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diff --git a/_build/html/_modules/arbdmodel/coords.html b/_build/html/_modules/arbdmodel/coords.html
index 66cd0352cc270bcdc08eb42f83f970620984b258..798a983841ffe813f32456df4faf8a0e8bf0513b 100644
--- a/_build/html/_modules/arbdmodel/coords.html
+++ b/_build/html/_modules/arbdmodel/coords.html
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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     <script>let toggleHintHide = 'Click to hide';</script>
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index 0e96a9ba36d38fcecf61cf023a801c5eeea2c957..d6ee79f69a2270a038e340148eb6ee7c874a8cd4 100644
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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diff --git a/_build/html/_modules/arbdmodel/grid.html b/_build/html/_modules/arbdmodel/grid.html
index 2b14aafa4a05033331261939a88d7f5ebfc97523..5062c1aab2738ce553a2bf8965859fa9a815f0eb 100644
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/html/_modules/arbdmodel/ibi.html b/_build/html/_modules/arbdmodel/ibi.html
index 28cd332671391c0f8851e477ed36415916daaf69..09a420f5565fe32fb32d5efc9e8853dc68a90d0a 100644
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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/html/_modules/arbdmodel/interactions.html b/_build/html/_modules/arbdmodel/interactions.html
index 402a72b9784f64af838122b4a770e7e99324ec8f..11fefccfbb966ebb9f10f09a151d6e4520854517 100644
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-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -60,9 +60,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -317,7 +317,6 @@ document.write(`
 <span class="sd">    Abstract base class for implementing interaction potentials.</span>
 <span class="sd">    This class defines the basic structure for creating and managing interaction potential</span>
 <span class="sd">    functions that can be written to files and used in simulations.</span>
-
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    range_ : tuple of (float, float or None)</span>
@@ -335,9 +334,20 @@ document.write(`
 <span class="sd">        - &#39;min&#39;: Zero is at the minimum value</span>
 <span class="sd">        - &#39;first&#39;: Zero is at the first point</span>
 <span class="sd">        - &#39;last&#39;: Zero is at the last point</span>
+<span class="sd">    Attributes</span>
+<span class="sd">    ----------</span>
+<span class="sd">    range_ : tuple of (float, float or None)</span>
+<span class="sd">        The range of distances for the potential.</span>
+<span class="sd">    resolution : float</span>
+<span class="sd">        The spacing between points in the discretized potential.</span>
+<span class="sd">    max_force : float or None</span>
+<span class="sd">        Maximum allowed force magnitude.</span>
+<span class="sd">    max_potential : float or None</span>
+<span class="sd">        Maximum allowed potential energy.</span>
+<span class="sd">    zero : str</span>
+<span class="sd">        Method to set the zero of the potential.</span>
 <span class="sd">    periodic : bool</span>
 <span class="sd">        Whether the potential is periodic (False by default).</span>
-
 <span class="sd">    Methods</span>
 <span class="sd">    -------</span>
 <span class="sd">    potential(r, types=None)</span>
@@ -348,11 +358,11 @@ document.write(`
 <span class="sd">    filename(types=None)</span>
 <span class="sd">        Abstract method that should be implemented by subclasses.</span>
 <span class="sd">        Returns a filename for the potential.</span>
-
 <span class="sd">    Notes</span>
 <span class="sd">    -----</span>
 <span class="sd">    Subclasses must implement at minimum the `potential` and `filename` methods.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot; Abstract class for writing potentials &quot;&quot;&quot;</span>
 
