 def water_density(temperature, pressure=0.1013):
     """Return the density of liquid water at a given temperature and pressure.
diff --git a/openmc/data/half_life.json b/openmc/data/half_life.json
index bb67da75d..4f670918b 100644
--- a/openmc/data/half_life.json
+++ b/openmc/data/half_life.json
@@ -1,3563 +1,3563 @@
 {
-    "H3": 388789600.0,
-    "H4": 9.90652e-23,
-    "H5": 7.99473e-23,
-    "H6": 2.84812e-22,
-    "H7": 2.3e-23,
-    "He5": 7.595e-22,
-    "He6": 0.8067,
-    "He7": 3.038e-21,
-    "He8": 0.1191,
-    "He9": 7e-21,
-    "He10": 1.519e-21,
-    "Li4": 7.55721e-23,
-    "Li5": 3.06868e-22,
-    "Li8": 0.838,
-    "Li9": 0.1783,
-    "Li10": 2e-21,
-    "Li11": 0.00859,
-    "Li12": 1e-08,
-    "Be5": 1e-09,
-    "Be6": 4.95326e-21,
-    "Be7": 4598208.0,
-    "Be8": 8.18132e-17,
-    "Be10": 47652000000000.0,
-    "Be11": 13.81,
-    "Be12": 0.0213,
-    "Be13": 2.7e-21,
-    "Be14": 0.00435,
-    "Be15": 2e-07,
-    "Be16": 2e-07,
-    "B6": 1e-09,
-    "B7": 3.255e-22,
-    "B8": 0.77,
-    "B9": 8.43888e-19,
-    "B12": 0.0202,
-    "B13": 0.01736,
-    "B14": 0.0125,
-    "B15": 0.00993,
-    "B16": 1.9e-10,
-    "B17": 0.00508,
-    "B18": 2.6e-08,
-    "B19": 0.00292,
-    "C8": 1.9813e-21,
-    "C9": 0.1265,
-    "C10": 19.29,
-    "C11": 1223.1,
-    "C14": 179878000000.0,
-    "C15": 2.449,
-    "C16": 0.747,
-    "C17": 0.193,
-    "C18": 0.092,
-    "C19": 0.049,
-    "C20": 0.0145,
-    "C21": 3e-08,
-    "C22": 0.0062,
-    "N10": 2e-22,
-    "N11": 3.12742e-22,
-    "N12": 0.011,
-    "N13": 597.9,
-    "N16": 7.13,
-    "N17": 4.171,
-    "N18": 0.624,
-    "N19": 0.271,
-    "N20": 0.13,
-    "N21": 0.085,
-    "N22": 0.024,
-    "N23": 0.0145,
-    "N24": 5.2e-08,
-    "N25": 2.6e-07,
-    "O12": 1.13925e-21,
-    "O13": 0.00858,
-    "O14": 70.606,
-    "O15": 122.24,
-    "O19": 26.88,
-    "O20": 13.51,
-    "O21": 3.42,
-    "O22": 2.25,
-    "O23": 0.0905,
-    "O24": 0.065,
-    "O25": 5e-08,
-    "O26": 4e-08,
-    "O27": 2.6e-07,
-    "O28": 1e-07,
-    "F14": 5.0007e-22,
-    "F15": 4.557e-22,
-    "F16": 1.13925e-20,
-    "F17": 64.49,
-    "F18": 6586.2,
-    "F20": 11.163,
-    "F21": 4.158,
-    "F22": 4.23,
-    "F23": 2.23,
-    "F24": 0.39,
-    "F25": 0.05,
-    "F26": 0.0096,
-    "F27": 0.005,
-    "F28": 4e-08,
-    "F29": 0.0025,
-    "F30": 2.6e-07,
-    "F31": 2.5e-07,
-    "Ne16": 3.73524e-21,
-    "Ne17": 0.1092,
-    "Ne18": 1.672,
-    "Ne19": 17.22,
-    "Ne23": 37.24,
-    "Ne24": 202.8,
-    "Ne25": 0.602,
-    "Ne26": 0.197,
-    "Ne27": 0.032,
-    "Ne28": 0.0189,
-    "Ne29": 0.0148,
-    "Ne30": 0.0073,
-    "Ne31": 0.0034,
-    "Ne32": 0.0035,
-    "Ne33": 1.8e-07,
-    "Ne34": 6e-08,
-    "Na18": 1.3e-21,
-    "Na19": 4e-08,
-    "Na20": 0.4479,
-    "Na21": 22.49,
-    "Na22": 82134970.0,
-    "Na24": 53989.2,
-    "Na24_m1": 0.02018,
-    "Na25": 59.1,
-    "Na26": 1.077,
-    "Na27": 0.301,
-    "Na28": 0.0305,
-    "Na29": 0.0449,
-    "Na30": 0.048,
-    "Na31": 0.017,
-    "Na32": 0.0132,
-    "Na33": 0.008,
-    "Na34": 0.0055,
-    "Na35": 0.0015,
-    "Na36": 1.8e-07,
-    "Na37": 6e-08,
-    "Mg19": 4e-12,
-    "Mg20": 0.0908,
-    "Mg21": 0.122,
-    "Mg22": 3.8755,
-    "Mg23": 11.317,
-    "Mg27": 567.48,
-    "Mg28": 75294.0,
-    "Mg29": 1.3,
-    "Mg30": 0.335,
-    "Mg31": 0.232,
-    "Mg32": 0.086,
-    "Mg33": 0.0905,
-    "Mg34": 0.02,
-    "Mg35": 0.07,
-    "Mg36": 0.0039,
-    "Mg37": 2.6e-07,
-    "Mg38": 2.6e-07,
-    "Mg39": 1.8e-07,
-    "Mg40": 1.7e-07,
-    "Al21": 3.5e-08,
-    "Al22": 0.059,
-    "Al23": 0.47,
-    "Al24": 2.053,
-    "Al24_m1": 0.13,
-    "Al25": 7.183,
-    "Al26": 22626800000000.0,
-    "Al26_m1": 6.3452,
-    "Al28": 134.484,
-    "Al29": 393.6,
-    "Al30": 3.62,
-    "Al31": 0.644,
-    "Al32": 0.033,
-    "Al33": 0.0417,
-    "Al34": 0.042,
-    "Al35": 0.0386,
-    "Al36": 0.09,
-    "Al37": 0.0107,
-    "Al38": 0.0076,
-    "Al39": 7.6e-06,
-    "Al40": 2.6e-07,
-    "Al41": 2.6e-07,
-    "Al42": 1.7e-07,
-    "Si22": 0.029,
-    "Si23": 0.0423,
-    "Si24": 0.14,
-    "Si25": 0.22,
-    "Si26": 2.234,
-    "Si27": 4.16,
-    "Si31": 9438.0,
-    "Si32": 4828310000.0,
-    "Si33": 6.11,
-    "Si34": 2.77,
-    "Si35": 0.78,
-    "Si36": 0.45,
-    "Si37": 0.09,
-    "Si38": 1e-06,
-    "Si39": 0.0475,
-    "Si40": 0.033,
-    "Si41": 0.02,
-    "Si42": 0.0125,
-    "Si43": 6e-08,
-    "Si44": 3.6e-07,
-    "P24": 0.0074,
-    "P25": 3e-08,
-    "P26": 0.0437,
-    "P27": 0.26,
-    "P28": 0.2703,
-    "P29": 4.142,
-    "P30": 149.88,
-    "P32": 1232323.0,
-    "P33": 2189376.0,
-    "P34": 12.43,
-    "P35": 47.3,
-    "P36": 5.6,
-    "P37": 2.31,
-    "P38": 0.64,
-    "P39": 0.28,
-    "P40": 0.125,
-    "P41": 0.1,
-    "P42": 0.0485,
-    "P43": 0.0365,
-    "P44": 0.0185,
-    "P45": 2e-07,
-    "P46": 2e-07,
-    "S26": 0.01,
-    "S27": 0.0155,
-    "S28": 0.125,
-    "S29": 0.187,
-    "S30": 1.178,
-    "S31": 2.572,
-    "S35": 7560864.0,
-    "S37": 303.0,
-    "S38": 10218.0,
-    "S39": 11.5,
-    "S40": 8.8,
-    "S41": 1.99,
-    "S42": 1.013,
-    "S43": 0.28,
-    "S44": 0.1,
-    "S45": 0.068,
-    "S46": 0.05,
-    "S48": 2e-07,
-    "S49": 2e-07,
-    "Cl28": 0.0017,
-    "Cl29": 2e-08,
-    "Cl30": 3e-08,
-    "Cl31": 0.15,
-    "Cl32": 0.298,
-    "Cl33": 2.511,
-    "Cl34": 1.5264,
-    "Cl34_m1": 1920.0,
-    "Cl36": 9498840000000.0,
-    "Cl38": 2233.8,
-    "Cl38_m1": 0.715,
-    "Cl39": 3336.0,
-    "Cl40": 81.0,
-    "Cl41": 38.4,
-    "Cl42": 6.8,
-    "Cl43": 3.13,
-    "Cl44": 0.56,
-    "Cl45": 0.413,
-    "Cl46": 0.232,
-    "Cl47": 0.101,
-    "Cl48": 2e-07,
-    "Cl49": 1.7e-07,
-    "Cl50": 0.02,
-    "Cl51": 2e-07,
-    "Ar30": 2e-08,
-    "Ar31": 0.0151,
-    "Ar32": 0.098,
-    "Ar33": 0.173,
-    "Ar34": 0.8445,
-    "Ar35": 1.775,
-    "Ar37": 3027456.0,
-    "Ar39": 8488990000.0,
-    "Ar41": 6576.6,
-    "Ar42": 1038250000.0,
-    "Ar43": 322.2,
-    "Ar44": 712.2,
-    "Ar45": 21.48,
-    "Ar46": 8.4,
-    "Ar47": 1.23,
-    "Ar48": 0.475,
-    "Ar49": 0.17,
-    "Ar50": 0.085,
-    "Ar51": 2e-07,
-    "Ar52": 0.01,
-    "Ar53": 0.003,
-    "K32": 0.0033,
-    "K33": 2.5e-08,
-    "K34": 2.5e-08,
-    "K35": 0.178,
-    "K36": 0.342,
-    "K37": 1.226,
-    "K38": 458.16,
-    "K38_m1": 0.924,
-    "K40": 3.93839e16,
-    "K42": 44496.0,
-    "K43": 80280.0,
-    "K44": 1327.8,
-    "K45": 1068.6,
-    "K46": 105.0,
-    "K47": 17.5,
-    "K48": 6.8,
-    "K49": 1.26,
-    "K50": 0.472,
-    "K51": 0.365,
-    "K52": 0.105,
-    "K53": 0.03,
-    "K54": 0.01,
-    "K55": 0.003,
-    "Ca34": 3.5e-08,
-    "Ca35": 0.0257,
-    "Ca36": 0.102,
-    "Ca37": 0.1811,
-    "Ca38": 0.44,
-    "Ca39": 0.8596,
-    "Ca41": 3218880000000.0,
-    "Ca45": 14049500.0,
-    "Ca47": 391910.4,
-    "Ca48": 7.25824e26,
-    "Ca49": 523.08,
-    "Ca50": 13.9,
-    "Ca51": 10.0,
-    "Ca52": 4.6,
-    "Ca53": 0.09,
-    "Ca54": 0.086,
-    "Ca55": 0.022,
-    "Ca56": 0.01,
-    "Ca57": 0.005,
-    "Sc36": 0.0088,
-    "Sc37": 0.056,
-    "Sc38": 0.0423,
-    "Sc39": 3e-07,
-    "Sc40": 0.1823,
-    "Sc41": 0.5963,
-    "Sc42": 0.6808,
-    "Sc42_m1": 62.0,
-    "Sc43": 14007.6,
-    "Sc44": 14292.0,
-    "Sc44_m1": 210996.0,
-    "Sc45_m1": 0.318,
-    "Sc46": 7239456.0,
-    "Sc46_m1": 18.75,
-    "Sc47": 289370.9,
-    "Sc48": 157212.0,
-    "Sc49": 3430.8,
-    "Sc50": 102.5,
-    "Sc50_m1": 0.35,
-    "Sc51": 12.4,
-    "Sc52": 8.2,
-    "Sc53": 3.0,
-    "Sc54": 0.36,
-    "Sc55": 0.105,
-    "Sc56": 0.06,
-    "Sc57": 0.013,
-    "Sc58": 0.012,
-    "Sc59": 0.01,
-    "Sc60": 0.003,
-    "Ti38": 1.2e-07,
-    "Ti39": 0.032,
-    "Ti40": 0.0533,
-    "Ti41": 0.0804,
-    "Ti42": 0.199,
-    "Ti43": 0.509,
-    "Ti44": 1893460000.0,
-    "Ti45": 11088.0,
-    "Ti51": 345.6,
-    "Ti52": 102.0,
-    "Ti53": 32.7,
-    "Ti54": 1.5,
-    "Ti55": 1.3,
-    "Ti56": 0.2,
-    "Ti57": 0.06,
-    "Ti58": 0.059,
-    "Ti59": 0.03,
-    "Ti60": 0.022,
-    "Ti61": 3e-07,
-    "Ti62": 0.01,
-    "Ti63": 0.003,
-    "V40": 0.0077,
-    "V41": 0.0244,
-    "V42": 5.5e-08,
-    "V43": 0.8,
-    "V44": 0.111,
-    "V44_m1": 0.15,
-    "V45": 0.547,
-    "V46": 0.4225,
-    "V46_m1": 0.00102,
-    "V47": 1956.0,
-    "V48": 1380110.0,
-    "V49": 28512000.0,
-    "V50": 4.41806e24,
-    "V52": 224.58,
-    "V53": 92.58,
-    "V54": 49.8,
-    "V55": 6.54,
-    "V56": 0.216,
-    "V57": 0.35,
-    "V58": 0.185,
-    "V59": 0.075,
-    "V60": 0.068,
-    "V61": 0.047,
-    "V62": 1.5e-07,
-    "V63": 0.017,
-    "V64": 0.019,
-    "V65": 0.01,
-    "Cr42": 0.014,
-    "Cr43": 0.0216,
-    "Cr44": 0.0535,
-    "Cr45": 0.0609,
-    "Cr46": 0.26,
-    "Cr47": 0.5,
-    "Cr48": 77616.0,
-    "Cr49": 2538.0,
-    "Cr51": 2393366.0,
-    "Cr55": 209.82,
-    "Cr56": 356.4,
-    "Cr57": 21.1,
-    "Cr58": 7.0,
-    "Cr59": 0.46,
-    "Cr60": 0.49,
-    "Cr61": 0.27,
-    "Cr62": 0.19,
-    "Cr63": 0.129,
-    "Cr64": 0.043,
-    "Cr65": 0.027,
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From 3e61076715b9a15285b2d731127b968c600d7812 Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sat, 25 Jun 2022 14:38:19 +0200
Subject: [PATCH 045/119] Changing check for Tabular to use std. dev.

---
 tests/unit_tests/test_stats.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index f789a0dca..87d811881 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -165,14 +165,26 @@ def test_tabular():
 
     n_samples = 100_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(d.mean(), rel=1e-03)
+    diff = np.abs(samples - d.mean())
+    # within_1_sigma = np.count_nonzero(diff < samples.std())
+    # assert within_1_sigma / n_samples >= 0.68
+    within_2_sigma = np.count_nonzero(diff < 2*samples.std())
+    assert within_2_sigma / n_samples >= 0.95
+    within_3_sigma = np.count_nonzero(diff < 3*samples.std())
+    assert within_3_sigma / n_samples >= 0.99
 
     # test histogram sampling
     d = openmc.stats.Tabular(x, p, interpolation='histogram')
     d.normalize()
 
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(d.mean(), rel=1e-03)
+    diff = np.abs(samples - d.mean())
+    # within_1_sigma = np.count_nonzero(diff < samples.std())
+    # assert within_1_sigma / n_samples >= 0.68
+    within_2_sigma = np.count_nonzero(diff < 2*samples.std())
+    assert within_2_sigma / n_samples >= 0.95
+    within_3_sigma = np.count_nonzero(diff < 3*samples.std())
+    assert within_3_sigma / n_samples >= 0.99
 
 
 def test_legendre():

From e9eaf2edef09fe4cec82810d8669e6437d512a4d Mon Sep 17 00:00:00 2001
From: Patrick Shriwise <pshriwise@gmail.com>
Date: Sun, 26 Jun 2022 01:10:53 -0400
Subject: [PATCH 046/119] Using std. dev. of sampled mean for comparison

---
 tests/unit_tests/test_stats.py | 33 +++++++++++++++++++++++++--------
 1 file changed, 25 insertions(+), 8 deletions(-)

diff --git a/tests/unit_tests/test_stats.py b/tests/unit_tests/test_stats.py
index 87d811881..b57f9578a 100644
--- a/tests/unit_tests/test_stats.py
+++ b/tests/unit_tests/test_stats.py
@@ -36,8 +36,10 @@ def test_discrete():
     # sample discrete distribution
     n_samples = 1_000_000
     samples = d3.sample(n_samples, seed=100)
-    # check that the mean of the samples is close to the true mean
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples.mean()) < 3*std_dev
 
 
 def test_merge_discrete():
@@ -81,7 +83,10 @@ def test_uniform():
     exp_mean = 0.5 * (a + b)
     n_samples = 1_000_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples.mean()) < 3*std_dev
 
 
 def test_powerlaw():
@@ -100,7 +105,10 @@ def test_powerlaw():
     # sample power law distribution
     n_samples = 1_000_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples.mean()) < 3*std_dev
 
 
 def test_maxwell():
@@ -117,13 +125,19 @@ def test_maxwell():
     # sample maxwell distribution
     n_samples = 1_000_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-02)
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples.mean()) < 3*std_dev
 
     # A second sample with a different seed
     samples_2 = d.sample(n_samples, seed=200)
-    assert samples_2.mean() == pytest.approx(exp_mean, rel=1e-02)
-    assert samples_2.mean() != samples.mean()
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples_2.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples_2.mean()) < 3*std_dev
 
+    assert samples_2.mean() != samples.mean()
 
 
 def test_watt():
@@ -145,7 +159,10 @@ def test_watt():
     # sample Watt distribution
     n_samples = 1_000_000
     samples = d.sample(n_samples, seed=100)
-    assert samples.mean() == pytest.approx(exp_mean, rel=1e-03)
+    # check that the mean of the samples is within 3 std. dev.
+    # of the expected mean
+    std_dev = samples.std() / np.sqrt(n_samples)
+    assert np.abs(exp_mean - samples.mean()) < 3*std_dev
 
 
 def test_tabular():

From a4f98b489c161ed4b7ac26cca4e945d535ccaba3 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Mon, 23 May 2022 14:20:01 -0500
Subject: [PATCH 047/119] Change values in dict returned by
 Material.get_nuclide_atom_densities

---
 openmc/cell.py                              |  8 ++++----
 openmc/deplete/operator.py                  | 15 +++++++--------
 openmc/material.py                          | 20 ++++++++++++--------
 openmc/plotter.py                           | 12 ++++--------
 tests/unit_tests/test_deplete_activation.py |  2 +-
 tests/unit_tests/test_material.py           | 15 +++++++--------
 tests/unit_tests/test_model.py              | 18 ++++++++----------
 7 files changed, 43 insertions(+), 47 deletions(-)

diff --git a/openmc/cell.py b/openmc/cell.py
index 103a34fe6..4b419e1c6 100644
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -214,8 +214,8 @@ class Cell(IDManagerMixin):
                 self._atoms = self._fill.get_nuclide_atom_densities()
 
                 # Convert to total number of atoms
-                for key, nuclide in self._atoms.items():
-                    atom = nuclide[1] * self._volume * 1.0e+24
+                for key, atom_per_bcm in self._atoms.items():
+                    atom = atom_per_bcm * self._volume * 1.0e+24
                     self._atoms[key] = atom
 
             elif self.fill_type == 'distribmat':
@@ -224,12 +224,12 @@ class Cell(IDManagerMixin):
                 partial_volume = self.volume / len(self.fill)
                 self._atoms = OrderedDict()
                 for mat in self.fill:
-                    for key, nuclide in mat.get_nuclide_atom_densities().items():
+                    for key, atom_per_bcm in mat.get_nuclide_atom_densities().items():
                         # To account for overlap of nuclides between distribmat
                         # we need to append new atoms to any existing value
                         # hence it is necessary to ask for default.
                         atom = self._atoms.setdefault(key, 0)
-                        atom += nuclide[1] * partial_volume * 1.0e+24
+                        atom += atom_per_bcm * partial_volume * 1.0e+24
                         self._atoms[key] = atom
 
             else:
diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
index 327c762e0..7ef874e87 100644
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -528,9 +528,9 @@ class Operator(TransportOperator):
         """
         mat_id = str(mat.id)
 
