From e8e8b9d48f1649b31d0202d7bdecce2fff8daa6c Mon Sep 17 00:00:00 2001
From: Jon Walsh <walshjon@mit.edu>
Date: Sat, 21 Jun 2014 21:22:48 -0600
Subject: [PATCH 1/2] added examples for other nuclear data libraries, changed
 all to 300 K

---
 examples/basic/{ => jeff}/geometry.xml        |  0
 examples/basic/jeff/materials.xml             | 18 +++++
 examples/basic/{ => jeff}/settings.xml        |  0
 examples/basic/{ => jeff}/tallies.xml         |  0
 examples/basic/mcnp/geometry.xml              | 15 ++++
 examples/basic/{ => mcnp}/materials.xml       |  0
 examples/basic/mcnp/settings.xml              | 18 +++++
 examples/basic/mcnp/tallies.xml               | 22 ++++++
 examples/basic/nndc/geometry.xml              | 15 ++++
 examples/basic/nndc/materials.xml             | 18 +++++
 examples/basic/nndc/settings.xml              | 18 +++++
 examples/basic/nndc/tallies.xml               | 22 ++++++
 examples/basic/serpent/geometry.xml           | 15 ++++
 examples/basic/serpent/materials.xml          | 18 +++++
 examples/basic/serpent/settings.xml           | 18 +++++
 examples/basic/serpent/tallies.xml            | 22 ++++++
 .../lattice/nested/{ => jeff}/geometry.xml    |  0
 examples/lattice/nested/jeff/materials.xml    | 19 +++++
 examples/lattice/nested/{ => jeff}/plots.xml  |  0
 .../lattice/nested/{ => jeff}/settings.xml    |  0
 .../lattice/nested/{ => jeff}/tallies.xml     |  0
 examples/lattice/nested/mcnp/geometry.xml     | 45 ++++++++++++
 .../lattice/nested/{ => mcnp}/materials.xml   |  0
 .../lattice/{simple => nested/mcnp}/plots.xml |  0
 .../{simple => nested/mcnp}/settings.xml      |  0
 .../{simple => nested/mcnp}/tallies.xml       |  0
 examples/lattice/nested/nndc/geometry.xml     | 45 ++++++++++++
 examples/lattice/nested/nndc/materials.xml    | 19 +++++
 examples/lattice/nested/nndc/plots.xml        | 10 +++
 examples/lattice/nested/nndc/settings.xml     | 18 +++++
 examples/lattice/nested/nndc/tallies.xml      | 16 +++++
 examples/lattice/nested/serpent/geometry.xml  | 45 ++++++++++++
 examples/lattice/nested/serpent/materials.xml | 19 +++++
 examples/lattice/nested/serpent/plots.xml     | 10 +++
 examples/lattice/nested/serpent/settings.xml  | 18 +++++
 examples/lattice/nested/serpent/tallies.xml   | 16 +++++
 .../lattice/simple/{ => jeff}/geometry.xml    |  0
 examples/lattice/simple/jeff/materials.xml    | 19 +++++
 examples/lattice/simple/jeff/plots.xml        | 10 +++
 examples/lattice/simple/jeff/settings.xml     | 18 +++++
 examples/lattice/simple/jeff/tallies.xml      | 16 +++++
 examples/lattice/simple/mcnp/geometry.xml     | 33 +++++++++
 .../lattice/simple/{ => mcnp}/materials.xml   |  0
 examples/lattice/simple/mcnp/plots.xml        | 10 +++
 examples/lattice/simple/mcnp/settings.xml     | 18 +++++
 examples/lattice/simple/mcnp/tallies.xml      | 16 +++++
 examples/lattice/simple/nndc/geometry.xml     | 33 +++++++++
 examples/lattice/simple/nndc/materials.xml    | 19 +++++
 examples/lattice/simple/nndc/plots.xml        | 10 +++
 examples/lattice/simple/nndc/settings.xml     | 18 +++++
 examples/lattice/simple/nndc/tallies.xml      | 16 +++++
 examples/lattice/simple/serpent/geometry.xml  | 33 +++++++++
 examples/lattice/simple/serpent/materials.xml | 19 +++++
 examples/lattice/simple/serpent/plots.xml     | 10 +++
 examples/lattice/simple/serpent/settings.xml  | 18 +++++
 examples/lattice/simple/serpent/tallies.xml   | 16 +++++
 examples/pincell/{ => jeff}/geometry.xml      |  0
 examples/pincell/jeff/materials.xml           | 70 +++++++++++++++++++
 examples/pincell/{ => jeff}/settings.xml      |  0
 examples/pincell/{ => jeff}/tallies.xml       |  0
 examples/pincell/mcnp/geometry.xml            | 27 +++++++
 examples/pincell/mcnp/materials.xml           | 70 +++++++++++++++++++
 examples/pincell/mcnp/settings.xml            | 32 +++++++++
 examples/pincell/mcnp/tallies.xml             | 16 +++++
 examples/pincell/nndc/geometry.xml            | 27 +++++++
 examples/pincell/{ => nndc}/materials.xml     |  6 +-
 examples/pincell/nndc/settings.xml            | 32 +++++++++
 examples/pincell/nndc/tallies.xml             | 16 +++++
 examples/pincell/serpent/geometry.xml         | 27 +++++++
 examples/pincell/serpent/materials.xml        | 70 +++++++++++++++++++
 examples/pincell/serpent/settings.xml         | 32 +++++++++
 examples/pincell/serpent/tallies.xml          | 16 +++++
 examples/reflective/{ => jeff}/geometry.xml   |  0
 examples/reflective/jeff/materials.xml        | 11 +++
 examples/reflective/{ => jeff}/settings.xml   |  0
 examples/reflective/mcnp/geometry.xml         | 19 +++++
 examples/reflective/{ => mcnp}/materials.xml  |  0
 examples/reflective/mcnp/settings.xml         | 18 +++++
 examples/reflective/nndc/geometry.xml         | 19 +++++
 examples/reflective/nndc/materials.xml        | 11 +++
 examples/reflective/nndc/settings.xml         | 18 +++++
 examples/reflective/serpent/geometry.xml      | 19 +++++
 examples/reflective/serpent/materials.xml     | 11 +++
 examples/reflective/serpent/settings.xml      | 18 +++++
 84 files changed, 1413 insertions(+), 3 deletions(-)
 rename examples/basic/{ => jeff}/geometry.xml (100%)
 create mode 100644 examples/basic/jeff/materials.xml
 rename examples/basic/{ => jeff}/settings.xml (100%)
 rename examples/basic/{ => jeff}/tallies.xml (100%)
 create mode 100644 examples/basic/mcnp/geometry.xml
 rename examples/basic/{ => mcnp}/materials.xml (100%)
 create mode 100644 examples/basic/mcnp/settings.xml
 create mode 100644 examples/basic/mcnp/tallies.xml
 create mode 100644 examples/basic/nndc/geometry.xml
 create mode 100644 examples/basic/nndc/materials.xml
 create mode 100644 examples/basic/nndc/settings.xml
 create mode 100644 examples/basic/nndc/tallies.xml
 create mode 100644 examples/basic/serpent/geometry.xml
 create mode 100644 examples/basic/serpent/materials.xml
 create mode 100644 examples/basic/serpent/settings.xml
 create mode 100644 examples/basic/serpent/tallies.xml
 rename examples/lattice/nested/{ => jeff}/geometry.xml (100%)
 create mode 100644 examples/lattice/nested/jeff/materials.xml
 rename examples/lattice/nested/{ => jeff}/plots.xml (100%)
 rename examples/lattice/nested/{ => jeff}/settings.xml (100%)
 rename examples/lattice/nested/{ => jeff}/tallies.xml (100%)
 create mode 100644 examples/lattice/nested/mcnp/geometry.xml
 rename examples/lattice/nested/{ => mcnp}/materials.xml (100%)
 rename examples/lattice/{simple => nested/mcnp}/plots.xml (100%)
 rename examples/lattice/{simple => nested/mcnp}/settings.xml (100%)
 rename examples/lattice/{simple => nested/mcnp}/tallies.xml (100%)
 create mode 100644 examples/lattice/nested/nndc/geometry.xml
 create mode 100644 examples/lattice/nested/nndc/materials.xml
 create mode 100644 examples/lattice/nested/nndc/plots.xml
 create mode 100644 examples/lattice/nested/nndc/settings.xml
 create mode 100644 examples/lattice/nested/nndc/tallies.xml
 create mode 100644 examples/lattice/nested/serpent/geometry.xml
 create mode 100644 examples/lattice/nested/serpent/materials.xml
 create mode 100644 examples/lattice/nested/serpent/plots.xml
 create mode 100644 examples/lattice/nested/serpent/settings.xml
 create mode 100644 examples/lattice/nested/serpent/tallies.xml
 rename examples/lattice/simple/{ => jeff}/geometry.xml (100%)
 create mode 100644 examples/lattice/simple/jeff/materials.xml
 create mode 100644 examples/lattice/simple/jeff/plots.xml
 create mode 100644 examples/lattice/simple/jeff/settings.xml
 create mode 100644 examples/lattice/simple/jeff/tallies.xml
 create mode 100644 examples/lattice/simple/mcnp/geometry.xml
 rename examples/lattice/simple/{ => mcnp}/materials.xml (100%)
 create mode 100644 examples/lattice/simple/mcnp/plots.xml
 create mode 100644 examples/lattice/simple/mcnp/settings.xml
 create mode 100644 examples/lattice/simple/mcnp/tallies.xml
 create mode 100644 examples/lattice/simple/nndc/geometry.xml
 create mode 100644 examples/lattice/simple/nndc/materials.xml
 create mode 100644 examples/lattice/simple/nndc/plots.xml
 create mode 100644 examples/lattice/simple/nndc/settings.xml
 create mode 100644 examples/lattice/simple/nndc/tallies.xml
 create mode 100644 examples/lattice/simple/serpent/geometry.xml
 create mode 100644 examples/lattice/simple/serpent/materials.xml
 create mode 100644 examples/lattice/simple/serpent/plots.xml
 create mode 100644 examples/lattice/simple/serpent/settings.xml
 create mode 100644 examples/lattice/simple/serpent/tallies.xml
 rename examples/pincell/{ => jeff}/geometry.xml (100%)
 create mode 100644 examples/pincell/jeff/materials.xml
 rename examples/pincell/{ => jeff}/settings.xml (100%)
 rename examples/pincell/{ => jeff}/tallies.xml (100%)
 create mode 100644 examples/pincell/mcnp/geometry.xml
 create mode 100644 examples/pincell/mcnp/materials.xml
 create mode 100644 examples/pincell/mcnp/settings.xml
 create mode 100644 examples/pincell/mcnp/tallies.xml
 create mode 100644 examples/pincell/nndc/geometry.xml
 rename examples/pincell/{ => nndc}/materials.xml (96%)
 create mode 100644 examples/pincell/nndc/settings.xml
 create mode 100644 examples/pincell/nndc/tallies.xml
 create mode 100644 examples/pincell/serpent/geometry.xml
 create mode 100644 examples/pincell/serpent/materials.xml
 create mode 100644 examples/pincell/serpent/settings.xml
 create mode 100644 examples/pincell/serpent/tallies.xml
 rename examples/reflective/{ => jeff}/geometry.xml (100%)
 create mode 100644 examples/reflective/jeff/materials.xml
 rename examples/reflective/{ => jeff}/settings.xml (100%)
 create mode 100644 examples/reflective/mcnp/geometry.xml
 rename examples/reflective/{ => mcnp}/materials.xml (100%)
 create mode 100644 examples/reflective/mcnp/settings.xml
 create mode 100644 examples/reflective/nndc/geometry.xml
 create mode 100644 examples/reflective/nndc/materials.xml
 create mode 100644 examples/reflective/nndc/settings.xml
 create mode 100644 examples/reflective/serpent/geometry.xml
 create mode 100644 examples/reflective/serpent/materials.xml
 create mode 100644 examples/reflective/serpent/settings.xml

diff --git a/examples/basic/geometry.xml b/examples/basic/jeff/geometry.xml
similarity index 100%
rename from examples/basic/geometry.xml
rename to examples/basic/jeff/geometry.xml
diff --git a/examples/basic/jeff/materials.xml b/examples/basic/jeff/materials.xml
new file mode 100644
index 0000000000..e5b7e2044c
--- /dev/null
+++ b/examples/basic/jeff/materials.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>31c</default_xs>
+
+  <material id="40">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="41">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1" ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwtr01" xs="31t" />
+  </material>
+
+</materials>
diff --git a/examples/basic/settings.xml b/examples/basic/jeff/settings.xml
similarity index 100%
rename from examples/basic/settings.xml
rename to examples/basic/jeff/settings.xml
diff --git a/examples/basic/tallies.xml b/examples/basic/jeff/tallies.xml
similarity index 100%
rename from examples/basic/tallies.xml
rename to examples/basic/jeff/tallies.xml
diff --git a/examples/basic/mcnp/geometry.xml b/examples/basic/mcnp/geometry.xml
new file mode 100644
index 0000000000..e9483306c0
--- /dev/null
+++ b/examples/basic/mcnp/geometry.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1" universe="0" fill="37" surfaces="-2" />
+  <cell id="100" universe="37" material="40" surfaces="-1" />
+  <cell id="101" universe="37" material="41" surfaces="1" />
+  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
+  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
+  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
+    
+</geometry>
diff --git a/examples/basic/materials.xml b/examples/basic/mcnp/materials.xml
similarity index 100%
rename from examples/basic/materials.xml
rename to examples/basic/mcnp/materials.xml
diff --git a/examples/basic/mcnp/settings.xml b/examples/basic/mcnp/settings.xml
new file mode 100644
index 0000000000..eb9f5bd56d
--- /dev/null
+++ b/examples/basic/mcnp/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>15</batches>
+    <inactive>5</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/basic/mcnp/tallies.xml b/examples/basic/mcnp/tallies.xml
new file mode 100644
index 0000000000..fb1dfbc9ce
--- /dev/null
+++ b/examples/basic/mcnp/tallies.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <tally id="1">
+    <filter type="cell" bins="100" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="2">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="3">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <filter type="energyout" bins="0 20.0" />
+    <scores>scatter nu-scatter nu-fission</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/basic/nndc/geometry.xml b/examples/basic/nndc/geometry.xml
new file mode 100644
index 0000000000..e9483306c0
--- /dev/null
+++ b/examples/basic/nndc/geometry.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1" universe="0" fill="37" surfaces="-2" />
+  <cell id="100" universe="37" material="40" surfaces="-1" />
+  <cell id="101" universe="37" material="41" surfaces="1" />
+  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
+  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
+  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
+    
+</geometry>
diff --git a/examples/basic/nndc/materials.xml b/examples/basic/nndc/materials.xml
new file mode 100644
index 0000000000..75ab74dbba
--- /dev/null
+++ b/examples/basic/nndc/materials.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>71c</default_xs>
+
+  <material id="40">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="41">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1" ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="HH2O" xs="71t" />
+  </material>
+
+</materials>
diff --git a/examples/basic/nndc/settings.xml b/examples/basic/nndc/settings.xml
new file mode 100644
index 0000000000..eb9f5bd56d
--- /dev/null
+++ b/examples/basic/nndc/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>15</batches>
+    <inactive>5</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/basic/nndc/tallies.xml b/examples/basic/nndc/tallies.xml
new file mode 100644
index 0000000000..fb1dfbc9ce
--- /dev/null
+++ b/examples/basic/nndc/tallies.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <tally id="1">
+    <filter type="cell" bins="100" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="2">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="3">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <filter type="energyout" bins="0 20.0" />
+    <scores>scatter nu-scatter nu-fission</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/basic/serpent/geometry.xml b/examples/basic/serpent/geometry.xml
new file mode 100644
index 0000000000..e9483306c0
--- /dev/null
