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diff --git a/docs/build/doctrees/beam/msgpi.ms.beam.Beam.doctree b/docs/build/doctrees/beam/msgpi.ms.beam.Beam.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/ref_manual.doctree b/docs/build/doctrees/ref_manual.doctree
diff --git a/docs/build/doctrees/user_guide.doctree b/docs/build/doctrees/user_guide.doctree
diff --git a/docs/build/doctrees/user_io_tools.doctree b/docs/build/doctrees/user_io_tools.doctree
diff --git a/docs/build/html/_sources/beam/msgpi.ms.beam.Beam.rst.txt b/docs/build/html/_sources/beam/msgpi.ms.beam.Beam.rst.txt
@@ -17,6 +17,7 @@
       ~Beam.echo
       ~Beam.findPtCoordByName
       ~Beam.findSectionByName
+      ~Beam.writeGmshMsh
 
 
 

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -3,26 +3,18 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to msgpi documentation!
-========================================
+msgpi documentation
+===================
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: Content
 
-   sg_structuregene
-   sg_materialsection
-   methods
-   beam
-   beam_methods
-   utils
+   user_guide
+   ref_manual
 
 
 
-.. sg_module
-.. ms_module
-.. utils
-
 Indices and tables
 ==================
 

diff --git a/docs/build/html/_sources/ref_manual.rst.txt b/docs/build/html/_sources/ref_manual.rst.txt
@@ -0,0 +1,13 @@
+Reference
+=========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   sg_structuregene
+   sg_materialsection
+   methods
+   beam
+   beam_methods
+   utils
diff --git a/docs/build/html/_sources/user_guide.rst.txt b/docs/build/html/_sources/user_guide.rst.txt
@@ -0,0 +1,9 @@
+User Guide
+==========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Content
+
+   user_io_tools
+
diff --git a/docs/build/html/_sources/user_io_tools.rst.txt b/docs/build/html/_sources/user_io_tools.rst.txt
@@ -0,0 +1,5 @@
+IO Tools
+========
+
+
+
diff --git a/docs/build/html/analysis/msgpi.analysis.run.html b/docs/build/html/analysis/msgpi.analysis.run.html
@@ -89,19 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../methods.html">Methods</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="../methods.html#input-output">Input/Output</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../methods.html#preprocessing">Preprocessing</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../methods.html#analysis">Analysis</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -150,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../methods.html">Methods</a> &raquo;</li>
 
       <li>msgpi.analysis.run</li>

diff --git a/docs/build/html/analysis/msgpi.analysis.solve.html b/docs/build/html/analysis/msgpi.analysis.solve.html
@@ -89,19 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../methods.html">Methods</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="../methods.html#input-output">Input/Output</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../methods.html#preprocessing">Preprocessing</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../methods.html#analysis">Analysis</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -150,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../methods.html">Methods</a> &raquo;</li>
 
       <li>msgpi.analysis.solve</li>

diff --git a/docs/build/html/beam.html b/docs/build/html/beam.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="methods.html">Methods</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">A Simple Beam Class</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#beamsegment">BeamSegment</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#beam">Beam</a></li>
+<li class="toctree-l1"><a class="reference internal" href="user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="methods.html">Methods</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">A Simple Beam Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="beam_methods.html">Beam Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="ref_manual.html">Reference</a> &raquo;</li>
+
       <li>A Simple Beam Class</li>
 
 

diff --git a/docs/build/html/beam/msgpi.ms.analysis.runGEBT.html b/docs/build/html/beam/msgpi.ms.analysis.runGEBT.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../methods.html">Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a><ul class="current">
-<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods_gebt.html">GEBT</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../beam_methods_dymore.html">Dymore</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../beam_methods.html">Beam Methods</a> &raquo;</li>
 
           <li><a href="../beam_methods_gebt.html">GEBT</a> &raquo;</li>

diff --git a/docs/build/html/beam/msgpi.ms.analysis.solveGEBT.html b/docs/build/html/beam/msgpi.ms.analysis.solveGEBT.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../methods.html">Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a><ul class="current">
-<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods_gebt.html">GEBT</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../beam_methods_dymore.html">Dymore</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../beam_methods.html">Beam Methods</a> &raquo;</li>
 
           <li><a href="../beam_methods_gebt.html">GEBT</a> &raquo;</li>

diff --git a/docs/build/html/beam/msgpi.ms.analysis.solvePLECS.html b/docs/build/html/beam/msgpi.ms.analysis.solvePLECS.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../methods.html">Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a><ul class="current">
-<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods_gebt.html">GEBT</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../beam_methods_dymore.html">Dymore</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../beam_methods.html">Beam Methods</a> &raquo;</li>
 
           <li><a href="../beam_methods_gebt.html">GEBT</a> &raquo;</li>

diff --git a/docs/build/html/beam/msgpi.ms.beam.Beam.analysis_type.html b/docs/build/html/beam/msgpi.ms.beam.Beam.analysis_type.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../methods.html">Methods</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../beam.html">A Simple Beam Class</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="../beam.html#beamsegment">BeamSegment</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../beam.html#beam">Beam</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../beam.html">A Simple Beam Class</a> &raquo;</li>
 
       <li>msgpi.ms.beam.Beam.analysis_type</li>

diff --git a/docs/build/html/beam/msgpi.ms.beam.Beam.angular_velocity.html b/docs/build/html/beam/msgpi.ms.beam.Beam.angular_velocity.html
@@ -89,18 +89,18 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">Content</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../methods.html">Methods</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../beam.html">A Simple Beam Class</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="../beam.html#beamsegment">BeamSegment</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../beam.html#beam">Beam</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide.html">User Guide</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../ref_manual.html">Reference</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../sg_structuregene.html">StructureGene</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sg_materialsection.html">MaterialSection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../methods.html">Methods</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../beam.html">A Simple Beam Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="../beam_methods.html">Beam Methods</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../utils.html">Utility Functions</a></li>
 </ul>
 
 
@@ -149,6 +149,8 @@
 
       <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
 
+          <li><a href="../ref_manual.html">Reference</a> &raquo;</li>
+
           <li><a href="../beam.html">A Simple Beam Class</a> &raquo;</li>
 
       <li>msgpi.ms.beam.Beam.angular_velocity</li>