-        for nuclide, density in mat.get_nuclide_atom_densities().values():
-            number = density * 1.0e24
-            self.number.set_atom_density(mat_id, nuclide, number)
+        for nuclide, atom_per_bcm in mat.get_nuclide_atom_densities().items():
+            atom_per_cc = atom_per_bcm * 1.0e24
+            self.number.set_atom_density(mat_id, nuclide, atom_per_cc)
 
     def _set_number_from_results(self, mat, prev_res):
         """Extracts material nuclides and number densities.
@@ -556,16 +556,15 @@ class Operator(TransportOperator):
         # Merge lists of nuclides, with the same order for every calculation
         geom_nuc_densities.update(depl_nuc)
 
-        for nuclide in geom_nuc_densities.keys():
+        for nuclide, atom_per_bcm in geom_nuc_densities.items():
             if nuclide in depl_nuc:
                 concentration = prev_res.get_atoms(mat_id, nuclide)[1][-1]
                 volume = prev_res[-1].volume[mat_id]
-                number = concentration / volume
+                atom_per_cc = concentration / volume
             else:
-                density = geom_nuc_densities[nuclide][1]
-                number = density * 1.0e24
+                atom_per_cc = atom_per_bcm * 1.0e24
 
-            self.number.set_atom_density(mat_id, nuclide, number)
+            self.number.set_atom_density(mat_id, nuclide, atom_per_cc)
 
     def initial_condition(self):
         """Performs final setup and returns initial condition.
diff --git a/openmc/material.py b/openmc/material.py
index 3c2a98ffd..073dab712 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -259,10 +259,10 @@ class Material(IDManagerMixin):
         if self.volume is None:
             raise ValueError("Volume must be set in order to determine mass.")
         density = 0.0
-        for nuc, atoms_per_cc in self.get_nuclide_atom_densities().values():
+        for nuc, atoms_per_bcm in self.get_nuclide_atom_densities().items():
             Z = openmc.data.zam(nuc)[0]
             if Z >= 90:
-                density += 1e24 * atoms_per_cc * openmc.data.atomic_mass(nuc) \
+                density += 1e24 * atoms_per_bcm * openmc.data.atomic_mass(nuc) \
                            / openmc.data.AVOGADRO
         return density*self.volume
 
@@ -786,11 +786,15 @@ class Material(IDManagerMixin):
         """Returns all nuclides in the material and their atomic densities in
         units of atom/b-cm
 
+        .. versionchanged:: 0.13.1
+            The values in the dictionary were changed from a tuple containing
+            the nuclide name and the density to just the density.
+
         Returns
         -------
         nuclides : dict
-            Dictionary whose keys are nuclide names and values are tuples of
-            (nuclide, density in atom/b-cm)
+            Dictionary whose keys are nuclide names and values are densities in
+            [atom/b-cm]
 
         """
 
@@ -850,7 +854,7 @@ class Material(IDManagerMixin):
 
         nuclides = OrderedDict()
         for n, nuc in enumerate(nucs):
-            nuclides[nuc] = (nuc, nuc_densities[n])
+            nuclides[nuc] = nuc_densities[n]
 
         return nuclides
 
@@ -870,9 +874,9 @@ class Material(IDManagerMixin):
 
         """
         mass_density = 0.0
-        for nuc, atoms_per_cc in self.get_nuclide_atom_densities().values():
+        for nuc, atoms_per_bcm in self.get_nuclide_atom_densities().items():
             if nuclide is None or nuclide == nuc:
-                density_i = 1e24 * atoms_per_cc * openmc.data.atomic_mass(nuc) \
+                density_i = 1e24 * atoms_per_bcm * openmc.data.atomic_mass(nuc) \
                             / openmc.data.AVOGADRO
                 mass_density += density_i
         return mass_density
@@ -1092,7 +1096,7 @@ class Material(IDManagerMixin):
         nuclides_per_cc = defaultdict(float)
         mass_per_cc = defaultdict(float)
         for mat, wgt in zip(materials, wgts):
-            for nuc, atoms_per_bcm in mat.get_nuclide_atom_densities().values():
+            for nuc, atoms_per_bcm in mat.get_nuclide_atom_densities().items():
                 nuc_per_cc = wgt*1.e24*atoms_per_bcm
                 nuclides_per_cc[nuc] += nuc_per_cc
                 mass_per_cc[nuc] += nuc_per_cc*openmc.data.atomic_mass(nuc) / \
diff --git a/openmc/plotter.py b/openmc/plotter.py
index 92acaf5bb..16760868e 100644
--- a/openmc/plotter.py
+++ b/openmc/plotter.py
@@ -542,15 +542,11 @@ def _calculate_cexs_elem_mat(this, types, temperature=294.,
 
     if isinstance(this, openmc.Material):
         # Expand elements in to nuclides with atomic densities
-        nuclides = this.get_nuclide_atom_densities()
-        # For ease of processing split out the nuclide and its fraction
-        nuc_fractions = {nuclide[1][0]: nuclide[1][1]
-                         for nuclide in nuclides.items()}
+        nuc_fractions = this.get_nuclide_atom_densities()
         # Create a dict of [nuclide name] = nuclide object to carry forward
         # with a common nuclides format between openmc.Material and
         # openmc.Element objects
-        nuclides = {nuclide[1][0]: nuclide[1][0]
-                    for nuclide in nuclides.items()}
+        nuclides = {nuclide: nuclide for nuclide in nuc_fractions}
     else:
         # Expand elements in to nuclides with atomic densities
         nuclides = this.expand(1., 'ao', enrichment=enrichment,
@@ -885,13 +881,13 @@ def _calculate_mgxs_elem_mat(this, types, library, orders=None,
         # Check to see if we have nuclides/elements or a macroscopic object
         if this._macroscopic is not None:
             # We have macroscopics
-            nuclides = {this._macroscopic: (this._macroscopic, this.density)}
+            nuclides = {this._macroscopic: this.density}
         else:
             # Expand elements in to nuclides with atomic densities
             nuclides = this.get_nuclide_atom_densities()
 
         # For ease of processing split out nuc and nuc_density
-        nuc_fraction = [nuclide[1][1] for nuclide in nuclides.items()]
+        nuc_fraction = list(nuclides.values())
     else:
         T = temperature
         # Expand elements in to nuclides with atomic densities
diff --git a/tests/unit_tests/test_deplete_activation.py b/tests/unit_tests/test_deplete_activation.py
index 0b82a5fbc..cb3b86b9c 100644
--- a/tests/unit_tests/test_deplete_activation.py
+++ b/tests/unit_tests/test_deplete_activation.py
@@ -92,7 +92,7 @@ def test_activation(run_in_tmpdir, model, reaction_rate_mode, reaction_rate_opts
 
     w = model.geometry.get_materials_by_name('tungsten')[0]
     atom_densities = w.get_nuclide_atom_densities()
-    atom_per_cc = 1e24 * atom_densities['W186'][1]  # Density in atom/cm^3
+    atom_per_cc = 1e24 * atom_densities['W186']  # Density in atom/cm^3
     n0 = atom_per_cc * w.volume  # Absolute number of atoms
 
     # Pick a random irradiation time and then determine necessary source rate to
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index c15a4b9e5..374b5a3d8 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -100,7 +100,7 @@ def test_add_elements_by_formula():
     m.add_elements_from_formula('Li4SiO4')
     # checking the ratio of elements is 4:1:4 for Li:Si:O
     elem = defaultdict(float)
-    for nuclide, adens in m.get_nuclide_atom_densities().values():
+    for nuclide, adens in m.get_nuclide_atom_densities().items():
         if nuclide.startswith("Li"):
             elem["Li"] += adens
         if nuclide.startswith("Si"):
@@ -117,7 +117,7 @@ def test_add_elements_by_formula():
                 'O16': 0.443386, 'O17': 0.000168}
     nuc_dens = m.get_nuclide_atom_densities()
     for nuclide in ref_dens:
-        assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
+        assert nuc_dens[nuclide] == pytest.approx(ref_dens[nuclide], 1e-2)
 
     # testing the correct nuclides are added to the Material when enriched
     m = openmc.Material()
@@ -129,7 +129,7 @@ def test_add_elements_by_formula():
                 'O16': 0.443386, 'O17': 0.000168}
     nuc_dens = m.get_nuclide_atom_densities()
     for nuclide in ref_dens:
-        assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
+        assert nuc_dens[nuclide] == pytest.approx(ref_dens[nuclide], 1e-2)
 
     # testing the use of brackets
     m = openmc.Material()
@@ -137,7 +137,7 @@ def test_add_elements_by_formula():
 
     # checking the ratio of elements is 2:2:6 for Mg:N:O
     elem = defaultdict(float)
-    for nuclide, adens in m.get_nuclide_atom_densities().values():
+    for nuclide, adens in m.get_nuclide_atom_densities().items():
         if nuclide.startswith("Mg"):
             elem["Mg"] += adens
         if nuclide.startswith("N"):
@@ -155,7 +155,7 @@ def test_add_elements_by_formula():
                 'O16': 0.599772, 'O17': 0.000227}
     nuc_dens = m.get_nuclide_atom_densities()
     for nuclide in ref_dens:
-        assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
+        assert nuc_dens[nuclide] == pytest.approx(ref_dens[nuclide], 1e-2)
 
     # testing non integer multiplier results in a value error
     m = openmc.Material()
@@ -289,8 +289,7 @@ def test_get_nuclide_densities(uo2):
 
 
 def test_get_nuclide_atom_densities(uo2):
-    nucs = uo2.get_nuclide_atom_densities()
-    for nuc, density in nucs.values():
+    for nuc, density in uo2.get_nuclide_atom_densities().items():
         assert nuc in ('U235', 'O16')
         assert density > 0
 
@@ -341,7 +340,7 @@ def test_borated_water():
                 'O16':2.4672e-02}
     nuc_dens = m.get_nuclide_atom_densities()
     for nuclide in ref_dens:
-        assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
+        assert nuc_dens[nuclide] == pytest.approx(ref_dens[nuclide], 1e-2)
     assert m.id == 50
 
     # Test the Celsius conversion.
diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py
index 10417b20e..9b05ed2a5 100644
--- a/tests/unit_tests/test_model.py
+++ b/tests/unit_tests/test_model.py
@@ -391,16 +391,14 @@ def test_py_lib_attributes(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
     assert openmc.lib.materials[1].get_density('atom/b-cm') == \
         pytest.approx(0.06891296988603757, abs=1e-13)
     mat_a_dens = np.sum(
-        [v[1] for v in test_model.materials[0].
-            get_nuclide_atom_densities().values()])
+        list(test_model.materials[0].get_nuclide_atom_densities().values()))
     assert mat_a_dens == pytest.approx(0.06891296988603757, abs=1e-8)
     # Change the density
     test_model.update_densities(['UO2'], 2.)
     assert openmc.lib.materials[1].get_density('atom/b-cm') == \
         pytest.approx(2., abs=1e-13)
     mat_a_dens = np.sum(
-        [v[1] for v in test_model.materials[0].
-            get_nuclide_atom_densities().values()])
+        list(test_model.materials[0].get_nuclide_atom_densities().values()))
     assert mat_a_dens == pytest.approx(2., abs=1e-8)
 
     # Now lets do the cell temperature updates.
@@ -441,7 +439,7 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
     test_model = openmc.Model(geom, mats, settings, tals, plots)
 
     initial_mat = mats[0].clone()
-    initial_u = initial_mat.get_nuclide_atom_densities()['U235'][1]
+    initial_u = initial_mat.get_nuclide_atom_densities()['U235']
 
     # Note that the chain file includes only U-235 fission to a stable Xe136 w/
     # a yield of 100%. Thus all the U235 we lose becomes Xe136
@@ -453,8 +451,8 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
                        operator_kwargs=op_kwargs,
                        power=1., output=False)
     # Get the new Xe136 and U235 atom densities
-    after_xe = mats[0].get_nuclide_atom_densities()['Xe136'][1]
-    after_u = mats[0].get_nuclide_atom_densities()['U235'][1]
+    after_xe = mats[0].get_nuclide_atom_densities()['Xe136']
+    after_u = mats[0].get_nuclide_atom_densities()['U235']
     assert after_xe + after_u == pytest.approx(initial_u, abs=1e-15)
     assert test_model.is_initialized is False
 
@@ -462,7 +460,7 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
     mats[0].nuclides.clear()
     densities = initial_mat.get_nuclide_atom_densities()
     tot_density = 0.
-    for nuc, density in densities.values():
+    for nuc, density in densities.items():
         mats[0].add_nuclide(nuc, density)
         tot_density += density
     mats[0].set_density('atom/b-cm', tot_density)
@@ -473,8 +471,8 @@ def test_deplete(run_in_tmpdir, pin_model_attributes, mpi_intracomm):
                        operator_kwargs=op_kwargs,
                        power=1., output=False)
     # Get the new Xe136 and U235 atom densities
-    after_lib_xe = mats[0].get_nuclide_atom_densities()['Xe136'][1]
-    after_lib_u = mats[0].get_nuclide_atom_densities()['U235'][1]
+    after_lib_xe = mats[0].get_nuclide_atom_densities()['Xe136']
+    after_lib_u = mats[0].get_nuclide_atom_densities()['U235']
     assert after_lib_xe + after_lib_u == pytest.approx(initial_u, abs=1e-15)
     assert test_model.is_initialized is True
 

From 7fcc20472690c49cf2b0508b099dc440b6249dc4 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Mon, 23 May 2022 14:43:34 -0500
Subject: [PATCH 048/119] Implement Material.get_nuclide_atoms method

---
 openmc/material.py                | 19 +++++++++++++++++++
 tests/unit_tests/test_material.py | 10 ++++++++++
 2 files changed, 29 insertions(+)

diff --git a/openmc/material.py b/openmc/material.py
index 073dab712..ea42d64b1 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -858,6 +858,25 @@ class Material(IDManagerMixin):
 
         return nuclides
 
+    def get_nuclide_atoms(self):
+        """Return number of atoms of each nuclide in the material
+
+        .. versionadded:: 0.13.1
+
+        Returns
+        -------
+        dict
+            Dictionary whose keys are nuclide names and values are number of
+            atoms present in the material.
+
+        """
+        if self.volume is None:
+            raise ValueError("Volume must be set in order to determine atoms.")
+        atoms = {}
+        for nuclide, atom_per_bcm in self.get_nuclide_atom_densities().items():
+            atoms[nuclide] = 1.0e24 * atom_per_bcm * self.volume
+        return atoms
+
     def get_mass_density(self, nuclide=None):
         """Return mass density of one or all nuclides
 
diff --git a/tests/unit_tests/test_material.py b/tests/unit_tests/test_material.py
index 374b5a3d8..fd0e4f624 100644
--- a/tests/unit_tests/test_material.py
+++ b/tests/unit_tests/test_material.py
@@ -294,6 +294,16 @@ def test_get_nuclide_atom_densities(uo2):
         assert density > 0
 
 
+def test_get_nuclide_atoms():
+    mat = openmc.Material()
+    mat.add_nuclide('Li6', 1.0)
+    mat.set_density('atom/cm3', 3.26e20)
+    mat.volume = 100.0
+
+    atoms = mat.get_nuclide_atoms()
+    assert atoms['Li6'] == pytest.approx(mat.density * mat.volume)
+
+
 def test_mass():
     m = openmc.Material()
     m.add_nuclide('Zr90', 1.0, 'wo')

From 19494cccd022cdf9ee9c0c8e6461bea494d95e69 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 24 May 2022 12:47:36 -0500
Subject: [PATCH 049/119] Add check in Decay.decay_constant for erroneous
 half-life

---
 openmc/data/decay.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/openmc/data/decay.py b/openmc/data/decay.py
index 5ca2b235a..51a594bc8 100644
--- a/openmc/data/decay.py
+++ b/openmc/data/decay.py
@@ -465,11 +465,10 @@ class Decay(EqualityMixin):
 
     @property
     def decay_constant(self):
-        if hasattr(self.half_life, 'n'):
-            return log(2.)/self.half_life
-        else:
-            mu, sigma = self.half_life
-            return ufloat(log(2.)/mu, log(2.)/mu**2*sigma)
+        if self.half_life.n == 0.0:
+            name = self.nuclide['name']
+            raise ValueError(f"{name} is listed as unstable but has a zero half-life.")
+        return log(2.)/self.half_life
 
     @property
     def decay_energy(self):

From 3c20b1e415e89b1b2b2b8e4953710f0b6851fb62 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 28 Jun 2022 08:00:16 -0500
Subject: [PATCH 050/119] Fix use of get_nuclide_atom_densities in
 Material.activity property

---
 openmc/material.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/openmc/material.py b/openmc/material.py
index ea42d64b1..1341746dc 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -86,6 +86,9 @@ class Material(IDManagerMixin):
     fissionable_mass : float
         Mass of fissionable nuclides in the material in [g]. Requires that the
         :attr:`volume` attribute is set.
+    activity : float
+        Activity of the material in [Bq]. Requires that the :attr:`volume`
+        attribute is set.
 
     """
 
@@ -152,7 +155,7 @@ class Material(IDManagerMixin):
         for key, value in atoms_per_barn_cm.items():
             half_life = openmc.data.half_life(key)
             if half_life:
-                total_activity += value[1] / half_life
+                total_activity += value / half_life
         total_activity *= math.log(2) * 1e24 * self.volume
 
         return total_activity

From fc615451d04c358d0f32bb72837fc52992fb39b0 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 15:54:49 +0200
Subject: [PATCH 051/119] added method to Tally

---
 openmc/tallies.py | 86 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index d0355f14e..f559c392c 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -8,6 +8,8 @@ from pathlib import Path
 from xml.etree import ElementTree as ET
 
 import h5py
+import vtk
+import vtk.util.numpy_support as nps
 import numpy as np
 import pandas as pd
 import scipy.sparse as sps
@@ -457,6 +459,54 @@ class Tally(IDManagerMixin):
                 self._std_dev = np.reshape(self._std_dev.toarray(), self.shape)
             self._sparse = False
 
+    def write_to_vtk(self, filename):
+        mesh = None
+        for f in self.filters:
+            if isinstance(f, openmc.MeshFilter):
+                if isinstance(f.mesh, (openmc.RegularMesh, openmc.CylindricalMesh)):
+                    mesh = f.mesh
+                    break
+
+        if not mesh:
+            raise ValueError(
+                "write_to_vtk only works with openmc.RegularMesh, openmc.CylindricalMesh"
+            )
+
+        if isinstance(mesh, openmc.RegularMesh):
+            vtk_grid = voxels_to_vtk(
+                x_vals=np.linspace(
+                    mesh.lower_left[0],
+                    mesh.upper_right[0],
+                    num=mesh.dimension[0] + 1,
+                ),
+                y_vals=np.linspace(
+                    mesh.lower_left[1],
+                    mesh.upper_right[1],
+                    num=mesh.dimension[1] + 1,
+                ),
+                z_vals=np.linspace(
+                    mesh.lower_left[2],
+                    mesh.upper_right[2],
+                    num=mesh.dimension[2] + 1,
+                ),
+                mean=self.mean,
+                std_dev=self.std_dev,
+                cylindrical=False,
+            )
+        elif isinstance(mesh, openmc.CylindricalMesh):
+            vtk_grid = voxels_to_vtk(
+                x_vals=mesh.r_grid,
+                y_vals=mesh.phi_grid,
+                z_vals=mesh.z_grid,
+                mean=self.mean,
+                std_dev=self.std_dev,
+                cylindrical=True,
+            )
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
+
     def remove_score(self, score):
         """Remove a score from the tally
 
@@ -3229,3 +3279,39 @@ class Tallies(cv.CheckedList):
             tallies.append(tally)
 
         return cls(tallies)
+
+
+def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
+    vtk_box = vtk.vtkStructuredGrid()
+
+    vtk_box.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
+
+    # points
+    points = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
+    if cylindrical:
+        points_cartesian = np.copy(points)
+        r = points[:, 0]
+        phi = points[:, 1]
+        z = points[:, 2]
+        points_cartesian[:, 0] = r * np.cos(phi)
+        points_cartesian[:, 1] = r * np.sin(phi)
+        points_cartesian[:, 2] = z
+
+    vtkPts = vtk.vtkPoints()
+    vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))
+
+    vtk_box.SetPoints(vtkPts)
+
+    # # data
+    mean_array = vtk.vtkDoubleArray()
+    mean_array.SetName("mean")
+    mean_array.SetArray(mean, mean.size, True)
+
+    std_dev_array = vtk.vtkDoubleArray()
+    std_dev_array.SetName("std_dev")
+    std_dev_array.SetArray(std_dev, std_dev.size, True)
+
+    vtk_box.GetCellData().AddArray(mean_array)
+    vtk_box.GetCellData().AddArray(std_dev_array)
+
+    return vtk_box

From e870ab2040e6d2a9894eb99e413a5174f83ae546 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:00:54 +0200
Subject: [PATCH 052/119] added RectilinearMesh