+++ b/examples/basic/serpent/geometry.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1" universe="0" fill="37" surfaces="-2" />
+  <cell id="100" universe="37" material="40" surfaces="-1" />
+  <cell id="101" universe="37" material="41" surfaces="1" />
+  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
+  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
+  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
+    
+</geometry>
diff --git a/examples/basic/serpent/materials.xml b/examples/basic/serpent/materials.xml
new file mode 100644
index 0000000000..21c3555e8c
--- /dev/null
+++ b/examples/basic/serpent/materials.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>03c</default_xs>
+
+  <material id="40">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="41">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1" ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwe7" xs="00t" />
+  </material>
+
+</materials>
diff --git a/examples/basic/serpent/settings.xml b/examples/basic/serpent/settings.xml
new file mode 100644
index 0000000000..eb9f5bd56d
--- /dev/null
+++ b/examples/basic/serpent/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>15</batches>
+    <inactive>5</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/basic/serpent/tallies.xml b/examples/basic/serpent/tallies.xml
new file mode 100644
index 0000000000..fb1dfbc9ce
--- /dev/null
+++ b/examples/basic/serpent/tallies.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <tally id="1">
+    <filter type="cell" bins="100" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="2">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
+  </tally>
+
+  <tally id="3">
+    <filter type="cell" bins="100" />
+    <filter type="energy" bins="0 20.0" />
+    <filter type="energyout" bins="0 20.0" />
+    <scores>scatter nu-scatter nu-fission</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/nested/geometry.xml b/examples/lattice/nested/jeff/geometry.xml
similarity index 100%
rename from examples/lattice/nested/geometry.xml
rename to examples/lattice/nested/jeff/geometry.xml
diff --git a/examples/lattice/nested/jeff/materials.xml b/examples/lattice/nested/jeff/materials.xml
new file mode 100644
index 0000000000..5de4135b4a
--- /dev/null
+++ b/examples/lattice/nested/jeff/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>31c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwtr01" xs="31t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/nested/plots.xml b/examples/lattice/nested/jeff/plots.xml
similarity index 100%
rename from examples/lattice/nested/plots.xml
rename to examples/lattice/nested/jeff/plots.xml
diff --git a/examples/lattice/nested/settings.xml b/examples/lattice/nested/jeff/settings.xml
similarity index 100%
rename from examples/lattice/nested/settings.xml
rename to examples/lattice/nested/jeff/settings.xml
diff --git a/examples/lattice/nested/tallies.xml b/examples/lattice/nested/jeff/tallies.xml
similarity index 100%
rename from examples/lattice/nested/tallies.xml
rename to examples/lattice/nested/jeff/tallies.xml
diff --git a/examples/lattice/nested/mcnp/geometry.xml b/examples/lattice/nested/mcnp/geometry.xml
new file mode 100644
index 0000000000..f223cf3bb4
--- /dev/null
+++ b/examples/lattice/nested/mcnp/geometry.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
+  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <!-- 4 x 4 assembly -->
+  <lattice id="4">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-1.0 -1.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2
+      2 3
+    </universes>
+  </lattice>
+
+  <!-- 4 x 4 core -->
+  <lattice id="6">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>2.0 2.0</width>
+    <universes>
+      5 5
+      5 5
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/nested/materials.xml b/examples/lattice/nested/mcnp/materials.xml
similarity index 100%
rename from examples/lattice/nested/materials.xml
rename to examples/lattice/nested/mcnp/materials.xml
diff --git a/examples/lattice/simple/plots.xml b/examples/lattice/nested/mcnp/plots.xml
similarity index 100%
rename from examples/lattice/simple/plots.xml
rename to examples/lattice/nested/mcnp/plots.xml
diff --git a/examples/lattice/simple/settings.xml b/examples/lattice/nested/mcnp/settings.xml
similarity index 100%
rename from examples/lattice/simple/settings.xml
rename to examples/lattice/nested/mcnp/settings.xml
diff --git a/examples/lattice/simple/tallies.xml b/examples/lattice/nested/mcnp/tallies.xml
similarity index 100%
rename from examples/lattice/simple/tallies.xml
rename to examples/lattice/nested/mcnp/tallies.xml
diff --git a/examples/lattice/nested/nndc/geometry.xml b/examples/lattice/nested/nndc/geometry.xml
new file mode 100644
index 0000000000..f223cf3bb4
--- /dev/null
+++ b/examples/lattice/nested/nndc/geometry.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
+  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <!-- 4 x 4 assembly -->
+  <lattice id="4">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-1.0 -1.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2
+      2 3
+    </universes>
+  </lattice>
+
+  <!-- 4 x 4 core -->
+  <lattice id="6">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>2.0 2.0</width>
+    <universes>
+      5 5
+      5 5
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/nested/nndc/materials.xml b/examples/lattice/nested/nndc/materials.xml
new file mode 100644
index 0000000000..b649221366
--- /dev/null
+++ b/examples/lattice/nested/nndc/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>71c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="HH2O" xs="71t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/nested/nndc/plots.xml b/examples/lattice/nested/nndc/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/nested/nndc/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/nested/nndc/settings.xml b/examples/lattice/nested/nndc/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/nested/nndc/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/nested/nndc/tallies.xml b/examples/lattice/nested/nndc/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/nested/nndc/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/nested/serpent/geometry.xml b/examples/lattice/nested/serpent/geometry.xml
new file mode 100644
index 0000000000..f223cf3bb4
--- /dev/null
+++ b/examples/lattice/nested/serpent/geometry.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
+  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <!-- 4 x 4 assembly -->
+  <lattice id="4">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-1.0 -1.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2
+      2 3
+    </universes>
+  </lattice>
+
+  <!-- 4 x 4 core -->
+  <lattice id="6">
+    <type>rectangular</type>
+    <dimension>2 2</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>2.0 2.0</width>
+    <universes>
+      5 5
+      5 5
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/nested/serpent/materials.xml b/examples/lattice/nested/serpent/materials.xml
new file mode 100644
index 0000000000..29534b8003
--- /dev/null
+++ b/examples/lattice/nested/serpent/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>03c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwe7" xs="00t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/nested/serpent/plots.xml b/examples/lattice/nested/serpent/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/nested/serpent/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/nested/serpent/settings.xml b/examples/lattice/nested/serpent/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/nested/serpent/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/nested/serpent/tallies.xml b/examples/lattice/nested/serpent/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/nested/serpent/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/simple/geometry.xml b/examples/lattice/simple/jeff/geometry.xml
similarity index 100%
rename from examples/lattice/simple/geometry.xml
rename to examples/lattice/simple/jeff/geometry.xml
diff --git a/examples/lattice/simple/jeff/materials.xml b/examples/lattice/simple/jeff/materials.xml
new file mode 100644
index 0000000000..5de4135b4a
--- /dev/null
+++ b/examples/lattice/simple/jeff/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>31c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwtr01" xs="31t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/simple/jeff/plots.xml b/examples/lattice/simple/jeff/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/simple/jeff/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/simple/jeff/settings.xml b/examples/lattice/simple/jeff/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/simple/jeff/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/simple/jeff/tallies.xml b/examples/lattice/simple/jeff/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/simple/jeff/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/simple/mcnp/geometry.xml b/examples/lattice/simple/mcnp/geometry.xml
new file mode 100644
index 0000000000..b5bad90b9c
--- /dev/null
+++ b/examples/lattice/simple/mcnp/geometry.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <lattice id="5">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2 1 2
+      2 3 2 3
+      1 2 1 2
+      2 3 2 3
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/simple/materials.xml b/examples/lattice/simple/mcnp/materials.xml
similarity index 100%
rename from examples/lattice/simple/materials.xml
rename to examples/lattice/simple/mcnp/materials.xml
diff --git a/examples/lattice/simple/mcnp/plots.xml b/examples/lattice/simple/mcnp/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/simple/mcnp/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/simple/mcnp/settings.xml b/examples/lattice/simple/mcnp/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/simple/mcnp/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/simple/mcnp/tallies.xml b/examples/lattice/simple/mcnp/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/simple/mcnp/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/simple/nndc/geometry.xml b/examples/lattice/simple/nndc/geometry.xml
new file mode 100644
index 0000000000..b5bad90b9c
--- /dev/null
+++ b/examples/lattice/simple/nndc/geometry.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <lattice id="5">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2 1 2
+      2 3 2 3
+      1 2 1 2
+      2 3 2 3
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/simple/nndc/materials.xml b/examples/lattice/simple/nndc/materials.xml
new file mode 100644
index 0000000000..b649221366
--- /dev/null
+++ b/examples/lattice/simple/nndc/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>71c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="HH2O" xs="71t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/simple/nndc/plots.xml b/examples/lattice/simple/nndc/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/simple/nndc/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/simple/nndc/settings.xml b/examples/lattice/simple/nndc/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/simple/nndc/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/simple/nndc/tallies.xml b/examples/lattice/simple/nndc/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/simple/nndc/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/lattice/simple/serpent/geometry.xml b/examples/lattice/simple/serpent/geometry.xml
new file mode 100644
index 0000000000..b5bad90b9c
--- /dev/null
+++ b/examples/lattice/simple/serpent/geometry.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
+  <cell id="101" universe="1" material="1" surfaces="-5" />
+  <cell id="102" universe="1" material="2" surfaces="5" />
+  <cell id="201" universe="2" material="1" surfaces="-6" />
+  <cell id="202" universe="2" material="2" surfaces="6" />
+  <cell id="301" universe="3" material="1" surfaces="-7" />
+  <cell id="302" universe="3" material="2" surfaces="7" />
+
+  <lattice id="5">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+    <universes>
+      1 2 1 2
+      2 3 2 3
+      1 2 1 2
+      2 3 2 3
+    </universes>
+  </lattice>
+
+  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
+  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
+  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
+  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
+  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
+
+</geometry>
diff --git a/examples/lattice/simple/serpent/materials.xml b/examples/lattice/simple/serpent/materials.xml
new file mode 100644
index 0000000000..29534b8003
--- /dev/null
+++ b/examples/lattice/simple/serpent/materials.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>03c</default_xs>
+
+  <!-- Definition of materials -->
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="1.0" units="g/cc" />
+    <nuclide name="H-1"  ao="2.0" />
+    <nuclide name="O-16" ao="1.0" />
+    <sab name="lwe7" xs="00t" />
+  </material>
+
+</materials>
diff --git a/examples/lattice/simple/serpent/plots.xml b/examples/lattice/simple/serpent/plots.xml
new file mode 100644
index 0000000000..a8c6fbb7c5
--- /dev/null
+++ b/examples/lattice/simple/serpent/plots.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<plots>
+
+  <plot id="1" color="mat">
+    <origin>0. 0. 0.</origin>
+    <width>4.0 4.0</width>
+    <pixels>400 400</pixels>
+  </plot>
+
+</plots>
diff --git a/examples/lattice/simple/serpent/settings.xml b/examples/lattice/simple/serpent/settings.xml
new file mode 100644
index 0000000000..2a6aaaf426
--- /dev/null
+++ b/examples/lattice/simple/serpent/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>20</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/lattice/simple/serpent/tallies.xml b/examples/lattice/simple/serpent/tallies.xml
new file mode 100644
index 0000000000..5730e6b12c
--- /dev/null
+++ b/examples/lattice/simple/serpent/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>4 4</dimension>
+    <lower_left>-2.0 -2.0</lower_left>
+    <width>1.0 1.0</width>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <scores>total</scores>
+  </tally>
+
+</tallies>
diff --git a/examples/pincell/geometry.xml b/examples/pincell/jeff/geometry.xml
similarity index 100%
rename from examples/pincell/geometry.xml
rename to examples/pincell/jeff/geometry.xml
diff --git a/examples/pincell/jeff/materials.xml b/examples/pincell/jeff/materials.xml
new file mode 100644
index 0000000000..02ec6fca38
--- /dev/null
+++ b/examples/pincell/jeff/materials.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<materials>
+
+  <!-- By default, use 300K cross sections -->
+  <default_xs>31c</default_xs>
+
+  <!--
+      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
+      atom densities for O-17 and O-18 in any materials containing Oxygen.