     <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">range_</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="kc">None</span><span class="p">),</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> 
                  <span class="n">max_force</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">max_potential</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">zero</span><span class="o">=</span><span class="s1">&#39;last&#39;</span><span class="p">):</span>
@@ -477,37 +487,6 @@ document.write(`
 <div class="viewcode-block" id="LennardJones">
 <a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.LennardJones">[docs]</a>
 <span class="k">class</span><span class="w"> </span><span class="nc">LennardJones</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Lennard-Jones potential implementation.</span>
-
-<span class="sd">    This class implements the Lennard-Jones potential energy function:</span>
-<span class="sd">    U(r) = 4ε[(σ/r)^12 - (σ/r)^6]</span>
-
-<span class="sd">    where:</span>
-<span class="sd">    - ε (epsilon) is the depth of the potential well, calculated as the geometric mean </span>
-<span class="sd">        of the epsilon values of the two interacting particles</span>
-<span class="sd">    - σ (r0) is the distance at which the potential is zero, calculated as the average</span>
-<span class="sd">        of the radii of the two interacting particles</span>
-<span class="sd">    - r is the distance between particles in angstroms</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    r : numpy.ndarray</span>
-<span class="sd">            Distances between particles</span>
-<span class="sd">    types : tuple</span>
-<span class="sd">            Tuple containing two particle type objects (typeA, typeB), each with epsilon and</span>
-<span class="sd">            radius attributes</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">    -------</span>
-<span class="sd">    numpy.ndarray</span>
-<span class="sd">            Potential energy values for the given distances</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    -----</span>
-<span class="sd">    The function implements the standard form of the Lennard-Jones potential for pairwise</span>
-<span class="sd">    particle interactions.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
 <div class="viewcode-block" id="LennardJones.potential">
 <a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.LennardJones.potential">[docs]</a>
     <span class="k">def</span><span class="w"> </span><span class="nf">potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">types</span><span class="p">):</span>
diff --git a/_build/html/_modules/arbdmodel/kh_polymer_model.html b/_build/html/_modules/arbdmodel/kh_polymer_model.html
index 36a120ecce365f1edc66d4b94f0830b88e79ce81..d2036683648a90ed442cadc9720b9d5eb754088c 100644
--- a/_build/html/_modules/arbdmodel/kh_polymer_model.html
+++ b/_build/html/_modules/arbdmodel/kh_polymer_model.html
@@ -31,19 +31,19 @@
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
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     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/_modules/arbdmodel/logger.html b/_build/html/_modules/arbdmodel/logger.html
index 11b7b3f2c6dbe1140571b52fb072064b76d8e1c4..f75f469f82f3456df6dace30d28470996dc94502 100644
--- a/_build/html/_modules/arbdmodel/logger.html
+++ b/_build/html/_modules/arbdmodel/logger.html
@@ -31,19 +31,19 @@
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/_modules/arbdmodel/mesh_process_surface.html b/_build/html/_modules/arbdmodel/mesh_process_surface.html
index e78aac8c3b10d0258805ccf2f5f8dc33a1efe392..82b7cfa934cc0049d9a7fa4f71d272dd8c0b5eed 100644
--- a/_build/html/_modules/arbdmodel/mesh_process_surface.html
+++ b/_build/html/_modules/arbdmodel/mesh_process_surface.html
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/html/_modules/arbdmodel/mesh_rigidbody.html b/_build/html/_modules/arbdmodel/mesh_rigidbody.html
index 3646e22af78f285a3c1e89ebcd21a66add731327..3b3cb20f8aacbb54aad5e8de8e2b4f00684a02d3 100644
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-    <script src="../../_static/js/micromodal.min.js"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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diff --git a/_build/html/_modules/arbdmodel/model.html b/_build/html/_modules/arbdmodel/model.html
index cebae80423bcabc55acefc141307ba10548d707c..6e89ccb5434c29f023dbe42d7522dc9e3947926e 100644
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
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+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
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+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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+    <script src="../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
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diff --git a/_build/html/api/core/index.html b/_build/html/api/core/index.html
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diff --git a/_build/html/api/core/model.html b/_build/html/api/core/model.html
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diff --git a/_build/html/api/core/sim_config.html b/_build/html/api/core/sim_config.html
index e59f52b87aaedff3f0672413226c67d12a96324f..744c946af50de4b8f313e12ef1cc401099bff1f7 100644
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-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
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@@ -347,46 +347,15 @@ document.write(`
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_steps"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_steps</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.output_period"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.output_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.pressure"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.pressure</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.viscosity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.solvent_density</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_heavy_cluster</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.Properties"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.Properties</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.temperature"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf"><code class="docutils literal notranslate"><span class="pre">SimConf</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_steps"><code class="docutils literal notranslate"><span class="pre">SimConf.num_steps</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.output_period"><code class="docutils literal notranslate"><span class="pre">SimConf.output_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.integrator</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.timestep"><code class="docutils literal notranslate"><span class="pre">SimConf.timestep</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.thermostat"><code class="docutils literal notranslate"><span class="pre">SimConf.thermostat</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.barostat"><code class="docutils literal notranslate"><span class="pre">SimConf.barostat</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pressure"><code class="docutils literal notranslate"><span class="pre">SimConf.pressure</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.cutoff"><code class="docutils literal notranslate"><span class="pre">SimConf.cutoff</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pairlist_distance"><code class="docutils literal notranslate"><span class="pre">SimConf.pairlist_distance</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.decomp_period"><code class="docutils literal notranslate"><span class="pre">SimConf.decomp_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.gpu"><code class="docutils literal notranslate"><span class="pre">SimConf.gpu</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.seed"><code class="docutils literal notranslate"><span class="pre">SimConf.seed</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.restart_file"><code class="docutils literal notranslate"><span class="pre">SimConf.restart_file</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_integrator</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_grid_grid_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">SimConf.viscosity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">SimConf.solvent_density</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">SimConf.num_heavy_cluster</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -410,127 +379,10 @@ classes for configuring simulation parameters.</p>
 <dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DefaultSimConf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'MD'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thermostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Langevin'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">barostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">295</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pairlist_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decomp_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">40</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viscosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solvent_density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_heavy_cluster</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#DefaultSimConf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="reference internal" href="#arbdmodel.sim_config.SimConf" title="arbdmodel.sim_config.SimConf"><code class="xref py py-class docutils literal notranslate"><span class="pre">SimConf</span></code></a></p>
-<p>Generic class describing properties for a simulation with default binary paths.
-This class extends SimConf to provide default binary paths and configuration parameters
-for molecular dynamics simulations using ARBD.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>num_steps</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Number of simulation steps to run, default 1e5.</p></li>
-<li><p><strong>output_period</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Period for output generation, default 1e3.</p></li>
-<li><p><strong>integrator</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em>, </em><em>optional</em>) – Integration method, default ‘MD’.</p></li>
-<li><p><strong>timestep</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Simulation timestep in ns, default 20e-6.</p></li>
-<li><p><strong>thermostat</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em>, </em><em>optional</em>) – Thermostat type, default ‘Langevin’.</p></li>
-<li><p><strong>barostat</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Barostat type if any, default None.</p></li>
-<li><p><strong>temperature</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Simulation temperature in K, default 295.</p></li>
-<li><p><strong>pressure</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Pressure value for barostat if used, default 1.</p></li>
-<li><p><strong>cutoff</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Interaction cutoff distance, default 50.</p></li>
-<li><p><strong>pairlist_distance</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Pairlist buffer distance, default None.</p></li>
-<li><p><strong>decomp_period</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – Period for domain decomposition updates, default 40.</p></li>
-<li><p><strong>seed</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Random seed for simulation, default None (random).</p></li>
-<li><p><strong>restart_file</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Path to restart file if continuing a simulation, default None.</p></li>
-<li><p><strong>gpu</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – GPU device index to use, default 0.</p></li>
-<li><p><strong>viscosity</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Solvent viscosity, default 0.01.</p></li>
-<li><p><strong>solvent_density</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Density of the solvent, default 1.0.</p></li>
-<li><p><strong>num_heavy_cluster</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – Number of heavy atoms per cluster, default 3.</p></li>
-<li><p><strong>**kwargs</strong> – Additional keyword arguments to pass to SimConf.</p></li>
-</ul>
-</dd>
-</dl>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.num_steps">
-<span class="sig-name descname"><span class="pre">num_steps</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.num_steps" title="Link to this definition">#</a></dt>
-<dd><p>Number of simulation steps.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.output_period">
-<span class="sig-name descname"><span class="pre">output_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.output_period" title="Link to this definition">#</a></dt>
-<dd><p>Period for output generation.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.pressure">
-<span class="sig-name descname"><span class="pre">pressure</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.pressure" title="Link to this definition">#</a></dt>
-<dd><p>Pressure value for barostat if used.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.viscosity">
-<span class="sig-name descname"><span class="pre">viscosity</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.viscosity" title="Link to this definition">#</a></dt>
-<dd><p>Solvent viscosity.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.solvent_density">
-<span class="sig-name descname"><span class="pre">solvent_density</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density" title="Link to this definition">#</a></dt>
-<dd><p>Density of the solvent.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster">
-<span class="sig-name descname"><span class="pre">num_heavy_cluster</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster" title="Link to this definition">#</a></dt>
-<dd><p>Number of heavy atoms per cluster.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.Properties">
-<span class="sig-name descname"><span class="pre">Properties</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.Properties" title="Link to this definition">#</a></dt>
-<dd></dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py">
-<span class="sig-name descname"><span class="pre">----------</span></span></dt>
-<dd></dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.temperature">
-<span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.temperature" title="Link to this definition">#</a></dt>
-<dd><p>Simulation temperature with validation (must be positive).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<p class="rubric">Notes</p>
-<p>The class automatically searches for binary dependencies like ‘arbd’, ‘hydropro’, ‘apbs’,
-‘vmd’, and ‘namd’, and adds their paths to the configuration if found.
-Essential binaries (currently only ‘arbd’) will generate warnings if not found.</p>
+<p>Generic class describing properties for a simulation with default binary paths</p>
 <dl class="py property">
-<dt class="sig sig-object py" id="id0">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.temperature" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -539,263 +391,18 @@ Essential binaries (currently only ‘arbd’) will generate warnings if not fou
 <dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimConf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thermostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">barostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pairlist_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decomp_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rigid_body_integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rigid_body_grid_grid_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viscosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solvent_density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_heavy_cluster</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">arbd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">namd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hydropro_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmsh_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
-<p>Class describing properties for a simulation (ARBD or NAMD).
-This class stores various simulation parameters, manages binary paths, and provides
-methods to combine simulation configurations.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.num_steps">
-<span class="sig-name descname"><span class="pre">num_steps</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.num_steps" title="Link to this definition">#</a></dt>
-<dd><p>Total number of simulation steps.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.output_period">
-<span class="sig-name descname"><span class="pre">output_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.output_period" title="Link to this definition">#</a></dt>
-<dd><p>Frequency of output generation.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.integrator">
-<span class="sig-name descname"><span class="pre">integrator</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.integrator" title="Link to this definition">#</a></dt>
-<dd><p>Type of integrator used (e.g., ‘MD’, ‘BD’).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.timestep">
-<span class="sig-name descname"><span class="pre">timestep</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.timestep" title="Link to this definition">#</a></dt>
-<dd><p>Simulation time step.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.thermostat">
-<span class="sig-name descname"><span class="pre">thermostat</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.thermostat" title="Link to this definition">#</a></dt>
-<dd><p>Type of thermostat used.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.barostat">
-<span class="sig-name descname"><span class="pre">barostat</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.barostat" title="Link to this definition">#</a></dt>
-<dd><p>Type of barostat used.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.temperature">
-<span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.temperature" title="Link to this definition">#</a></dt>
-<dd><p>Simulation temperature (must be positive).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.pressure">
-<span class="sig-name descname"><span class="pre">pressure</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.pressure" title="Link to this definition">#</a></dt>
-<dd><p>Simulation pressure.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.cutoff">
-<span class="sig-name descname"><span class="pre">cutoff</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.cutoff" title="Link to this definition">#</a></dt>
-<dd><p>Cutoff distance for interactions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.pairlist_distance">
-<span class="sig-name descname"><span class="pre">pairlist_distance</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.pairlist_distance" title="Link to this definition">#</a></dt>
-<dd><p>Distance for generating pair lists.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.decomp_period">
-<span class="sig-name descname"><span class="pre">decomp_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.decomp_period" title="Link to this definition">#</a></dt>
-<dd><p>Period for decomposition.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.gpu">
-<span class="sig-name descname"><span class="pre">gpu</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.gpu" title="Link to this definition">#</a></dt>
-<dd><p>Whether to use GPU acceleration.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)">bool</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.seed">
-<span class="sig-name descname"><span class="pre">seed</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.seed" title="Link to this definition">#</a></dt>
-<dd><p>Random seed for reproducibility.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.restart_file">
-<span class="sig-name descname"><span class="pre">restart_file</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.restart_file" title="Link to this definition">#</a></dt>
-<dd><p>Path to restart file.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py">
-<span class="sig-name descname"><span class="pre">#</span> <span class="pre">ARBD-specific</span> <span class="pre">parameters</span></span></dt>
-<dd></dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.rigid_body_integrator">
-<span class="sig-name descname"><span class="pre">rigid_body_integrator</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator" title="Link to this definition">#</a></dt>
-<dd><p>Type of rigid body integrator.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period">
-<span class="sig-name descname"><span class="pre">rigid_body_grid_grid_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period" title="Link to this definition">#</a></dt>
-<dd><p>Period for rigid body grid updates.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py">
-<span class="sig-name descname"><span class="pre">#</span> <span class="pre">SimpleARBD</span> <span class="pre">parameters</span></span></dt>
-<dd></dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.viscosity">
-<span class="sig-name descname"><span class="pre">viscosity</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.viscosity" title="Link to this definition">#</a></dt>
-<dd><p>Solvent viscosity.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.solvent_density">
-<span class="sig-name descname"><span class="pre">solvent_density</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.solvent_density" title="Link to this definition">#</a></dt>
-<dd><p>Solvent density. in g/cm^3</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.num_heavy_cluster">
-<span class="sig-name descname"><span class="pre">num_heavy_cluster</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster" title="Link to this definition">#</a></dt>
-<dd><p>Number of heavy clusters.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.get_binary">
-<span class="sig-name descname"><span class="pre">get_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.get_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.get_binary" title="Link to this definition">#</a></dt>
-<dd><p>Get the path to a specific binary.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.set_binary">
-<span class="sig-name descname"><span class="pre">set_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.set_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.set_binary" title="Link to this definition">#</a></dt>
-<dd><p>Set the path to a specific binary.</p>
-</dd></dl>
-
+<p>Class describing properties for a (ARBD or NAMD) simulation</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.combine">
 <span class="sig-name descname"><span class="pre">combine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">policy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'override'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.combine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.combine" title="Link to this definition">#</a></dt>
-<dd><p>Combine two SimConf objects.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.items">
-<span class="sig-name descname"><span class="pre">items</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.items"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.items" title="Link to this definition">#</a></dt>
-<dd><p>Iterate over attribute name-value pairs.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="id1">
-<span class="sig-name descname"><span class="pre">combine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">policy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'override'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.combine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt>
 <dd><p>Creates a new SimConf object whose properties are
 initialized to be from “self”, but are overridden with
 properties in “other”, provided they are not None</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id2">
-<span class="sig-name descname"><span class="pre">get_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.get_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.get_binary">
+<span class="sig-name descname"><span class="pre">get_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.get_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.get_binary" title="Link to this definition">#</a></dt>
 <dd><p>Get the path to a specific binary with improved error handling.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -810,19 +417,19 @@ for graceful handling of missing optional dependencies.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id3">
-<span class="sig-name descname"><span class="pre">items</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.items"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id3" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.items">
+<span class="sig-name descname"><span class="pre">items</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.items"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.items" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id4">
-<span class="sig-name descname"><span class="pre">set_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.set_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id4" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.set_binary">
+<span class="sig-name descname"><span class="pre">set_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.set_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.set_binary" title="Link to this definition">#</a></dt>
 <dd><p>Set the path to a specific binary.</p>
 </dd></dl>
 
 <dl class="py property">
-<dt class="sig sig-object py" id="id5">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#id5" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.temperature" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -876,46 +483,15 @@ for graceful handling of missing optional dependencies.</p>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_steps"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_steps</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.output_period"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.output_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.pressure"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.pressure</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.viscosity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.solvent_density</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_heavy_cluster</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.Properties"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.Properties</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.temperature"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf"><code class="docutils literal notranslate"><span class="pre">SimConf</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_steps"><code class="docutils literal notranslate"><span class="pre">SimConf.num_steps</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.output_period"><code class="docutils literal notranslate"><span class="pre">SimConf.output_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.integrator</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.timestep"><code class="docutils literal notranslate"><span class="pre">SimConf.timestep</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.thermostat"><code class="docutils literal notranslate"><span class="pre">SimConf.thermostat</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.barostat"><code class="docutils literal notranslate"><span class="pre">SimConf.barostat</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
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-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.cutoff"><code class="docutils literal notranslate"><span class="pre">SimConf.cutoff</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pairlist_distance"><code class="docutils literal notranslate"><span class="pre">SimConf.pairlist_distance</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.decomp_period"><code class="docutils literal notranslate"><span class="pre">SimConf.decomp_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.gpu"><code class="docutils literal notranslate"><span class="pre">SimConf.gpu</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.seed"><code class="docutils literal notranslate"><span class="pre">SimConf.seed</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.restart_file"><code class="docutils literal notranslate"><span class="pre">SimConf.restart_file</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_integrator</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_grid_grid_period</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">SimConf.viscosity</span></code></a></li>
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-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">SimConf.num_heavy_cluster</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
 </ul>
 </li>
 </ul>
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-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -347,14 +347,20 @@ document.write(`
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.resolution"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.resolution</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_force"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_force</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_potential</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.zero"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.zero</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential</span></code></a><ul class="nav section-nav flex-column">
@@ -443,12 +449,14 @@ document.write(`
 <dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>Abstract base class for implementing interaction potentials.
 This class defines the basic structure for creating and managing interaction potential
-functions that can be written to files and used in simulations.</p>
+functions that can be written to files and used in simulations.
+:param <a href="#id1"><span class="problematic" id="id2">range_</span></a>: The range of distances for the potential (min, max).</p>
+<blockquote>
+<div><p>If max is None, potential extends to infinity.</p>
+</div></blockquote>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>range</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a><em> of </em><em>(</em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>)</em>) – The range of distances for the potential (min, max).
-If max is None, potential extends to infinity.</p></li>
 <li><p><strong>resolution</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The spacing between points in the discretized potential. Default is 0.1.</p></li>
 <li><p><strong>max_force</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Maximum allowed force magnitude. If provided, forces exceeding this value will be capped.</p></li>
 <li><p><strong>max_potential</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Maximum allowed potential energy. If provided, the potential will be modified
@@ -457,10 +465,75 @@ to ensure it doesn’t exceed this value.</p></li>
 - ‘min’: Zero is at the minimum value
 - ‘first’: Zero is at the first point
 - ‘last’: Zero is at the last point</p></li>
-<li><p><strong>periodic</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Whether the potential is periodic (False by default).</p></li>
 </ul>
 </dd>
 </dl>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.range_">
+<span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.range_" title="Link to this definition">#</a></dt>
+<dd><p>The range of distances for the potential.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)">tuple</a> of (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a>, <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.resolution">
+<span class="sig-name descname"><span class="pre">resolution</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.resolution" title="Link to this definition">#</a></dt>
+<dd><p>The spacing between points in the discretized potential.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.max_force">
+<span class="sig-name descname"><span class="pre">max_force</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.max_force" title="Link to this definition">#</a></dt>
+<dd><p>Maximum allowed force magnitude.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.max_potential">
+<span class="sig-name descname"><span class="pre">max_potential</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.max_potential" title="Link to this definition">#</a></dt>
+<dd><p>Maximum allowed potential energy.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.zero">
+<span class="sig-name descname"><span class="pre">zero</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.zero" title="Link to this definition">#</a></dt>
+<dd><p>Method to set the zero of the potential.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.periodic">
+<span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.periodic" title="Link to this definition">#</a></dt>
+<dd><p>Whether the potential is periodic (False by default).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)">bool</a></p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.potential">
 <span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.potential" title="Link to this definition">#</a></dt>
@@ -489,23 +562,23 @@ Returns a filename for the potential.</p>
 <dd></dd></dl>
 