---
 openmc/tallies.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index f559c392c..20e6e3996 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -463,13 +463,13 @@ class Tally(IDManagerMixin):
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):
-                if isinstance(f.mesh, (openmc.RegularMesh, openmc.CylindricalMesh)):
+                if isinstance(f.mesh, (openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh)):
                     mesh = f.mesh
                     break
 
         if not mesh:
             raise ValueError(
-                "write_to_vtk only works with openmc.RegularMesh, openmc.CylindricalMesh"
+                "write_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
             )
 
         if isinstance(mesh, openmc.RegularMesh):
@@ -493,6 +493,15 @@ class Tally(IDManagerMixin):
                 std_dev=self.std_dev,
                 cylindrical=False,
             )
+        if isinstance(mesh, openmc.RectilinearMesh):
+            vtk_grid = voxels_to_vtk(
+                x_vals=mesh.x_grid,
+                y_vals=mesh.y_grid,
+                z_vals=mesh.z_grid,
+                mean=self.mean,
+                std_dev=self.std_dev,
+                cylindrical=False,
+            )
         elif isinstance(mesh, openmc.CylindricalMesh):
             vtk_grid = voxels_to_vtk(
                 x_vals=mesh.r_grid,

From 06c5d3ec584c9ef9a62b08c561945b34e2e6b4e9 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:04:33 +0200
Subject: [PATCH 053/119] added comments

---
 openmc/tallies.py | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 20e6e3996..6797253e1 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -460,6 +460,7 @@ class Tally(IDManagerMixin):
             self._sparse = False
 
     def write_to_vtk(self, filename):
+        # check that tally has a MeshFilter
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):
@@ -511,6 +512,8 @@ class Tally(IDManagerMixin):
                 std_dev=self.std_dev,
                 cylindrical=True,
             )
+        
+        # write the .vtk file
         writer = vtk.vtkStructuredGridWriter()
         writer.SetFileName(filename)
         writer.SetInputData(vtk_grid)
@@ -3291,36 +3294,32 @@ class Tallies(cv.CheckedList):
 
 
 def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
-    vtk_box = vtk.vtkStructuredGrid()
+    vtk_grid = vtk.vtkStructuredGrid()
 
-    vtk_box.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
+    vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
 
-    # points
+    # create points
     points = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
-    if cylindrical:
+    if cylindrical:  # transform points to cartesian coordinates
         points_cartesian = np.copy(points)
-        r = points[:, 0]
-        phi = points[:, 1]
-        z = points[:, 2]
+        r, phi, z = points[:, 0], points[:, 1], points[:, 2]
         points_cartesian[:, 0] = r * np.cos(phi)
         points_cartesian[:, 1] = r * np.sin(phi)
         points_cartesian[:, 2] = z
 
     vtkPts = vtk.vtkPoints()
     vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))
+    vtk_grid.SetPoints(vtkPts)
 
-    vtk_box.SetPoints(vtkPts)
-
-    # # data
+    # add mean and std dev data
     mean_array = vtk.vtkDoubleArray()
     mean_array.SetName("mean")
     mean_array.SetArray(mean, mean.size, True)
+    vtk_grid.GetCellData().AddArray(mean_array)
 
     std_dev_array = vtk.vtkDoubleArray()
     std_dev_array.SetName("std_dev")
     std_dev_array.SetArray(std_dev, std_dev.size, True)
+    vtk_grid.GetCellData().AddArray(std_dev_array)
 
-    vtk_box.GetCellData().AddArray(mean_array)
-    vtk_box.GetCellData().AddArray(std_dev_array)
-
-    return vtk_box
+    return vtk_grid

From 30b06fa2910a51ac04a249170bff27d54cb3f26a Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:08:36 +0200
Subject: [PATCH 054/119] docstrings

---
 openmc/tallies.py | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 6797253e1..77f0b8cd3 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -460,6 +460,15 @@ class Tally(IDManagerMixin):
             self._sparse = False
 
     def write_to_vtk(self, filename):
+        """Writes the tally to a vtk file
+
+        Args:
+            filename (str): the filename (must end with .vtk)
+
+        Raises:
+            ValueError: if no MeshFilter with appropriate mesh was found 
+                (SphericalMesh not supported)
+        """
         # check that tally has a MeshFilter
         mesh = None
         for f in self.filters:
@@ -512,7 +521,7 @@ class Tally(IDManagerMixin):
                 std_dev=self.std_dev,
                 cylindrical=True,
             )
-        
+
         # write the .vtk file
         writer = vtk.vtkStructuredGridWriter()
         writer.SetFileName(filename)
@@ -3294,6 +3303,20 @@ class Tallies(cv.CheckedList):
 
 
 def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
+    """Creates a vtk object from a list of X, Y, Z values and mean/std_dev data.
+
+    Args:
+        x_vals (list): X values.
+        y_vals (list): Y values.
+        z_vals (list): Z values.
+        mean (np.array): the tally mean.
+        std_dev (np.array): the tally standard deviation.
+        cylindrical (bool, optional): If set to True, cylindrical coordinates
+            (r, phi, z) are assumed. Defaults to True.
+
+    Returns:
+        vtkStructuredGrid: a vtk object containing tally data on the appropriate grid
+    """
     vtk_grid = vtk.vtkStructuredGrid()
 
     vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))

From 06c6bcd7d269aa3b3317c8d64f9cf4318170468c Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:09:32 +0200
Subject: [PATCH 055/119] added TODO

---
 openmc/tallies.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 77f0b8cd3..c0f410524 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3317,6 +3317,9 @@ def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
     Returns:
         vtkStructuredGrid: a vtk object containing tally data on the appropriate grid
     """
+
+    # TODO: should this be a method of Tally?
+
     vtk_grid = vtk.vtkStructuredGrid()
 
     vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))

From 877a62c0af072e14c3b62991f21a6648352dc8bb Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:43:42 +0200
Subject: [PATCH 056/119] fixed cylindrical

---
 openmc/tallies.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index c0f410524..2e31e8ee2 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3332,6 +3332,7 @@ def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
         points_cartesian[:, 0] = r * np.cos(phi)
         points_cartesian[:, 1] = r * np.sin(phi)
         points_cartesian[:, 2] = z
+        points = points_cartesian
 
     vtkPts = vtk.vtkPoints()
     vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))

From 1eb8670f2b93cbbb42912dd7903c1d1ae18b1d33 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Tue, 28 Jun 2022 16:46:10 +0200
Subject: [PATCH 057/119] mean and std_dev are np.zeros if None (for testing
 without running a sim)

---
 openmc/tallies.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 2e31e8ee2..75c7ea8f3 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3341,11 +3341,23 @@ def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
     # add mean and std dev data
     mean_array = vtk.vtkDoubleArray()
     mean_array.SetName("mean")
+    if mean is None:
+        mean = np.zeros(
+            (len(x_vals) - 1)
+            * (len(y_vals) - 1)
+            * (len(z_vals) - 1)
+        )
     mean_array.SetArray(mean, mean.size, True)
     vtk_grid.GetCellData().AddArray(mean_array)
 
     std_dev_array = vtk.vtkDoubleArray()
     std_dev_array.SetName("std_dev")
+    if std_dev is None:
+        std_dev = np.zeros(
+            (len(x_vals) - 1)
+            * (len(y_vals) - 1)
+            * (len(z_vals) - 1)
+        )
     std_dev_array.SetArray(std_dev, std_dev.size, True)
     vtk_grid.GetCellData().AddArray(std_dev_array)
 

From 3d0b404b7a99388296dda50d087d267bf3c6f917 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 28 Jun 2022 16:06:17 +0100
Subject: [PATCH 058/119] added multi stages option

---
 Dockerfile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 755d9f2a0..152590161 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,7 +15,7 @@
 
 # sudo docker run image_name:tag_name or ID with no tag sudo docker run ID number
 
-FROM debian:bullseye-slim
+FROM debian:bullseye-slim AS dependencies
 
 # By default this Dockerfile builds OpenMC without DAGMC and LIBMESH support
 ARG build_dagmc=off
@@ -172,6 +172,8 @@ RUN if [ "$build_libmesh" = "on" ]; then \
         && rm -rf ${LIBMESH_INSTALL_DIR}/build ${LIBMESH_INSTALL_DIR}/libmesh ; \
     fi
 
+FROM dependencies as build
+
 # clone and install openmc
 RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
     && git clone --shallow-submodules --recurse-submodules --single-branch -b ${openmc_branch} --depth=1 ${OPENMC_REPO} \
@@ -207,5 +209,7 @@ RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
     && cd ../openmc && pip install .[test,depletion-mpi] \
     && python -c "import openmc"
 
+FROM build as release
+
 # Download cross sections (NNDC and WMP) and ENDF data needed by test suite
 RUN ${HOME}/OpenMC/openmc/tools/ci/download-xs.sh

From 419351bb260f837386bcd5c6e798405638820e17 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 28 Jun 2022 16:14:52 +0100
Subject: [PATCH 059/119] uppercase AS

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 152590161..341390c9a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -172,7 +172,7 @@ RUN if [ "$build_libmesh" = "on" ]; then \
         && rm -rf ${LIBMESH_INSTALL_DIR}/build ${LIBMESH_INSTALL_DIR}/libmesh ; \
     fi
 
-FROM dependencies as build
+FROM dependencies AS build
 
 # clone and install openmc
 RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
@@ -209,7 +209,7 @@ RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
     && cd ../openmc && pip install .[test,depletion-mpi] \
     && python -c "import openmc"
 
-FROM build as release
+FROM build AS release
 
 # Download cross sections (NNDC and WMP) and ENDF data needed by test suite
 RUN ${HOME}/OpenMC/openmc/tools/ci/download-xs.sh

From 782d987fc836494166ffb66ab9e9f81888666582 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Tue, 28 Jun 2022 20:18:52 +0200
Subject: [PATCH 060/119] Optional vtk import

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
---
 openmc/tallies.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 75c7ea8f3..b795fc83a 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -8,8 +8,6 @@ from pathlib import Path
 from xml.etree import ElementTree as ET
 
 import h5py
-import vtk
-import vtk.util.numpy_support as nps
 import numpy as np
 import pandas as pd
 import scipy.sparse as sps
@@ -470,6 +468,12 @@ class Tally(IDManagerMixin):
                 (SphericalMesh not supported)
         """
         # check that tally has a MeshFilter
+        try:
+            import vtk
+            import vtk.util.numpy_support as nps
+        except ImportError:
+            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
+            raise ImportError(msg)
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):

From 7723ea492c12e17c2a8e2bef8f301386410b15a3 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 28 Jun 2022 09:45:38 -0500
Subject: [PATCH 061/119] Add Material.get_nuclide_activity method and
 decay_constant function

---
 docs/source/pythonapi/data.rst     |  1 +
 openmc/data/data.py                | 35 ++++++++++++++++++++++++++++--
 openmc/material.py                 | 30 +++++++++++++++----------
 tests/unit_tests/test_data_misc.py | 13 ++++++++++-
 4 files changed, 64 insertions(+), 15 deletions(-)

diff --git a/docs/source/pythonapi/data.rst b/docs/source/pythonapi/data.rst
index 6f5c006c2..287738774 100644
--- a/docs/source/pythonapi/data.rst
+++ b/docs/source/pythonapi/data.rst
@@ -61,6 +61,7 @@ Core Functions
 
     atomic_mass
     atomic_weight
+    decay_constant
     dose_coefficients
     gnd_name
     half_life
diff --git a/openmc/data/data.py b/openmc/data/data.py
index 3a3cf5826..71b93293e 100644
--- a/openmc/data/data.py
+++ b/openmc/data/data.py
@@ -3,7 +3,7 @@ import json
 import os
 import re
 from pathlib import Path
-from math import sqrt
+from math import sqrt, log
 from warnings import warn
 
 # Isotopic abundances from Meija J, Coplen T B, et al, "Isotopic compositions
@@ -202,7 +202,7 @@ _GND_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)')
 
 # Used in half_life function as a cache
 _HALF_LIFE = {}
-
+_LOG_TWO = log(2.0)
 
 def atomic_mass(isotope):
     """Return atomic mass of isotope in atomic mass units.
@@ -283,6 +283,8 @@ def half_life(isotope):
     Half-life values are from the `ENDF/B-VIII.0 decay sublibrary
     <https://www.nndc.bnl.gov/endf-b8.0/download.html>`_.
 
+    .. versionadded:: 0.13.1
+
     Parameters
     ----------
     isotope : str
@@ -302,6 +304,35 @@ def half_life(isotope):
 
     return _HALF_LIFE.get(isotope.lower())
 
+
+def decay_constant(isotope):
+    """Return decay constant of isotope in [s^-1]
+
+    Decay constants are based on half-life values from the
+    :func:`~openmc.data.half_life` function. When the isotope is stable, a decay
+    constant of zero is returned.
+
+    .. versionadded:: 0.13.1
+
+    Parameters
+    ----------
+    isotope : str
+        Name of isotope, e.g., 'Pu239'
+
+    Returns
+    -------
+    float
+        Decay constant of isotope in [s^-1]
+
+    See also
+    --------
+    openmc.data.half_life
+
+    """
+    t = half_life(isotope)
+    return _LOG_TWO / t if t else 0.0
+
+
 def water_density(temperature, pressure=0.1013):
     """Return the density of liquid water at a given temperature and pressure.
 
diff --git a/openmc/material.py b/openmc/material.py
index 1341746dc..e8285de7c 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,7 +3,6 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
-import math
 import re
 import warnings
 from xml.etree import ElementTree as ET
@@ -145,20 +144,10 @@ class Material(IDManagerMixin):
 
         return string
 
-
     @property
     def activity(self):
         """Returns the total activity of the material in Becquerels."""
-
-        atoms_per_barn_cm = self.get_nuclide_atom_densities()
-        total_activity = 0
-        for key, value in atoms_per_barn_cm.items():
-            half_life = openmc.data.half_life(key)
-            if half_life:
-                total_activity += value / half_life
-        total_activity *= math.log(2) * 1e24 * self.volume
-
-        return total_activity
+        return sum(self.get_nuclide_activity().values())
 
     @property
     def name(self):
@@ -861,6 +850,23 @@ class Material(IDManagerMixin):
 
         return nuclides
 
+    def get_nuclide_activity(self):
+        """Return activity in [Bq] for each nuclide in the material
+
+        .. versionadded:: 0.13.1
+
+        Returns
+        -------
+        dict
+            Dictionary whose keys are nuclide names and values are activity in
+            [Bq].
+        """
+        activity = {}
+        for nuclide, atoms in self.get_nuclide_atoms().items():
+            inv_seconds = openmc.data.decay_constant(nuclide)
+            activity[nuclide] = inv_seconds * atoms
+        return activity
+
     def get_nuclide_atoms(self):
         """Return number of atoms of each nuclide in the material
 
diff --git a/tests/unit_tests/test_data_misc.py b/tests/unit_tests/test_data_misc.py
index 6a81fb1e0..c3f7e3cff 100644
--- a/tests/unit_tests/test_data_misc.py
+++ b/tests/unit_tests/test_data_misc.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from collections.abc import Mapping
+from math import log
 import os
 from pathlib import Path
 
@@ -126,3 +126,14 @@ def test_zam():
     assert openmc.data.zam('Am242_m10') == (95, 242, 10)
     with pytest.raises(ValueError):
         openmc.data.zam('garbage')
+
+
+def test_half_life():
+    assert openmc.data.half_life('H2') is None
+    assert openmc.data.half_life('U235') == pytest.approx(2.22102e16)
+    assert openmc.data.half_life('Am242') == pytest.approx(57672.0)
+    assert openmc.data.half_life('Am242_m1') == pytest.approx(4449622000.0)
+    assert openmc.data.decay_constant('H2') == 0.0
+    assert openmc.data.decay_constant('U235') == pytest.approx(log(2.0)/2.22102e16)
+    assert openmc.data.decay_constant('Am242') == pytest.approx(log(2.0)/57672.0)
+    assert openmc.data.decay_constant('Am242_m1') == pytest.approx(log(2.0)/4449622000.0)

From 6eaab920eeaddac452ad07e25015357c3658f139 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 08:18:10 +0200
Subject: [PATCH 062/119] better error catching

---
 openmc/tallies.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index b795fc83a..faa7c3efe 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -471,9 +471,12 @@ class Tally(IDManagerMixin):
         try:
             import vtk
             import vtk.util.numpy_support as nps
-        except ImportError:
+        except ModuleNotFoundError:
             msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
-            raise ImportError(msg)
+            raise ModuleNotFoundError(msg)
+        except ImportError as err:
+            raise err
+
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):

From fb40ba894addb3ab87226e80e631aaa6288dafa6 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 08:18:22 +0200
Subject: [PATCH 063/119] moved comment statement

---
 openmc/tallies.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index faa7c3efe..bec0ddc6f 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -467,7 +467,6 @@ class Tally(IDManagerMixin):
             ValueError: if no MeshFilter with appropriate mesh was found 
                 (SphericalMesh not supported)
         """
-        # check that tally has a MeshFilter
         try:
             import vtk
             import vtk.util.numpy_support as nps
@@ -477,6 +476,7 @@ class Tally(IDManagerMixin):
         except ImportError as err:
             raise err
 
+        # check that tally has a MeshFilter
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):

From dacd3b75b855d8f28da8f7eedea4e6508c20fd80 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 08:20:25 +0200
Subject: [PATCH 064/119] moved import to voxels_to_vtk

---
 openmc/tallies.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index bec0ddc6f..fbf2962b9 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -467,15 +467,6 @@ class Tally(IDManagerMixin):
             ValueError: if no MeshFilter with appropriate mesh was found 
                 (SphericalMesh not supported)
         """
-        try:
-            import vtk
-            import vtk.util.numpy_support as nps
-        except ModuleNotFoundError:
-            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
-            raise ModuleNotFoundError(msg)
-        except ImportError as err:
-            raise err
-
         # check that tally has a MeshFilter
         mesh = None
         for f in self.filters:
@@ -3324,7 +3315,14 @@ def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
     Returns:
         vtkStructuredGrid: a vtk object containing tally data on the appropriate grid
     """
-
+    try:
+        import vtk
+        import vtk.util.numpy_support as nps
+    except ModuleNotFoundError:
+        msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
+        raise ModuleNotFoundError(msg)
+    except ImportError as err:
+        raise err
     # TODO: should this be a method of Tally?
 
     vtk_grid = vtk.vtkStructuredGrid()

From 9ec0a0a3df1a90783e1b0e60701f972275ffd17e Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 08:42:32 +0200
Subject: [PATCH 065/119] refactoring

---
 openmc/tallies.py | 105 +++++++++++++++++++++++-----------------------
 1 file changed, 53 insertions(+), 52 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index fbf2962b9..a25d535e5 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -464,61 +464,29 @@ class Tally(IDManagerMixin):
             filename (str): the filename (must end with .vtk)
 
         Raises:
-            ValueError: if no MeshFilter with appropriate mesh was found 
-                (SphericalMesh not supported)
+            ValueError: if no MeshFilter was found
         """
+        try:
+            import vtk
+        except ModuleNotFoundError:
+            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
+            raise ModuleNotFoundError(msg)
+        except ImportError as err:
+            raise err
+
         # check that tally has a MeshFilter
         mesh = None
         for f in self.filters:
             if isinstance(f, openmc.MeshFilter):
-                if isinstance(f.mesh, (openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh)):
-                    mesh = f.mesh
-                    break
+                mesh = f.mesh
+                break
 
         if not mesh:
             raise ValueError(
-                "write_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
+                "write_to_vtk requires a MeshFilter in the tally filters"
             )
 
-        if isinstance(mesh, openmc.RegularMesh):
-            vtk_grid = voxels_to_vtk(
-                x_vals=np.linspace(
-                    mesh.lower_left[0],
-                    mesh.upper_right[0],
-                    num=mesh.dimension[0] + 1,
-                ),
-                y_vals=np.linspace(
-                    mesh.lower_left[1],
-                    mesh.upper_right[1],
-                    num=mesh.dimension[1] + 1,
-                ),
-                z_vals=np.linspace(
-                    mesh.lower_left[2],
-                    mesh.upper_right[2],
-                    num=mesh.dimension[2] + 1,
-                ),
-                mean=self.mean,
-                std_dev=self.std_dev,
-                cylindrical=False,
-            )
-        if isinstance(mesh, openmc.RectilinearMesh):
-            vtk_grid = voxels_to_vtk(
-                x_vals=mesh.x_grid,
-                y_vals=mesh.y_grid,
-                z_vals=mesh.z_grid,
-                mean=self.mean,
-                std_dev=self.std_dev,
-                cylindrical=False,
-            )
-        elif isinstance(mesh, openmc.CylindricalMesh):
-            vtk_grid = voxels_to_vtk(
-                x_vals=mesh.r_grid,
-                y_vals=mesh.phi_grid,
-                z_vals=mesh.z_grid,
-                mean=self.mean,
-                std_dev=self.std_dev,
-                cylindrical=True,
-            )
+        vtk_grid = voxels_to_vtk(mesh, self.mean, self.std_dev)
 
         # write the .vtk file
         writer = vtk.vtkStructuredGridWriter()
@@ -3300,20 +3268,20 @@ class Tallies(cv.CheckedList):
         return cls(tallies)
 
 
-def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
+def voxels_to_vtk(mesh, mean, std_dev):
     """Creates a vtk object from a list of X, Y, Z values and mean/std_dev data.
 