+  -->
+
+  <!-- UO2 fuel at 2.4 wt% enrichment -->
+  <material id="1">
+    <density value="10.29769" units="g/cm3" />
+    <nuclide name="U-234"  ao="4.4843e-06" />
+    <nuclide name="U-235"  ao="5.5815e-04" />
+    <nuclide name="U-238"  ao="2.2408e-02" />
+    <nuclide name="O-16"   ao="4.5829e-02" />
+    <nuclide name="O-17"   ao="1.1164e-04" />
+  </material>
+
+  <!-- Helium for gap -->
+  <material id="2">
+    <density value="0.001598" units="g/cm3" />
+    <nuclide name="He-4"   ao="2.4044e-04" />
+  </material>
+
+  <!-- Zircaloy 4 -->
+  <material id="3">
+    <density value="6.55" units="g/cm3" />
+    <nuclide name="O-16"   ao="3.0743e-04" />
+    <nuclide name="O-17"   ao="7.4887e-07" />
+    <nuclide name="Cr-50"  ao="3.2962e-06" />
+    <nuclide name="Cr-52"  ao="6.3564e-05" />
+    <nuclide name="Cr-53"  ao="7.2076e-06" />
+    <nuclide name="Cr-54"  ao="1.7941e-06" />
+    <nuclide name="Fe-54"  ao="8.6699e-06" />
+    <nuclide name="Fe-56"  ao="1.3610e-04" />
+    <nuclide name="Fe-57"  ao="3.1431e-06" />
+    <nuclide name="Fe-58"  ao="4.1829e-07" />
+    <nuclide name="Zr-90"  ao="2.1827e-02" />
+    <nuclide name="Zr-91"  ao="4.7600e-03" />
+    <nuclide name="Zr-92"  ao="7.2758e-03" />
+    <nuclide name="Zr-94"  ao="7.3734e-03" />
+    <nuclide name="Zr-96"  ao="1.1879e-03" />
+    <nuclide name="Sn-112" ao="4.6735e-06" />
+    <nuclide name="Sn-114" ao="3.1799e-06" />
+    <nuclide name="Sn-115" ao="1.6381e-06" />
+    <nuclide name="Sn-116" ao="7.0055e-05" />
+    <nuclide name="Sn-117" ao="3.7003e-05" />
+    <nuclide name="Sn-118" ao="1.1669e-04" />
+    <nuclide name="Sn-119" ao="4.1387e-05" />
+    <nuclide name="Sn-120" ao="1.5697e-04" />
+    <nuclide name="Sn-122" ao="2.2308e-05" />
+    <nuclide name="Sn-124" ao="2.7897e-05" />
+  </material>
+    
+  <!-- Borated water at 975 ppm -->
+  <material id="4">
+    <density value="0.740582" units="g/cm3" />
+    <nuclide name="B-10"  ao="8.0042e-06" />
+    <nuclide name="B-11"  ao="3.2218e-05" />
+    <nuclide name="H-1"   ao="4.9457e-02" />
+    <nuclide name="H-2"   ao="7.4196e-06" />
+    <nuclide name="O-16"  ao="2.4672e-02" />
+    <nuclide name="O-17"  ao="6.0099e-05" />
+    <sab name="lwtr01" xs="31t" />
+  </material>
+
+</materials>
diff --git a/examples/pincell/settings.xml b/examples/pincell/jeff/settings.xml
similarity index 100%
rename from examples/pincell/settings.xml
rename to examples/pincell/jeff/settings.xml
diff --git a/examples/pincell/tallies.xml b/examples/pincell/jeff/tallies.xml
similarity index 100%
rename from examples/pincell/tallies.xml
rename to examples/pincell/jeff/tallies.xml
diff --git a/examples/pincell/mcnp/geometry.xml b/examples/pincell/mcnp/geometry.xml
new file mode 100644
index 0000000000..53cb2f15dc
--- /dev/null
+++ b/examples/pincell/mcnp/geometry.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!--
+      This is a simple pin cell model based on dimensions from the MIT BEAVRS
+      (Benchmarking for Evaluation and Validation of Reactor Simulations)
+      benchmark.
+  -->
+
+  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
+  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
+  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
+  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
+
+  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
+       cm (taken from Table 2 in BEAVRS). -->
+  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
+  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
+
+  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
+  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
+  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
+  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
+
+</geometry>
diff --git a/examples/pincell/mcnp/materials.xml b/examples/pincell/mcnp/materials.xml
new file mode 100644
index 0000000000..a0673418ca
--- /dev/null
+++ b/examples/pincell/mcnp/materials.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<materials>
+
+  <!-- By default, use 300K cross sections -->
+  <default_xs>70c</default_xs>
+
+  <!--
+      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
+      atom densities for O-17 and O-18 in any materials containing Oxygen.
+  -->
+
+  <!-- UO2 fuel at 2.4 wt% enrichment -->
+  <material id="1">
+    <density value="10.29769" units="g/cm3" />
+    <nuclide name="U-234"  ao="4.4843e-06" />
+    <nuclide name="U-235"  ao="5.5815e-04" />
+    <nuclide name="U-238"  ao="2.2408e-02" />
+    <nuclide name="O-16"   ao="4.5829e-02" />
+    <nuclide name="O-17"   ao="1.1164e-04" />
+  </material>
+
+  <!-- Helium for gap -->
+  <material id="2">
+    <density value="0.001598" units="g/cm3" />
+    <nuclide name="He-4"   ao="2.4044e-04" />
+  </material>
+
+  <!-- Zircaloy 4 -->
+  <material id="3">
+    <density value="6.55" units="g/cm3" />
+    <nuclide name="O-16"   ao="3.0743e-04" />
+    <nuclide name="O-17"   ao="7.4887e-07" />
+    <nuclide name="Cr-50"  ao="3.2962e-06" />
+    <nuclide name="Cr-52"  ao="6.3564e-05" />
+    <nuclide name="Cr-53"  ao="7.2076e-06" />
+    <nuclide name="Cr-54"  ao="1.7941e-06" />
+    <nuclide name="Fe-54"  ao="8.6699e-06" />
+    <nuclide name="Fe-56"  ao="1.3610e-04" />
+    <nuclide name="Fe-57"  ao="3.1431e-06" />
+    <nuclide name="Fe-58"  ao="4.1829e-07" />
+    <nuclide name="Zr-90"  ao="2.1827e-02" />
+    <nuclide name="Zr-91"  ao="4.7600e-03" />
+    <nuclide name="Zr-92"  ao="7.2758e-03" />
+    <nuclide name="Zr-94"  ao="7.3734e-03" />
+    <nuclide name="Zr-96"  ao="1.1879e-03" />
+    <nuclide name="Sn-112" ao="4.6735e-06" />
+    <nuclide name="Sn-114" ao="3.1799e-06" />
+    <nuclide name="Sn-115" ao="1.6381e-06" />
+    <nuclide name="Sn-116" ao="7.0055e-05" />
+    <nuclide name="Sn-117" ao="3.7003e-05" />
+    <nuclide name="Sn-118" ao="1.1669e-04" />
+    <nuclide name="Sn-119" ao="4.1387e-05" />
+    <nuclide name="Sn-120" ao="1.5697e-04" />
+    <nuclide name="Sn-122" ao="2.2308e-05" />
+    <nuclide name="Sn-124" ao="2.7897e-05" />
+  </material>
+    
+  <!-- Borated water at 975 ppm -->
+  <material id="4">
+    <density value="0.740582" units="g/cm3" />
+    <nuclide name="B-10"  ao="8.0042e-06" />
+    <nuclide name="B-11"  ao="3.2218e-05" />
+    <nuclide name="H-1"   ao="4.9457e-02" />
+    <nuclide name="H-2"   ao="7.4196e-06" />
+    <nuclide name="O-16"  ao="2.4672e-02" />
+    <nuclide name="O-17"  ao="6.0099e-05" />
+    <sab name="lwtr" xs="10t" />
+  </material>
+
+</materials>
diff --git a/examples/pincell/mcnp/settings.xml b/examples/pincell/mcnp/settings.xml
new file mode 100644
index 0000000000..443af9cde2
--- /dev/null
+++ b/examples/pincell/mcnp/settings.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Define how many particles to run and for how many batches -->
+  <eigenvalue>
+    <batches>100</batches>
+    <inactive>10</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <!-- The starting source is a uniform distribution over the entire pin
+       cell. Note that since this is effectively a 2D model, the z coordinates
+       are inconsequential -->
+  <source>
+    <space type="box">
+      <parameters>
+        -0.62992 -0.62992 -1.
+         0.62992  0.62992  1.
+      </parameters>
+    </space>
+  </source>
+
+  <!-- To assess convergence of the source distribution, we need to define the
+       bounds for a mesh over which the Shannon entropy should be
+       calculated. The extent in the z direction is made arbitrarily large. -->
+  <entropy>
+    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
+    <upper_right>0.39218  0.39218  1.e50</upper_right>
+    <dimension>10 10 1</dimension>
+  </entropy>
+
+</settings>
\ No newline at end of file
diff --git a/examples/pincell/mcnp/tallies.xml b/examples/pincell/mcnp/tallies.xml
new file mode 100644
index 0000000000..bbfd588360
--- /dev/null
+++ b/examples/pincell/mcnp/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1" type="rectangular">
+    <dimension>100 100 1</dimension>
+    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
+    <upper_right>0.62992  0.62992  1.e50</upper_right>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <filter type="energy" bins="0. 4.e-6 20.0" />
+    <scores>flux fission nu-fission</scores>
+  </tally>
+
+</tallies>
\ No newline at end of file
diff --git a/examples/pincell/nndc/geometry.xml b/examples/pincell/nndc/geometry.xml
new file mode 100644
index 0000000000..53cb2f15dc
--- /dev/null
+++ b/examples/pincell/nndc/geometry.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!--
+      This is a simple pin cell model based on dimensions from the MIT BEAVRS
+      (Benchmarking for Evaluation and Validation of Reactor Simulations)
+      benchmark.