 <dl class="py property">
-<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.periodic">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.periodic" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="id1">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id1">
-<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="id2">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py property">
-<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.range_">
-<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.range_" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="id3">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#id3" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id2">
-<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#AbstractPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="id4">
+<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#AbstractPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id4" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -646,40 +719,6 @@ for consistency with the AbstractPotential interface.</p>
 <dt class="sig sig-object py" id="arbdmodel.interactions.LennardJones">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LennardJones</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">range_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">None)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_potential</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zero</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'last'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#LennardJones"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.LennardJones" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="reference internal" href="#arbdmodel.interactions.AbstractPotential" title="arbdmodel.interactions.AbstractPotential"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a></p>
-<p>Lennard-Jones potential implementation.</p>
-<p>This class implements the Lennard-Jones potential energy function:
-U(r) = 4ε[(σ/r)^12 - (σ/r)^6]</p>
-<p>where:
-- ε (epsilon) is the depth of the potential well, calculated as the geometric mean</p>
-<blockquote>
-<div><p>of the epsilon values of the two interacting particles</p>
-</div></blockquote>
-<ul class="simple">
-<li><dl class="simple">
-<dt>σ (r0) is the distance at which the potential is zero, calculated as the average</dt><dd><p>of the radii of the two interacting particles</p>
-</dd>
-</dl>
-</li>
-<li><p>r is the distance between particles in angstroms</p></li>
-</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>r</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – Distances between particles</p></li>
-<li><p><strong>types</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a>) – Tuple containing two particle type objects (typeA, typeB), each with epsilon and
-radius attributes</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>Potential energy values for the given distances</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)">numpy.ndarray</a></p>
-</dd>
-</dl>
-<p class="rubric">Notes</p>
-<p>The function implements the standard form of the Lennard-Jones potential for pairwise
-particle interactions.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.interactions.LennardJones.potential">
 <span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#LennardJones.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.LennardJones.potential" title="Link to this definition">#</a></dt>
@@ -814,14 +853,20 @@ particle interactions.</p>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.resolution"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.resolution</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_force"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_force</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_potential</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.zero"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.zero</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential</span></code></a><ul class="nav section-nav flex-column">
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index 8babd4b9dd5d1df29c6510559c0ea606bb7b501b..64a5b45512e8fc57f5690e8a14876faf2e8a8c0f 100644
--- a/_build/html/api/polymer_modeling/fjc_polymer_model.html
+++ b/_build/html/api/polymer_modeling/fjc_polymer_model.html
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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index 5f13b6fd7d98625a9b64da9c39476bb81e4a0999..8b1e2842379dc66b94d65b2501673ffb0bf94366 100644
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/html/api/polymer_modeling/index.html b/_build/html/api/polymer_modeling/index.html
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+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/onck_polymer_model.html b/_build/html/api/polymer_modeling/onck_polymer_model.html
index b95148bcda67979906b92126675252a4fe39568e..c651531d7bd453cbdec2b018f6174643f67e415c 100644
--- a/_build/html/api/polymer_modeling/onck_polymer_model.html
+++ b/_build/html/api/polymer_modeling/onck_polymer_model.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/polymer.html b/_build/html/api/polymer_modeling/polymer.html
index a1e9504fbd6c412a36e9201e3b5e9d05dd189b68..3c00dc073280c440ff894ff1fa43a90b20414af3 100644
--- a/_build/html/api/polymer_modeling/polymer.html
+++ b/_build/html/api/polymer_modeling/polymer.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -347,15 +347,9 @@ document.write(`
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement"><code class="docutils literal notranslate"><span class="pre">ConnectableElement</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.locations</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.connection_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.connection_locations</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.connections"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.connections</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_location_at"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_location_at"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.Connection"><code class="docutils literal notranslate"><span class="pre">Connection</span></code></a><ul class="nav section-nav flex-column">
@@ -393,45 +387,21 @@ document.write(`
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection"><code class="docutils literal notranslate"><span class="pre">PolymerSection</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.segname"><code class="docutils literal notranslate"><span class="pre">PolymerSection.segname</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.num_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.num_monomers</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_length"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_length</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.start_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.start_position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.end_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.end_position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.start_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.start_orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.position_spline_params"><code class="docutils literal notranslate"><span class="pre">PolymerSection.position_spline_params</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.quaternion_spline_params"><code class="docutils literal notranslate"><span class="pre">PolymerSection.quaternion_spline_params</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.sequence"><code class="docutils literal notranslate"><span class="pre">PolymerSection.sequence</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_center"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.insert_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.remove_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.translate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.rotate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.add_location"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_monomer_index"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_monomer_index()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_position()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_tangent"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_tangent()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_center"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_contour_sorted_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.add_location"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.insert_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">PolymerSection.iterate_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_monomer_index()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_tangent()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id8"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id9"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_contour_sorted_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id10"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id11"><code class="docutils literal notranslate"><span class="pre">PolymerSection.iterate_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id12"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id13"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id14"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id15"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id16"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id17"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.remove_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.rotate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.translate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -452,81 +422,22 @@ document.write(`
 <dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ConnectableElement</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">connection_locations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">connections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
-<p>ConnectableElement is an abstract base class that represents an object that can be connected to other objects.
-This class provides functionality for managing connections between objects, where connections are typically made between ‘Location’ objects that are associated with the ConnectableElement.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.locations">
-<span class="sig-name descname"><span class="pre">locations</span></span><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.locations" title="Link to this definition">#</a></dt>
-<dd><p>A list of Location objects associated with this element. Alias for connection_locations.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)">list</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.connection_locations">
-<span class="sig-name descname"><span class="pre">connection_locations</span></span><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.connection_locations" title="Link to this definition">#</a></dt>
-<dd><p>A list of Location objects associated with this element.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)">list</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.connections">
-<span class="sig-name descname"><span class="pre">connections</span></span><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.connections" title="Link to this definition">#</a></dt>
-<dd><p>A list of Connection objects that this element is a part of.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)">list</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.get_locations">
-<span class="sig-name descname"><span class="pre">get_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.get_locations" title="Link to this definition">#</a></dt>
-<dd><p>Returns locations of a specified type, excluding certain types.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.get_location_at">
-<span class="sig-name descname"><span class="pre">get_location_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contour_position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_fwd_strand</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'crossover'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_location_at"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.get_location_at" title="Link to this definition">#</a></dt>
-<dd><p>Returns a location at a specific contour position and strand orientation,
-creating one if necessary.</p>
-</dd></dl>
-
+<p>Abstract base class</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.get_connections_and_locations">
 <span class="sig-name descname"><span class="pre">get_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">connection_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.get_connections_and_locations" title="Link to this definition">#</a></dt>
-<dd><p>Returns a list of [connection, location_in_self, location_in_other] for each connection.</p>
-</dd></dl>
-
-<p class="rubric">Notes</p>
-<ul class="simple">
-<li><p>The class is designed to be subclassed.</p></li>
-<li><p>It appears to be part of a system for modeling polymer structures, possibly DNA origami or similar structures.</p></li>
-<li><p>The class enforces that objects cannot be connected to themselves directly.</p></li>
-</ul>
-<dl class="py method">
-<dt class="sig sig-object py" id="id0">
-<span class="sig-name descname"><span class="pre">get_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">connection_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt>
 <dd><p>Returns a list with each entry of the form:
 connection, location_in_self, location_in_other</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id1">
-<span class="sig-name descname"><span class="pre">get_location_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contour_position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_fwd_strand</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'crossover'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_location_at"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.get_location_at">
+<span class="sig-name descname"><span class="pre">get_location_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contour_position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_fwd_strand</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'crossover'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_location_at"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.get_location_at" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id2">
-<span class="sig-name descname"><span class="pre">get_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.ConnectableElement.get_locations">
+<span class="sig-name descname"><span class="pre">get_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#ConnectableElement.get_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.ConnectableElement.get_locations" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -664,253 +575,45 @@ connection, location_in_self, location_in_other</p>
 <dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PolymerSection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_monomers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">monomer_length</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_position</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end_position</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="reference internal" href="#arbdmodel.polymer.ConnectableElement" title="arbdmodel.polymer.ConnectableElement"><code class="xref py py-class docutils literal notranslate"><span class="pre">ConnectableElement</span></code></a></p>
-<p>Base class that describes a linear section of a polymer.
-A PolymerSection represents a continuous section of a polymer, defined by the number of monomers
-and their spatial properties. It handles spatial transformations, contour-to-position mapping,
-and manages connections to other polymer elements.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.segname">
-<span class="sig-name descname"><span class="pre">segname</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.segname" title="Link to this definition">#</a></dt>
-<dd><p>Name of the polymer section.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.num_monomers">
-<span class="sig-name descname"><span class="pre">num_monomers</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.num_monomers" title="Link to this definition">#</a></dt>
-<dd><p>Number of monomers in this polymer section.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.monomer_length">
-<span class="sig-name descname"><span class="pre">monomer_length</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.monomer_length" title="Link to this definition">#</a></dt>
-<dd><p>Length of each monomer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.start_position">
-<span class="sig-name descname"><span class="pre">start_position</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.start_position" title="Link to this definition">#</a></dt>
-<dd><p>3D coordinates of the section’s starting point.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>ndarray</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.end_position">
-<span class="sig-name descname"><span class="pre">end_position</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.end_position" title="Link to this definition">#</a></dt>
-<dd><p>3D coordinates of the section’s ending point.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>ndarray</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.start_orientation">
-<span class="sig-name descname"><span class="pre">start_orientation</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.start_orientation" title="Link to this definition">#</a></dt>
-<dd><p>Initial orientation matrix.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>ndarray, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.position_spline_params">
-<span class="sig-name descname"><span class="pre">position_spline_params</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.position_spline_params" title="Link to this definition">#</a></dt>
-<dd><p>Spline parameters for position interpolation.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)">tuple</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.quaternion_spline_params">
-<span class="sig-name descname"><span class="pre">quaternion_spline_params</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.quaternion_spline_params" title="Link to this definition">#</a></dt>
-<dd><p>Spline parameters for orientation interpolation.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)">tuple</a>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.sequence">
-<span class="sig-name descname"><span class="pre">sequence</span></span><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.sequence" title="Link to this definition">#</a></dt>
-<dd><p>Sequence of monomers if applicable.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)">list</a>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.set_splines">
-<span class="sig-name descname"><span class="pre">set_splines</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.set_splines" title="Link to this definition">#</a></dt>
-<dd><p>Define position splines from contours and coordinates.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.set_orientation_splines">
-<span class="sig-name descname"><span class="pre">set_orientation_splines</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_orientation_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines" title="Link to this definition">#</a></dt>
-<dd><p>Define orientation splines from contours and quaternions.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.get_center">
-<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.get_center" title="Link to this definition">#</a></dt>
-<dd><p>Get the center point of the polymer section.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.insert_monomers">
-<span class="sig-name descname"><span class="pre">insert_monomers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.insert_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.insert_monomers" title="Link to this definition">#</a></dt>
-<dd><p>Insert monomers at a specified position.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>at_monomer</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>)</p></li>
-<li><p><strong>num_monomer</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>)</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.remove_monomers">
-<span class="sig-name descname"><span class="pre">remove_monomers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.remove_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.remove_monomers" title="Link to this definition">#</a></dt>
-<dd><p>Remove a range of monomers from the section.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>first_monomer</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>)</p></li>
-<li><p><strong>last_monomer</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>)</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.translate">
-<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.translate" title="Link to this definition">#</a></dt>
-<dd><p>Apply a translation to the polymer section, with optional filtering.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.rotate">
-<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.rotate" title="Link to this definition">#</a></dt>
-<dd><p>Apply a rotation to the polymer section, with optional filtering.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_monomer_index">
-<span class="sig-name descname"><span class="pre">contour_to_monomer_index</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_monomer_index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_monomer_index" title="Link to this definition">#</a></dt>
-<dd><p>Convert contour position to monomer index.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.monomer_index_to_contour">
-<span class="sig-name descname"><span class="pre">monomer_index_to_contour</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.monomer_index_to_contour"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour" title="Link to this definition">#</a></dt>
-<dd><p>Convert monomer index to contour position.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_position">
-<span class="sig-name descname"><span class="pre">contour_to_position</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_position" title="Link to this definition">#</a></dt>
-<dd><p>Get 3D position from contour parameter.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_tangent">
-<span class="sig-name descname"><span class="pre">contour_to_tangent</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_tangent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_tangent" title="Link to this definition">#</a></dt>
-<dd><p>Get tangent vector at contour position.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_orientation">
-<span class="sig-name descname"><span class="pre">contour_to_orientation</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_orientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation" title="Link to this definition">#</a></dt>
-<dd><p>Get orientation matrix at contour position.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">
-<span class="sig-name descname"><span class="pre">get_contour_sorted_connections_and_locations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_contour_sorted_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations" title="Link to this definition">#</a></dt>
-<dd><p>Get sorted connections and locations by type.</p>
-</dd></dl>
-
+<p>Base class that describes a linear section of a polymer</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.add_location">
-<span class="sig-name descname"><span class="pre">add_location</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.add_location"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.add_location" title="Link to this definition">#</a></dt>
-<dd><p>Add a new location at a specific monomer position.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.iterate_connections_and_locations">
-<span class="sig-name descname"><span class="pre">iterate_connections_and_locations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.iterate_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations" title="Link to this definition">#</a></dt>
-<dd><p>Iterate through all connections and locations.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="id3">
-<span class="sig-name descname"><span class="pre">add_location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_fwd_strand</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.add_location"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id3" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">add_location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_fwd_strand</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.add_location"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.add_location" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id4">
-<span class="sig-name descname"><span class="pre">contour_to_monomer_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contour_pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nearest_monomer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_monomer_index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id4" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_monomer_index">
+<span class="sig-name descname"><span class="pre">contour_to_monomer_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contour_pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nearest_monomer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_monomer_index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_monomer_index" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id5">
-<span class="sig-name descname"><span class="pre">contour_to_orientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_orientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id5" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_orientation">
+<span class="sig-name descname"><span class="pre">contour_to_orientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_orientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id6">
-<span class="sig-name descname"><span class="pre">contour_to_position</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id6" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_position">
+<span class="sig-name descname"><span class="pre">contour_to_position</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_position" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id7">
-<span class="sig-name descname"><span class="pre">contour_to_tangent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_tangent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id7" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.contour_to_tangent">
+<span class="sig-name descname"><span class="pre">contour_to_tangent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.contour_to_tangent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.contour_to_tangent" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id8">
-<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id8" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.get_center">
+<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.get_center" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id9">
-<span class="sig-name descname"><span class="pre">get_contour_sorted_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_contour_sorted_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id9" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">
+<span class="sig-name descname"><span class="pre">get_contour_sorted_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.get_contour_sorted_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id10">
-<span class="sig-name descname"><span class="pre">insert_monomers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">at_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.insert_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id10" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.insert_monomers">
+<span class="sig-name descname"><span class="pre">insert_monomers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">at_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.insert_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.insert_monomers" title="Link to this definition">#</a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -922,18 +625,18 @@ and manages connections to other polymer elements.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id11">
-<span class="sig-name descname"><span class="pre">iterate_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.iterate_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id11" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.iterate_connections_and_locations">
+<span class="sig-name descname"><span class="pre">iterate_connections_and_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.iterate_connections_and_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id12">
-<span class="sig-name descname"><span class="pre">monomer_index_to_contour</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">monomer_pos</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.monomer_index_to_contour"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id12" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.monomer_index_to_contour">
+<span class="sig-name descname"><span class="pre">monomer_index_to_contour</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">monomer_pos</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.monomer_index_to_contour"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id13">
-<span class="sig-name descname"><span class="pre">remove_monomers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">first_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">last_monomer</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.remove_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id13" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.remove_monomers">
+<span class="sig-name descname"><span class="pre">remove_monomers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">first_monomer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">last_monomer</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.remove_monomers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.remove_monomers" title="Link to this definition">#</a></dt>
 <dd><p>Removes nucleotides between first_monomer and last_monomer, inclusive</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -946,23 +649,23 @@ and manages connections to other polymer elements.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id14">
-<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contour_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id14" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.rotate">
+<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contour_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.rotate" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id15">
-<span class="sig-name descname"><span class="pre">set_orientation_splines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contours</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quaternions</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_orientation_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id15" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.set_orientation_splines">
+<span class="sig-name descname"><span class="pre">set_orientation_splines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contours</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quaternions</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_orientation_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id16">
-<span class="sig-name descname"><span class="pre">set_splines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contours</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id16" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.set_splines">
+<span class="sig-name descname"><span class="pre">set_splines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contours</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.set_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.set_splines" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="id17">
-<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">translation_vector</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contour_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id17" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerSection.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">translation_vector</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contour_filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerSection.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerSection.translate" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
@@ -1016,15 +719,9 @@ and manages connections to other polymer elements.</p>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement"><code class="docutils literal notranslate"><span class="pre">ConnectableElement</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.locations</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.connection_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.connection_locations</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.connections"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.connections</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_location_at"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_location_at"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_location_at()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.ConnectableElement.get_locations"><code class="docutils literal notranslate"><span class="pre">ConnectableElement.get_locations()</span></code></a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.Connection"><code class="docutils literal notranslate"><span class="pre">Connection</span></code></a><ul class="nav section-nav flex-column">
@@ -1062,45 +759,21 @@ and manages connections to other polymer elements.</p>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection"><code class="docutils literal notranslate"><span class="pre">PolymerSection</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.segname"><code class="docutils literal notranslate"><span class="pre">PolymerSection.segname</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.num_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.num_monomers</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_length"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_length</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.start_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.start_position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.end_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.end_position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.start_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.start_orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.position_spline_params"><code class="docutils literal notranslate"><span class="pre">PolymerSection.position_spline_params</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.quaternion_spline_params"><code class="docutils literal notranslate"><span class="pre">PolymerSection.quaternion_spline_params</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.sequence"><code class="docutils literal notranslate"><span class="pre">PolymerSection.sequence</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_center"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.insert_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.remove_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.translate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.rotate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.add_location"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_monomer_index"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_monomer_index()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_position"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_position()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_tangent"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_tangent()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.contour_to_orientation"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_center"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_contour_sorted_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.add_location"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.insert_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations"><code class="docutils literal notranslate"><span class="pre">PolymerSection.iterate_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">PolymerSection.add_location()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_monomer_index()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_orientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">PolymerSection.contour_to_tangent()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id8"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_center()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id9"><code class="docutils literal notranslate"><span class="pre">PolymerSection.get_contour_sorted_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id10"><code class="docutils literal notranslate"><span class="pre">PolymerSection.insert_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id11"><code class="docutils literal notranslate"><span class="pre">PolymerSection.iterate_connections_and_locations()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id12"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id13"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id14"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id15"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id16"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id17"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.monomer_index_to_contour"><code class="docutils literal notranslate"><span class="pre">PolymerSection.monomer_index_to_contour()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.remove_monomers"><code class="docutils literal notranslate"><span class="pre">PolymerSection.remove_monomers()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.rotate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_orientation_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_orientation_splines()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.set_splines"><code class="docutils literal notranslate"><span class="pre">PolymerSection.set_splines()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.polymer.PolymerSection.translate"><code class="docutils literal notranslate"><span class="pre">PolymerSection.translate()</span></code></a></li>
 </ul>
 </li>
 </ul>
diff --git a/_build/html/api/polymer_modeling/sali_polymer_model.html b/_build/html/api/polymer_modeling/sali_polymer_model.html
index 2742a95159799b42a3e6453d8e00a13e1d0d96f2..1feeb534e607b5fcf5ee9fb59232955ecbc29cb2 100644
--- a/_build/html/api/polymer_modeling/sali_polymer_model.html
+++ b/_build/html/api/polymer_modeling/sali_polymer_model.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
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     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -539,7 +539,7 @@ document.write(`
 