     Args:
-        x_vals (list): X values.
-        y_vals (list): Y values.
-        z_vals (list): Z values.
+        mesh (openmc.StructuredMesh): The tallied mesh (SphericalMesh is not yet supported).
         mean (np.array): the tally mean.
         std_dev (np.array): the tally standard deviation.
-        cylindrical (bool, optional): If set to True, cylindrical coordinates
-            (r, phi, z) are assumed. Defaults to True.
 
     Returns:
         vtkStructuredGrid: a vtk object containing tally data on the appropriate grid
+
+    Raises:
+        ValueError: if mesh is not openmc.RegularMesh, openmc.RectilinearMesh or
+            openmc.CylindricalMesh
     """
     try:
         import vtk
@@ -3325,13 +3293,46 @@ def voxels_to_vtk(x_vals, y_vals, z_vals, mean, std_dev, cylindrical=True):
         raise err
     # TODO: should this be a method of Tally?
 
+    system_of_coordinates = "cartesian"
+
+    if isinstance(mesh, openmc.RegularMesh):
+        print('coucou')
+        x_vals = np.linspace(
+            mesh.lower_left[0],
+            mesh.upper_right[0],
+            num=mesh.dimension[0] + 1,
+        )
+        y_vals = np.linspace(
+            mesh.lower_left[1],
+            mesh.upper_right[1],
+            num=mesh.dimension[1] + 1,
+        )
+        z_vals = np.linspace(
+            mesh.lower_left[2],
+            mesh.upper_right[2],
+            num=mesh.dimension[2] + 1,
+        )
+    elif isinstance(mesh, openmc.RectilinearMesh):
+        x_vals = mesh.x_grid
+        y_vals = mesh.y_grid
+        z_vals = mesh.z_grid
+    elif isinstance(mesh, openmc.CylindricalMesh):
+        x_vals = mesh.r_grid
+        y_vals = mesh.phi_grid
+        z_vals = mesh.z_grid
+        system_of_coordinates = "cylindrical"
+    else:
+        print(type(mesh))
+        raise ValueError(
+                "voxels_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
+            )
     vtk_grid = vtk.vtkStructuredGrid()
 
     vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
 
     # create points
     points = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
-    if cylindrical:  # transform points to cartesian coordinates
+    if system_of_coordinates == "cylindrical":  # transform points to cartesian coordinates
         points_cartesian = np.copy(points)
         r, phi, z = points[:, 0], points[:, 1], points[:, 2]
         points_cartesian[:, 0] = r * np.cos(phi)

From 11cee75e46ebc7e9756d81dbfae3452ff824cc10 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 09:12:28 +0200
Subject: [PATCH 066/119] put write_to_vtk method at the end

---
 openmc/tallies.py | 74 +++++++++++++++++++++++------------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index a25d535e5..198f5581b 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -457,43 +457,6 @@ class Tally(IDManagerMixin):
                 self._std_dev = np.reshape(self._std_dev.toarray(), self.shape)
             self._sparse = False
 
-    def write_to_vtk(self, filename):
-        """Writes the tally to a vtk file
-
-        Args:
-            filename (str): the filename (must end with .vtk)
-
-        Raises:
-            ValueError: if no MeshFilter was found
-        """
-        try:
-            import vtk
-        except ModuleNotFoundError:
-            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
-            raise ModuleNotFoundError(msg)
-        except ImportError as err:
-            raise err
-
-        # check that tally has a MeshFilter
-        mesh = None
-        for f in self.filters:
-            if isinstance(f, openmc.MeshFilter):
-                mesh = f.mesh
-                break
-
-        if not mesh:
-            raise ValueError(
-                "write_to_vtk requires a MeshFilter in the tally filters"
-            )
-
-        vtk_grid = voxels_to_vtk(mesh, self.mean, self.std_dev)
-
-        # write the .vtk file
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
     def remove_score(self, score):
         """Remove a score from the tally
 
@@ -3050,6 +3013,43 @@ class Tally(IDManagerMixin):
         new_tally.sparse = self.sparse
         return new_tally
 
+    def write_to_vtk(self, filename):
+        """Writes the tally to a vtk file
+
+        Args:
+            filename (str): the filename (must end with .vtk)
+
+        Raises:
+            ValueError: if no MeshFilter was found
+        """
+        try:
+            import vtk
+        except ModuleNotFoundError:
+            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
+            raise ModuleNotFoundError(msg)
+        except ImportError as err:
+            raise err
+
+        # check that tally has a MeshFilter
+        mesh = None
+        for f in self.filters:
+            if isinstance(f, openmc.MeshFilter):
+                mesh = f.mesh
+                break
+
+        if not mesh:
+            raise ValueError(
+                "write_to_vtk requires a MeshFilter in the tally filters"
+            )
+
+        vtk_grid = voxels_to_vtk(mesh, self.mean, self.std_dev)
+
+        # write the .vtk file
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
+
 
 class Tallies(cv.CheckedList):
     """Collection of Tallies used for an OpenMC simulation.

From bff8bc4b459030448749e587fb0fde2cf53d48f9 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 09:16:40 +0200
Subject: [PATCH 067/119] added tests

---
 tests/unit_tests/test_tallies.py | 62 ++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
index aeeb0612d..b6fc6cc47 100644
--- a/tests/unit_tests/test_tallies.py
+++ b/tests/unit_tests/test_tallies.py
@@ -1,4 +1,8 @@
 import numpy as np
+import pytest
+import vtk
+from os.path import exists
+
 import openmc
 
 
@@ -38,3 +42,61 @@ def test_xml_roundtrip(run_in_tmpdir):
     assert new_tally.triggers[0].trigger_type == tally.triggers[0].trigger_type
     assert new_tally.triggers[0].threshold == tally.triggers[0].threshold
     assert new_tally.triggers[0].scores == tally.triggers[0].scores
+
+
+cylinder_mesh = openmc.CylindricalMesh()
+cylinder_mesh.r_grid = np.linspace(1, 2, num=30)
+cylinder_mesh.phi_grid = np.linspace(0, np.pi / 2, num=50)
+cylinder_mesh.z_grid = np.linspace(0, 1, num=30)
+
+regular_mesh = openmc.RegularMesh()
+regular_mesh.lower_left = [0, 0, 0]
+regular_mesh.upper_right = [1, 1, 1]
+regular_mesh.dimension = [10, 5, 6]
+
+rectilinear_mesh = openmc.RectilinearMesh()
+rectilinear_mesh.x_grid = np.linspace(0, 1)
+rectilinear_mesh.y_grid = np.linspace(0, 1)
+rectilinear_mesh.z_grid = np.linspace(0, 1)
+
+
+@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh])
+def test_voxels_to_vtk(mesh):
+    vtk_grid = openmc.voxels_to_vtk(mesh, mean=None, std_dev=None)
+    assert isinstance(vtk_grid, vtk.vtkStructuredGrid)
+
+
+@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh])
+def test_write_to_vtk(mesh, tmpdir):
+    # build
+    tally = openmc.Tally()
+    tally.filters = [openmc.MeshFilter(mesh)]
+    filename = tmpdir / "out.vtk"
+    # run
+    tally.write_to_vtk(filename)
+    # test
+    assert exists(filename)
+
+
+def test_write_to_vtk_raises_error_when_no_meshfilter():
+    # build
+    tally = openmc.Tally()
+
+    # test
+    expected_err_msg = "write_to_vtk requires a MeshFilter in the tally filters"
+    with pytest.raises(ValueError, match=expected_err_msg):
+        tally.write_to_vtk("out.vtk")
+
+
+def test_voxel_to_vtk_raises_error_with_wrong_mesh():
+    # build
+    tally = openmc.Tally()
+    spherical_mesh = openmc.SphericalMesh()
+    spherical_mesh.r_grid = np.linspace(1, 2)
+    spherical_mesh.phi_grid = np.linspace(1, 2)
+    spherical_mesh.theta_grid = np.linspace(1, 2)
+    tally.filters = [openmc.MeshFilter(spherical_mesh)]
+    # test
+    expected_err_msg = "voxels_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
+    with pytest.raises(ValueError, match=expected_err_msg):
+        tally.write_to_vtk("out.vtk")
\ No newline at end of file

From b61ec91d781caf8e7ca593a98c76d916a8efa94e Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 09:50:28 +0200
Subject: [PATCH 068/119] removed print statement

---
 openmc/tallies.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 198f5581b..88f747249 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3296,7 +3296,6 @@ def voxels_to_vtk(mesh, mean, std_dev):
     system_of_coordinates = "cartesian"
 
     if isinstance(mesh, openmc.RegularMesh):
-        print('coucou')
         x_vals = np.linspace(
             mesh.lower_left[0],
             mesh.upper_right[0],

From cac84d6e1f76b69d28da8674fcf81011170cf446 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 09:50:42 +0200
Subject: [PATCH 069/119] removd print statement

---
 openmc/tallies.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 88f747249..020d4a3d9 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3321,7 +3321,6 @@ def voxels_to_vtk(mesh, mean, std_dev):
         z_vals = mesh.z_grid
         system_of_coordinates = "cylindrical"
     else:
-        print(type(mesh))
         raise ValueError(
                 "voxels_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
             )

From 7be28ef156a96fb4c525130d9c52e6966cf43539 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:08:58 +0200
Subject: [PATCH 070/119] added vtk_grid to meshes

---
 openmc/mesh.py | 99 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 7f7b07879..dbdfb10b0 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -621,7 +621,45 @@ class RegularMesh(StructuredMesh):
         root_cell.fill = lattice
 
         return root_cell, cells
+    
+    def vtk_grid(self, filename=None):
+        import vtk
+        from vtk.util import numpy_support as nps
 
+        x_vals = np.linspace(
+            self.lower_left[0],
+            self.upper_right[0],
+            num=self.dimension[0] + 1,
+        )
+        y_vals = np.linspace(
+            self.lower_left[1],
+            self.upper_right[1],
+            num=self.dimension[1] + 1,
+        )
+        z_vals = np.linspace(
+            self.lower_left[2],
+            self.upper_right[2],
+            num=self.dimension[2] + 1,
+        )
+        vtk_grid = vtk.vtkStructuredGrid()
+
+        vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
+
+        # create points
+        pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
+
+        vtkPts = vtk.vtkPoints()
+        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
+        vtk_grid.SetPoints(vtkPts)
+
+        if filename:
+            # write the .vtk file
+            writer = vtk.vtkStructuredGridWriter()
+            writer.SetFileName(filename)
+            writer.SetInputData(vtk_grid)
+            writer.Write()
+
+        return vtk_grid
 
 def Mesh(*args, **kwargs):
     warnings.warn("Mesh has been renamed RegularMesh. Future versions of "
@@ -821,6 +859,33 @@ class RectilinearMesh(StructuredMesh):
 
         return element
 
+    def vtk_grid(self, filename=None):
+        import vtk
+        from vtk.util import numpy_support as nps
+
+        x_vals = self.x_grid
+        y_vals = self.y_grid
+        z_vals = self.z_grid
+        vtk_grid = vtk.vtkStructuredGrid()
+
+        vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
+
+        # create points
+        pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
+
+        vtkPts = vtk.vtkPoints()
+        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
+        vtk_grid.SetPoints(vtkPts)
+
+        if filename:
+            # write the .vtk file
+            writer = vtk.vtkStructuredGridWriter()
+            writer.SetFileName(filename)
+            writer.SetInputData(vtk_grid)
+            writer.Write()
+
+        return vtk_grid
+
 
 class CylindricalMesh(StructuredMesh):
     """A 3D cylindrical mesh
@@ -1012,6 +1077,37 @@ class CylindricalMesh(StructuredMesh):
 
         return np.multiply.outer(np.outer(V_r, V_p), V_z)
 
+    def vtk_grid(self, filename=None):
+        import vtk
+        from vtk.util import numpy_support as nps
+
+        r_vals = self.r_grid
+        phi_vals = self.phi_grid
+        z_vals = self.z_grid
+        vtk_grid = vtk.vtkStructuredGrid()
+
+        vtk_grid.SetDimensions(len(r_vals), len(phi_vals), len(z_vals))
+
+        # create points
+        pts_cylindrical = np.array([[r, phi, z] for z in z_vals for phi in phi_vals for r in r_vals])
+        pts_cartesian = np.copy(pts_cylindrical)
+        r, phi, z = pts_cylindrical[:, 0], pts_cylindrical[:, 1], pts_cylindrical[:, 2]
+        pts_cartesian[:, 0] = r * np.cos(phi)
+        pts_cartesian[:, 1] = r * np.sin(phi)
+        pts_cartesian[:, 2] = z
+
+        vtkPts = vtk.vtkPoints()
+        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
+        vtk_grid.SetPoints(vtkPts)
+
+        if filename:
+            # write the .vtk file
+            writer = vtk.vtkStructuredGridWriter()
+            writer.SetFileName(filename)
+            writer.SetInputData(vtk_grid)
+            writer.Write()
+
+        return vtk_grid
 
 class SphericalMesh(StructuredMesh):
     """A 3D spherical mesh
@@ -1204,6 +1300,9 @@ class SphericalMesh(StructuredMesh):
 
         return np.multiply.outer(np.outer(V_r, V_t), V_p)
 
+    def vtk_grid(self, filename=None):
+        raise NotImplementedError("vtk_grid not implemented for SphericalMesh")
+
 
 class UnstructuredMesh(MeshBase):
     """A 3D unstructured mesh

From 4ab6617bc4fe681bff68bce6dd4b22bf57a821d9 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:09:18 +0200
Subject: [PATCH 071/119] write_to_vtk makes use of mesh.vtk_grid()

---
 openmc/tallies.py | 113 +++++-----------------------------------------
 1 file changed, 12 insertions(+), 101 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index 020d4a3d9..e67365df6 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3042,7 +3042,18 @@ class Tally(IDManagerMixin):
                 "write_to_vtk requires a MeshFilter in the tally filters"
             )
 
-        vtk_grid = voxels_to_vtk(mesh, self.mean, self.std_dev)
+        vtk_grid = mesh.vtk_grid()
+
+        # add mean and std dev data
+        mean_array = vtk.vtkDoubleArray()
+        mean_array.SetName("mean")
+        mean_array.SetArray(self.mean, self.mean.size, True)
+        vtk_grid.GetCellData().AddArray(mean_array)
+
+        std_dev_array = vtk.vtkDoubleArray()
+        std_dev_array.SetName("std_dev")
+        std_dev_array.SetArray(self.std_dev, self.std_dev.size, True)
+        vtk_grid.GetCellData().AddArray(std_dev_array)
 
         # write the .vtk file
         writer = vtk.vtkStructuredGridWriter()
@@ -3266,103 +3277,3 @@ class Tallies(cv.CheckedList):
             tallies.append(tally)
 
         return cls(tallies)
-
-
-def voxels_to_vtk(mesh, mean, std_dev):
-    """Creates a vtk object from a list of X, Y, Z values and mean/std_dev data.
-
-    Args:
-        mesh (openmc.StructuredMesh): The tallied mesh (SphericalMesh is not yet supported).
-        mean (np.array): the tally mean.
-        std_dev (np.array): the tally standard deviation.
-
-    Returns:
-        vtkStructuredGrid: a vtk object containing tally data on the appropriate grid
-
-    Raises:
-        ValueError: if mesh is not openmc.RegularMesh, openmc.RectilinearMesh or
-            openmc.CylindricalMesh
-    """
-    try:
-        import vtk
-        import vtk.util.numpy_support as nps
-    except ModuleNotFoundError:
-        msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
-        raise ModuleNotFoundError(msg)
-    except ImportError as err:
-        raise err
-    # TODO: should this be a method of Tally?
-
-    system_of_coordinates = "cartesian"
-
-    if isinstance(mesh, openmc.RegularMesh):
-        x_vals = np.linspace(
-            mesh.lower_left[0],
-            mesh.upper_right[0],
-            num=mesh.dimension[0] + 1,
-        )
-        y_vals = np.linspace(
-            mesh.lower_left[1],
-            mesh.upper_right[1],
-            num=mesh.dimension[1] + 1,
-        )
-        z_vals = np.linspace(
-            mesh.lower_left[2],
-            mesh.upper_right[2],
-            num=mesh.dimension[2] + 1,
-        )
-    elif isinstance(mesh, openmc.RectilinearMesh):
-        x_vals = mesh.x_grid
-        y_vals = mesh.y_grid
-        z_vals = mesh.z_grid
-    elif isinstance(mesh, openmc.CylindricalMesh):
-        x_vals = mesh.r_grid
-        y_vals = mesh.phi_grid
-        z_vals = mesh.z_grid
-        system_of_coordinates = "cylindrical"
-    else:
-        raise ValueError(
-                "voxels_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
-            )
-    vtk_grid = vtk.vtkStructuredGrid()
-
-    vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
-
-    # create points
-    points = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
-    if system_of_coordinates == "cylindrical":  # transform points to cartesian coordinates
-        points_cartesian = np.copy(points)
-        r, phi, z = points[:, 0], points[:, 1], points[:, 2]
-        points_cartesian[:, 0] = r * np.cos(phi)
-        points_cartesian[:, 1] = r * np.sin(phi)
-        points_cartesian[:, 2] = z
-        points = points_cartesian
-
-    vtkPts = vtk.vtkPoints()
-    vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))
-    vtk_grid.SetPoints(vtkPts)
-
-    # add mean and std dev data
-    mean_array = vtk.vtkDoubleArray()
-    mean_array.SetName("mean")
-    if mean is None:
-        mean = np.zeros(
-            (len(x_vals) - 1)
-            * (len(y_vals) - 1)
-            * (len(z_vals) - 1)
-        )
-    mean_array.SetArray(mean, mean.size, True)
-    vtk_grid.GetCellData().AddArray(mean_array)
-
-    std_dev_array = vtk.vtkDoubleArray()
-    std_dev_array.SetName("std_dev")
-    if std_dev is None:
-        std_dev = np.zeros(
-            (len(x_vals) - 1)
-            * (len(y_vals) - 1)
-            * (len(z_vals) - 1)
-        )
-    std_dev_array.SetArray(std_dev, std_dev.size, True)
-    vtk_grid.GetCellData().AddArray(std_dev_array)
-
-    return vtk_grid

From 8958b74da73e47757147ab80b22b325926291142 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:09:32 +0200
Subject: [PATCH 072/119] adapted tests

---
 tests/unit_tests/test_tallies.py | 29 ++++++++++++++++++++---------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
index b6fc6cc47..e49596f6d 100644
--- a/tests/unit_tests/test_tallies.py
+++ b/tests/unit_tests/test_tallies.py
@@ -43,6 +43,23 @@ def test_xml_roundtrip(run_in_tmpdir):
     assert new_tally.triggers[0].threshold == tally.triggers[0].threshold
     assert new_tally.triggers[0].scores == tally.triggers[0].scores
 
+def run_dummy_sim(tally):
+    mat = openmc.Material()
+    mat.add_nuclide('Zr90', 1.0)
+    mat.set_density('g/cm3', 1.0)
+
+    model = openmc.Model()
+    sph = openmc.Sphere(r=25.0, boundary_type='vacuum')
+    cell = openmc.Cell(fill=mat, region=-sph)
+    model.geometry = openmc.Geometry([cell])
+
+    model.settings.run_mode = 'fixed source'
+    model.settings.batches = 2
+    model.settings.particles = 50
+
+    model.tallies = openmc.Tallies([tally])
+
+    model.run()
 
 cylinder_mesh = openmc.CylindricalMesh()
 cylinder_mesh.r_grid = np.linspace(1, 2, num=30)
@@ -59,19 +76,13 @@ rectilinear_mesh.x_grid = np.linspace(0, 1)
 rectilinear_mesh.y_grid = np.linspace(0, 1)
 rectilinear_mesh.z_grid = np.linspace(0, 1)
 
-
-@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh])
-def test_voxels_to_vtk(mesh):
-    vtk_grid = openmc.voxels_to_vtk(mesh, mean=None, std_dev=None)
-    assert isinstance(vtk_grid, vtk.vtkStructuredGrid)
-
-
 @pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh])
 def test_write_to_vtk(mesh, tmpdir):
     # build
     tally = openmc.Tally()
     tally.filters = [openmc.MeshFilter(mesh)]
     filename = tmpdir / "out.vtk"
+    run_dummy_sim(tally)
     # run
     tally.write_to_vtk(filename)
     # test
@@ -97,6 +108,6 @@ def test_voxel_to_vtk_raises_error_with_wrong_mesh():
     spherical_mesh.theta_grid = np.linspace(1, 2)
     tally.filters = [openmc.MeshFilter(spherical_mesh)]
     # test
-    expected_err_msg = "voxels_to_vtk only works with openmc.RegularMesh, openmc.RectilinearMesh, openmc.CylindricalMesh"
-    with pytest.raises(ValueError, match=expected_err_msg):
+    expected_err_msg = "vtk_grid not implemented for SphericalMesh"
+    with pytest.raises(NotImplementedError, match=expected_err_msg):
         tally.write_to_vtk("out.vtk")
\ No newline at end of file