+  -->
+
+  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
+  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
+  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
+  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
+
+  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
+       cm (taken from Table 2 in BEAVRS). -->
+  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
+  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
+
+  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
+  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
+  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
+  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
+
+</geometry>
diff --git a/examples/pincell/materials.xml b/examples/pincell/nndc/materials.xml
similarity index 96%
rename from examples/pincell/materials.xml
rename to examples/pincell/nndc/materials.xml
index 1fca23090d..427fc175d4 100644
--- a/examples/pincell/materials.xml
+++ b/examples/pincell/nndc/materials.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <materials>
 
-  <!-- By default, use 600K cross sections -->
+  <!-- By default, use 300K cross sections -->
   <default_xs>71c</default_xs>
 
   <!--
@@ -64,7 +64,7 @@
     <nuclide name="H-2"   ao="7.4196e-06" />
     <nuclide name="O-16"  ao="2.4672e-02" />
     <nuclide name="O-17"  ao="6.0099e-05" />
-    <sab name="lwtr" xs="15t" />
+    <sab name="HH2O" xs="71t" />
   </material>
 
-</materials>
\ No newline at end of file
+</materials>
diff --git a/examples/pincell/nndc/settings.xml b/examples/pincell/nndc/settings.xml
new file mode 100644
index 0000000000..443af9cde2
--- /dev/null
+++ b/examples/pincell/nndc/settings.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Define how many particles to run and for how many batches -->
+  <eigenvalue>
+    <batches>100</batches>
+    <inactive>10</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <!-- The starting source is a uniform distribution over the entire pin
+       cell. Note that since this is effectively a 2D model, the z coordinates
+       are inconsequential -->
+  <source>
+    <space type="box">
+      <parameters>
+        -0.62992 -0.62992 -1.
+         0.62992  0.62992  1.
+      </parameters>
+    </space>
+  </source>
+
+  <!-- To assess convergence of the source distribution, we need to define the
+       bounds for a mesh over which the Shannon entropy should be
+       calculated. The extent in the z direction is made arbitrarily large. -->
+  <entropy>
+    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
+    <upper_right>0.39218  0.39218  1.e50</upper_right>
+    <dimension>10 10 1</dimension>
+  </entropy>
+
+</settings>
\ No newline at end of file
diff --git a/examples/pincell/nndc/tallies.xml b/examples/pincell/nndc/tallies.xml
new file mode 100644
index 0000000000..bbfd588360
--- /dev/null
+++ b/examples/pincell/nndc/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1" type="rectangular">
+    <dimension>100 100 1</dimension>
+    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
+    <upper_right>0.62992  0.62992  1.e50</upper_right>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <filter type="energy" bins="0. 4.e-6 20.0" />
+    <scores>flux fission nu-fission</scores>
+  </tally>
+
+</tallies>
\ No newline at end of file
diff --git a/examples/pincell/serpent/geometry.xml b/examples/pincell/serpent/geometry.xml
new file mode 100644
index 0000000000..53cb2f15dc
--- /dev/null
+++ b/examples/pincell/serpent/geometry.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!--
+      This is a simple pin cell model based on dimensions from the MIT BEAVRS
+      (Benchmarking for Evaluation and Validation of Reactor Simulations)
+      benchmark.
+  -->
+
+  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
+  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
+  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
+  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
+
+  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
+       cm (taken from Table 2 in BEAVRS). -->
+  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
+  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
+  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
+
+  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
+  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
+  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
+  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
+
+</geometry>
diff --git a/examples/pincell/serpent/materials.xml b/examples/pincell/serpent/materials.xml
new file mode 100644
index 0000000000..348c870d6b
--- /dev/null
+++ b/examples/pincell/serpent/materials.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<materials>
+
+  <!-- By default, use 300K cross sections -->
+  <default_xs>03c</default_xs>
+
+  <!--
+      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
+      atom densities for O-17 and O-18 in any materials containing Oxygen.
+  -->
+
+  <!-- UO2 fuel at 2.4 wt% enrichment -->
+  <material id="1">
+    <density value="10.29769" units="g/cm3" />
+    <nuclide name="U-234"  ao="4.4843e-06" />
+    <nuclide name="U-235"  ao="5.5815e-04" />
+    <nuclide name="U-238"  ao="2.2408e-02" />
+    <nuclide name="O-16"   ao="4.5829e-02" />
+    <nuclide name="O-17"   ao="1.1164e-04" />
+  </material>
+
+  <!-- Helium for gap -->
+  <material id="2">
+    <density value="0.001598" units="g/cm3" />
+    <nuclide name="He-4"   ao="2.4044e-04" />
+  </material>
+
+  <!-- Zircaloy 4 -->
+  <material id="3">
+    <density value="6.55" units="g/cm3" />
+    <nuclide name="O-16"   ao="3.0743e-04" />
+    <nuclide name="O-17"   ao="7.4887e-07" />
+    <nuclide name="Cr-50"  ao="3.2962e-06" />
+    <nuclide name="Cr-52"  ao="6.3564e-05" />
+    <nuclide name="Cr-53"  ao="7.2076e-06" />
+    <nuclide name="Cr-54"  ao="1.7941e-06" />
+    <nuclide name="Fe-54"  ao="8.6699e-06" />
+    <nuclide name="Fe-56"  ao="1.3610e-04" />
+    <nuclide name="Fe-57"  ao="3.1431e-06" />
+    <nuclide name="Fe-58"  ao="4.1829e-07" />
+    <nuclide name="Zr-90"  ao="2.1827e-02" />
+    <nuclide name="Zr-91"  ao="4.7600e-03" />
+    <nuclide name="Zr-92"  ao="7.2758e-03" />
+    <nuclide name="Zr-94"  ao="7.3734e-03" />
+    <nuclide name="Zr-96"  ao="1.1879e-03" />
+    <nuclide name="Sn-112" ao="4.6735e-06" />
+    <nuclide name="Sn-114" ao="3.1799e-06" />
+    <nuclide name="Sn-115" ao="1.6381e-06" />
+    <nuclide name="Sn-116" ao="7.0055e-05" />
+    <nuclide name="Sn-117" ao="3.7003e-05" />
+    <nuclide name="Sn-118" ao="1.1669e-04" />
+    <nuclide name="Sn-119" ao="4.1387e-05" />
+    <nuclide name="Sn-120" ao="1.5697e-04" />
+    <nuclide name="Sn-122" ao="2.2308e-05" />
+    <nuclide name="Sn-124" ao="2.7897e-05" />
+  </material>
+    
+  <!-- Borated water at 975 ppm -->
+  <material id="4">
+    <density value="0.740582" units="g/cm3" />
+    <nuclide name="B-10"  ao="8.0042e-06" />
+    <nuclide name="B-11"  ao="3.2218e-05" />
+    <nuclide name="H-1"   ao="4.9457e-02" />
+    <nuclide name="H-2"   ao="7.4196e-06" />
+    <nuclide name="O-16"  ao="2.4672e-02" />
+    <nuclide name="O-17"  ao="6.0099e-05" />
+    <sab name="lwe7" xs="00t" />
+  </material>
+
+</materials>
diff --git a/examples/pincell/serpent/settings.xml b/examples/pincell/serpent/settings.xml
new file mode 100644
index 0000000000..443af9cde2
--- /dev/null
+++ b/examples/pincell/serpent/settings.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Define how many particles to run and for how many batches -->
+  <eigenvalue>
+    <batches>100</batches>
+    <inactive>10</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <!-- The starting source is a uniform distribution over the entire pin
+       cell. Note that since this is effectively a 2D model, the z coordinates
+       are inconsequential -->
+  <source>
+    <space type="box">
+      <parameters>
+        -0.62992 -0.62992 -1.
+         0.62992  0.62992  1.
+      </parameters>
+    </space>
+  </source>
+
+  <!-- To assess convergence of the source distribution, we need to define the
+       bounds for a mesh over which the Shannon entropy should be
+       calculated. The extent in the z direction is made arbitrarily large. -->
+  <entropy>
+    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
+    <upper_right>0.39218  0.39218  1.e50</upper_right>
+    <dimension>10 10 1</dimension>
+  </entropy>
+
+</settings>
\ No newline at end of file
diff --git a/examples/pincell/serpent/tallies.xml b/examples/pincell/serpent/tallies.xml
new file mode 100644
index 0000000000..bbfd588360
--- /dev/null
+++ b/examples/pincell/serpent/tallies.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1" type="rectangular">
+    <dimension>100 100 1</dimension>
+    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
+    <upper_right>0.62992  0.62992  1.e50</upper_right>
+  </mesh>
+
+  <tally id="1">
+    <filter type="mesh" bins="1" />
+    <filter type="energy" bins="0. 4.e-6 20.0" />
+    <scores>flux fission nu-fission</scores>
+  </tally>
+
+</tallies>
\ No newline at end of file
diff --git a/examples/reflective/geometry.xml b/examples/reflective/jeff/geometry.xml
similarity index 100%
rename from examples/reflective/geometry.xml
rename to examples/reflective/jeff/geometry.xml
diff --git a/examples/reflective/jeff/materials.xml b/examples/reflective/jeff/materials.xml
new file mode 100644
index 0000000000..538751eb6e
--- /dev/null
+++ b/examples/reflective/jeff/materials.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>31c</default_xs>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+</materials>
diff --git a/examples/reflective/settings.xml b/examples/reflective/jeff/settings.xml
similarity index 100%
rename from examples/reflective/settings.xml
rename to examples/reflective/jeff/settings.xml
diff --git a/examples/reflective/mcnp/geometry.xml b/examples/reflective/mcnp/geometry.xml
new file mode 100644
index 0000000000..664ef0705f
--- /dev/null
+++ b/examples/reflective/mcnp/geometry.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1">
+    <universe>0</universe>
+    <material>1</material>
+    <surfaces>1 -2 3 -4 5 -6</surfaces>
+  </cell>
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
+  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
+    
+</geometry>
diff --git a/examples/reflective/materials.xml b/examples/reflective/mcnp/materials.xml
similarity index 100%
rename from examples/reflective/materials.xml
rename to examples/reflective/mcnp/materials.xml
diff --git a/examples/reflective/mcnp/settings.xml b/examples/reflective/mcnp/settings.xml
new file mode 100644
index 0000000000..9f8cf8e959
--- /dev/null
+++ b/examples/reflective/mcnp/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>500</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/reflective/nndc/geometry.xml b/examples/reflective/nndc/geometry.xml
new file mode 100644
index 0000000000..664ef0705f
--- /dev/null
+++ b/examples/reflective/nndc/geometry.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1">
+    <universe>0</universe>
+    <material>1</material>
+    <surfaces>1 -2 3 -4 5 -6</surfaces>
+  </cell>
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
+  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
+    
+</geometry>
diff --git a/examples/reflective/nndc/materials.xml b/examples/reflective/nndc/materials.xml
new file mode 100644
index 0000000000..6da53a9b60
--- /dev/null
+++ b/examples/reflective/nndc/materials.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>71c</default_xs>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+</materials>
diff --git a/examples/reflective/nndc/settings.xml b/examples/reflective/nndc/settings.xml
new file mode 100644
index 0000000000..9f8cf8e959
--- /dev/null
+++ b/examples/reflective/nndc/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>500</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>
diff --git a/examples/reflective/serpent/geometry.xml b/examples/reflective/serpent/geometry.xml
new file mode 100644
index 0000000000..664ef0705f
--- /dev/null
+++ b/examples/reflective/serpent/geometry.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Definition of Cells -->
+  <cell id="1">
+    <universe>0</universe>
+    <material>1</material>
+    <surfaces>1 -2 3 -4 5 -6</surfaces>
+  </cell>
+
+  <!-- Defition of Surfaces -->
+  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
+  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
+  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
+  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
+  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
+    
+</geometry>
diff --git a/examples/reflective/serpent/materials.xml b/examples/reflective/serpent/materials.xml
new file mode 100644
index 0000000000..036dafe254
--- /dev/null
+++ b/examples/reflective/serpent/materials.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<materials>
+
+  <default_xs>03c</default_xs>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" ao="1.0" />
+  </material>
+
+</materials>
diff --git a/examples/reflective/serpent/settings.xml b/examples/reflective/serpent/settings.xml
new file mode 100644
index 0000000000..9f8cf8e959
--- /dev/null
+++ b/examples/reflective/serpent/settings.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <!-- Parameters for k-eigenvalue calculation -->
+  <eigenvalue>
+    <batches>500</batches>
+    <inactive>10</inactive>
+    <particles>10000</particles>
+  </eigenvalue>
+
+  <!-- Starting source -->
+  <source>
+    <space type="box">
+      <parameters>-1 -1 -1  1  1  1</parameters>
+    </space>
+  </source>
+
+</settings>

From bd73ca023a27f7527853633ca0a31c5c043dbc1a Mon Sep 17 00:00:00 2001
From: Jon Walsh <walshjon@mit.edu>
Date: Sun, 22 Jun 2014 21:15:58 -0600
Subject: [PATCH 2/2] delete example inputs for all data libraries except those
 from nndc

---
 examples/basic/{jeff => }/geometry.xml        |  0
 examples/basic/jeff/materials.xml             | 18 -----
 examples/basic/{nndc => }/materials.xml       |  0
 examples/basic/mcnp/geometry.xml              | 15 ----
 examples/basic/mcnp/materials.xml             | 18 -----
 examples/basic/mcnp/settings.xml              | 18 -----
 examples/basic/mcnp/tallies.xml               | 22 ------
 examples/basic/nndc/geometry.xml              | 15 ----
 examples/basic/nndc/settings.xml              | 18 -----
 examples/basic/nndc/tallies.xml               | 22 ------
 examples/basic/serpent/geometry.xml           | 15 ----
 examples/basic/serpent/materials.xml          | 18 -----