 <dl class="py method">
 <dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine.write_simulation_files">
-<span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_pqr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy_ff_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">PosixPath('/Users/pinyili/Documents/research/arbdmodel-simple/arbdmodel/resources/charmm36.nbfix')</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine.write_simulation_files" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_pqr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy_ff_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">PosixPath('/data/server10/pinyili2/arbdmodel-simple/arbdmodel/resources/charmm36.nbfix')</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine.write_simulation_files" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </dd></dl>
diff --git a/_build/html/api/simulation_engines/index.html b/_build/html/api/simulation_engines/index.html
index 550c28923e8b14d77c07b9c1f5decccc78cdd46b..2dec772f8a93eed9e1686cd7f157d8db0dcdff31 100644
--- a/_build/html/api/simulation_engines/index.html
+++ b/_build/html/api/simulation_engines/index.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/simulation_engines/parmed_bd.html b/_build/html/api/simulation_engines/parmed_bd.html
index b0e495c1d213c8675fe3e5c6ac1a4038f54d57ed..c99edfd8f447345fac7e5e3226c42f3f934362ee 100644
--- a/_build/html/api/simulation_engines/parmed_bd.html
+++ b/_build/html/api/simulation_engines/parmed_bd.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/binary_manager.html b/_build/html/api/utilities/binary_manager.html
index 8a861bedf804c0a0d45f3d829ab729f328e1d969..cdf5ceaef2b137d1fba3e181ec878f861559b782 100644
--- a/_build/html/api/utilities/binary_manager.html
+++ b/_build/html/api/utilities/binary_manager.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/coords.html b/_build/html/api/utilities/coords.html
index 185f75e3ca14a19bbdad70c9ee492e8d64d34aee..1e2da889a84bd5f1f6a30235ba76c176297186e4 100644
--- a/_build/html/api/utilities/coords.html
+++ b/_build/html/api/utilities/coords.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
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     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/grid.html b/_build/html/api/utilities/grid.html
index f4626ec8eb99b31cecc1fc0532e03006d05b7596..e9731a0660bd4ed47bf9ec1ca997c8e5840f2707 100644
--- a/_build/html/api/utilities/grid.html
+++ b/_build/html/api/utilities/grid.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/index.html b/_build/html/api/utilities/index.html
index 7690f4ecec8585895f2f9317710f6ff41fd76545..4ce4aa5d8948d249a1cfeb912f46af5b89c85dd4 100644
--- a/_build/html/api/utilities/index.html
+++ b/_build/html/api/utilities/index.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -61,9 +61,9 @@
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     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/logger.html b/_build/html/api/utilities/logger.html
index 521b3ed392a0df800d8fa476389efc6e859185b7..b2019818b85ebaa370635bf6ed2d0b831a843568 100644
--- a/_build/html/api/utilities/logger.html
+++ b/_build/html/api/utilities/logger.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -61,9 +61,9 @@
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     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/version.html b/_build/html/api/utilities/version.html
index 63b2cdfefc749166d64c1dfc04f91aa4ffd9e879..4ffe2535c2cd64764a3bda79974f171e5bea75d5 100644
--- a/_build/html/api/utilities/version.html
+++ b/_build/html/api/utilities/version.html
@@ -32,19 +32,19 @@
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     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="../../_static/tabs.js?v=3ee01567"></script>
-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/html/genindex.html b/_build/html/genindex.html
index adbb8b21ded27aa39f130df98e4b910eb72e43d9..27ad7dc64b3a6a401bfe57f4f0dc9671a0a96bbc 100644
--- a/_build/html/genindex.html
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-    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css" />
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-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -60,9 +60,9 @@
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     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="_static/tabs.js?v=3ee01567"></script>
-    <script src="_static/js/hoverxref.js"></script>
-    <script src="_static/js/tooltipster.bundle.min.js"></script>
-    <script src="_static/js/micromodal.min.js"></script>
+    <script src="_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -325,6 +325,7 @@ document.write(`
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  | <a href="#V"><strong>V</strong></a>
  | <a href="#W"><strong>W</strong></a>
+ | <a href="#Z"><strong>Z</strong></a>
  