From 2a78c06cf512e579eaeef007a63a2c90da9cb4ed Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:21:45 +0200
Subject: [PATCH 073/119] added docstrings

---
 openmc/mesh.py | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index dbdfb10b0..f6e395328 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -623,6 +623,15 @@ class RegularMesh(StructuredMesh):
         return root_cell, cells
     
     def vtk_grid(self, filename=None):
+        """Creates a VTK object of the mesh
+
+        Args:
+            filename (str, optional): Name of the vtk file to write =
+                (must end with .vtk). Defaults to None.
+
+        Returns:
+            vtk.vtkStructuredGrid: the VTK object
+        """
         import vtk
         from vtk.util import numpy_support as nps
 
@@ -860,6 +869,15 @@ class RectilinearMesh(StructuredMesh):
         return element
 
     def vtk_grid(self, filename=None):
+        """Creates a VTK object of the mesh
+
+        Args:
+            filename (str, optional): Name of the vtk file to write =
+                (must end with .vtk). Defaults to None.
+
+        Returns:
+            vtk.vtkStructuredGrid: the VTK object
+        """
         import vtk
         from vtk.util import numpy_support as nps
 
@@ -1078,6 +1096,15 @@ class CylindricalMesh(StructuredMesh):
         return np.multiply.outer(np.outer(V_r, V_p), V_z)
 
     def vtk_grid(self, filename=None):
+        """Creates a VTK object of the mesh
+
+        Args:
+            filename (str, optional): Name of the vtk file to write =
+                (must end with .vtk). Defaults to None.
+
+        Returns:
+            vtk.vtkStructuredGrid: the VTK object
+        """
         import vtk
         from vtk.util import numpy_support as nps
 
@@ -1301,6 +1328,16 @@ class SphericalMesh(StructuredMesh):
         return np.multiply.outer(np.outer(V_r, V_t), V_p)
 
     def vtk_grid(self, filename=None):
+        """Creates a VTK object of the mesh
+
+        Args:
+            filename (str, optional): Name of the vtk file to write =
+                (must end with .vtk). Defaults to None.
+
+        Returns:
+            vtk.vtkStructuredGrid: the VTK object
+        """
+        # FIXME
         raise NotImplementedError("vtk_grid not implemented for SphericalMesh")
 
 

From 913bc99564b97490d90152aa68ed9a65838bdc3e Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:33:17 +0200
Subject: [PATCH 074/119] minor refactore

---
 openmc/mesh.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index f6e395328..d89a980ac 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1108,15 +1108,12 @@ class CylindricalMesh(StructuredMesh):
         import vtk
         from vtk.util import numpy_support as nps
 
-        r_vals = self.r_grid
-        phi_vals = self.phi_grid
-        z_vals = self.z_grid
         vtk_grid = vtk.vtkStructuredGrid()
 
-        vtk_grid.SetDimensions(len(r_vals), len(phi_vals), len(z_vals))
+        vtk_grid.SetDimensions(len(self.r_grid), len(self.phi_grid), len(self.z_grid))
 
         # create points
-        pts_cylindrical = np.array([[r, phi, z] for z in z_vals for phi in phi_vals for r in r_vals])
+        pts_cylindrical = np.array([[r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid])
         pts_cartesian = np.copy(pts_cylindrical)
         r, phi, z = pts_cylindrical[:, 0], pts_cylindrical[:, 1], pts_cylindrical[:, 2]
         pts_cartesian[:, 0] = r * np.cos(phi)

From aeb66509098b597a5cd53fca88d5e21096c691a0 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:54:52 +0200
Subject: [PATCH 075/119] implemented spherical grid

---
 openmc/mesh.py | 29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index d89a980ac..260ed5f43 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1334,8 +1334,33 @@ class SphericalMesh(StructuredMesh):
         Returns:
             vtk.vtkStructuredGrid: the VTK object
         """
-        # FIXME
-        raise NotImplementedError("vtk_grid not implemented for SphericalMesh")
+        import vtk
+        from vtk.util import numpy_support as nps
+
+        vtk_grid = vtk.vtkStructuredGrid()
+
+        vtk_grid.SetDimensions(len(self.r_grid), len(self.theta_grid), len(self.phi_grid))
+
+        # create points
+        pts_cylindrical = np.array([[r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid])
+        pts_cartesian = np.copy(pts_cylindrical)
+        r, theta, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1], pts_cylindrical[:, 2]
+        pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta)
+        pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta)
+        pts_cartesian[:, 2] = r * np.cos(phi)
+
+        vtkPts = vtk.vtkPoints()
+        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
+        vtk_grid.SetPoints(vtkPts)
+
+        if filename:
+            # write the .vtk file
+            writer = vtk.vtkStructuredGridWriter()
+            writer.SetFileName(filename)
+            writer.SetInputData(vtk_grid)
+            writer.Write()
+
+        return vtk_grid
 
 
 class UnstructuredMesh(MeshBase):

From 7de718a85c1ceaa0a6c485184829357d0f5c6372 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 11:56:32 +0200
Subject: [PATCH 076/119] adapted tests

---
 tests/unit_tests/test_tallies.py | 21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
index e49596f6d..e3f9a486d 100644
--- a/tests/unit_tests/test_tallies.py
+++ b/tests/unit_tests/test_tallies.py
@@ -76,7 +76,12 @@ rectilinear_mesh.x_grid = np.linspace(0, 1)
 rectilinear_mesh.y_grid = np.linspace(0, 1)
 rectilinear_mesh.z_grid = np.linspace(0, 1)
 
-@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh])
+spherical_mesh = openmc.SphericalMesh()
+spherical_mesh.r_grid = np.linspace(1, 2)
+spherical_mesh.phi_grid = np.linspace(1, 2)
+spherical_mesh.theta_grid = np.linspace(1, 2)
+
+@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
 def test_write_to_vtk(mesh, tmpdir):
     # build
     tally = openmc.Tally()
@@ -97,17 +102,3 @@ def test_write_to_vtk_raises_error_when_no_meshfilter():
     expected_err_msg = "write_to_vtk requires a MeshFilter in the tally filters"
     with pytest.raises(ValueError, match=expected_err_msg):
         tally.write_to_vtk("out.vtk")
-
-
-def test_voxel_to_vtk_raises_error_with_wrong_mesh():
-    # build
-    tally = openmc.Tally()
-    spherical_mesh = openmc.SphericalMesh()
-    spherical_mesh.r_grid = np.linspace(1, 2)
-    spherical_mesh.phi_grid = np.linspace(1, 2)
-    spherical_mesh.theta_grid = np.linspace(1, 2)
-    tally.filters = [openmc.MeshFilter(spherical_mesh)]
-    # test
-    expected_err_msg = "vtk_grid not implemented for SphericalMesh"
-    with pytest.raises(NotImplementedError, match=expected_err_msg):
-        tally.write_to_vtk("out.vtk")
\ No newline at end of file

From 0f23bf2109505f1ebb2de692552f096b25a5e93b Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:21:59 +0200
Subject: [PATCH 077/119] write_data_to_vtk SphericalMesh

---
 openmc/mesh.py | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 260ed5f43..c780827ea 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1324,7 +1324,7 @@ class SphericalMesh(StructuredMesh):
 
         return np.multiply.outer(np.outer(V_r, V_t), V_p)
 
-    def vtk_grid(self, filename=None):
+    def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
         Args:
@@ -1337,6 +1337,19 @@ class SphericalMesh(StructuredMesh):
         import vtk
         from vtk.util import numpy_support as nps
 
+        if self.volumes is None and volume_normalization:
+            raise RuntimeError("No volume data is present on this "
+                               "unstructured mesh. Please load the "
+                               " mesh information from a statepoint file.")
+
+        # check that the data sets are appropriately sized
+        for label, dataset in datasets.items():
+            if isinstance(dataset, np.ndarray):
+                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            else:
+                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            cv.check_type('label', label, str)
+
         vtk_grid = vtk.vtkStructuredGrid()
 
         vtk_grid.SetDimensions(len(self.r_grid), len(self.theta_grid), len(self.phi_grid))
@@ -1353,12 +1366,26 @@ class SphericalMesh(StructuredMesh):
         vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
         vtk_grid.SetPoints(vtkPts)
 
-        if filename:
-            # write the .vtk file
-            writer = vtk.vtkStructuredGridWriter()
-            writer.SetFileName(filename)
-            writer.SetInputData(vtk_grid)
-            writer.Write()
+        # create VTK arrays for each of
+        # the data sets
+        for label, dataset in datasets.items():
+            dataset = np.asarray(dataset).flatten()
+
+            if volume_normalization:
+                dataset /= self.volumes.flatten()
+
+            dataset_array = vtk.vtkDoubleArray()
+            dataset_array.SetName(label)
+            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
+                           dataset.size,
+                           True)
+            vtk_grid.GetCellData().AddArray(dataset_array)
+
+        # write the .vtk file
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
 
         return vtk_grid
 

From 15cc2a0804d3fa146bf6e337f4987ae634490513 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:23:55 +0200
Subject: [PATCH 078/119] fixed variable name

---
 openmc/mesh.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index c780827ea..3dbc170d6 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1355,9 +1355,9 @@ class SphericalMesh(StructuredMesh):
         vtk_grid.SetDimensions(len(self.r_grid), len(self.theta_grid), len(self.phi_grid))
 
         # create points
-        pts_cylindrical = np.array([[r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid])
-        pts_cartesian = np.copy(pts_cylindrical)
-        r, theta, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1], pts_cylindrical[:, 2]
+        pts_spherical = np.array([[r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid])
+        pts_cartesian = np.copy(pts_spherical)
+        r, theta, phi = pts_spherical[:, 0], pts_spherical[:, 1], pts_spherical[:, 2]
         pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta)
         pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta)
         pts_cartesian[:, 2] = r * np.cos(phi)

From 3b1d1756e4716e5e70f58a3142dc7efaed2d7913 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:26:29 +0200
Subject: [PATCH 079/119] write_data_to_vtk CylindricalMesh

---
 openmc/mesh.py | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 3dbc170d6..029d714f0 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1095,7 +1095,7 @@ class CylindricalMesh(StructuredMesh):
 
         return np.multiply.outer(np.outer(V_r, V_p), V_z)
 
-    def vtk_grid(self, filename=None):
+    def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
         Args:
@@ -1108,6 +1108,19 @@ class CylindricalMesh(StructuredMesh):
         import vtk
         from vtk.util import numpy_support as nps
 
+        if self.volumes is None and volume_normalization:
+            raise RuntimeError("No volume data is present on this "
+                               "unstructured mesh. Please load the "
+                               " mesh information from a statepoint file.")
+
+        # check that the data sets are appropriately sized
+        for label, dataset in datasets.items():
+            if isinstance(dataset, np.ndarray):
+                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            else:
+                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            cv.check_type('label', label, str)
+
         vtk_grid = vtk.vtkStructuredGrid()
 
         vtk_grid.SetDimensions(len(self.r_grid), len(self.phi_grid), len(self.z_grid))
@@ -1124,12 +1137,26 @@ class CylindricalMesh(StructuredMesh):
         vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
         vtk_grid.SetPoints(vtkPts)
 
-        if filename:
-            # write the .vtk file
-            writer = vtk.vtkStructuredGridWriter()
-            writer.SetFileName(filename)
-            writer.SetInputData(vtk_grid)
-            writer.Write()
+        # create VTK arrays for each of
+        # the data sets
+        for label, dataset in datasets.items():
+            dataset = np.asarray(dataset).flatten()
+
+            if volume_normalization:
+                dataset /= self.volumes.flatten()
+
+            dataset_array = vtk.vtkDoubleArray()
+            dataset_array.SetName(label)
+            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
+                           dataset.size,
+                           True)
+            vtk_grid.GetCellData().AddArray(dataset_array)
+
+
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
 
         return vtk_grid
 

From 722b572dc314ba3dc5802da57a43e0d124323556 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:31:35 +0200
Subject: [PATCH 080/119] write_data_to_vtk RegularMesh

---
 openmc/mesh.py | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 029d714f0..179e9a171 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -622,7 +622,7 @@ class RegularMesh(StructuredMesh):
 
         return root_cell, cells
     
-    def vtk_grid(self, filename=None):
+    def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
         Args:
@@ -635,6 +635,19 @@ class RegularMesh(StructuredMesh):
         import vtk
         from vtk.util import numpy_support as nps
 
+        if self.volumes is None and volume_normalization:
+            raise RuntimeError("No volume data is present on this "
+                               "unstructured mesh. Please load the "
+                               " mesh information from a statepoint file.")
+
+        # check that the data sets are appropriately sized
+        for label, dataset in datasets.items():
+            if isinstance(dataset, np.ndarray):
+                assert dataset.size == self.dimension[0] * self.dimension[1] * self.dimension[2]
+            else:
+                assert len(dataset) == self.dimension[0] * self.dimension[1] * self.dimension[2]
+            cv.check_type('label', label, str)
+
         x_vals = np.linspace(
             self.lower_left[0],
             self.upper_right[0],
@@ -661,12 +674,26 @@ class RegularMesh(StructuredMesh):
         vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
         vtk_grid.SetPoints(vtkPts)
 
-        if filename:
-            # write the .vtk file
-            writer = vtk.vtkStructuredGridWriter()
-            writer.SetFileName(filename)
-            writer.SetInputData(vtk_grid)
-            writer.Write()
+        # create VTK arrays for each of
+        # the data sets
+        for label, dataset in datasets.items():
+            dataset = np.asarray(dataset).flatten()
+
+            if volume_normalization:
+                dataset /= self.volumes.flatten()
+
+            dataset_array = vtk.vtkDoubleArray()
+            dataset_array.SetName(label)
+            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
+                           dataset.size,
+                           True)
+            vtk_grid.GetCellData().AddArray(dataset_array)
+
+        # write the .vtk file
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
 
         return vtk_grid
 

From 5ecac76b6960f635f375fd48f3cb567733073d3f Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:34:05 +0200
Subject: [PATCH 081/119] write_data_to_vtk rectilinear mesh

---
 openmc/mesh.py | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 179e9a171..db2e1593c 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -895,7 +895,7 @@ class RectilinearMesh(StructuredMesh):
 
         return element
 
-    def vtk_grid(self, filename=None):
+    def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
         Args:
@@ -908,6 +908,19 @@ class RectilinearMesh(StructuredMesh):
         import vtk
         from vtk.util import numpy_support as nps
 
+        if self.volumes is None and volume_normalization:
+            raise RuntimeError("No volume data is present on this "
+                               "unstructured mesh. Please load the "
+                               " mesh information from a statepoint file.")
+
+        # check that the data sets are appropriately sized
+        for label, dataset in datasets.items():
+            if isinstance(dataset, np.ndarray):
+                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            else:
+                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+            cv.check_type('label', label, str)
+
         x_vals = self.x_grid
         y_vals = self.y_grid
         z_vals = self.z_grid
@@ -922,12 +935,26 @@ class RectilinearMesh(StructuredMesh):
         vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
         vtk_grid.SetPoints(vtkPts)
 
-        if filename:
-            # write the .vtk file
-            writer = vtk.vtkStructuredGridWriter()
-            writer.SetFileName(filename)
-            writer.SetInputData(vtk_grid)
-            writer.Write()
+        # create VTK arrays for each of
+        # the data sets
+        for label, dataset in datasets.items():
+            dataset = np.asarray(dataset).flatten()
+
+            if volume_normalization:
+                dataset /= self.volumes.flatten()
+
+            dataset_array = vtk.vtkDoubleArray()
+            dataset_array.SetName(label)
+            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
+                           dataset.size,
+                           True)
+            vtk_grid.GetCellData().AddArray(dataset_array)
+
+        # write the .vtk file
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(filename)
+        writer.SetInputData(vtk_grid)
+        writer.Write()
 
         return vtk_grid
 

From 3233ffc759708b6df7a12c8234404897fa329e51 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 12:34:58 +0200
Subject: [PATCH 082/119] removed Tally.write_to_vtk

---
 openmc/tallies.py | 48 -----------------------------------------------
 1 file changed, 48 deletions(-)

diff --git a/openmc/tallies.py b/openmc/tallies.py
index e67365df6..d0355f14e 100644
--- a/openmc/tallies.py
+++ b/openmc/tallies.py
@@ -3013,54 +3013,6 @@ class Tally(IDManagerMixin):
         new_tally.sparse = self.sparse
         return new_tally
 
-    def write_to_vtk(self, filename):
-        """Writes the tally to a vtk file
-
-        Args:
-            filename (str): the filename (must end with .vtk)
-
-        Raises:
-            ValueError: if no MeshFilter was found
-        """
-        try:
-            import vtk
-        except ModuleNotFoundError:
-            msg = 'Python package vtk was not found, please install vtk to use Tally.write_to_vtk.'
-            raise ModuleNotFoundError(msg)
-        except ImportError as err:
-            raise err
-
-        # check that tally has a MeshFilter
-        mesh = None
-        for f in self.filters:
-            if isinstance(f, openmc.MeshFilter):
-                mesh = f.mesh
-                break
-
-        if not mesh:
-            raise ValueError(
-                "write_to_vtk requires a MeshFilter in the tally filters"
-            )
-
-        vtk_grid = mesh.vtk_grid()
-
-        # add mean and std dev data
-        mean_array = vtk.vtkDoubleArray()
-        mean_array.SetName("mean")
-        mean_array.SetArray(self.mean, self.mean.size, True)
-        vtk_grid.GetCellData().AddArray(mean_array)
-
-        std_dev_array = vtk.vtkDoubleArray()
-        std_dev_array.SetName("std_dev")
-        std_dev_array.SetArray(self.std_dev, self.std_dev.size, True)
-        vtk_grid.GetCellData().AddArray(std_dev_array)
-
-        # write the .vtk file
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
 
 class Tallies(cv.CheckedList):
     """Collection of Tallies used for an OpenMC simulation.