 examples/basic/serpent/settings.xml           | 18 -----
 examples/basic/serpent/tallies.xml            | 22 ------
 examples/basic/{jeff => }/settings.xml        |  0
 examples/basic/{jeff => }/tallies.xml         |  0
 .../lattice/nested/{jeff => }/geometry.xml    |  0
 examples/lattice/nested/jeff/materials.xml    | 19 -----
 .../lattice/nested/{nndc => }/materials.xml   |  0
 examples/lattice/nested/mcnp/geometry.xml     | 45 ------------
 examples/lattice/nested/mcnp/materials.xml    | 19 -----
 examples/lattice/nested/nndc/geometry.xml     | 45 ------------
 examples/lattice/nested/nndc/plots.xml        | 10 ---
 examples/lattice/nested/nndc/settings.xml     | 18 -----
 examples/lattice/nested/nndc/tallies.xml      | 16 -----
 examples/lattice/nested/{jeff => }/plots.xml  |  0
 examples/lattice/nested/serpent/geometry.xml  | 45 ------------
 examples/lattice/nested/serpent/materials.xml | 19 -----
 examples/lattice/nested/serpent/plots.xml     | 10 ---
 examples/lattice/nested/serpent/settings.xml  | 18 -----
 examples/lattice/nested/serpent/tallies.xml   | 16 -----
 .../lattice/nested/{jeff => }/settings.xml    |  0
 .../lattice/nested/{jeff => }/tallies.xml     |  0
 .../lattice/simple/{jeff => }/geometry.xml    |  0
 examples/lattice/simple/jeff/materials.xml    | 19 -----
 examples/lattice/simple/jeff/plots.xml        | 10 ---
 examples/lattice/simple/jeff/settings.xml     | 18 -----
 examples/lattice/simple/jeff/tallies.xml      | 16 -----
 .../lattice/simple/{nndc => }/materials.xml   |  0
 examples/lattice/simple/mcnp/geometry.xml     | 33 ---------
 examples/lattice/simple/mcnp/materials.xml    | 19 -----
 examples/lattice/simple/mcnp/plots.xml        | 10 ---
 examples/lattice/simple/mcnp/settings.xml     | 18 -----
 examples/lattice/simple/mcnp/tallies.xml      | 16 -----
 examples/lattice/simple/nndc/geometry.xml     | 33 ---------
 examples/lattice/simple/nndc/plots.xml        | 10 ---
 examples/lattice/simple/nndc/settings.xml     | 18 -----
 examples/lattice/simple/nndc/tallies.xml      | 16 -----
 .../lattice/{nested/mcnp => simple}/plots.xml |  0
 examples/lattice/simple/serpent/geometry.xml  | 33 ---------
 examples/lattice/simple/serpent/materials.xml | 19 -----
 examples/lattice/simple/serpent/plots.xml     | 10 ---
 examples/lattice/simple/serpent/settings.xml  | 18 -----
 examples/lattice/simple/serpent/tallies.xml   | 16 -----
 .../{nested/mcnp => simple}/settings.xml      |  0
 .../{nested/mcnp => simple}/tallies.xml       |  0
 examples/pincell/{jeff => }/geometry.xml      |  0
 examples/pincell/jeff/materials.xml           | 70 -------------------
 examples/pincell/{nndc => }/materials.xml     |  0
 examples/pincell/mcnp/geometry.xml            | 27 -------
 examples/pincell/mcnp/materials.xml           | 70 -------------------
 examples/pincell/mcnp/settings.xml            | 32 ---------
 examples/pincell/mcnp/tallies.xml             | 16 -----
 examples/pincell/nndc/geometry.xml            | 27 -------
 examples/pincell/nndc/settings.xml            | 32 ---------
 examples/pincell/nndc/tallies.xml             | 16 -----
 examples/pincell/serpent/geometry.xml         | 27 -------
 examples/pincell/serpent/materials.xml        | 70 -------------------
 examples/pincell/serpent/settings.xml         | 32 ---------
 examples/pincell/serpent/tallies.xml          | 16 -----
 examples/pincell/{jeff => }/settings.xml      |  0
 examples/pincell/{jeff => }/tallies.xml       |  0
 examples/reflective/{jeff => }/geometry.xml   |  0
 examples/reflective/jeff/materials.xml        | 11 ---
 examples/reflective/{nndc => }/materials.xml  |  0
 examples/reflective/mcnp/geometry.xml         | 19 -----
 examples/reflective/mcnp/materials.xml        | 11 ---
 examples/reflective/mcnp/settings.xml         | 18 -----
 examples/reflective/nndc/geometry.xml         | 19 -----
 examples/reflective/nndc/settings.xml         | 18 -----
 examples/reflective/serpent/geometry.xml      | 19 -----
 examples/reflective/serpent/materials.xml     | 11 ---
 examples/reflective/serpent/settings.xml      | 18 -----
 examples/reflective/{jeff => }/settings.xml   |  0
 84 files changed, 1410 deletions(-)
 rename examples/basic/{jeff => }/geometry.xml (100%)
 delete mode 100644 examples/basic/jeff/materials.xml
 rename examples/basic/{nndc => }/materials.xml (100%)
 delete mode 100644 examples/basic/mcnp/geometry.xml
 delete mode 100644 examples/basic/mcnp/materials.xml
 delete mode 100644 examples/basic/mcnp/settings.xml
 delete mode 100644 examples/basic/mcnp/tallies.xml
 delete mode 100644 examples/basic/nndc/geometry.xml
 delete mode 100644 examples/basic/nndc/settings.xml
 delete mode 100644 examples/basic/nndc/tallies.xml
 delete mode 100644 examples/basic/serpent/geometry.xml
 delete mode 100644 examples/basic/serpent/materials.xml
 delete mode 100644 examples/basic/serpent/settings.xml
 delete mode 100644 examples/basic/serpent/tallies.xml
 rename examples/basic/{jeff => }/settings.xml (100%)
 rename examples/basic/{jeff => }/tallies.xml (100%)
 rename examples/lattice/nested/{jeff => }/geometry.xml (100%)
 delete mode 100644 examples/lattice/nested/jeff/materials.xml
 rename examples/lattice/nested/{nndc => }/materials.xml (100%)
 delete mode 100644 examples/lattice/nested/mcnp/geometry.xml
 delete mode 100644 examples/lattice/nested/mcnp/materials.xml
 delete mode 100644 examples/lattice/nested/nndc/geometry.xml
 delete mode 100644 examples/lattice/nested/nndc/plots.xml
 delete mode 100644 examples/lattice/nested/nndc/settings.xml
 delete mode 100644 examples/lattice/nested/nndc/tallies.xml
 rename examples/lattice/nested/{jeff => }/plots.xml (100%)
 delete mode 100644 examples/lattice/nested/serpent/geometry.xml
 delete mode 100644 examples/lattice/nested/serpent/materials.xml
 delete mode 100644 examples/lattice/nested/serpent/plots.xml
 delete mode 100644 examples/lattice/nested/serpent/settings.xml
 delete mode 100644 examples/lattice/nested/serpent/tallies.xml
 rename examples/lattice/nested/{jeff => }/settings.xml (100%)
 rename examples/lattice/nested/{jeff => }/tallies.xml (100%)
 rename examples/lattice/simple/{jeff => }/geometry.xml (100%)
 delete mode 100644 examples/lattice/simple/jeff/materials.xml
 delete mode 100644 examples/lattice/simple/jeff/plots.xml
 delete mode 100644 examples/lattice/simple/jeff/settings.xml
 delete mode 100644 examples/lattice/simple/jeff/tallies.xml
 rename examples/lattice/simple/{nndc => }/materials.xml (100%)
 delete mode 100644 examples/lattice/simple/mcnp/geometry.xml
 delete mode 100644 examples/lattice/simple/mcnp/materials.xml
 delete mode 100644 examples/lattice/simple/mcnp/plots.xml
 delete mode 100644 examples/lattice/simple/mcnp/settings.xml
 delete mode 100644 examples/lattice/simple/mcnp/tallies.xml
 delete mode 100644 examples/lattice/simple/nndc/geometry.xml
 delete mode 100644 examples/lattice/simple/nndc/plots.xml
 delete mode 100644 examples/lattice/simple/nndc/settings.xml
 delete mode 100644 examples/lattice/simple/nndc/tallies.xml
 rename examples/lattice/{nested/mcnp => simple}/plots.xml (100%)
 delete mode 100644 examples/lattice/simple/serpent/geometry.xml
 delete mode 100644 examples/lattice/simple/serpent/materials.xml
 delete mode 100644 examples/lattice/simple/serpent/plots.xml
 delete mode 100644 examples/lattice/simple/serpent/settings.xml
 delete mode 100644 examples/lattice/simple/serpent/tallies.xml
 rename examples/lattice/{nested/mcnp => simple}/settings.xml (100%)
 rename examples/lattice/{nested/mcnp => simple}/tallies.xml (100%)
 rename examples/pincell/{jeff => }/geometry.xml (100%)
 delete mode 100644 examples/pincell/jeff/materials.xml
 rename examples/pincell/{nndc => }/materials.xml (100%)
 delete mode 100644 examples/pincell/mcnp/geometry.xml
 delete mode 100644 examples/pincell/mcnp/materials.xml
 delete mode 100644 examples/pincell/mcnp/settings.xml
 delete mode 100644 examples/pincell/mcnp/tallies.xml
 delete mode 100644 examples/pincell/nndc/geometry.xml
 delete mode 100644 examples/pincell/nndc/settings.xml
 delete mode 100644 examples/pincell/nndc/tallies.xml
 delete mode 100644 examples/pincell/serpent/geometry.xml
 delete mode 100644 examples/pincell/serpent/materials.xml
 delete mode 100644 examples/pincell/serpent/settings.xml
 delete mode 100644 examples/pincell/serpent/tallies.xml
 rename examples/pincell/{jeff => }/settings.xml (100%)
 rename examples/pincell/{jeff => }/tallies.xml (100%)
 rename examples/reflective/{jeff => }/geometry.xml (100%)
 delete mode 100644 examples/reflective/jeff/materials.xml
 rename examples/reflective/{nndc => }/materials.xml (100%)
 delete mode 100644 examples/reflective/mcnp/geometry.xml
 delete mode 100644 examples/reflective/mcnp/materials.xml
 delete mode 100644 examples/reflective/mcnp/settings.xml
 delete mode 100644 examples/reflective/nndc/geometry.xml
 delete mode 100644 examples/reflective/nndc/settings.xml
 delete mode 100644 examples/reflective/serpent/geometry.xml
 delete mode 100644 examples/reflective/serpent/materials.xml
 delete mode 100644 examples/reflective/serpent/settings.xml
 rename examples/reflective/{jeff => }/settings.xml (100%)

diff --git a/examples/basic/jeff/geometry.xml b/examples/basic/geometry.xml
similarity index 100%
rename from examples/basic/jeff/geometry.xml
rename to examples/basic/geometry.xml
diff --git a/examples/basic/jeff/materials.xml b/examples/basic/jeff/materials.xml
deleted file mode 100644
index e5b7e2044c..0000000000
--- a/examples/basic/jeff/materials.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>31c</default_xs>
-
-  <material id="40">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="41">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1" ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr01" xs="31t" />
-  </material>
-
-</materials>
diff --git a/examples/basic/nndc/materials.xml b/examples/basic/materials.xml
similarity index 100%
rename from examples/basic/nndc/materials.xml
rename to examples/basic/materials.xml
diff --git a/examples/basic/mcnp/geometry.xml b/examples/basic/mcnp/geometry.xml
deleted file mode 100644
index e9483306c0..0000000000
--- a/examples/basic/mcnp/geometry.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1" universe="0" fill="37" surfaces="-2" />
-  <cell id="100" universe="37" material="40" surfaces="-1" />
-  <cell id="101" universe="37" material="41" surfaces="1" />
-  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
-  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
-  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
-    
-</geometry>
diff --git a/examples/basic/mcnp/materials.xml b/examples/basic/mcnp/materials.xml
deleted file mode 100644
index e50a423112..0000000000
--- a/examples/basic/mcnp/materials.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>70c</default_xs>
-
-  <material id="40">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="41">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1" ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr" xs="10t" />
-  </material>
-
-</materials>
diff --git a/examples/basic/mcnp/settings.xml b/examples/basic/mcnp/settings.xml
deleted file mode 100644
index eb9f5bd56d..0000000000
--- a/examples/basic/mcnp/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>15</batches>
-    <inactive>5</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-4 -4 -4  4  4  4</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/basic/mcnp/tallies.xml b/examples/basic/mcnp/tallies.xml
deleted file mode 100644
index fb1dfbc9ce..0000000000
--- a/examples/basic/mcnp/tallies.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <tally id="1">
-    <filter type="cell" bins="100" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="2">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="3">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <filter type="energyout" bins="0 20.0" />
-    <scores>scatter nu-scatter nu-fission</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/basic/nndc/geometry.xml b/examples/basic/nndc/geometry.xml
deleted file mode 100644
index e9483306c0..0000000000
--- a/examples/basic/nndc/geometry.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1" universe="0" fill="37" surfaces="-2" />
-  <cell id="100" universe="37" material="40" surfaces="-1" />
-  <cell id="101" universe="37" material="41" surfaces="1" />
-  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
-  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
-  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
-    
-</geometry>
diff --git a/examples/basic/nndc/settings.xml b/examples/basic/nndc/settings.xml
deleted file mode 100644
index eb9f5bd56d..0000000000
--- a/examples/basic/nndc/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>15</batches>
-    <inactive>5</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-4 -4 -4  4  4  4</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/basic/nndc/tallies.xml b/examples/basic/nndc/tallies.xml
deleted file mode 100644
index fb1dfbc9ce..0000000000
--- a/examples/basic/nndc/tallies.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <tally id="1">
-    <filter type="cell" bins="100" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="2">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="3">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <filter type="energyout" bins="0 20.0" />
-    <scores>scatter nu-scatter nu-fission</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/basic/serpent/geometry.xml b/examples/basic/serpent/geometry.xml
deleted file mode 100644
index e9483306c0..0000000000
--- a/examples/basic/serpent/geometry.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1" universe="0" fill="37" surfaces="-2" />
-  <cell id="100" universe="37" material="40" surfaces="-1" />
-  <cell id="101" universe="37" material="41" surfaces="1" />
-  <cell id="2" universe="0" material="41" surfaces = "2 -3" />
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="z-cylinder" coeffs="0 0 7" />
-  <surface id="2" type="z-cylinder" coeffs="0 0 9" />
-  <surface id="3" type="z-cylinder" coeffs="0 0 11" boundary="vacuum" />
-    
-</geometry>
diff --git a/examples/basic/serpent/materials.xml b/examples/basic/serpent/materials.xml
deleted file mode 100644
index 21c3555e8c..0000000000
--- a/examples/basic/serpent/materials.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>03c</default_xs>
-
-  <material id="40">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="41">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1" ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwe7" xs="00t" />