 </div>
 <h2 id="A">A</h2>
@@ -366,7 +367,7 @@ document.write(`
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_improper">add_improper() (Parent method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.add_location">add_location() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id3">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.add_location">add_location() (PolymerSection method)</a>
 </li>
       <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.add_nonbonded_interaction">add_nonbonded_interaction() (ArbdModel method)</a>
 </li>
@@ -612,15 +613,13 @@ document.write(`
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.b">b (DnaStrandBeads attribute)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.barostat">barostat (SimConf attribute)</a>
 </li>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.bins">bins (AbstractIBIpotential attribute)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondAngleDof">BondAngleDof (class in arbdmodel.ibi)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondDof">BondDof (class in arbdmodel.ibi)</a>
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.Bound_grid">Bound_grid() (in module arbdmodel.grid)</a>
@@ -665,7 +664,7 @@ document.write(`
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.clone">clone() (Group method)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.combine">combine() (SimConf method)</a>, <a href="api/core/sim_config.html#id1">[1]</a>
+      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.combine">combine() (SimConf method)</a>
 </li>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AngleDof.compute_volume">compute_volume() (AngleDof method)</a>
 
@@ -686,20 +685,16 @@ document.write(`
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement">ConnectableElement (class in arbdmodel.polymer)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection">Connection (class in arbdmodel.polymer)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.connection_locations">connection_locations (ConnectableElement attribute)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.connections">connections (ConnectableElement attribute)</a>
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.constant_force">constant_force() (in module arbdmodel.grid)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_monomer_index">contour_to_monomer_index() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id4">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_monomer_index">contour_to_monomer_index() (PolymerSection method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_orientation">contour_to_orientation() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id5">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_orientation">contour_to_orientation() (PolymerSection method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_position">contour_to_position() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id6">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_position">contour_to_position() (PolymerSection method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_tangent">contour_to_tangent() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id7">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_tangent">contour_to_tangent() (PolymerSection method)</a>
 </li>
       <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg">convert_sod_to_mg() (ParmedArbd static method)</a>
 </li>
@@ -716,8 +711,6 @@ document.write(`
       <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.create_model">create_model() (SimpleArbdConfig method)</a>
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.Create_null">Create_null() (in module arbdmodel.grid)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.cutoff">cutoff (SimConf attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -731,8 +724,6 @@ document.write(`
         <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.debye_length">(OnckNonbonded attribute)</a>
 </li>
       </ul></li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.decomp_period">decomp_period (SimConf attribute)</a>
-</li>
       <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.default_binary">default_binary (ArbdEngine property)</a>
 
       <ul>
@@ -747,10 +738,10 @@ document.write(`
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.delete">delete() (Connection method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType">DiffusiveRigidBodyType (class in arbdmodel.structure_rigidbody)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DihedralDof">DihedralDof (class in arbdmodel.ibi)</a>
 </li>
       <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.dimensions_from_structure">dimensions_from_structure() (ArbdModel method)</a>
@@ -779,8 +770,6 @@ document.write(`
 <h2 id="E">E</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.end_position">end_position (PolymerSection attribute)</a>
-</li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.excludedAttributes">excludedAttributes (ParticleType attribute)</a>
 </li>
   </ul></td>
@@ -865,7 +854,7 @@ document.write(`
         <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles">(SurfaceMeshProcessor method)</a>
 </li>
       </ul></li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.get_binary">get_binary() (SimConf method)</a>, <a href="api/core/sim_config.html#id2">[1]</a>
+      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.get_binary">get_binary() (SimConf method)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bond_angles">get_bond_angles() (Parent method)</a>
 </li>
@@ -878,7 +867,7 @@ document.write(`
 </li>
         <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_center">(PolymerGroup method)</a>
 </li>
-        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_center">(PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id8">[1]</a>
+        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_center">(PolymerSection method)</a>
 </li>
       </ul></li>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution">get_cg_distribution() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id2">[1]</a>
@@ -893,11 +882,11 @@ document.write(`
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_connections">get_connections() (PolymerGroup method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_connections_and_locations">get_connections_and_locations() (ConnectableElement method)</a>, <a href="api/polymer_modeling/polymer.html#id0">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_connections_and_locations">get_connections_and_locations() (ConnectableElement method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id9">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>
 </li>
       <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.get_default_conf">get_default_conf() (ArbdEngine method)</a>
 
@@ -915,9 +904,9 @@ document.write(`
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_impropers">get_impropers() (Parent method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_location_at">get_location_at() (ConnectableElement method)</a>, <a href="api/polymer_modeling/polymer.html#id1">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_location_at">get_location_at() (ConnectableElement method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_locations">get_locations() (ConnectableElement method)</a>, <a href="api/polymer_modeling/polymer.html#id2">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_locations">get_locations() (ConnectableElement method)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.get_monomer_index">get_monomer_index() (Location method)</a>
 </li>
@@ -956,8 +945,6 @@ document.write(`
       <li><a href="api/utilities/version.html#arbdmodel.version.get_version">get_version() (in module arbdmodel.version)</a>
 </li>
       <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.getParticleTypesAndCounts">getParticleTypesAndCounts() (ArbdModel method)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.gpu">gpu (SimConf attribute)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group">Group (class in arbdmodel.core_objects)</a>
 </li>
@@ -1008,14 +995,12 @@ document.write(`
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.index">index() (Parent method)</a>
 </li>
       <li><a href="api/utilities/binary_manager.html#arbdmodel.binary_manager.initialize_binary_paths">initialize_binary_paths() (in module arbdmodel.binary_manager)</a>
-</li>
-      <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.insert">insert() (Parent method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.insert_monomers">insert_monomers() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id10">[1]</a>
+      <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.insert">insert() (Parent method)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.integrator">integrator (SimConf attribute)</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.insert_monomers">insert_monomers() (PolymerSection method)</a>
 </li>
       <li><a href="api/utilities/version.html#arbdmodel.version.is_dirty">is_dirty() (in module arbdmodel.version)</a>
 </li>
@@ -1023,9 +1008,9 @@ document.write(`
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.isotropic_kernel">isotropic_kernel() (in module arbdmodel.grid)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.items">items() (SimConf method)</a>, <a href="api/core/sim_config.html#id3">[1]</a>
+      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.items">items() (SimConf method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations">iterate_connections_and_locations() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id11">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations">iterate_connections_and_locations() (PolymerSection method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -1070,8 +1055,6 @@ document.write(`
       <li><a href="api/utilities/grid.html#arbdmodel.grid.loadGrid">loadGrid() (in module arbdmodel.grid)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location">Location (class in arbdmodel.polymer)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.locations">locations (ConnectableElement attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -1081,12 +1064,16 @@ document.write(`
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.main">main() (in module arbdmodel.simplearbd)</a>
 </li>
-      <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.max_force">max_force (KhNonbonded attribute)</a>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.max_force">max_force (AbstractPotential attribute)</a>
 
       <ul>
+        <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.max_force">(KhNonbonded attribute)</a>
+</li>
         <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.max_force">(OnckNonbonded attribute)</a>
 </li>
       </ul></li>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.max_potential">max_potential (AbstractPotential attribute)</a>
+</li>
       <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor">MeshProcessor (class in arbdmodel.mesh_process_volume)</a>
 </li>
       <li><a href="api/rigidbody_models/mesh_rigidbody.html#arbdmodel.mesh_rigidbody.MeshRigidBodyType">MeshRigidBodyType (class in arbdmodel.mesh_rigidbody)</a>
@@ -1160,9 +1147,7 @@ document.write(`
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.monomer_index_to_contour">monomer_index_to_contour() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id12">[1]</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.monomer_length">monomer_length (PolymerSection attribute)</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.monomer_index_to_contour">monomer_index_to_contour() (PolymerSection method)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads.monomers_per_bead_group">monomers_per_bead_group (PolymerBeads property)</a>
 </li>
@@ -1182,6 +1167,8 @@ document.write(`
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.neighborhood_average">neighborhood_average() (in module arbdmodel.grid)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt">nt (DnaStrandBeads attribute)</a>
 </li>
       <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential">NullPotential (class in arbdmodel.interactions)</a>
@@ -1189,22 +1176,6 @@ document.write(`
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads.num_bead_groups">num_bead_groups (PolymerBeads property)</a>
 </li>
   </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster">num_heavy_cluster (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.num_heavy_cluster">(SimConf attribute)</a>
-</li>
-      </ul></li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.num_monomers">num_monomers (PolymerSection attribute)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.num_steps">num_steps (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.num_steps">(SimConf attribute)</a>
-</li>
-      </ul></li>
-  </ul></td>
 </tr></table>
 