From c58465214b96f7245979f792f4bf98201551e560 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 13:01:47 +0200
Subject: [PATCH 083/119] removed tally tests

---
 tests/unit_tests/test_tallies.py | 63 --------------------------------
 1 file changed, 63 deletions(-)

diff --git a/tests/unit_tests/test_tallies.py b/tests/unit_tests/test_tallies.py
index e3f9a486d..bfff741a9 100644
--- a/tests/unit_tests/test_tallies.py
+++ b/tests/unit_tests/test_tallies.py
@@ -1,7 +1,4 @@
 import numpy as np
-import pytest
-import vtk
-from os.path import exists
 
 import openmc
 
@@ -42,63 +39,3 @@ def test_xml_roundtrip(run_in_tmpdir):
     assert new_tally.triggers[0].trigger_type == tally.triggers[0].trigger_type
     assert new_tally.triggers[0].threshold == tally.triggers[0].threshold
     assert new_tally.triggers[0].scores == tally.triggers[0].scores
-
-def run_dummy_sim(tally):
-    mat = openmc.Material()
-    mat.add_nuclide('Zr90', 1.0)
-    mat.set_density('g/cm3', 1.0)
-
-    model = openmc.Model()
-    sph = openmc.Sphere(r=25.0, boundary_type='vacuum')
-    cell = openmc.Cell(fill=mat, region=-sph)
-    model.geometry = openmc.Geometry([cell])
-
-    model.settings.run_mode = 'fixed source'
-    model.settings.batches = 2
-    model.settings.particles = 50
-
-    model.tallies = openmc.Tallies([tally])
-
-    model.run()
-
-cylinder_mesh = openmc.CylindricalMesh()
-cylinder_mesh.r_grid = np.linspace(1, 2, num=30)
-cylinder_mesh.phi_grid = np.linspace(0, np.pi / 2, num=50)
-cylinder_mesh.z_grid = np.linspace(0, 1, num=30)
-
-regular_mesh = openmc.RegularMesh()
-regular_mesh.lower_left = [0, 0, 0]
-regular_mesh.upper_right = [1, 1, 1]
-regular_mesh.dimension = [10, 5, 6]
-
-rectilinear_mesh = openmc.RectilinearMesh()
-rectilinear_mesh.x_grid = np.linspace(0, 1)
-rectilinear_mesh.y_grid = np.linspace(0, 1)
-rectilinear_mesh.z_grid = np.linspace(0, 1)
-
-spherical_mesh = openmc.SphericalMesh()
-spherical_mesh.r_grid = np.linspace(1, 2)
-spherical_mesh.phi_grid = np.linspace(1, 2)
-spherical_mesh.theta_grid = np.linspace(1, 2)
-
-@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
-def test_write_to_vtk(mesh, tmpdir):
-    # build
-    tally = openmc.Tally()
-    tally.filters = [openmc.MeshFilter(mesh)]
-    filename = tmpdir / "out.vtk"
-    run_dummy_sim(tally)
-    # run
-    tally.write_to_vtk(filename)
-    # test
-    assert exists(filename)
-
-
-def test_write_to_vtk_raises_error_when_no_meshfilter():
-    # build
-    tally = openmc.Tally()
-
-    # test
-    expected_err_msg = "write_to_vtk requires a MeshFilter in the tally filters"
-    with pytest.raises(ValueError, match=expected_err_msg):
-        tally.write_to_vtk("out.vtk")

From 15b98ea541fd27f6e02b5939bd482155cf44b56b Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 13:02:12 +0200
Subject: [PATCH 084/119] added a test to meshes

---
 tests/unit_tests/test_mesh_to_vtk.py | 35 ++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 tests/unit_tests/test_mesh_to_vtk.py

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
new file mode 100644
index 000000000..b5c8ca60a
--- /dev/null
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -0,0 +1,35 @@
+import numpy as np
+from os.path import exists
+import pytest
+
+import openmc
+
+
+regular_mesh = openmc.RegularMesh()
+regular_mesh.lower_left = (0, 0, 0)
+regular_mesh.upper_right = (1, 1, 1)
+regular_mesh.dimension = [30, 20, 10]
+
+rectilinear_mesh = openmc.RectilinearMesh()
+rectilinear_mesh.x_grid = np.linspace(1, 2, num=30)
+rectilinear_mesh.y_grid = np.linspace(1, 2, num=30)
+rectilinear_mesh.z_grid = np.linspace(1, 2, num=30)
+
+cylinder_mesh = openmc.CylindricalMesh()
+cylinder_mesh.r_grid = np.linspace(1, 2, num=30)
+cylinder_mesh.phi_grid = np.linspace(0, np.pi, num=50)
+cylinder_mesh.z_grid = np.linspace(0, 1, num=30)
+
+spherical_mesh = openmc.SphericalMesh()
+spherical_mesh.r_grid = np.linspace(1, 2, num=30)
+spherical_mesh.phi_grid = np.linspace(0, np.pi, num=50)
+spherical_mesh.theta_grid = np.linspace(0, np.pi / 2, num=30)
+
+@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
+def test_write_data_to_vtk(mesh, tmpdir):
+    filename = tmpdir / "out.vtk"
+
+    data = np.random.random(mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2])
+
+    mesh.write_data_to_vtk(filename=filename, datasets={"label": data})
+    assert exists(filename)
\ No newline at end of file

From 5174145c1ec9daacac8cfcd33e4b9212d9889fa1 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 13:21:36 +0200
Subject: [PATCH 085/119] added checks to test

---
 tests/unit_tests/test_mesh_to_vtk.py | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index b5c8ca60a..e487b3668 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -1,6 +1,8 @@
 import numpy as np
 from os.path import exists
 import pytest
+import vtk
+from vtk.util import numpy_support as nps
 
 import openmc
 
@@ -27,9 +29,30 @@ spherical_mesh.theta_grid = np.linspace(0, np.pi / 2, num=30)
 
 @pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
 def test_write_data_to_vtk(mesh, tmpdir):
+    # BUILD
     filename = tmpdir / "out.vtk"
 
     data = np.random.random(mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2])
 
-    mesh.write_data_to_vtk(filename=filename, datasets={"label": data})
-    assert exists(filename)
\ No newline at end of file
+    # RUN
+    mesh.write_data_to_vtk(filename=filename, datasets={"label1": data, "label2": data})
+
+    # TEST
+    assert exists(filename)
+
+    # read file
+    reader = vtk.vtkStructuredGridReader()
+    reader.SetFileName(filename)
+    reader.Update()
+
+    # check name of datasets
+    vtk_grid = reader.GetOutput()
+    array1 = vtk_grid.GetCellData().GetArray(0)
+    array2 = vtk_grid.GetCellData().GetArray(1)
+
+    assert array1.GetName() == "label1"
+    assert array2.GetName() == "label2"
+
+    # check size of datasets
+    assert nps.vtk_to_numpy(array1).size == data.size
+    assert nps.vtk_to_numpy(array2).size == data.size
\ No newline at end of file

From 5603e328b8650e874b2cf0235bba6fe792850129 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 13:24:44 +0200
Subject: [PATCH 086/119] docstrings

---
 openmc/mesh.py | 48 ++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 40 insertions(+), 8 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index db2e1593c..1372c5196 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -626,8 +626,16 @@ class RegularMesh(StructuredMesh):
         """Creates a VTK object of the mesh
 
         Args:
-            filename (str, optional): Name of the vtk file to write =
-                (must end with .vtk). Defaults to None.
+            filename (str): Name of the VTK file to write.
+            datasets (dict): Dictionary whose keys are the data labels
+                and values are the data sets.
+            volume_normalization (bool, optional): Whether or not to
+                normalize the data by the volume of the mesh elements.
+                Defaults to True.
+
+        Raises:
+            RuntimeError: when no volume data is found and volume_normalisation
+                is required
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
@@ -899,8 +907,16 @@ class RectilinearMesh(StructuredMesh):
         """Creates a VTK object of the mesh
 
         Args:
-            filename (str, optional): Name of the vtk file to write =
-                (must end with .vtk). Defaults to None.
+            filename (str): Name of the VTK file to write.
+            datasets (dict): Dictionary whose keys are the data labels
+                and values are the data sets.
+            volume_normalization (bool, optional): Whether or not to
+                normalize the data by the volume of the mesh elements.
+                Defaults to True.
+
+        Raises:
+            RuntimeError: when no volume data is found and volume_normalisation
+                is required
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
@@ -1153,8 +1169,16 @@ class CylindricalMesh(StructuredMesh):
         """Creates a VTK object of the mesh
 
         Args:
-            filename (str, optional): Name of the vtk file to write =
-                (must end with .vtk). Defaults to None.
+            filename (str): Name of the VTK file to write.
+            datasets (dict): Dictionary whose keys are the data labels
+                and values are the data sets.
+            volume_normalization (bool, optional): Whether or not to
+                normalize the data by the volume of the mesh elements.
+                Defaults to True.
+
+        Raises:
+            RuntimeError: when no volume data is found and volume_normalisation
+                is required
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
@@ -1409,8 +1433,16 @@ class SphericalMesh(StructuredMesh):
         """Creates a VTK object of the mesh
 
         Args:
-            filename (str, optional): Name of the vtk file to write =
-                (must end with .vtk). Defaults to None.
+            filename (str): Name of the VTK file to write.
+            datasets (dict): Dictionary whose keys are the data labels
+                and values are the data sets.
+            volume_normalization (bool, optional): Whether or not to
+                normalize the data by the volume of the mesh elements.
+                Defaults to True.
+
+        Raises:
+            RuntimeError: when no volume data is found and volume_normalisation
+                is required
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object

From c77eb6097d6584820256ad497520273669299f9a Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:18:31 +0200
Subject: [PATCH 087/119] removed check volume for structured meshes

---
 openmc/mesh.py | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 1372c5196..a63834941 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -633,21 +633,12 @@ class RegularMesh(StructuredMesh):
                 normalize the data by the volume of the mesh elements.
                 Defaults to True.
 
-        Raises:
-            RuntimeError: when no volume data is found and volume_normalisation
-                is required
-
         Returns:
             vtk.vtkStructuredGrid: the VTK object
         """
         import vtk
         from vtk.util import numpy_support as nps
 
-        if self.volumes is None and volume_normalization:
-            raise RuntimeError("No volume data is present on this "
-                               "unstructured mesh. Please load the "
-                               " mesh information from a statepoint file.")
-
         # check that the data sets are appropriately sized
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
@@ -914,21 +905,12 @@ class RectilinearMesh(StructuredMesh):
                 normalize the data by the volume of the mesh elements.
                 Defaults to True.
 
-        Raises:
-            RuntimeError: when no volume data is found and volume_normalisation
-                is required
-
         Returns:
             vtk.vtkStructuredGrid: the VTK object
         """
         import vtk
         from vtk.util import numpy_support as nps
 
-        if self.volumes is None and volume_normalization:
-            raise RuntimeError("No volume data is present on this "
-                               "unstructured mesh. Please load the "
-                               " mesh information from a statepoint file.")
-
         # check that the data sets are appropriately sized
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
@@ -1176,21 +1158,12 @@ class CylindricalMesh(StructuredMesh):
                 normalize the data by the volume of the mesh elements.
                 Defaults to True.
 
-        Raises:
-            RuntimeError: when no volume data is found and volume_normalisation
-                is required
-
         Returns:
             vtk.vtkStructuredGrid: the VTK object
         """
         import vtk
         from vtk.util import numpy_support as nps
 
-        if self.volumes is None and volume_normalization:
-            raise RuntimeError("No volume data is present on this "
-                               "unstructured mesh. Please load the "
-                               " mesh information from a statepoint file.")
-
         # check that the data sets are appropriately sized
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
@@ -1440,21 +1413,12 @@ class SphericalMesh(StructuredMesh):
                 normalize the data by the volume of the mesh elements.
                 Defaults to True.
 
-        Raises:
-            RuntimeError: when no volume data is found and volume_normalisation
-                is required
-
         Returns:
             vtk.vtkStructuredGrid: the VTK object
         """
         import vtk
         from vtk.util import numpy_support as nps
 
-        if self.volumes is None and volume_normalization:
-            raise RuntimeError("No volume data is present on this "
-                               "unstructured mesh. Please load the "
-                               " mesh information from a statepoint file.")
-
         # check that the data sets are appropriately sized
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):

From 1a7c0791bf92e46475343323d7ac0b939bcb9a5a Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:19:12 +0200
Subject: [PATCH 088/119] z is unchanged

---
 openmc/mesh.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index a63834941..1ccb6e86e 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1179,10 +1179,9 @@ class CylindricalMesh(StructuredMesh):
         # create points
         pts_cylindrical = np.array([[r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid])
         pts_cartesian = np.copy(pts_cylindrical)
-        r, phi, z = pts_cylindrical[:, 0], pts_cylindrical[:, 1], pts_cylindrical[:, 2]
+        r, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1]
         pts_cartesian[:, 0] = r * np.cos(phi)
         pts_cartesian[:, 1] = r * np.sin(phi)
-        pts_cartesian[:, 2] = z
 
         vtkPts = vtk.vtkPoints()
         vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))

From 9867a4340abbbd2fa093acb1fd04ed1745ab6513 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 14:19:56 +0200
Subject: [PATCH 089/119] [skip ci] use .num_mesh_cells

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 tests/unit_tests/test_mesh_to_vtk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index e487b3668..b57235edd 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -32,7 +32,7 @@ def test_write_data_to_vtk(mesh, tmpdir):
     # BUILD
     filename = tmpdir / "out.vtk"
 
-    data = np.random.random(mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2])
+    data = np.random.random(mesh.num_mesh_cells)
 
     # RUN
     mesh.write_data_to_vtk(filename=filename, datasets={"label1": data, "label2": data})

From 7e074fe354fc60887c8c4d6540c28e1a6a338ebc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 14:20:17 +0200
Subject: [PATCH 090/119] [skip ci] str(filename)

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/mesh.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 1372c5196..e024710b4 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -699,7 +699,7 @@ class RegularMesh(StructuredMesh):
 
         # write the .vtk file
         writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
+        writer.SetFileName(str(filename))
         writer.SetInputData(vtk_grid)
         writer.Write()
 

From 1155ffb739d8a80e5520c1013596864874a57cf5 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:21:15 +0200
Subject: [PATCH 091/119] added pathlib import

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

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index e487b3668..cfb0407ca 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -1,5 +1,6 @@
 import numpy as np
 from os.path import exists
+from pathlib import Path
 import pytest
 import vtk
 from vtk.util import numpy_support as nps

From aeeb078344023ebb47ec7238b763c89a541a05fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 14:22:01 +0200
Subject: [PATCH 092/119] [skip ci] pathlib instead of os

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 tests/unit_tests/test_mesh_to_vtk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index b57235edd..3b7ccf9fa 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -30,7 +30,7 @@ spherical_mesh.theta_grid = np.linspace(0, np.pi / 2, num=30)
 @pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
 def test_write_data_to_vtk(mesh, tmpdir):
     # BUILD
-    filename = tmpdir / "out.vtk"
+    filename = Path(tmpdir) / "out.vtk"
 
     data = np.random.random(mesh.num_mesh_cells)
 

From f99e93b5839f4166972fa8e83d93de6eccb5b619 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 14:22:26 +0200
Subject: [PATCH 093/119] [skip ci] is_file() instead of exists()

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 tests/unit_tests/test_mesh_to_vtk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 3b7ccf9fa..31fbd4c88 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -38,7 +38,7 @@ def test_write_data_to_vtk(mesh, tmpdir):
     mesh.write_data_to_vtk(filename=filename, datasets={"label1": data, "label2": data})
 
     # TEST
-    assert exists(filename)
+    assert filename.is_file()
 
     # read file
     reader = vtk.vtkStructuredGridReader()

From 1266e433c8bd3f525e6b1ea9bafef174238be09c Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:23:06 +0200
Subject: [PATCH 094/119] removed unused import

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

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 572834f84..5da62cdef 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -1,5 +1,4 @@
 import numpy as np
-from os.path import exists
 from pathlib import Path
 import pytest
 import vtk

From 58ccb82cf50a5ba76e622f96969ba4db6752a885 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:26:27 +0200
Subject: [PATCH 095/119] back to .dimension

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

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 5da62cdef..451c869c2 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -32,7 +32,7 @@ def test_write_data_to_vtk(mesh, tmpdir):
     # BUILD
     filename = Path(tmpdir) / "out.vtk"
 
-    data = np.random.random(mesh.num_mesh_cells)
+    data = np.random.random(mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2])
 
     # RUN
     mesh.write_data_to_vtk(filename=filename, datasets={"label1": data, "label2": data})

From 890c3ad0d58fa59532dc143e56c0100e4540fd0d Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:26:46 +0200
Subject: [PATCH 096/119] pytest.importorskip

---
 tests/unit_tests/test_mesh_to_vtk.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 451c869c2..f651f5acb 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -1,7 +1,8 @@
 import numpy as np
 from pathlib import Path
 import pytest
-import vtk
+
+vtk = pytest.importorskip("vtk")
 from vtk.util import numpy_support as nps
 
 import openmc

From 48a0d15b1aa6bbbfa2f3b3c85252a9d05c923028 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:36:54 +0200
Subject: [PATCH 097/119] added error raise + new test

---
 openmc/mesh.py                       | 53 ++++++++++++++++++++++------
 tests/unit_tests/test_mesh_to_vtk.py | 17 ++++++++-
 2 files changed, 59 insertions(+), 11 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index b883a4a09..ada69887a 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -635,16 +635,22 @@ class RegularMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
+        
+        Raises:
+            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
         import vtk
         from vtk.util import numpy_support as nps
 
         # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
-                assert dataset.size == self.dimension[0] * self.dimension[1] * self.dimension[2]
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             else:
-                assert len(dataset) == self.dimension[0] * self.dimension[1] * self.dimension[2]
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             cv.check_type('label', label, str)
 
         x_vals = np.linspace(
@@ -907,16 +913,22 @@ class RectilinearMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
+
+        Raises:
+            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
         import vtk
         from vtk.util import numpy_support as nps
 
         # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
-                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             else:
-                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             cv.check_type('label', label, str)
 
         x_vals = self.x_grid
@@ -1160,16 +1172,22 @@ class CylindricalMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
+
+        Raises:
+            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
         import vtk
         from vtk.util import numpy_support as nps
 
         # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
-                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             else:
-                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             cv.check_type('label', label, str)
 
         vtk_grid = vtk.vtkStructuredGrid()
@@ -1414,16 +1432,23 @@ class SphericalMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
+
+        Raises:
+            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
         import vtk
         from vtk.util import numpy_support as nps
 
         # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
-                assert dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             else:
-                assert len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
+
             cv.check_type('label', label, str)
 
         vtk_grid = vtk.vtkStructuredGrid()
@@ -1642,6 +1667,11 @@ class UnstructuredMesh(MeshBase):
         volume_normalization : bool
             Whether or not to normalize the data by the
             volume of the mesh elements
+
+        Raises
+        ------
+            RuntimeError
+                when the size of a dataset doesn't match the number of cells 
         """
 
         import vtk
@@ -1658,11 +1688,14 @@ class UnstructuredMesh(MeshBase):
                                " mesh information from a statepoint file.")
 
         # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
         for label, dataset in datasets.items():
             if isinstance(dataset, np.ndarray):
-                assert dataset.size == self.n_elements
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             else:
-                assert len(dataset) == self.n_elements
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
             cv.check_type('label', label, str)
 
         # create data arrays for the cells/points
diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index f651f5acb..9022feecd 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -56,4 +56,19 @@ def test_write_data_to_vtk(mesh, tmpdir):
 
     # check size of datasets
     assert nps.vtk_to_numpy(array1).size == data.size
-    assert nps.vtk_to_numpy(array2).size == data.size
\ No newline at end of file
+    assert nps.vtk_to_numpy(array2).size == data.size
+
+@pytest.mark.parametrize("mesh", [cylinder_mesh, regular_mesh, rectilinear_mesh, spherical_mesh])
+def test_write_data_to_vtk_size_mismatch(mesh):
+    """Checks that an error is raised when the size of the dataset
+    doesn't match the mesh number of cells
+
+    Args:
+        mesh (openmc.StructuredMesh): the mesh to test
+    """
+    right_size = mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2]
+    data = np.random.random(right_size + 1)
+
+    expected_error_msg = "The size of the dataset label should be equal to the number of cells"
+    with pytest.raises(RuntimeError, match=expected_error_msg):
+        mesh.write_data_to_vtk(filename="out.vtk", datasets={"label": data})
\ No newline at end of file

From 8857b769324f299ad410926b2542c7b7a24a895f Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:50:28 +0200
Subject: [PATCH 098/119] refactored by adding
 StructuredMesh.write_data_to_vtk()

---
 openmc/mesh.py | 260 +++++++++++++------------------------------------
 1 file changed, 70 insertions(+), 190 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index ada69887a..5083b215c 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -193,6 +193,51 @@ class StructuredMesh(MeshBase):
         s1 = (slice(1, None),)*ndim + (slice(None),)
         return (vertices[s0] + vertices[s1]) / 2
 
+    def write_data_to_vtk(self, points, filename, datasets, volume_normalization=True):
+        import vtk
+        from vtk.util import numpy_support as nps
+
+        # check that the data sets are appropriately sized
+        errmsg = "The size of the dataset {} should be equal to the number of cells"
+        for label, dataset in datasets.items():
+            if isinstance(dataset, np.ndarray):
+                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
+            else:
+                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
+                    raise RuntimeError(errmsg.format(label))
+            cv.check_type('label', label, str)
+
+        vtk_grid = vtk.vtkStructuredGrid()
+
+        vtk_grid.SetDimensions(*self.dimension)
+
+        vtkPts = vtk.vtkPoints()
+        vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))
+        vtk_grid.SetPoints(vtkPts)
+
+        # create VTK arrays for each of
+        # the data sets
+        for label, dataset in datasets.items():
+            dataset = np.asarray(dataset).flatten()
+
+            if volume_normalization:
+                dataset /= self.volumes.flatten()
+
+            dataset_array = vtk.vtkDoubleArray()
+            dataset_array.SetName(label)
+            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
+                           dataset.size,
+                           True)
+            vtk_grid.GetCellData().AddArray(dataset_array)
+
+        # write the .vtk file
+        writer = vtk.vtkStructuredGridWriter()
+        writer.SetFileName(str(filename))
+        writer.SetInputData(vtk_grid)
+        writer.Write()
+
+        return vtk_grid
 
 class RegularMesh(StructuredMesh):
     """A regular Cartesian mesh in one, two, or three dimensions
@@ -635,23 +680,7 @@ class RegularMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
-        
-        Raises:
-            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
-        import vtk
-        from vtk.util import numpy_support as nps
-
-        # check that the data sets are appropriately sized
-        errmsg = "The size of the dataset {} should be equal to the number of cells"
-        for label, dataset in datasets.items():
-            if isinstance(dataset, np.ndarray):
-                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            else:
-                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            cv.check_type('label', label, str)
 
         x_vals = np.linspace(
             self.lower_left[0],
@@ -668,39 +697,16 @@ class RegularMesh(StructuredMesh):
             self.upper_right[2],
             num=self.dimension[2] + 1,
         )
-        vtk_grid = vtk.vtkStructuredGrid()
-
-        vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
 