-  </material>
-
-</materials>
diff --git a/examples/basic/serpent/settings.xml b/examples/basic/serpent/settings.xml
deleted file mode 100644
index eb9f5bd56d..0000000000
--- a/examples/basic/serpent/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>15</batches>
-    <inactive>5</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-4 -4 -4  4  4  4</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/basic/serpent/tallies.xml b/examples/basic/serpent/tallies.xml
deleted file mode 100644
index fb1dfbc9ce..0000000000
--- a/examples/basic/serpent/tallies.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <tally id="1">
-    <filter type="cell" bins="100" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="2">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <scores>total scatter nu-scatter absorption fission nu-fission</scores>
-  </tally>
-
-  <tally id="3">
-    <filter type="cell" bins="100" />
-    <filter type="energy" bins="0 20.0" />
-    <filter type="energyout" bins="0 20.0" />
-    <scores>scatter nu-scatter nu-fission</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/basic/jeff/settings.xml b/examples/basic/settings.xml
similarity index 100%
rename from examples/basic/jeff/settings.xml
rename to examples/basic/settings.xml
diff --git a/examples/basic/jeff/tallies.xml b/examples/basic/tallies.xml
similarity index 100%
rename from examples/basic/jeff/tallies.xml
rename to examples/basic/tallies.xml
diff --git a/examples/lattice/nested/jeff/geometry.xml b/examples/lattice/nested/geometry.xml
similarity index 100%
rename from examples/lattice/nested/jeff/geometry.xml
rename to examples/lattice/nested/geometry.xml
diff --git a/examples/lattice/nested/jeff/materials.xml b/examples/lattice/nested/jeff/materials.xml
deleted file mode 100644
index 5de4135b4a..0000000000
--- a/examples/lattice/nested/jeff/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>31c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr01" xs="31t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/nested/nndc/materials.xml b/examples/lattice/nested/materials.xml
similarity index 100%
rename from examples/lattice/nested/nndc/materials.xml
rename to examples/lattice/nested/materials.xml
diff --git a/examples/lattice/nested/mcnp/geometry.xml b/examples/lattice/nested/mcnp/geometry.xml
deleted file mode 100644
index f223cf3bb4..0000000000
--- a/examples/lattice/nested/mcnp/geometry.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
-  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <!-- 4 x 4 assembly -->
-  <lattice id="4">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-1.0 -1.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2
-      2 3
-    </universes>
-  </lattice>
-
-  <!-- 4 x 4 core -->
-  <lattice id="6">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>2.0 2.0</width>
-    <universes>
-      5 5
-      5 5
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/nested/mcnp/materials.xml b/examples/lattice/nested/mcnp/materials.xml
deleted file mode 100644
index dcf6ed2b89..0000000000
--- a/examples/lattice/nested/mcnp/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>70c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr" xs="10t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/nested/nndc/geometry.xml b/examples/lattice/nested/nndc/geometry.xml
deleted file mode 100644
index f223cf3bb4..0000000000
--- a/examples/lattice/nested/nndc/geometry.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
-  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <!-- 4 x 4 assembly -->
-  <lattice id="4">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-1.0 -1.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2
-      2 3
-    </universes>
-  </lattice>
-
-  <!-- 4 x 4 core -->
-  <lattice id="6">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>2.0 2.0</width>
-    <universes>
-      5 5
-      5 5
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/nested/nndc/plots.xml b/examples/lattice/nested/nndc/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/nested/nndc/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/nested/nndc/settings.xml b/examples/lattice/nested/nndc/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/nested/nndc/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/nested/nndc/tallies.xml b/examples/lattice/nested/nndc/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/nested/nndc/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/nested/jeff/plots.xml b/examples/lattice/nested/plots.xml
similarity index 100%
rename from examples/lattice/nested/jeff/plots.xml
rename to examples/lattice/nested/plots.xml
diff --git a/examples/lattice/nested/serpent/geometry.xml b/examples/lattice/nested/serpent/geometry.xml
deleted file mode 100644
index f223cf3bb4..0000000000
--- a/examples/lattice/nested/serpent/geometry.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1"                fill="6" surfaces="1 -2 3 -4" />
-  <cell id="2"   universe="5" fill="4" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <!-- 4 x 4 assembly -->
-  <lattice id="4">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-1.0 -1.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2
-      2 3
-    </universes>
-  </lattice>
-
-  <!-- 4 x 4 core -->
-  <lattice id="6">
-    <type>rectangular</type>
-    <dimension>2 2</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>2.0 2.0</width>
-    <universes>
-      5 5
-      5 5
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/nested/serpent/materials.xml b/examples/lattice/nested/serpent/materials.xml
deleted file mode 100644
index 29534b8003..0000000000
--- a/examples/lattice/nested/serpent/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>03c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwe7" xs="00t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/nested/serpent/plots.xml b/examples/lattice/nested/serpent/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/nested/serpent/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/nested/serpent/settings.xml b/examples/lattice/nested/serpent/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/nested/serpent/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/nested/serpent/tallies.xml b/examples/lattice/nested/serpent/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/nested/serpent/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/nested/jeff/settings.xml b/examples/lattice/nested/settings.xml
similarity index 100%
rename from examples/lattice/nested/jeff/settings.xml
rename to examples/lattice/nested/settings.xml
diff --git a/examples/lattice/nested/jeff/tallies.xml b/examples/lattice/nested/tallies.xml
similarity index 100%
rename from examples/lattice/nested/jeff/tallies.xml
rename to examples/lattice/nested/tallies.xml
diff --git a/examples/lattice/simple/jeff/geometry.xml b/examples/lattice/simple/geometry.xml
similarity index 100%
rename from examples/lattice/simple/jeff/geometry.xml
rename to examples/lattice/simple/geometry.xml
diff --git a/examples/lattice/simple/jeff/materials.xml b/examples/lattice/simple/jeff/materials.xml
deleted file mode 100644
index 5de4135b4a..0000000000
--- a/examples/lattice/simple/jeff/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>31c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr01" xs="31t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/simple/jeff/plots.xml b/examples/lattice/simple/jeff/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/simple/jeff/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/simple/jeff/settings.xml b/examples/lattice/simple/jeff/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/simple/jeff/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/simple/jeff/tallies.xml b/examples/lattice/simple/jeff/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/simple/jeff/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/simple/nndc/materials.xml b/examples/lattice/simple/materials.xml
similarity index 100%
rename from examples/lattice/simple/nndc/materials.xml
rename to examples/lattice/simple/materials.xml
diff --git a/examples/lattice/simple/mcnp/geometry.xml b/examples/lattice/simple/mcnp/geometry.xml
deleted file mode 100644
index b5bad90b9c..0000000000
--- a/examples/lattice/simple/mcnp/geometry.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <lattice id="5">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2 1 2
-      2 3 2 3
-      1 2 1 2
-      2 3 2 3
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/simple/mcnp/materials.xml b/examples/lattice/simple/mcnp/materials.xml
deleted file mode 100644
index dcf6ed2b89..0000000000
--- a/examples/lattice/simple/mcnp/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>70c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwtr" xs="10t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/simple/mcnp/plots.xml b/examples/lattice/simple/mcnp/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/simple/mcnp/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/simple/mcnp/settings.xml b/examples/lattice/simple/mcnp/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/simple/mcnp/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/simple/mcnp/tallies.xml b/examples/lattice/simple/mcnp/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/simple/mcnp/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/simple/nndc/geometry.xml b/examples/lattice/simple/nndc/geometry.xml
deleted file mode 100644
index b5bad90b9c..0000000000
--- a/examples/lattice/simple/nndc/geometry.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <lattice id="5">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2 1 2
-      2 3 2 3
-      1 2 1 2
-      2 3 2 3
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/simple/nndc/plots.xml b/examples/lattice/simple/nndc/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/simple/nndc/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/simple/nndc/settings.xml b/examples/lattice/simple/nndc/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/simple/nndc/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/simple/nndc/tallies.xml b/examples/lattice/simple/nndc/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/simple/nndc/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/nested/mcnp/plots.xml b/examples/lattice/simple/plots.xml
similarity index 100%
rename from examples/lattice/nested/mcnp/plots.xml
rename to examples/lattice/simple/plots.xml
diff --git a/examples/lattice/simple/serpent/geometry.xml b/examples/lattice/simple/serpent/geometry.xml
deleted file mode 100644
index b5bad90b9c..0000000000
--- a/examples/lattice/simple/serpent/geometry.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <cell id="1" fill="5" surfaces="1 -2 3 -4" />
-  <cell id="101" universe="1" material="1" surfaces="-5" />
-  <cell id="102" universe="1" material="2" surfaces="5" />
-  <cell id="201" universe="2" material="1" surfaces="-6" />
-  <cell id="202" universe="2" material="2" surfaces="6" />
-  <cell id="301" universe="3" material="1" surfaces="-7" />
-  <cell id="302" universe="3" material="2" surfaces="7" />
-
-  <lattice id="5">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-    <universes>
-      1 2 1 2
-      2 3 2 3
-      1 2 1 2
-      2 3 2 3
-    </universes>
-  </lattice>
-
-  <surface id="1" type="x-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-2.0" boundary="vacuum" />
-  <surface id="4" type="y-plane" coeffs="2.0" boundary="vacuum" />
-  <surface id="5" type="z-cylinder" coeffs="0.0 0.0 0.4" />
-  <surface id="6" type="z-cylinder" coeffs="0.0 0.0 0.3" />
-  <surface id="7" type="z-cylinder" coeffs="0.0 0.0 0.2" />
-
-</geometry>
diff --git a/examples/lattice/simple/serpent/materials.xml b/examples/lattice/simple/serpent/materials.xml
deleted file mode 100644
index 29534b8003..0000000000
--- a/examples/lattice/simple/serpent/materials.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>03c</default_xs>
-
-  <!-- Definition of materials -->
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-  <material id="2">
-    <density value="1.0" units="g/cc" />
-    <nuclide name="H-1"  ao="2.0" />
-    <nuclide name="O-16" ao="1.0" />
-    <sab name="lwe7" xs="00t" />
-  </material>
-
-</materials>
diff --git a/examples/lattice/simple/serpent/plots.xml b/examples/lattice/simple/serpent/plots.xml
deleted file mode 100644
index a8c6fbb7c5..0000000000
--- a/examples/lattice/simple/serpent/plots.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<plots>
-
-  <plot id="1" color="mat">
-    <origin>0. 0. 0.</origin>
-    <width>4.0 4.0</width>
-    <pixels>400 400</pixels>
-  </plot>
-
-</plots>
diff --git a/examples/lattice/simple/serpent/settings.xml b/examples/lattice/simple/serpent/settings.xml
deleted file mode 100644
index 2a6aaaf426..0000000000
--- a/examples/lattice/simple/serpent/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>20</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/lattice/simple/serpent/tallies.xml b/examples/lattice/simple/serpent/tallies.xml
deleted file mode 100644
index 5730e6b12c..0000000000
--- a/examples/lattice/simple/serpent/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1">
-    <type>rectangular</type>
-    <dimension>4 4</dimension>
-    <lower_left>-2.0 -2.0</lower_left>
-    <width>1.0 1.0</width>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <scores>total</scores>
-  </tally>
-
-</tallies>
diff --git a/examples/lattice/nested/mcnp/settings.xml b/examples/lattice/simple/settings.xml
similarity index 100%
rename from examples/lattice/nested/mcnp/settings.xml
rename to examples/lattice/simple/settings.xml
diff --git a/examples/lattice/nested/mcnp/tallies.xml b/examples/lattice/simple/tallies.xml
similarity index 100%
rename from examples/lattice/nested/mcnp/tallies.xml
rename to examples/lattice/simple/tallies.xml
diff --git a/examples/pincell/jeff/geometry.xml b/examples/pincell/geometry.xml
similarity index 100%
rename from examples/pincell/jeff/geometry.xml
rename to examples/pincell/geometry.xml
diff --git a/examples/pincell/jeff/materials.xml b/examples/pincell/jeff/materials.xml
deleted file mode 100644
index 02ec6fca38..0000000000
--- a/examples/pincell/jeff/materials.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <!-- By default, use 300K cross sections -->
-  <default_xs>31c</default_xs>
-
-  <!--
-      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
-      atom densities for O-17 and O-18 in any materials containing Oxygen.