 <h2 id="O">O</h2>
@@ -1213,19 +1184,13 @@ document.write(`
       <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads">OnckBeads (class in arbdmodel.onck_polymer_model)</a>
 </li>
       <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckModel">OnckModel (class in arbdmodel.onck_polymer_model)</a>
-</li>
-      <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">OnckNonbonded (class in arbdmodel.onck_polymer_model)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.other">other() (Connection method)</a>
+      <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">OnckNonbonded (class in arbdmodel.onck_polymer_model)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.output_period">output_period (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.output_period">(SimConf attribute)</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.other">other() (Connection method)</a>
 </li>
-      </ul></li>
   </ul></td>
 </tr></table>
 
@@ -1235,8 +1200,6 @@ document.write(`
       <li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.p">p (DnaStrandBeads attribute)</a>
 </li>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.PairDistributionDof">PairDistributionDof (class in arbdmodel.ibi)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.pairlist_distance">pairlist_distance (SimConf attribute)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent">Parent (class in arbdmodel.core_objects)</a>
 </li>
@@ -1252,9 +1215,11 @@ document.write(`
 </li>
       <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.peptide_bond">peptide_bond (OnckBeads attribute)</a>
 </li>
-      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.periodic">periodic (AbstractPotential property)</a>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.periodic">periodic (AbstractPotential attribute)</a>
 
       <ul>
+        <li><a href="api/interaction_potentials/interactions.html#id1">(AbstractPotential property)</a>
+</li>
         <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicDihedral.periodic">(HarmonicDihedral property)</a>
 </li>
         <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBIDihedral.periodic">(IBIDihedral property)</a>
@@ -1271,15 +1236,13 @@ document.write(`
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerModel">PolymerModel (class in arbdmodel.polymer)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection">PolymerSection (class in arbdmodel.polymer)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.position_spline_params">position_spline_params (PolymerSection attribute)</a>
 </li>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.potential">potential (AbstractIBIpotential attribute)</a>
 </li>
       <li><a href="api/interaction_potentials/ibi.html#id0">potential() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id4">[1]</a>
 
       <ul>
-        <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id1">[1]</a>
+        <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id2">[1]</a>
 </li>
         <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.potential">(BoundaryPotential method)</a>
 </li>
@@ -1318,12 +1281,6 @@ document.write(`
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.prepare_for_simulation">prepare_for_simulation() (ArbdModel method)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.pressure">pressure (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.pressure">(SimConf attribute)</a>
-</li>
-      </ul></li>
       <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject.process">process() (StaticObject method)</a>
 </li>
       <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.process_mesh_file">process_mesh_file() (in module arbdmodel.mesh_process_volume)</a>
@@ -1331,8 +1288,6 @@ document.write(`
       <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.process_structure">process_structure() (StructureProcessor method)</a>
 </li>
       <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.process_surface_mesh">process_surface_mesh() (in module arbdmodel.mesh_process_surface)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.Properties">Properties (DefaultSimConf attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -1351,8 +1306,6 @@ document.write(`
       <li><a href="api/utilities/coords.html#arbdmodel.coords.quaternion_product">quaternion_product() (in module arbdmodel.coords)</a>
 </li>
       <li><a href="api/utilities/coords.html#arbdmodel.coords.quaternion_slerp">quaternion_slerp() (in module arbdmodel.coords)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.quaternion_spline_params">quaternion_spline_params (PolymerSection attribute)</a>
 </li>
       <li><a href="api/utilities/coords.html#arbdmodel.coords.quaternion_to_matrix">quaternion_to_matrix() (in module arbdmodel.coords)</a>
 </li>
@@ -1364,8 +1317,12 @@ document.write(`
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.RadiusDof">RadiusDof (class in arbdmodel.ibi)</a>
 </li>
-      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.range_">range_ (AbstractPotential property)</a>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.range_">range_ (AbstractPotential attribute)</a>
+
+      <ul>
+        <li><a href="api/interaction_potentials/interactions.html#id3">(AbstractPotential property)</a>
 </li>
+      </ul></li>
       <li><a href="api/utilities/coords.html#arbdmodel.coords.read_arbd_coordinates">read_arbd_coordinates() (in module arbdmodel.coords)</a>
 </li>
       <li><a href="api/utilities/coords.html#arbdmodel.coords.read_average_arbd_coordinates">read_average_arbd_coordinates() (in module arbdmodel.coords)</a>
@@ -1384,17 +1341,13 @@ document.write(`
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.remove">remove() (Parent method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.remove_monomers">remove_monomers() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id13">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.remove_monomers">remove_monomers() (PolymerSection method)</a>
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.replace_false_with_distance">replace_false_with_distance() (in module arbdmodel.grid)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.restart_file">restart_file (SimConf attribute)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period">rigid_body_grid_grid_period (SimConf attribute)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.rigid_body_integrator">rigid_body_integrator (SimConf attribute)</a>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.resolution">resolution (AbstractPotential attribute)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody">RigidBody (class in arbdmodel.core_objects)</a>
 </li>
@@ -1403,7 +1356,7 @@ document.write(`
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.rotate">rotate() (PolymerGroup method)</a>
 
       <ul>
-        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.rotate">(PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id14">[1]</a>
+        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.rotate">(PolymerSection method)</a>
 </li>
         <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.rotate">(Transformable method)</a>
 </li>
@@ -1454,17 +1407,9 @@ document.write(`
         <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb">(SurfaceMeshProcessor method)</a>
 </li>
       </ul></li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.seed">seed (SimConf attribute)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.segname">segname (PolymerSection attribute)</a>
-</li>
       <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.sequence">sequence (OnckBeads attribute)</a>
-
-      <ul>
-        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.sequence">(PolymerSection attribute)</a>
 </li>
-      </ul></li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">set_binary() (SimConf method)</a>, <a href="api/core/sim_config.html#id4">[1]</a>
+      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">set_binary() (SimConf method)</a>
 </li>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.set_connection">set_connection() (Location method)</a>
 </li>
@@ -1480,18 +1425,18 @@ document.write(`
         <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckModel.set_damping_coefficient">(OnckModel method)</a>
 </li>
       </ul></li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_orientation_splines">set_orientation_splines() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id15">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_orientation_splines">set_orientation_splines() (PolymerSection method)</a>
 </li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_splines">set_splines() (PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id16">[1]</a>
+      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_splines">set_splines() (PolymerSection method)</a>
 </li>
       <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.setup_and_run">setup_and_run() (ShapeCGModel method)</a>
 </li>
       <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects">setup_diffusible_objects() (SimpleArbdConfig method)</a>
-</li>
-      <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">setup_static_objects() (SimpleArbdConfig method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">setup_static_objects() (SimpleArbdConfig method)</a>
+</li>
       <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory">ShapeCGFactory (class in arbdmodel.shape_cg)</a>
 </li>
       <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel">ShapeCGModel (class in arbdmodel.shape_cg)</a>
@@ -1516,12 +1461,6 @@ document.write(`
       </ul></li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.slab_potential_z">slab_potential_z() (in module arbdmodel.grid)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.solvent_density">solvent_density (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.solvent_density">(SimConf attribute)</a>
-</li>
-      </ul></li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.spherical_confinement">spherical_confinement() (in module arbdmodel.grid)</a>
 </li>
       <li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsModel.spring_constant">spring_constant (HpsModel attribute)</a>
@@ -1534,10 +1473,6 @@ document.write(`
         <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.spring_constant">(OnckBeads attribute)</a>
 </li>
       </ul></li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.start_orientation">start_orientation (PolymerSection attribute)</a>
-</li>
-      <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.start_position">start_position (PolymerSection attribute)</a>
-</li>
       <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject">StaticObject (class in arbdmodel.structure_rigidbody)</a>
 </li>
       <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor">StructureProcessor (class in arbdmodel.structure_from_pdb)</a>
@@ -1554,38 +1489,30 @@ document.write(`
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.TabulatedNonbonded">TabulatedNonbonded (class in arbdmodel.interactions)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.temperature">temperature (DefaultSimConf attribute)</a>
+      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.temperature">temperature (DefaultSimConf property)</a>
 
       <ul>
-        <li><a href="api/core/sim_config.html#id0">(DefaultSimConf property)</a>
-</li>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf attribute)</a>
-</li>
-        <li><a href="api/core/sim_config.html#id5">(SimConf property)</a>
+        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf property)</a>
 </li>
       </ul></li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids.test_average_grids">test_average_grids() (TestAverageGrids method)</a>
 </li>
       <li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids">TestAverageGrids (class in arbdmodel.grid)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.thermostat">thermostat (SimConf attribute)</a>
-</li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.timestep">timestep (SimConf attribute)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.transform">transform() (Transformable method)</a>
 </li>
       <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable">Transformable (class in arbdmodel.core_objects)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.translate">translate() (PolymerGroup method)</a>
 
       <ul>
-        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.translate">(PolymerSection method)</a>, <a href="api/polymer_modeling/polymer.html#id17">[1]</a>
+        <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.translate">(PolymerSection method)</a>
 </li>
         <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.translate">(Transformable method)</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicAngle.type_">type_ (HarmonicAngle property)</a>
 
       <ul>
@@ -1636,12 +1563,6 @@ document.write(`
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.version">version (OnckBeads attribute)</a>
 </li>
-      <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.viscosity">viscosity (DefaultSimConf attribute)</a>
-
-      <ul>
-        <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.viscosity">(SimConf attribute)</a>
-</li>
-      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.vmd_cylinder_tcl">vmd_cylinder_tcl() (PolymerGroup method)</a>
@@ -1677,7 +1598,7 @@ document.write(`
       <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_file">write_file() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id7">[1]</a>
 
       <ul>
-        <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id2">[1]</a>
+        <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id4">[1]</a>
 </li>
         <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.write_file">(BoundaryPotential method)</a>
 </li>
@@ -1717,6 +1638,14 @@ document.write(`
   </ul></td>
 </tr></table>
 
+<h2 id="Z">Z</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.zero">zero (AbstractPotential attribute)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 
 