         # create points
         pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
 
-        vtkPts = vtk.vtkPoints()
-        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
-        vtk_grid.SetPoints(vtkPts)
-
-        # create VTK arrays for each of
-        # the data sets
-        for label, dataset in datasets.items():
-            dataset = np.asarray(dataset).flatten()
-
-            if volume_normalization:
-                dataset /= self.volumes.flatten()
-
-            dataset_array = vtk.vtkDoubleArray()
-            dataset_array.SetName(label)
-            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
-                           dataset.size,
-                           True)
-            vtk_grid.GetCellData().AddArray(dataset_array)
-
-        # write the .vtk file
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(str(filename))
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
-        return vtk_grid
+        return super().write_data_to_vtk(
+            points=pts_cartesian,
+            filename=filename,
+            datasets=datasets,
+            volume_normalization=volume_normalization
+        )
 
 def Mesh(*args, **kwargs):
     warnings.warn("Mesh has been renamed RegularMesh. Future versions of "
@@ -913,60 +919,16 @@ class RectilinearMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
-
-        Raises:
-            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
-        import vtk
-        from vtk.util import numpy_support as nps
-
-        # check that the data sets are appropriately sized
-        errmsg = "The size of the dataset {} should be equal to the number of cells"
-        for label, dataset in datasets.items():
-            if isinstance(dataset, np.ndarray):
-                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            else:
-                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            cv.check_type('label', label, str)
-
-        x_vals = self.x_grid
-        y_vals = self.y_grid
-        z_vals = self.z_grid
-        vtk_grid = vtk.vtkStructuredGrid()
-
-        vtk_grid.SetDimensions(len(x_vals), len(y_vals), len(z_vals))
-
         # create points
-        pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])
+        pts_cartesian = np.array([[x, y, z] for z in self.z_grid for y in self.y_grid for x in self.x_grid])
 
-        vtkPts = vtk.vtkPoints()
-        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
-        vtk_grid.SetPoints(vtkPts)
-
-        # create VTK arrays for each of
-        # the data sets
-        for label, dataset in datasets.items():
-            dataset = np.asarray(dataset).flatten()
-
-            if volume_normalization:
-                dataset /= self.volumes.flatten()
-
-            dataset_array = vtk.vtkDoubleArray()
-            dataset_array.SetName(label)
-            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
-                           dataset.size,
-                           True)
-            vtk_grid.GetCellData().AddArray(dataset_array)
-
-        # write the .vtk file
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
-        return vtk_grid
+        return super().write_data_to_vtk(
+            points=pts_cartesian,
+            filename=filename,
+            datasets=datasets,
+            volume_normalization=volume_normalization
+        )
 
 
 class CylindricalMesh(StructuredMesh):
@@ -1172,28 +1134,7 @@ class CylindricalMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
-
-        Raises:
-            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
-        import vtk
-        from vtk.util import numpy_support as nps
-
-        # check that the data sets are appropriately sized
-        errmsg = "The size of the dataset {} should be equal to the number of cells"
-        for label, dataset in datasets.items():
-            if isinstance(dataset, np.ndarray):
-                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            else:
-                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            cv.check_type('label', label, str)
-
-        vtk_grid = vtk.vtkStructuredGrid()
-
-        vtk_grid.SetDimensions(len(self.r_grid), len(self.phi_grid), len(self.z_grid))
-
         # create points
         pts_cylindrical = np.array([[r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid])
         pts_cartesian = np.copy(pts_cylindrical)
@@ -1201,32 +1142,12 @@ class CylindricalMesh(StructuredMesh):
         pts_cartesian[:, 0] = r * np.cos(phi)
         pts_cartesian[:, 1] = r * np.sin(phi)
 
-        vtkPts = vtk.vtkPoints()
-        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
-        vtk_grid.SetPoints(vtkPts)
-
-        # create VTK arrays for each of
-        # the data sets
-        for label, dataset in datasets.items():
-            dataset = np.asarray(dataset).flatten()
-
-            if volume_normalization:
-                dataset /= self.volumes.flatten()
-
-            dataset_array = vtk.vtkDoubleArray()
-            dataset_array.SetName(label)
-            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
-                           dataset.size,
-                           True)
-            vtk_grid.GetCellData().AddArray(dataset_array)
-
-
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
-        return vtk_grid
+        return super().write_data_to_vtk(
+            points=pts_cartesian,
+            filename=filename,
+            datasets=datasets,
+            volume_normalization=volume_normalization
+        )
 
 class SphericalMesh(StructuredMesh):
     """A 3D spherical mesh
@@ -1432,28 +1353,7 @@ class SphericalMesh(StructuredMesh):
 
         Returns:
             vtk.vtkStructuredGrid: the VTK object
-
-        Raises:
-            RuntimeError: when the size of a dataset doesn't match the number of cells 
         """
-        import vtk
-        from vtk.util import numpy_support as nps
-
-        # check that the data sets are appropriately sized
-        errmsg = "The size of the dataset {} should be equal to the number of cells"
-        for label, dataset in datasets.items():
-            if isinstance(dataset, np.ndarray):
-                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-            else:
-                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
-                    raise RuntimeError(errmsg.format(label))
-
-            cv.check_type('label', label, str)
-
-        vtk_grid = vtk.vtkStructuredGrid()
-
-        vtk_grid.SetDimensions(len(self.r_grid), len(self.theta_grid), len(self.phi_grid))
 
         # create points
         pts_spherical = np.array([[r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid])
@@ -1463,32 +1363,12 @@ class SphericalMesh(StructuredMesh):
         pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta)
         pts_cartesian[:, 2] = r * np.cos(phi)
 
-        vtkPts = vtk.vtkPoints()
-        vtkPts.SetData(nps.numpy_to_vtk(pts_cartesian, deep=True))
-        vtk_grid.SetPoints(vtkPts)
-
-        # create VTK arrays for each of
-        # the data sets
-        for label, dataset in datasets.items():
-            dataset = np.asarray(dataset).flatten()
-
-            if volume_normalization:
-                dataset /= self.volumes.flatten()
-
-            dataset_array = vtk.vtkDoubleArray()
-            dataset_array.SetName(label)
-            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
-                           dataset.size,
-                           True)
-            vtk_grid.GetCellData().AddArray(dataset_array)
-
-        # write the .vtk file
-        writer = vtk.vtkStructuredGridWriter()
-        writer.SetFileName(filename)
-        writer.SetInputData(vtk_grid)
-        writer.Write()
-
-        return vtk_grid
+        return super().write_data_to_vtk(
+            points=pts_cartesian,
+            filename=filename,
+            datasets=datasets,
+            volume_normalization=volume_normalization
+        )
 
 
 class UnstructuredMesh(MeshBase):

From 0c4de41f5076acbd93efaad6cdb970e26c890964 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 14:56:27 +0200
Subject: [PATCH 099/119] docstrings

---
 openmc/mesh.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 5083b215c..449edb8d6 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -194,6 +194,24 @@ class StructuredMesh(MeshBase):
         return (vertices[s0] + vertices[s1]) / 2
 
     def write_data_to_vtk(self, points, filename, datasets, volume_normalization=True):
+        """Creates a VTK object of the mesh
+
+        Args:
+            points (list or np.array): List of (X,Y,Y) tuples.
+            filename (str): Name of the VTK file to write.
+            datasets (dict): Dictionary whose keys are the data labels
+                and values are the data sets.
+            volume_normalization (bool, optional): Whether or not to
+                normalize the data by the volume of the mesh elements.
+                Defaults to True.
+
+        Raises:
+            RuntimeError: when the size of a dataset doesn't match the number of cells
+
+        Returns:
+            vtk.vtkStructuredGrid: the VTK object
+        """
+
         import vtk
         from vtk.util import numpy_support as nps
 

From ad73f03a0d712311b0d5ef80f0456d2c35b61dbe Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 15:02:20 +0200
Subject: [PATCH 100/119] converted docstrings to numpy style

---
 openmc/mesh.py | 129 +++++++++++++++++++++++++++++++------------------
 1 file changed, 81 insertions(+), 48 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 449edb8d6..aa338f97e 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -196,20 +196,29 @@ class StructuredMesh(MeshBase):
     def write_data_to_vtk(self, points, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
-        Args:
-            points (list or np.array): List of (X,Y,Y) tuples.
-            filename (str): Name of the VTK file to write.
-            datasets (dict): Dictionary whose keys are the data labels
-                and values are the data sets.
-            volume_normalization (bool, optional): Whether or not to
-                normalize the data by the volume of the mesh elements.
-                Defaults to True.
+        Parameters
+        ----------
+        points : list or np.array
+            List of (X,Y,Y) tuples.
+        filename : str
+            Name of the VTK file to write.
+        datasets : dict
+            Dictionary whose keys are the data labels
+            and values are the data sets.
+        volume_normalization : bool, optional
+            Whether or not to normalize the data by
+            the volume of the mesh elements.
+            Defaults to True.
 
-        Raises:
-            RuntimeError: when the size of a dataset doesn't match the number of cells
+        Raises
+        ------
+        RuntimeError
+            When the size of a dataset doesn't match the number of cells
 
-        Returns:
-            vtk.vtkStructuredGrid: the VTK object
+        Returns
+        -------
+        vtk.vtkStructuredGrid
+            the VTK object
         """
 
         import vtk
@@ -688,16 +697,22 @@ class RegularMesh(StructuredMesh):
     def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
-        Args:
-            filename (str): Name of the VTK file to write.
-            datasets (dict): Dictionary whose keys are the data labels
-                and values are the data sets.
-            volume_normalization (bool, optional): Whether or not to
-                normalize the data by the volume of the mesh elements.
-                Defaults to True.
+        Parameters
+        ----------
+        filename : str
+            Name of the VTK file to write.
+        datasets : dict
+            Dictionary whose keys are the data labels
+            and values are the data sets.
+        volume_normalization : bool, optional
+            Whether or not to normalize the data by
+            the volume of the mesh elements.
+            Defaults to True.
 
-        Returns:
-            vtk.vtkStructuredGrid: the VTK object
+        Returns
+        -------
+        vtk.vtkStructuredGrid
+            the VTK object
         """
 
         x_vals = np.linspace(
@@ -927,16 +942,22 @@ class RectilinearMesh(StructuredMesh):
     def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
-        Args:
-            filename (str): Name of the VTK file to write.
-            datasets (dict): Dictionary whose keys are the data labels
-                and values are the data sets.
-            volume_normalization (bool, optional): Whether or not to
-                normalize the data by the volume of the mesh elements.
-                Defaults to True.
+        Parameters
+        ----------
+        filename : str
+            Name of the VTK file to write.
+        datasets : dict
+            Dictionary whose keys are the data labels
+            and values are the data sets.
+        volume_normalization : bool, optional
+            Whether or not to normalize the data by
+            the volume of the mesh elements.
+            Defaults to True.
 
-        Returns:
-            vtk.vtkStructuredGrid: the VTK object
+        Returns
+        -------
+        vtk.vtkStructuredGrid
+            the VTK object
         """
         # create points
         pts_cartesian = np.array([[x, y, z] for z in self.z_grid for y in self.y_grid for x in self.x_grid])
@@ -1142,16 +1163,22 @@ class CylindricalMesh(StructuredMesh):
     def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
-        Args:
-            filename (str): Name of the VTK file to write.
-            datasets (dict): Dictionary whose keys are the data labels
-                and values are the data sets.
-            volume_normalization (bool, optional): Whether or not to
-                normalize the data by the volume of the mesh elements.
-                Defaults to True.
+        Parameters
+        ----------
+        filename : str
+            Name of the VTK file to write.
+        datasets : dict
+            Dictionary whose keys are the data labels
+            and values are the data sets.
+        volume_normalization : bool, optional
+            Whether or not to normalize the data by
+            the volume of the mesh elements.
+            Defaults to True.
 
-        Returns:
-            vtk.vtkStructuredGrid: the VTK object
+        Returns
+        -------
+        vtk.vtkStructuredGrid
+            the VTK object
         """
         # create points
         pts_cylindrical = np.array([[r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid])
@@ -1361,16 +1388,22 @@ class SphericalMesh(StructuredMesh):
     def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
-        Args:
-            filename (str): Name of the VTK file to write.
-            datasets (dict): Dictionary whose keys are the data labels
-                and values are the data sets.
-            volume_normalization (bool, optional): Whether or not to
-                normalize the data by the volume of the mesh elements.
-                Defaults to True.
+        Parameters
+        ----------
+        filename : str
+            Name of the VTK file to write.
+        datasets : dict
+            Dictionary whose keys are the data labels
+            and values are the data sets.
+        volume_normalization : bool, optional
+            Whether or not to normalize the data by
+            the volume of the mesh elements.
+            Defaults to True.
 
-        Returns:
-            vtk.vtkStructuredGrid: the VTK object
+        Returns
+        -------
+        vtk.vtkStructuredGrid
+            the VTK object
         """
 
         # create points

From a2299063f5b4061a2eb2cd762004439fadbab57c Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 15:02:52 +0200
Subject: [PATCH 101/119] converted docstrings to numpy style

---
 tests/unit_tests/test_mesh_to_vtk.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 9022feecd..9247540a0 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -63,8 +63,10 @@ def test_write_data_to_vtk_size_mismatch(mesh):
     """Checks that an error is raised when the size of the dataset
     doesn't match the mesh number of cells
 
-    Args:
-        mesh (openmc.StructuredMesh): the mesh to test
+    Parameters
+    ----------
+    mesh : openmc.StructuredMesh
+        The mesh to test
     """
     right_size = mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2]
     data = np.random.random(right_size + 1)

From d80bf7bdb596a7169f0e28d42b363d1886c43448 Mon Sep 17 00:00:00 2001
From: Patrick Myers <90068356+myerspat@users.noreply.github.com>
Date: Wed, 29 Jun 2022 09:25:59 -0500
Subject: [PATCH 102/119] Added comments explaining reasoning for 2D xtensor xs
 in photon.h

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 include/openmc/photon.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/include/openmc/photon.h b/include/openmc/photon.h
index 50ee228c4..09fb3ba01 100644
--- a/include/openmc/photon.h
+++ b/include/openmc/photon.h
@@ -79,7 +79,9 @@ public:
   Tabulated1D coherent_anomalous_real_;
   Tabulated1D coherent_anomalous_imag_;
 
-  // Photoionization and atomic relaxation data
+  // Photoionization and atomic relaxation data. Subshell cross sections are
+  // stored separately to improve memory access pattern when calculating the
+  // total cross section
   vector<ElectronSubshell> shells_;
   xt::xtensor<double, 2> cross_sections_;
 

From 2c5a845897aeb973448f31cea2d9256754262e3e Mon Sep 17 00:00:00 2001
From: Patrick Myers <90068356+myerspat@users.noreply.github.com>
Date: Wed, 29 Jun 2022 09:26:36 -0500
Subject: [PATCH 103/119] Removed an include from photon.cpp

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 src/photon.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/photon.cpp b/src/photon.cpp
index 85bd435c9..a127ac2fe 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -17,7 +17,6 @@
 #include "xtensor/xmath.hpp"
 #include "xtensor/xoperation.hpp"
 #include "xtensor/xslice.hpp"
-#include "xtensor/xtensor_forward.hpp"
 #include "xtensor/xview.hpp"
 
 #include <cmath>

From c38ed4d8759704e829454abfc12dfa2189dd4bf1 Mon Sep 17 00:00:00 2001
From: myerspat <myerspat@umich.edu>
Date: Wed, 29 Jun 2022 09:37:18 -0500
Subject: [PATCH 104/119] used placeholders namespace and added comment about
 variables initialized

---
 src/photon.cpp  | 6 ++++--
 src/physics.cpp | 3 ++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/photon.cpp b/src/photon.cpp
index a127ac2fe..2f9bc5e3d 100644
--- a/src/photon.cpp
+++ b/src/photon.cpp
@@ -46,6 +46,8 @@ vector<unique_ptr<PhotonInteraction>> elements;
 
 PhotonInteraction::PhotonInteraction(hid_t group)
 {
+  using namespace xt::placeholders;
+
   // Set index of element in global vector
   index_ = data::elements.size();
 
@@ -164,8 +166,8 @@ PhotonInteraction::PhotonInteraction(hid_t group)
     close_dataset(dset);
     read_dataset(tgroup, "xs", xs);
 
-    auto cross_section = xt::view(
-      cross_sections_, xt::range(shell.threshold, xt::placeholders::_), i);
+    auto cross_section =
+      xt::view(cross_sections_, xt::range(shell.threshold, _), i);
     cross_section = xt::where(xs > 0, xt::log(xs), 0);
 
     if (object_exists(tgroup, "transitions")) {
diff --git a/src/physics.cpp b/src/physics.cpp
index cc712affd..bcdcf7ecf 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -347,7 +347,8 @@ void sample_photon_reaction(Particle& p)
   double prob_after = prob + micro.photoelectric;
 
   if (prob_after > cutoff) {
-
+    // Get grid index, interpolation factor, and bounding subshell
+    // cross sections
     int i_grid = micro.index_grid;
     double f = micro.interp_factor;
     const auto& xs_lower = xt::row(element.cross_sections_, i_grid);

From 7cba2ad03012658481c6edbc04f070892e90dd3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 18:46:10 +0200
Subject: [PATCH 105/119] [skip ci] X Y Y typo

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/mesh.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index aa338f97e..90f4c55a9 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -199,7 +199,7 @@ class StructuredMesh(MeshBase):
         Parameters
         ----------
         points : list or np.array
-            List of (X,Y,Y) tuples.
+            List of (X,Y,Z) tuples.
         filename : str
             Name of the VTK file to write.
         datasets : dict

From 5180ab3f8a6031cfbcd708c04e7fd23f8936085a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 18:46:43 +0200
Subject: [PATCH 106/119] [skip ci] removed default value

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/mesh.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 90f4c55a9..73a49bfc1 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -208,7 +208,6 @@ class StructuredMesh(MeshBase):
         volume_normalization : bool, optional
             Whether or not to normalize the data by
             the volume of the mesh elements.
-            Defaults to True.
 