-  -->
-
-  <!-- UO2 fuel at 2.4 wt% enrichment -->
-  <material id="1">
-    <density value="10.29769" units="g/cm3" />
-    <nuclide name="U-234"  ao="4.4843e-06" />
-    <nuclide name="U-235"  ao="5.5815e-04" />
-    <nuclide name="U-238"  ao="2.2408e-02" />
-    <nuclide name="O-16"   ao="4.5829e-02" />
-    <nuclide name="O-17"   ao="1.1164e-04" />
-  </material>
-
-  <!-- Helium for gap -->
-  <material id="2">
-    <density value="0.001598" units="g/cm3" />
-    <nuclide name="He-4"   ao="2.4044e-04" />
-  </material>
-
-  <!-- Zircaloy 4 -->
-  <material id="3">
-    <density value="6.55" units="g/cm3" />
-    <nuclide name="O-16"   ao="3.0743e-04" />
-    <nuclide name="O-17"   ao="7.4887e-07" />
-    <nuclide name="Cr-50"  ao="3.2962e-06" />
-    <nuclide name="Cr-52"  ao="6.3564e-05" />
-    <nuclide name="Cr-53"  ao="7.2076e-06" />
-    <nuclide name="Cr-54"  ao="1.7941e-06" />
-    <nuclide name="Fe-54"  ao="8.6699e-06" />
-    <nuclide name="Fe-56"  ao="1.3610e-04" />
-    <nuclide name="Fe-57"  ao="3.1431e-06" />
-    <nuclide name="Fe-58"  ao="4.1829e-07" />
-    <nuclide name="Zr-90"  ao="2.1827e-02" />
-    <nuclide name="Zr-91"  ao="4.7600e-03" />
-    <nuclide name="Zr-92"  ao="7.2758e-03" />
-    <nuclide name="Zr-94"  ao="7.3734e-03" />
-    <nuclide name="Zr-96"  ao="1.1879e-03" />
-    <nuclide name="Sn-112" ao="4.6735e-06" />
-    <nuclide name="Sn-114" ao="3.1799e-06" />
-    <nuclide name="Sn-115" ao="1.6381e-06" />
-    <nuclide name="Sn-116" ao="7.0055e-05" />
-    <nuclide name="Sn-117" ao="3.7003e-05" />
-    <nuclide name="Sn-118" ao="1.1669e-04" />
-    <nuclide name="Sn-119" ao="4.1387e-05" />
-    <nuclide name="Sn-120" ao="1.5697e-04" />
-    <nuclide name="Sn-122" ao="2.2308e-05" />
-    <nuclide name="Sn-124" ao="2.7897e-05" />
-  </material>
-    
-  <!-- Borated water at 975 ppm -->
-  <material id="4">
-    <density value="0.740582" units="g/cm3" />
-    <nuclide name="B-10"  ao="8.0042e-06" />
-    <nuclide name="B-11"  ao="3.2218e-05" />
-    <nuclide name="H-1"   ao="4.9457e-02" />
-    <nuclide name="H-2"   ao="7.4196e-06" />
-    <nuclide name="O-16"  ao="2.4672e-02" />
-    <nuclide name="O-17"  ao="6.0099e-05" />
-    <sab name="lwtr01" xs="31t" />
-  </material>
-
-</materials>
diff --git a/examples/pincell/nndc/materials.xml b/examples/pincell/materials.xml
similarity index 100%
rename from examples/pincell/nndc/materials.xml
rename to examples/pincell/materials.xml
diff --git a/examples/pincell/mcnp/geometry.xml b/examples/pincell/mcnp/geometry.xml
deleted file mode 100644
index 53cb2f15dc..0000000000
--- a/examples/pincell/mcnp/geometry.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!--
-      This is a simple pin cell model based on dimensions from the MIT BEAVRS
-      (Benchmarking for Evaluation and Validation of Reactor Simulations)
-      benchmark.
-  -->
-
-  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
-  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
-  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
-  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
-
-  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
-       cm (taken from Table 2 in BEAVRS). -->
-  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
-  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
-
-  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
-  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
-  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
-  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
-
-</geometry>
diff --git a/examples/pincell/mcnp/materials.xml b/examples/pincell/mcnp/materials.xml
deleted file mode 100644
index a0673418ca..0000000000
--- a/examples/pincell/mcnp/materials.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <!-- By default, use 300K cross sections -->
-  <default_xs>70c</default_xs>
-
-  <!--
-      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
-      atom densities for O-17 and O-18 in any materials containing Oxygen.
-  -->
-
-  <!-- UO2 fuel at 2.4 wt% enrichment -->
-  <material id="1">
-    <density value="10.29769" units="g/cm3" />
-    <nuclide name="U-234"  ao="4.4843e-06" />
-    <nuclide name="U-235"  ao="5.5815e-04" />
-    <nuclide name="U-238"  ao="2.2408e-02" />
-    <nuclide name="O-16"   ao="4.5829e-02" />
-    <nuclide name="O-17"   ao="1.1164e-04" />
-  </material>
-
-  <!-- Helium for gap -->
-  <material id="2">
-    <density value="0.001598" units="g/cm3" />
-    <nuclide name="He-4"   ao="2.4044e-04" />
-  </material>
-
-  <!-- Zircaloy 4 -->
-  <material id="3">
-    <density value="6.55" units="g/cm3" />
-    <nuclide name="O-16"   ao="3.0743e-04" />
-    <nuclide name="O-17"   ao="7.4887e-07" />
-    <nuclide name="Cr-50"  ao="3.2962e-06" />
-    <nuclide name="Cr-52"  ao="6.3564e-05" />
-    <nuclide name="Cr-53"  ao="7.2076e-06" />
-    <nuclide name="Cr-54"  ao="1.7941e-06" />
-    <nuclide name="Fe-54"  ao="8.6699e-06" />
-    <nuclide name="Fe-56"  ao="1.3610e-04" />
-    <nuclide name="Fe-57"  ao="3.1431e-06" />
-    <nuclide name="Fe-58"  ao="4.1829e-07" />
-    <nuclide name="Zr-90"  ao="2.1827e-02" />
-    <nuclide name="Zr-91"  ao="4.7600e-03" />
-    <nuclide name="Zr-92"  ao="7.2758e-03" />
-    <nuclide name="Zr-94"  ao="7.3734e-03" />
-    <nuclide name="Zr-96"  ao="1.1879e-03" />
-    <nuclide name="Sn-112" ao="4.6735e-06" />
-    <nuclide name="Sn-114" ao="3.1799e-06" />
-    <nuclide name="Sn-115" ao="1.6381e-06" />
-    <nuclide name="Sn-116" ao="7.0055e-05" />
-    <nuclide name="Sn-117" ao="3.7003e-05" />
-    <nuclide name="Sn-118" ao="1.1669e-04" />
-    <nuclide name="Sn-119" ao="4.1387e-05" />
-    <nuclide name="Sn-120" ao="1.5697e-04" />
-    <nuclide name="Sn-122" ao="2.2308e-05" />
-    <nuclide name="Sn-124" ao="2.7897e-05" />
-  </material>
-    
-  <!-- Borated water at 975 ppm -->
-  <material id="4">
-    <density value="0.740582" units="g/cm3" />
-    <nuclide name="B-10"  ao="8.0042e-06" />
-    <nuclide name="B-11"  ao="3.2218e-05" />
-    <nuclide name="H-1"   ao="4.9457e-02" />
-    <nuclide name="H-2"   ao="7.4196e-06" />
-    <nuclide name="O-16"  ao="2.4672e-02" />
-    <nuclide name="O-17"  ao="6.0099e-05" />
-    <sab name="lwtr" xs="10t" />
-  </material>
-
-</materials>
diff --git a/examples/pincell/mcnp/settings.xml b/examples/pincell/mcnp/settings.xml
deleted file mode 100644
index 443af9cde2..0000000000
--- a/examples/pincell/mcnp/settings.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Define how many particles to run and for how many batches -->
-  <eigenvalue>
-    <batches>100</batches>
-    <inactive>10</inactive>
-    <particles>1000</particles>
-  </eigenvalue>
-
-  <!-- The starting source is a uniform distribution over the entire pin
-       cell. Note that since this is effectively a 2D model, the z coordinates
-       are inconsequential -->
-  <source>
-    <space type="box">
-      <parameters>
-        -0.62992 -0.62992 -1.
-         0.62992  0.62992  1.
-      </parameters>
-    </space>
-  </source>
-
-  <!-- To assess convergence of the source distribution, we need to define the
-       bounds for a mesh over which the Shannon entropy should be
-       calculated. The extent in the z direction is made arbitrarily large. -->
-  <entropy>
-    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
-    <upper_right>0.39218  0.39218  1.e50</upper_right>
-    <dimension>10 10 1</dimension>
-  </entropy>
-
-</settings>
\ No newline at end of file
diff --git a/examples/pincell/mcnp/tallies.xml b/examples/pincell/mcnp/tallies.xml
deleted file mode 100644
index bbfd588360..0000000000
--- a/examples/pincell/mcnp/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1" type="rectangular">
-    <dimension>100 100 1</dimension>
-    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
-    <upper_right>0.62992  0.62992  1.e50</upper_right>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <filter type="energy" bins="0. 4.e-6 20.0" />
-    <scores>flux fission nu-fission</scores>
-  </tally>
-
-</tallies>
\ No newline at end of file
diff --git a/examples/pincell/nndc/geometry.xml b/examples/pincell/nndc/geometry.xml
deleted file mode 100644
index 53cb2f15dc..0000000000
--- a/examples/pincell/nndc/geometry.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!--
-      This is a simple pin cell model based on dimensions from the MIT BEAVRS
-      (Benchmarking for Evaluation and Validation of Reactor Simulations)
-      benchmark.
-  -->
-
-  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
-  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
-  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
-  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
-
-  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
-       cm (taken from Table 2 in BEAVRS). -->
-  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
-  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
-
-  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
-  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
-  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
-  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
-
-</geometry>
diff --git a/examples/pincell/nndc/settings.xml b/examples/pincell/nndc/settings.xml
deleted file mode 100644
index 443af9cde2..0000000000
--- a/examples/pincell/nndc/settings.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Define how many particles to run and for how many batches -->
-  <eigenvalue>
-    <batches>100</batches>
-    <inactive>10</inactive>
-    <particles>1000</particles>
-  </eigenvalue>
-
-  <!-- The starting source is a uniform distribution over the entire pin
-       cell. Note that since this is effectively a 2D model, the z coordinates
-       are inconsequential -->
-  <source>
-    <space type="box">
-      <parameters>
-        -0.62992 -0.62992 -1.
-         0.62992  0.62992  1.