                 </article>
diff --git a/_build/html/intro.html b/_build/html/intro.html
index 204712db74a591400bb9cc0a1d4c937880774fc5..753237cd058dac596899227ba10636e2407315b6 100644
--- a/_build/html/intro.html
+++ b/_build/html/intro.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="_static/copybutton.js?v=f281be69"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="_static/tabs.js?v=3ee01567"></script>
-    <script src="_static/js/hoverxref.js"></script>
-    <script src="_static/js/tooltipster.bundle.min.js"></script>
-    <script src="_static/js/micromodal.min.js"></script>
+    <script src="_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/objects.inv b/_build/html/objects.inv
index d27a5f3a7a25c5e137eea15c249db257124b96c3..a1dfc9269e7fcad8244e23bad55f63f00cdd41ba 100644
Binary files a/_build/html/objects.inv and b/_build/html/objects.inv differ
diff --git a/_build/html/py-modindex.html b/_build/html/py-modindex.html
index 14e0e7ef0e82adb2f86ec694601cbbff2cfbe7fe..1b834c767a334015a740102faf386096a0ac7a05 100644
--- a/_build/html/py-modindex.html
+++ b/_build/html/py-modindex.html
@@ -31,19 +31,19 @@
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-examples.css?v=e236af4b" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -60,9 +60,9 @@
     <script src="_static/copybutton.js?v=f281be69"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script src="_static/tabs.js?v=3ee01567"></script>
-    <script src="_static/js/hoverxref.js"></script>
-    <script src="_static/js/tooltipster.bundle.min.js"></script>
-    <script src="_static/js/micromodal.min.js"></script>
+    <script src="_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/reports/tutorials/1-basics/1-basics.err.log b/_build/html/reports/tutorials/1-basics/1-basics.err.log
index 3e15033a3d2309f198f69a0a4d79781ba75f4080..0573077fb16df59b415b82c18a892b02a4b1301b 100644
--- a/_build/html/reports/tutorials/1-basics/1-basics.err.log
+++ b/_build/html/reports/tutorials/1-basics/1-basics.err.log
@@ -1,17 +1,17 @@
 Traceback (most recent call last):
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
     return future.result()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
     await self.async_execute_cell(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
     await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
     raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
 nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
 ------------------
diff --git a/_build/html/reports/tutorials/2-polymer-objects/2-polymer-objects.err.log b/_build/html/reports/tutorials/2-polymer-objects/2-polymer-objects.err.log
index c7726fc1032b581cb695d43ae1f26a1e035cbf30..ae83ae474334877a5cda54c26c2d10d9ea5cd23b 100644
--- a/_build/html/reports/tutorials/2-polymer-objects/2-polymer-objects.err.log
+++ b/_build/html/reports/tutorials/2-polymer-objects/2-polymer-objects.err.log
@@ -1,17 +1,17 @@
 Traceback (most recent call last):
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
     return future.result()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
     await self.async_execute_cell(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
     await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
     raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
 nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
 ------------------
diff --git a/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log b/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log
index 2f5f05bb605419ef18c18c567106ce970efe3e04..8b7dba58946c81a8415fcb03865b4c9513644081 100644
--- a/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log
+++ b/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log
@@ -1,113 +1,104 @@
 Traceback (most recent call last):
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
     return future.result()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
     await self.async_execute_cell(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
     await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
     raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
 nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
 ------------------
-
-temperature = 298.15
-ion_concentration = 250         # in mM
-gpu = 0
-
-decomp_period = 50
-skin_depth = 8
-## 3.2
-
-model_name = 'HPS'
-step = 1
-
-## units "sqrt(80 epsilon0 k K /(2 * (mM/particle) * e**2))" AA
-debye_length = 10
-
-polymers, sequences = create_arbd_polymer_objects()
-
-model = NupModel( polymers, sequences,
-                  debye_length = debye_length,
-                  temperature=temperature,
-                  damping_coefficient = 50000, # units of 1/ns
-                  decomp_period = decomp_period,
-                  pairlist_distance = 50+skin_depth,
-                  dimensions = dimensions
-                  )
-engine = ArbdEngine( integrator = 'Langevin',
-                     num_steps=1e7,
-                     output_period=1e4,
-                     gpu = 0
-                    )
-directory = f'1-one_bead_per_res-{model_name}'
-outname = 'run'
-
-if not Path(f'{directory}/output/{outname}.dcd').exists():
-    # """ "Minimization" """
-    # add_restraints(model,restraints)
-    # model.simulate(output_name='{}-min-{}'.format(model_name,step),
-    #                num_steps=1e3, output_period=500,
-    #                gpu=gpu,
-    # )
-    # coords = readArbdCoords('output/{}-min-{}.restart'.format(model_name,step))
-    # model.update_splines(coords)
-
-    """ Production """
-    model.set_damping_coefficient( 100 )
-    engine.simulate(model, output_name=outname,
-                    directory = directory
-                    )
+## Usually this script would be put in it's own python file so it can be imported into multiple other scripts
+import numpy as np
+from pathlib import Path
+from arbdmodel import ArbdEngine
+from arbdmodel.coords import readArbdCoords
+from arbdmodel.polymer import PolymerSection
+from arbdmodel.hps_polymer_model import _types
+from arbdmodel.hps_polymer_model import HpsModel as NupModel
+
+_seq = 'GLFG' * 8              # 10 repeats per polymer
+## We're going to tile polymers along x and y in a square lattice
+Nx = 5
+Ny = 5
+N_polymers = Nx*Ny
+
+density = 55                    # mg / mL
+
+""" Calculated parameters """
+polymer_mass = sum( [_types[aa].mass for aa in _seq] ) # in daltons
+## units "mg/ml" "dalton/AA**3"
+_conversion = 0.0006022142
+
+dimensions = (Nx*Ny*polymer_mass/(density*_conversion))**(1/3) # in Angstroms, the unit of length in ARBD
+dimensions = [dimensions]*3                                 # along x,y,z
+
+xs = np.linspace( -dimensions[0]*0.5, dimensions[0]*0.5, Nx+1 ) # row edges (one extra value)
+ys = np.linspace( -dimensions[1]*0.5, dimensions[1]*0.5, Ny+1 ) # column edges
+xs = (xs[1:] + xs[:-1])*0.5                                     # row centers
+ys = (ys[1:] + ys[:-1])*0.5                                     # column centers
+
+z = np.arange(len(_seq))*3.8*0.5         # times coordinate for every amino acid in a polymer, compressed a bit
+
+""" Build peptide list consisting of sequence, coordinates"""
+peptides = []
+
+for x in xs:
+    for y in ys:
+        r = np.empty( (len(_seq),3) ) # allocate array for coordinates of each amino acid in polymer
+        r[:,0] = x
+        r[:,1] = y
+        r[:,2] = z
+
+        peptides.append( (_seq, r ) )
+
+def create_arbd_polymer_objects():
+    polymers = []
+    sequences = []
+    segid = 0
+    chainid = 0
+    sequence_to_chain = dict()
+
+    ## Loop over peptides to be added to system
+    for seq,coords in peptides:
+        ## Get chain and segid for PDB
+        if seq not in sequence_to_chain:
+            sequence_to_chain[seq] = chainid
+            chainid = chainid+1
+        chain = sequence_to_chain[seq]
+        segid = segid+1
+
+
+        p = PolymerSection(name=seq[:4], # use first part of sequence to name the polymer
+                           num_monomers=len(seq),
+                           monomer_length = 3.8,
+                           segname = '{}{:03d}'.format( chr(65+chain), segid ),
+                           chain = chr(65+chain),
+
+        )
+        p.set_splines(np.linspace(0,1,len(coords)), coords)
+        polymers.append(p)
+        sequences.append(seq)
+    return polymers, sequences
 
 ------------------
 
 
 ---------------------------------------------------------------------------
-TypeError                                 Traceback (most recent call last)
-Cell In[2], line 17
-     13 debye_length = 10
-     15 polymers, sequences = create_arbd_polymer_objects()
----> 17 model = NupModel( polymers, sequences,
-     18                   debye_length = debye_length,
-     19                   temperature=temperature,
-     20                   damping_coefficient = 50000, # units of 1/ns
-     21                   decomp_period = decomp_period,
-     22                   pairlist_distance = 50+skin_depth,
-     23                   dimensions = dimensions
-     24                   )
-     25 engine = ArbdEngine( integrator = 'Langevin',
-     26                      num_steps=1e7,
-     27                      output_period=1e4,
-     28                      gpu = 0
-     29                     )
-     30 directory = f'1-one_bead_per_res-{model_name}'
-
-File ~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239, in HpsModel.__init__(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)
-    236 if sequences is None:
-    237     raise NotImplementedError("HpsModel must be provided a sequences argument")
---> 239 PolymerModel.__init__(self, polymers, sequences, monomers_per_bead_group=1, **kwargs)
-    241 """ Update type diffusion coefficients """
-    242 self.types = all_types = [t for key,t in _types.items()]
-
-File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703, in PolymerModel.__init__(self, polymers, sequences, monomers_per_bead_group, **kwargs)
-    701 self.sequences = sequences
-    702 self.monomers_per_bead_group = monomers_per_bead_group
---> 703 ArbdModel.__init__(self, [], **kwargs)
-    705 """ Generate beads """
-    706 self.generate_beads()
-
-File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231, in ArbdModel.__init__(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)
-    228     cell_origin = [0, 0, 0]
-    230 # Initialize parent class
---> 231 PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms,
-    232                  cell_vectors, cell_origin)
-    235 # Store origin which might be different from cell_origin
-    236 self.origin = cell_origin
-
-TypeError: __init__() takes from 1 to 4 positional arguments but 6 were given
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 4
+      2 import numpy as np
+      3 from pathlib import Path
+----> 4 from arbdmodel import ArbdEngine
+      5 from arbdmodel.coords import readArbdCoords
+      6 from arbdmodel.polymer import PolymerSection
+
+ModuleNotFoundError: No module named 'arbdmodel'
 
diff --git a/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log b/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log
index 11be0157bdbf7c0c198ae16f82694b1d14ba1596..8930c6d0dc89df322b03afa1483d9266bb56e0bc 100644
--- a/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log
+++ b/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log
@@ -1,69 +1,65 @@
 Traceback (most recent call last):
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1319, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
     return loop.run_until_complete(inner)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
     return future.result()
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 709, in async_execute
     await self.async_execute_cell(
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
     await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+  File "/data/server10/pinyili2/miniconda3/envs/pybd/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
     raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
 nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
 ------------------
-## Optionally simulate the DNA-only model to see how it performs and behaves
-model = make_dna_model()
-model.simulate(output_name='run',
-               directory='trombone-no_ssb',
-               num_steps=1e5, output_period=1e3,
-)
-------------------
+## Create a function to construct the DNA model (we'll repeat this a few times)
+from arbdmodel.polymer import PolymerSection
+from arbdmodel.ssdna_two_bead import DnaModel, _P, _B 
 
+def make_dna_model():
+    ## Create spline-based polymer
+    a = PolymerSection(name='loop', num_monomers=500, # 500 nt fragment
+                       monomer_length = 5,
+                       start_position = restraint1,
+                       end_position = restraint2,
+    )
+    coords = dna_coordinates
+    a.set_splines( np.linspace(0,1,len(coords)), coords )
+    
 
----------------------------------------------------------------------------
-TypeError                                 Traceback (most recent call last)
-Cell In[4], line 2
-      1 ## Optionally simulate the DNA-only model to see how it performs and behaves
-----> 2 model = make_dna_model()
-      3 model.simulate(output_name='run',
-      4                directory='trombone-no_ssb',
-      5                num_steps=1e5, output_period=1e3,
-      6 )
+    ## Our DNA model is conveniently already implemented. Here we add the
+    ##   steric replisome potential (based on cryo-EM density) to both
+    ##   bead types. Note this model represents poly(dT), and is not ideal
+    ##   for study of the replisome
+    _P.grid = (replisome_grid, 500)       # scale it up by a big factor
+    _B.grid = (replisome_grid, 500)
+
+    model = DnaModel([a], dimensions=(3000,3000,3000),
+                     timestep = 20e-6
+                     )
 
-Cell In[3], line 23, in make_dna_model()
-     20 _P.grid = (replisome_grid, 500)       # scale it up by a big factor
-     21 _B.grid = (replisome_grid, 500)
----> 23 model = DnaModel([a], dimensions=(3000,3000,3000),
-     24                  timestep = 20e-6
-     25                  )
-     27 ## Restrain DNA ends
-     28 end1 = model.strands[0].children[0].children[0]
+    ## Restrain DNA ends
+    end1 = model.strands[0].children[0].children[0]
+    end2 = model.strands[0].children[-1].children[0]
 