         Raises
         ------

From 94ef0c40abe6f4a208aaaccad36c17ff486dd9b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Wed, 29 Jun 2022 18:47:24 +0200
Subject: [PATCH 107/119] [skip ci] refactore upperright and lowerleft

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/mesh.py | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 73a49bfc1..7155b0ba0 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -714,21 +714,10 @@ class RegularMesh(StructuredMesh):
             the VTK object
         """
 
-        x_vals = np.linspace(
-            self.lower_left[0],
-            self.upper_right[0],
-            num=self.dimension[0] + 1,
-        )
-        y_vals = np.linspace(
-            self.lower_left[1],
-            self.upper_right[1],
-            num=self.dimension[1] + 1,
-        )
-        z_vals = np.linspace(
-            self.lower_left[2],
-            self.upper_right[2],
-            num=self.dimension[2] + 1,
-        )
+        ll, ur = self.lower_left, self.upper_right
+        x_vals = np.linspace(ll[0], ur[0], num=self.dimension[0] + 1)
+        y_vals = np.linspace(ll[1], ur[1], num=self.dimension[1] + 1)
+        z_vals = np.linspace(ll[2], ur[2], num=self.dimension[2] + 1)
 
         # create points
         pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals])

From 96c89f138daa97f78cb996449a32a88ca58754ff Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 19:01:39 +0200
Subject: [PATCH 108/119] multiple lines

---
 openmc/mesh.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 7155b0ba0..209002e42 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -1169,7 +1169,14 @@ class CylindricalMesh(StructuredMesh):
             the VTK object
         """
         # create points
-        pts_cylindrical = np.array([[r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid])
+        pts_cylindrical = np.array(
+            [
+                [r, phi, z]
+                for z in self.z_grid
+                for phi in self.phi_grid
+                for r in self.r_grid
+            ]
+        )
         pts_cartesian = np.copy(pts_cylindrical)
         r, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1]
         pts_cartesian[:, 0] = r * np.cos(phi)
@@ -1395,7 +1402,14 @@ class SphericalMesh(StructuredMesh):
         """
 
         # create points
-        pts_spherical = np.array([[r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid])
+        pts_spherical = np.array(
+            [
+                [r, theta, phi]
+                for phi in self.phi_grid
+                for theta in self.theta_grid
+                for r in self.r_grid
+            ]
+        )
         pts_cartesian = np.copy(pts_spherical)
         r, theta, phi = pts_spherical[:, 0], pts_spherical[:, 1], pts_spherical[:, 2]
         pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta)

From fabe3e607c92891ec740aefa632eba010428eef2 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Wed, 29 Jun 2022 19:02:25 +0200
Subject: [PATCH 109/119] pathlib

---
 openmc/mesh.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 209002e42..2a53c8a91 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -698,7 +698,7 @@ class RegularMesh(StructuredMesh):
 
         Parameters
         ----------
-        filename : str
+        filename : str or pathlib.Path
             Name of the VTK file to write.
         datasets : dict
             Dictionary whose keys are the data labels
@@ -932,7 +932,7 @@ class RectilinearMesh(StructuredMesh):
 
         Parameters
         ----------
-        filename : str
+        filename : str or pathlib.Path
             Name of the VTK file to write.
         datasets : dict
             Dictionary whose keys are the data labels
@@ -1153,7 +1153,7 @@ class CylindricalMesh(StructuredMesh):
 
         Parameters
         ----------
-        filename : str
+        filename : str or pathlib.Path
             Name of the VTK file to write.
         datasets : dict
             Dictionary whose keys are the data labels
@@ -1385,7 +1385,7 @@ class SphericalMesh(StructuredMesh):
 
         Parameters
         ----------
-        filename : str
+        filename : str or pathlib.Path
             Name of the VTK file to write.
         datasets : dict
             Dictionary whose keys are the data labels
@@ -1592,7 +1592,7 @@ class UnstructuredMesh(MeshBase):
 
         Parameters
         ----------
-        filename : str
+        filename : str or pathlib.Path
             Name of the VTK file to write.
         datasets : dict
             Dictionary whose keys are the data labels

From 0b0265cb592685d8e6daec688229996d7b7e9f5a Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 1 Jul 2022 11:37:16 +0200
Subject: [PATCH 110/119] adapted tests

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

diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py
index 9247540a0..26a393b41 100644
--- a/tests/unit_tests/test_mesh_to_vtk.py
+++ b/tests/unit_tests/test_mesh_to_vtk.py
@@ -33,7 +33,7 @@ def test_write_data_to_vtk(mesh, tmpdir):
     # BUILD
     filename = Path(tmpdir) / "out.vtk"
 
-    data = np.random.random(mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2])
+    data = np.random.random(mesh.num_mesh_cells)
 
     # RUN
     mesh.write_data_to_vtk(filename=filename, datasets={"label1": data, "label2": data})
@@ -68,7 +68,7 @@ def test_write_data_to_vtk_size_mismatch(mesh):
     mesh : openmc.StructuredMesh
         The mesh to test
     """
-    right_size = mesh.dimension[0]*mesh.dimension[1]*mesh.dimension[2]
+    right_size = mesh.num_mesh_cells
     data = np.random.random(right_size + 1)
 
     expected_error_msg = "The size of the dataset label should be equal to the number of cells"

From 9c892f04dbd36bc423a0560b72bb2da3a1b2a21a Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 1 Jul 2022 09:42:35 +0000
Subject: [PATCH 111/119] added num_mesh_cells property to StructuredMesh

---
 openmc/mesh.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 2a53c8a91..925a63aee 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -193,6 +193,10 @@ class StructuredMesh(MeshBase):
         s1 = (slice(1, None),)*ndim + (slice(None),)
         return (vertices[s0] + vertices[s1]) / 2
 
+    @property
+    def num_mesh_cells(self):
+        return np.prod(self.dimension)
+
     def write_data_to_vtk(self, points, filename, datasets, volume_normalization=True):
         """Creates a VTK object of the mesh
 
@@ -1547,6 +1551,7 @@ class UnstructuredMesh(MeshBase):
                                "been loaded from a statepoint file.")
         return len(self._centroids)
 
+
     @centroids.setter
     def centroids(self, centroids):
         cv.check_type("Unstructured mesh centroids", centroids,

From 52d59a4c1a924039ca6eb790a1786fe85fce7574 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 1 Jul 2022 09:43:44 +0000
Subject: [PATCH 112/119] minor refactoring

---
 openmc/mesh.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index 925a63aee..d5a460baa 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -348,10 +348,6 @@ class RegularMesh(StructuredMesh):
                 dims =  self._dimension
                 return [(u - l) / d for u, l, d in zip(us, ls, dims)]
 
-    @property
-    def num_mesh_cells(self):
-        return np.prod(self._dimension)
-
     @property
     def volumes(self):
         """Return Volumes for every mesh cell

From a95d02dd91c9ac51d16843f04c503df4ed9d4261 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Thu, 7 Jul 2022 22:29:56 -0500
Subject: [PATCH 113/119] Update version pins of sphinx and sphinx_rtd_theme

---
 docs/requirements-rtd.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/requirements-rtd.txt b/docs/requirements-rtd.txt
index c3d1c0372..9591d482f 100644
--- a/docs/requirements-rtd.txt
+++ b/docs/requirements-rtd.txt
@@ -1,4 +1,5 @@
-sphinx==4.3.0
+sphinx==5.0.2
+sphinx_rtd_theme==1.0.0
 sphinx-numfig
 jupyter
 sphinxcontrib-katex

From ff15c98b67dc231de6e4e22f70de1892f6ec7746 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 8 Jul 2022 08:05:51 -0500
Subject: [PATCH 114/119] Add test checking that collision/tracklength
 estimators agree for sph/cyl mesh

---
 tests/unit_tests/test_filter_mesh.py | 109 +++++++++++++++++++++++++++
 1 file changed, 109 insertions(+)
 create mode 100644 tests/unit_tests/test_filter_mesh.py

diff --git a/tests/unit_tests/test_filter_mesh.py b/tests/unit_tests/test_filter_mesh.py
new file mode 100644
index 000000000..265642360
--- /dev/null
+++ b/tests/unit_tests/test_filter_mesh.py
@@ -0,0 +1,109 @@
+import numpy as np
+import openmc
+from uncertainties import unumpy
+
+
+def test_spherical_mesh_estimators(run_in_tmpdir):
+    """Test that collision/tracklength estimators agree for SphericalMesh"""
+
+    mat = openmc.Material()
+    mat.add_nuclide('U235', 1.0)
+    mat.set_density('g/cm3', 10.0)
+
+    sphere = openmc.Sphere(r=10.0, boundary_type='vacuum')
+    cell = openmc.Cell(fill=mat, region=-sphere)
+    model = openmc.Model()
+    model.geometry = openmc.Geometry([cell])
+    model.settings.particles = 1_000
+    model.settings.inactive = 10
+    model.settings.batches = 20
+
+    sph_mesh = openmc.SphericalMesh()
+    sph_mesh.r_grid = np.linspace(0.0, 5.0**3, 20)**(1/3)
+    tally1 = openmc.Tally()
+    tally1.filters = [openmc.MeshFilter(sph_mesh)]
+    tally1.scores = ['flux']
+    tally1.estimator = 'collision'
+
+    sph_mesh = openmc.SphericalMesh()
+    sph_mesh.r_grid = np.linspace(0.0, 5.0**3, 20)**(1/3)
+    tally2 = openmc.Tally()
+    tally2.filters = [openmc.MeshFilter(sph_mesh)]
+    tally2.scores = ['flux']
+    tally2.estimator = 'tracklength'
+
+    model.tallies = openmc.Tallies([tally1, tally2])
+
+    # Run OpenMC
+    sp_filename = model.run()
+
+    # Get radial flux distribution
+    with openmc.StatePoint(sp_filename) as sp:
+        flux_collision = sp.tallies[tally1.id].mean.ravel()
+        flux_collision_unc = sp.tallies[tally1.id].std_dev.ravel()
+        flux_tracklength = sp.tallies[tally2.id].mean.ravel()
+        flux_tracklength_unc = sp.tallies[tally2.id].std_dev.ravel()
+
+    # Construct arrays with uncertainties
+    collision = unumpy.uarray(flux_collision, flux_collision_unc)
+    tracklength = unumpy.uarray(flux_tracklength, flux_tracklength_unc)
+    delta = collision - tracklength
+
+    # Check that difference is within uncertainty
+    diff = unumpy.nominal_values(delta)
+    std_dev = unumpy.std_devs(delta)
+    assert np.all(diff < 3*std_dev)
+
+
+def test_cylindrical_mesh_estimators(run_in_tmpdir):
+    """Test that collision/tracklength estimators agree for CylindricalMesh"""
+
+    mat = openmc.Material()
+    mat.add_nuclide('U235', 1.0)
+    mat.set_density('g/cm3', 10.0)
+
+    cyl = openmc.model.RightCircularCylinder((0., 0., -5.), 10., 10.0, boundary_type='vacuum')
+    cell = openmc.Cell(fill=mat, region=-cyl)
+    model = openmc.Model()
+    model.geometry = openmc.Geometry([cell])
+    model.settings.particles = 1_000
+    model.settings.inactive = 10
+    model.settings.batches = 20
+
+    cyl_mesh = openmc.CylindricalMesh()
+    cyl_mesh.r_grid = np.linspace(0.0, 5.0**3, 20)**(1/3)
+    cyl_mesh.z_grid = [-5., 5.]
+    tally1 = openmc.Tally()
+    tally1.filters = [openmc.MeshFilter(cyl_mesh)]
+    tally1.scores = ['flux']
+    tally1.estimator = 'collision'
+
+    cyl_mesh = openmc.CylindricalMesh()
+    cyl_mesh.r_grid = np.linspace(0.0, 5.0**3, 20)**(1/3)
+    cyl_mesh.z_grid = [-5., 5.]
+    tally2 = openmc.Tally()
+    tally2.filters = [openmc.MeshFilter(cyl_mesh)]
+    tally2.scores = ['flux']
+    tally2.estimator = 'tracklength'
+
+    model.tallies = openmc.Tallies([tally1, tally2])
+
+    # Run OpenMC
+    sp_filename = model.run()
+
+    # Get radial flux distribution
+    with openmc.StatePoint(sp_filename) as sp:
+        flux_collision = sp.tallies[tally1.id].mean.ravel()
+        flux_collision_unc = sp.tallies[tally1.id].std_dev.ravel()
+        flux_tracklength = sp.tallies[tally2.id].mean.ravel()
+        flux_tracklength_unc = sp.tallies[tally2.id].std_dev.ravel()
+
+    # Construct arrays with uncertainties
+    collision = unumpy.uarray(flux_collision, flux_collision_unc)
+    tracklength = unumpy.uarray(flux_tracklength, flux_tracklength_unc)
+    delta = collision - tracklength
+
+    # Check that difference is within uncertainty
+    diff = unumpy.nominal_values(delta)
+    std_dev = unumpy.std_devs(delta)
+    assert np.all(diff < 3*std_dev)

From 620aaec5ee46400f5bde6bc63906deedf031f56d Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 8 Jul 2022 08:09:16 -0500
Subject: [PATCH 115/119] Fix indexing bug in SphericalMesh and CylindricalMesh

---
 src/mesh.cpp                                       | 14 ++++++--------
 .../regression_tests/filter_mesh/results_true.dat  |  2 +-
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/mesh.cpp b/src/mesh.cpp
index de29233fb..e8f79aa37 100644
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -379,7 +379,7 @@ void StructuredMesh::raytrace_mesh(
   // TODO: when c++-17 is available, use "if constexpr ()" to compile-time
   // enable/disable tally calls for now, T template type needs to provide both
   // surface and track methods, which might be empty. modern optimizing
-  // compilers will (hopefully) eleminate the complete code (including
+  // compilers will (hopefully) eliminate the complete code (including
   // calculation of parameters) but for the future: be explicit
 
   // Compute the length of the entire track.
@@ -957,7 +957,7 @@ double CylindricalMesh::find_r_crossing(
   const Position& r, const Direction& u, double l, int shell) const
 {
 
-  if ((shell < 0) || (shell >= shape_[0]))
+  if ((shell < 0) || (shell > shape_[0]))
     return INFTY;
 
   // solve r.x^2 + r.y^2 == r0^2
@@ -1190,7 +1190,7 @@ StructuredMesh::MeshIndex SphericalMesh::get_indices(
 double SphericalMesh::find_r_crossing(
   const Position& r, const Direction& u, double l, int shell) const
 {
-  if ((shell < 0) || (shell >= shape_[0]))
+  if ((shell < 0) || (shell > shape_[0]))
     return INFTY;
 
   // solve |r+s*u| = r0
@@ -1312,20 +1312,17 @@ StructuredMesh::MeshDistance SphericalMesh::distance_to_grid_boundary(
 {
 
   if (i == 0) {
-
     return std::min(
       MeshDistance(ijk[i] + 1, true, find_r_crossing(r0, u, l, ijk[i])),
       MeshDistance(ijk[i] - 1, false, find_r_crossing(r0, u, l, ijk[i] - 1)));
 
   } else if (i == 1) {
-
     return std::min(MeshDistance(sanitize_theta(ijk[i] + 1), true,
                       find_theta_crossing(r0, u, l, ijk[i])),
       MeshDistance(sanitize_theta(ijk[i] - 1), false,
         find_theta_crossing(r0, u, l, ijk[i] - 1)));
 
   } else {
-
     return std::min(MeshDistance(sanitize_phi(ijk[i] + 1), true,
                       find_phi_crossing(r0, u, l, ijk[i])),
       MeshDistance(sanitize_phi(ijk[i] - 1), false,
@@ -2567,8 +2564,9 @@ void read_meshes(pugi::xml_node root)
     // Check to make sure multiple meshes in the same file don't share IDs
     int id = std::stoi(get_node_value(node, "id"));
     if (contains(mesh_ids, id)) {
-      fatal_error(
-        fmt::format("Two or more meshes use the same unique ID '{}' in the same input file", id));
+      fatal_error(fmt::format(
+        "Two or more meshes use the same unique ID '{}' in the same input file",
+        id));
     }
     mesh_ids.insert(id);
 
diff --git a/tests/regression_tests/filter_mesh/results_true.dat b/tests/regression_tests/filter_mesh/results_true.dat
index 97735130e..ef52af2c7 100644
--- a/tests/regression_tests/filter_mesh/results_true.dat
+++ b/tests/regression_tests/filter_mesh/results_true.dat
@@ -1 +1 @@
-6e02d01fc115c54e4c60477a9f963149bc83c82e6a7bdb2d29125b131546150c59de5ac3aae5b9469b89b343ecf2574f6c949b918ccb43231e8666ee2b7c1b7c
\ No newline at end of file
+70243ebdb882e4367bf821667a9f4d41dea03eaf8b27d734e014a13e14922b5158cd47b0a7edf3733d4e23ca6a5ab06457220c9138b7e9720acf547f2eaa06e2
\ No newline at end of file

From 7e890037051dad5760ea5f010165017b864f389f Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Fri, 8 Jul 2022 23:44:32 +0100
Subject: [PATCH 116/119] [skip ci] Apply suggestions from code review by
 @paulromano

Co-authored-by: Paul Romano <paul.k.romano@gmail.com>
---
 openmc/material.py | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/openmc/material.py b/openmc/material.py
index 352959fe9..3592a35e6 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -3,7 +3,6 @@ from collections.abc import Iterable
 from copy import deepcopy
 from numbers import Real
 from pathlib import Path
-
 import os
 import math
 import re
@@ -345,7 +344,7 @@ class Material(IDManagerMixin):
             raise ValueError('No volume information found for material ID={}.'
                 .format(self.id))
 
-    def set_density(self, units: str, density:Optional[float]=None):
+    def set_density(self, units: str, density: Optional[float] = None):
         """Set the density of the material
 
         Parameters
@@ -377,7 +376,7 @@ class Material(IDManagerMixin):
                           density, Real)
             self._density = density
 
-    def add_nuclide(self, nuclide: str, percent: float, percent_type: str='ao'):
+    def add_nuclide(self, nuclide: str, percent: float, percent_type: str = 'ao'):
         """Add a nuclide to the material
 
         Parameters
@@ -505,10 +504,10 @@ class Material(IDManagerMixin):
         if macroscopic == self._macroscopic:
             self._macroscopic = None
 
-    def add_element(self, element: str, percent: float, percent_type: str='ao',
-                    enrichment: Optional[float]=None,
-                    enrichment_target: Optional[str]=None,
-                    enrichment_type: Optional[str]=None):
+    def add_element(self, element: str, percent: float, percent_type: str = 'ao',
+                    enrichment: Optional[float] = None,
+                    enrichment_target: Optional[str] = None,
+                    enrichment_type: Optional[str] = None):
         """Add a natural element to the material
 
         Parameters
@@ -613,10 +612,10 @@ class Material(IDManagerMixin):
                                       enrichment_type):
             self.add_nuclide(*nuclide)
 
-    def add_elements_from_formula(self, formula: str, percent_type: str='ao',
-                                  enrichment: Optional[float]=None,
-                                  enrichment_target: Optional[float]=None,
-                                  enrichment_type: Optional[str]=None):
+    def add_elements_from_formula(self, formula: str, percent_type: str = 'ao',
+                                  enrichment: Optional[float] = None,
+                                  enrichment_target: Optional[str] = None,
+                                  enrichment_type: Optional[str] = None):
         """Add a elements from a chemical formula to the material.
 
         .. versionadded:: 0.12
@@ -713,7 +712,7 @@ class Material(IDManagerMixin):
             else:
                 self.add_element(element, percent, percent_type)
 
-    def add_s_alpha_beta(self, name: str, fraction: float=1.0):
+    def add_s_alpha_beta(self, name: str, fraction: float = 1.0):
         r"""Add an :math:`S(\alpha,\beta)` table to the material
 
         Parameters
@@ -862,7 +861,7 @@ class Material(IDManagerMixin):
 
         return nuclides
 
-    def get_mass_density(self, nuclide: Optional[str]=None):
+    def get_mass_density(self, nuclide: Optional[str] = None):
         """Return mass density of one or all nuclides
 
         Parameters
@@ -885,7 +884,7 @@ class Material(IDManagerMixin):
                 mass_density += density_i
         return mass_density
 
-    def get_mass(self, nuclide: Optional[str]=None):
+    def get_mass(self, nuclide: Optional[str] = None):
         """Return mass of one or all nuclides.
 
         Note that this method requires that the :attr:`Material.volume` has
@@ -907,7 +906,7 @@ class Material(IDManagerMixin):
             raise ValueError("Volume must be set in order to determine mass.")
         return self.volume*self.get_mass_density(nuclide)
 
-    def clone(self, memo: Optional[dict]=None):
+    def clone(self, memo: Optional[dict] = None):
         """Create a copy of this material with a new unique ID.
 
         Parameters
@@ -1031,7 +1030,7 @@ class Material(IDManagerMixin):
 
     @classmethod
     def mix_materials(cls, materials, fracs: typing.Iterable[float],
-                      percent_type: str='ao', name: Optional[str]=None):
+                      percent_type: str = 'ao', name: Optional[str] = None):
         """Mix materials together based on atom, weight, or volume fractions
 
         .. versionadded:: 0.12
@@ -1260,7 +1259,7 @@ class Materials(cv.CheckedList):
         for material in self:
             material.make_isotropic_in_lab()
 
-    def export_to_xml(self, path: Union[str, os.PathLike]='materials.xml'):
+    def export_to_xml(self, path: Union[str, os.PathLike] = 'materials.xml'):
         """Export material collection to an XML file.
 
         Parameters
@@ -1307,7 +1306,7 @@ class Materials(cv.CheckedList):
             fh.write('</materials>\n')
 
     @classmethod
-    def from_xml(cls, path: Union[str, os.PathLike]='materials.xml'):
+    def from_xml(cls, path: Union[str, os.PathLike] = 'materials.xml'):
         """Generate materials collection from XML file
 
         Parameters

From 69cb024882bd1d711c88370504833931a365424d Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Fri, 8 Jul 2022 23:52:27 +0100
Subject: [PATCH 117/119] Adding type hint h5py.Group

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

diff --git a/openmc/material.py b/openmc/material.py
index 3592a35e6..dcb33ff29 100644
--- a/openmc/material.py
+++ b/openmc/material.py
@@ -11,6 +11,7 @@ import warnings
 from typing import Optional, Union
 from xml.etree import ElementTree as ET
 
+import h5py
 import numpy as np
 
 import openmc
@@ -270,7 +271,7 @@ class Material(IDManagerMixin):
         return density*self.volume
 
     @classmethod
-    def from_hdf5(cls, group: str):
+    def from_hdf5(cls, group: h5py.Group):
         """Create material from HDF5 group
 
         Parameters

From 0fe895e195c8bfe916910f3219fcff6eec643d75 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Mon, 11 Jul 2022 12:29:10 +0000
Subject: [PATCH 118/119] Fixed number of dimensions in vtk file

---
 openmc/mesh.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/mesh.py b/openmc/mesh.py
index d5a460baa..1fe5429d0 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -240,7 +240,7 @@ class StructuredMesh(MeshBase):
 
         vtk_grid = vtk.vtkStructuredGrid()
 
-        vtk_grid.SetDimensions(*self.dimension)
+        vtk_grid.SetDimensions(*[dim + 1 for dim in self.dimension])
 
         vtkPts = vtk.vtkPoints()
         vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))

From ef452850bee91c7dc0d5a6ba2272c64e69ded873 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Mon, 11 Jul 2022 10:28:06 -0500
Subject: [PATCH 119/119] Don't skip CI for non-code files (reverting changes
 from #2010)

---
 .github/workflows/ci.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 670b76cd9..050c8e287 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,13 +5,6 @@ on:
   workflow_dispatch:
 
   pull_request:
-    paths-ignore:
-      - 'docs/**'
-      - 'examples/**'
-      - 'man/**'
-      - '**.md'
-      - CODEOWNERS
-      - LICENSE
     branches:
       - develop
       - master