-      </parameters>
-    </space>
-  </source>
-
-  <!-- To assess convergence of the source distribution, we need to define the
-       bounds for a mesh over which the Shannon entropy should be
-       calculated. The extent in the z direction is made arbitrarily large. -->
-  <entropy>
-    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
-    <upper_right>0.39218  0.39218  1.e50</upper_right>
-    <dimension>10 10 1</dimension>
-  </entropy>
-
-</settings>
\ No newline at end of file
diff --git a/examples/pincell/nndc/tallies.xml b/examples/pincell/nndc/tallies.xml
deleted file mode 100644
index bbfd588360..0000000000
--- a/examples/pincell/nndc/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1" type="rectangular">
-    <dimension>100 100 1</dimension>
-    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
-    <upper_right>0.62992  0.62992  1.e50</upper_right>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <filter type="energy" bins="0. 4.e-6 20.0" />
-    <scores>flux fission nu-fission</scores>
-  </tally>
-
-</tallies>
\ No newline at end of file
diff --git a/examples/pincell/serpent/geometry.xml b/examples/pincell/serpent/geometry.xml
deleted file mode 100644
index 53cb2f15dc..0000000000
--- a/examples/pincell/serpent/geometry.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!--
-      This is a simple pin cell model based on dimensions from the MIT BEAVRS
-      (Benchmarking for Evaluation and Validation of Reactor Simulations)
-      benchmark.
-  -->
-
-  <!-- Surfaces for fuel, gap, cladding. Dimensions from Figure 2 in BEAVRS -->
-  <surface id="1" type="z-cylinder" coeffs="0. 0. 0.39218" /> <!-- Fuel OR -->
-  <surface id="2" type="z-cylinder" coeffs="0. 0. 0.40005" /> <!-- Clad IR -->
-  <surface id="3" type="z-cylinder" coeffs="0. 0. 0.45720" /> <!-- Clad OR -->
-
-  <!-- Reflective surfaces on outside of pin-cell. The lattice pitch is 1.25984
-       cm (taken from Table 2 in BEAVRS). -->
-  <surface id="4" type="x-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="5" type="x-plane" coeffs=" 0.62992" boundary="reflective" />
-  <surface id="6" type="y-plane" coeffs="-0.62992" boundary="reflective" />
-  <surface id="7" type="y-plane" coeffs=" 0.62992" boundary="reflective" />
-
-  <cell id="1" material="1" surfaces="  -1" />        <!-- UO2 Fuel -->
-  <cell id="2" material="2" surfaces="1 -2" />        <!-- Helium gap -->
-  <cell id="3" material="3" surfaces="2 -3" />        <!-- Zircaloy cladding -->
-  <cell id="4" material="4" surfaces="3 4 -5 6 -7" /> <!-- Borated water -->
-
-</geometry>
diff --git a/examples/pincell/serpent/materials.xml b/examples/pincell/serpent/materials.xml
deleted file mode 100644
index 348c870d6b..0000000000
--- a/examples/pincell/serpent/materials.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <!-- By default, use 300K cross sections -->
-  <default_xs>03c</default_xs>
-
-  <!--
-      Since O-18 is not present in ENDF/B-VII, it was necessary to combine the
-      atom densities for O-17 and O-18 in any materials containing Oxygen.
-  -->
-
-  <!-- UO2 fuel at 2.4 wt% enrichment -->
-  <material id="1">
-    <density value="10.29769" units="g/cm3" />
-    <nuclide name="U-234"  ao="4.4843e-06" />
-    <nuclide name="U-235"  ao="5.5815e-04" />
-    <nuclide name="U-238"  ao="2.2408e-02" />
-    <nuclide name="O-16"   ao="4.5829e-02" />
-    <nuclide name="O-17"   ao="1.1164e-04" />
-  </material>
-
-  <!-- Helium for gap -->
-  <material id="2">
-    <density value="0.001598" units="g/cm3" />
-    <nuclide name="He-4"   ao="2.4044e-04" />
-  </material>
-
-  <!-- Zircaloy 4 -->
-  <material id="3">
-    <density value="6.55" units="g/cm3" />
-    <nuclide name="O-16"   ao="3.0743e-04" />
-    <nuclide name="O-17"   ao="7.4887e-07" />
-    <nuclide name="Cr-50"  ao="3.2962e-06" />
-    <nuclide name="Cr-52"  ao="6.3564e-05" />
-    <nuclide name="Cr-53"  ao="7.2076e-06" />
-    <nuclide name="Cr-54"  ao="1.7941e-06" />
-    <nuclide name="Fe-54"  ao="8.6699e-06" />
-    <nuclide name="Fe-56"  ao="1.3610e-04" />
-    <nuclide name="Fe-57"  ao="3.1431e-06" />
-    <nuclide name="Fe-58"  ao="4.1829e-07" />
-    <nuclide name="Zr-90"  ao="2.1827e-02" />
-    <nuclide name="Zr-91"  ao="4.7600e-03" />
-    <nuclide name="Zr-92"  ao="7.2758e-03" />
-    <nuclide name="Zr-94"  ao="7.3734e-03" />
-    <nuclide name="Zr-96"  ao="1.1879e-03" />
-    <nuclide name="Sn-112" ao="4.6735e-06" />
-    <nuclide name="Sn-114" ao="3.1799e-06" />
-    <nuclide name="Sn-115" ao="1.6381e-06" />
-    <nuclide name="Sn-116" ao="7.0055e-05" />
-    <nuclide name="Sn-117" ao="3.7003e-05" />
-    <nuclide name="Sn-118" ao="1.1669e-04" />
-    <nuclide name="Sn-119" ao="4.1387e-05" />
-    <nuclide name="Sn-120" ao="1.5697e-04" />
-    <nuclide name="Sn-122" ao="2.2308e-05" />
-    <nuclide name="Sn-124" ao="2.7897e-05" />
-  </material>
-    
-  <!-- Borated water at 975 ppm -->
-  <material id="4">
-    <density value="0.740582" units="g/cm3" />
-    <nuclide name="B-10"  ao="8.0042e-06" />
-    <nuclide name="B-11"  ao="3.2218e-05" />
-    <nuclide name="H-1"   ao="4.9457e-02" />
-    <nuclide name="H-2"   ao="7.4196e-06" />
-    <nuclide name="O-16"  ao="2.4672e-02" />
-    <nuclide name="O-17"  ao="6.0099e-05" />
-    <sab name="lwe7" xs="00t" />
-  </material>
-
-</materials>
diff --git a/examples/pincell/serpent/settings.xml b/examples/pincell/serpent/settings.xml
deleted file mode 100644
index 443af9cde2..0000000000
--- a/examples/pincell/serpent/settings.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Define how many particles to run and for how many batches -->
-  <eigenvalue>
-    <batches>100</batches>
-    <inactive>10</inactive>
-    <particles>1000</particles>
-  </eigenvalue>
-
-  <!-- The starting source is a uniform distribution over the entire pin
-       cell. Note that since this is effectively a 2D model, the z coordinates
-       are inconsequential -->
-  <source>
-    <space type="box">
-      <parameters>
-        -0.62992 -0.62992 -1.
-         0.62992  0.62992  1.
-      </parameters>
-    </space>
-  </source>
-
-  <!-- To assess convergence of the source distribution, we need to define the
-       bounds for a mesh over which the Shannon entropy should be
-       calculated. The extent in the z direction is made arbitrarily large. -->
-  <entropy>
-    <lower_left>-0.39218 -0.39218 -1.e50</lower_left>
-    <upper_right>0.39218  0.39218  1.e50</upper_right>
-    <dimension>10 10 1</dimension>
-  </entropy>
-
-</settings>
\ No newline at end of file
diff --git a/examples/pincell/serpent/tallies.xml b/examples/pincell/serpent/tallies.xml
deleted file mode 100644
index bbfd588360..0000000000
--- a/examples/pincell/serpent/tallies.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0"?>
-<tallies>
-
-  <mesh id="1" type="rectangular">
-    <dimension>100 100 1</dimension>
-    <lower_left>-0.62992 -0.62992 -1.e50</lower_left>
-    <upper_right>0.62992  0.62992  1.e50</upper_right>
-  </mesh>
-
-  <tally id="1">
-    <filter type="mesh" bins="1" />
-    <filter type="energy" bins="0. 4.e-6 20.0" />
-    <scores>flux fission nu-fission</scores>
-  </tally>
-
-</tallies>
\ No newline at end of file
diff --git a/examples/pincell/jeff/settings.xml b/examples/pincell/settings.xml
similarity index 100%
rename from examples/pincell/jeff/settings.xml
rename to examples/pincell/settings.xml
diff --git a/examples/pincell/jeff/tallies.xml b/examples/pincell/tallies.xml
similarity index 100%
rename from examples/pincell/jeff/tallies.xml
rename to examples/pincell/tallies.xml
diff --git a/examples/reflective/jeff/geometry.xml b/examples/reflective/geometry.xml
similarity index 100%
rename from examples/reflective/jeff/geometry.xml
rename to examples/reflective/geometry.xml
diff --git a/examples/reflective/jeff/materials.xml b/examples/reflective/jeff/materials.xml
deleted file mode 100644
index 538751eb6e..0000000000
--- a/examples/reflective/jeff/materials.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>31c</default_xs>
-
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-</materials>
diff --git a/examples/reflective/nndc/materials.xml b/examples/reflective/materials.xml
similarity index 100%
rename from examples/reflective/nndc/materials.xml
rename to examples/reflective/materials.xml
diff --git a/examples/reflective/mcnp/geometry.xml b/examples/reflective/mcnp/geometry.xml
deleted file mode 100644
index 664ef0705f..0000000000
--- a/examples/reflective/mcnp/geometry.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1">
-    <universe>0</universe>
-    <material>1</material>
-    <surfaces>1 -2 3 -4 5 -6</surfaces>
-  </cell>
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
-  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
-    
-</geometry>
diff --git a/examples/reflective/mcnp/materials.xml b/examples/reflective/mcnp/materials.xml
deleted file mode 100644
index 3ae574ff3e..0000000000
--- a/examples/reflective/mcnp/materials.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>70c</default_xs>
-
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-</materials>
diff --git a/examples/reflective/mcnp/settings.xml b/examples/reflective/mcnp/settings.xml
deleted file mode 100644
index 9f8cf8e959..0000000000
--- a/examples/reflective/mcnp/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>500</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/reflective/nndc/geometry.xml b/examples/reflective/nndc/geometry.xml
deleted file mode 100644
index 664ef0705f..0000000000
--- a/examples/reflective/nndc/geometry.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1">
-    <universe>0</universe>
-    <material>1</material>
-    <surfaces>1 -2 3 -4 5 -6</surfaces>
-  </cell>
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
-  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
-    
-</geometry>
diff --git a/examples/reflective/nndc/settings.xml b/examples/reflective/nndc/settings.xml
deleted file mode 100644
index 9f8cf8e959..0000000000
--- a/examples/reflective/nndc/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>500</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/reflective/serpent/geometry.xml b/examples/reflective/serpent/geometry.xml
deleted file mode 100644
index 664ef0705f..0000000000
--- a/examples/reflective/serpent/geometry.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<geometry>
-
-  <!-- Definition of Cells -->
-  <cell id="1">
-    <universe>0</universe>
-    <material>1</material>
-    <surfaces>1 -2 3 -4 5 -6</surfaces>
-  </cell>
-
-  <!-- Defition of Surfaces -->
-  <surface id="1" type="x-plane" coeffs="-1" boundary="vacuum" />
-  <surface id="2" type="x-plane" coeffs="1" boundary="vacuum" />
-  <surface id="3" type="y-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="4" type="y-plane" coeffs="1" boundary="reflective" />
-  <surface id="5" type="z-plane" coeffs="-1" boundary="reflective" /> 
-  <surface id="6" type="z-plane" coeffs="1" boundary="reflective" />
-    
-</geometry>
diff --git a/examples/reflective/serpent/materials.xml b/examples/reflective/serpent/materials.xml
deleted file mode 100644
index 036dafe254..0000000000
--- a/examples/reflective/serpent/materials.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0"?>
-<materials>
-
-  <default_xs>03c</default_xs>
-
-  <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" ao="1.0" />
-  </material>
-
-</materials>
diff --git a/examples/reflective/serpent/settings.xml b/examples/reflective/serpent/settings.xml
deleted file mode 100644
index 9f8cf8e959..0000000000
--- a/examples/reflective/serpent/settings.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<settings>
-
-  <!-- Parameters for k-eigenvalue calculation -->
-  <eigenvalue>
-    <batches>500</batches>
-    <inactive>10</inactive>
-    <particles>10000</particles>
-  </eigenvalue>
-
-  <!-- Starting source -->
-  <source>
-    <space type="box">
-      <parameters>-1 -1 -1  1  1  1</parameters>
-    </space>
-  </source>
-
-</settings>
diff --git a/examples/reflective/jeff/settings.xml b/examples/reflective/settings.xml
similarity index 100%
rename from examples/reflective/jeff/settings.xml
rename to examples/reflective/settings.xml