-File ~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164, in DnaModel.__init__(self, polymers, sequences, DEBUG, **kwargs)
-    161 if 'timestep' not in kwargs: kwargs['timestep'] = 20e-6
-    162 if 'cutoff' not in kwargs: kwargs['cutoff'] = 35
---> 164 PolymerModel.__init__(self, polymers, sequences, monomers_per_bead_group=1, **kwargs)
-    165 self.strands = self.children # make a nice alias
-    167 self.add_nonbonded_interaction( TabulatedNonbonded(get_resource_path('two_bead_model/NBBB.dat')), typeA=_B, typeB=_B )
+    end1.add_restraint( (10, restraint1) )
+    end2.add_restraint( (10, restraint2) )
+
+    return model
+------------------
 
-File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703, in PolymerModel.__init__(self, polymers, sequences, monomers_per_bead_group, **kwargs)
-    701 self.sequences = sequences
-    702 self.monomers_per_bead_group = monomers_per_bead_group
---> 703 ArbdModel.__init__(self, [], **kwargs)
-    705 """ Generate beads """
-    706 self.generate_beads()
 
-File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231, in ArbdModel.__init__(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)
-    228     cell_origin = [0, 0, 0]
-    230 # Initialize parent class
---> 231 PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms,
-    232                  cell_vectors, cell_origin)
-    235 # Store origin which might be different from cell_origin
-    236 self.origin = cell_origin
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[3], line 2
+      1 ## Create a function to construct the DNA model (we'll repeat this a few times)
+----> 2 from arbdmodel.polymer import PolymerSection
+      3 from arbdmodel.ssdna_two_bead import DnaModel, _P, _B 
+      5 def make_dna_model():
+      6     ## Create spline-based polymer
 
-TypeError: __init__() takes from 1 to 4 positional arguments but 6 were given
+ModuleNotFoundError: No module named 'arbdmodel'
 
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"connection_locations (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.connection_locations", false]], "connections (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.connections", false]], "constant_force() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.constant_force", false]], "contour_to_monomer_index() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_monomer_index", false], [15, "id4", false]], "contour_to_orientation() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_orientation", false], [15, "id5", false]], "contour_to_position() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_position", false], [15, "id6", false]], "contour_to_tangent() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_tangent", false], [15, "id7", false]], "convert_sod_to_mg() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg", false]], "convolve_kernel_truncate() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.convolve_kernel_truncate", false]], "create_bounding_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.create_bounding_grid", false]], "create_dual_topology() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology", false]], "create_dual_topology_model() (parmedarbd class method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model", false]], "create_engine() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_engine", false]], "create_model() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_model", false]], "create_null() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.Create_null", false]], "cutoff (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.cutoff", false]], "debye_length (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.debye_length", false]], "debye_length (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.debye_length", false]], "decomp_period (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.decomp_period", false]], "default_binary (arbdengine property)": [[27, "arbdmodel.engine.ArbdEngine.default_binary", false]], "default_binary (namdengine property)": [[27, "arbdmodel.engine.NamdEngine.default_binary", false]], "default_binary (simengine property)": [[27, "arbdmodel.engine.SimEngine.default_binary", false]], "defaultsimconf (class in arbdmodel.sim_config)": [[4, "arbdmodel.sim_config.DefaultSimConf", false]], "degreeoffreedom (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DegreeOfFreedom", false]], "delete() (connection method)": [[15, "arbdmodel.polymer.Connection.delete", false]], "diffusiverigidbodytype (class in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.DiffusiveRigidBodyType", false]], "dihedraldof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DihedralDof", false]], "dimensions_from_structure() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.dimensions_from_structure", false]], "dimensions_from_structure() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.dimensions_from_structure", false]], "display() (citation method)": [[35, "arbdmodel.version.Citation.display", false]], "dnamodel (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaModel", false]], "dnastrandbeads (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads", false]], "duplicate() (group method)": [[1, "arbdmodel.core_objects.Group.duplicate", false]], "duplicate() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.duplicate", false]], "duplicate() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.duplicate", false]], "end_position (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.end_position", false]], "excludedattributes (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.excludedAttributes", false]], "extend() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.extend", false]], "extend() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.extend", false]], "filename() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.filename", false], [6, "id1", false]], "filename() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.filename", false], [8, "id0", false]], "filename() (harmonicbondedpotential method)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.filename", false]], "filename() (nullpotential method)": [[8, "arbdmodel.interactions.NullPotential.filename", false]], "filename() (shapecgnonbonded method)": [[26, "arbdmodel.shape_cg.ShapeCGNonbonded.filename", false]], "filename() (wlcskpotential method)": [[8, "arbdmodel.interactions.WLCSKPotential.filename", false]], "fill_nans() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.fill_nans", false]], "find_shape_based_sites() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.find_shape_based_sites", false]], "fjcbeadsfrompolymer (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcBeadsFromPolymer", false]], "fjcmodel (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcModel", false]], "from_protein_list() (shapecgmodel class method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.from_protein_list", false]], "gaussian_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.gaussian_kernel", false]], "generate_beads() (polymermodel method)": [[15, "arbdmodel.polymer.PolymerModel.generate_beads", false]], "generate_beads() (salimodel method)": [[16, "arbdmodel.sali_polymer_model.SaliModel.generate_beads", false]], "generate_charge_distribution() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution", false]], "generate_coordinates() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_coordinates", false]], "generate_electrostatic_map() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map", false]], "generate_potential_grid() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid", false]], "generate_potential_grid() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid", false]], "generate_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.generate_protein", false]], "generate_random_protein_positions() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions", false]], "generate_spanning_vectors() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_spanning_vectors", false]], "generate_vdw_maps() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps", false]], "get_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_angles", false]], "get_attached_particles() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles", false]], "get_attached_particles() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles", false]], "get_binary() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.get_binary", false], [4, "id2", false]], "get_bond_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bond_angles", false]], "get_bonds() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bonds", false]], "get_center() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.get_center", false]], "get_center() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_center", false]], "get_center() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_center", false]], "get_center() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_center", false], [15, "id8", false]], "get_cg_distribution() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution", false], [6, "id2", false]], "get_coarse_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein", false]], "get_coarse_types() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types", false]], "get_collapsed_position() (transformable method)": [[1, "arbdmodel.core_objects.Transformable.get_collapsed_position", false]], "get_connected_location() (location method)": [[15, "arbdmodel.polymer.Location.get_connected_location", false]], "get_connections() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_connections", false]], "get_connections_and_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_connections_and_locations", false], [15, "id0", false]], "get_contour_sorted_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations", false], [15, "id9", false]], "get_default_conf() (arbdengine method)": [[27, "arbdmodel.engine.ArbdEngine.get_default_conf", false]], "get_default_conf() (namdengine method)": [[27, "arbdmodel.engine.NamdEngine.get_default_conf", false]], "get_default_conf() (simengine method)": [[27, "arbdmodel.engine.SimEngine.get_default_conf", false]], "get_dihedrals() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_dihedrals", false]], "get_exclusions() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_exclusions", false]], "get_grid_files() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files", false]], "get_impropers() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_impropers", false]], "get_location_at() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_location_at", false], [15, "id1", false]], "get_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_locations", false], [15, "id2", false]], "get_monomer_index() (location method)": [[15, "arbdmodel.polymer.Location.get_monomer_index", false]], "get_original_recursively() (clone method)": [[1, "arbdmodel.core_objects.Clone.get_original_recursively", false]], "get_particle_assignments() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.get_particle_assignments", false]], "get_product_potentials() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_product_potentials", false]], "get_protein_types() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.get_protein_types", false]], "get_resource_path() (in module 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"get_vector_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_vector_angles", false]], "get_version() (in module arbdmodel.version)": [[35, "arbdmodel.version.get_version", false]], "getparticletypesandcounts() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.getParticleTypesAndCounts", false]], "gpu (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.gpu", false]], "group (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Group", false]], "groupsite (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.GroupSite", false]], "halfharmonic (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HalfHarmonic", false]], "harmonicangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicAngle", false]], "harmonicbond (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBond", false]], "harmonicbondedpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBondedPotential", false]], "harmonicdihedral (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicDihedral", false]], "harmonicvectorangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicVectorAngle", false]], "hpsbeads (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsBeads", false]], "hpsmodel (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsModel", false]], "hpsnonbonded (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsNonbonded", false]], "hydroprorunner (class in arbdmodel.engine)": [[27, "arbdmodel.engine.HydroProRunner", false]], "ibiangle (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIAngle", false]], "ibibond (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIBond", false]], "ibidihedral (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIDihedral", false]], "ibinonbonded (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBINonbonded", false]], "index() (parent method)": [[1, "arbdmodel.core_objects.Parent.index", false]], "initialize_binary_paths() (in module arbdmodel.binary_manager)": [[30, "arbdmodel.binary_manager.initialize_binary_paths", false]], "insert() (parent method)": [[1, "arbdmodel.core_objects.Parent.insert", false]], "insert_monomers() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.insert_monomers", false], [15, "id10", false]], "integrator (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.integrator", false]], "is_dirty() (in module arbdmodel.version)": [[35, "arbdmodel.version.is_dirty", false]], "is_same_type() (particletype method)": [[1, "arbdmodel.core_objects.ParticleType.is_same_type", false]], "isotropic_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.isotropic_kernel", false]], "items() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.items", false], [4, "id3", false]], "iterate_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.iterate_connections_and_locations", false], [15, "id11", false]], "khbeads (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhBeads", false]], "khmodel (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhModel", false]], "khnonbonded (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded", false]], "kscale (harmonicangle property)": [[8, "arbdmodel.interactions.HarmonicAngle.kscale", false]], "kscale (harmonicbond property)": [[8, "arbdmodel.interactions.HarmonicBond.kscale", false]], "kscale (harmonicbondedpotential property)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.kscale", false]], "kscale (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.kscale", false]], "kscale (harmonicvectorangle property)": [[8, "arbdmodel.interactions.HarmonicVectorAngle.kscale", false]], "lennardjones (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.LennardJones", false]], "linearbond (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.LinearBond", false]], "load_structure() (parmedarbd method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.load_structure", false]], "load_target_ibi_distributions() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.load_target_IBI_distributions", false]], "loadgrid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.loadGrid", false]], "location (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Location", false]], "locations (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.locations", false]], "main() (in module arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.main", false]], "max_force (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.max_force", false]], "max_force (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.max_force", false]], "meshprocessor (class in arbdmodel.mesh_process_volume)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor", false]], "meshrigidbodytype (class in arbdmodel.mesh_rigidbody)": [[21, "arbdmodel.mesh_rigidbody.MeshRigidBodyType", false]], "micron_to_angstrom (meshprocessor attribute)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM", false]], "micron_to_angstrom (surfacemeshprocessor attribute)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM", false]], "minimizermsd() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.minimizeRmsd", false]], "module": [[1, "module-arbdmodel.core_objects", false], [3, "module-arbdmodel.model", false], [4, "module-arbdmodel.sim_config", false], [6, "module-arbdmodel.ibi", false], [8, "module-arbdmodel.interactions", false], [9, "module-arbdmodel.fjc_polymer_model", false], [10, "module-arbdmodel.hps_polymer_model", false], [12, "module-arbdmodel.kh_polymer_model", false], [13, "module-arbdmodel.mpipi_polymer", false], [14, "module-arbdmodel.onck_polymer_model", false], [15, "module-arbdmodel.polymer", false], [16, "module-arbdmodel.sali_polymer_model", false], [17, "module-arbdmodel.ssdna_two_bead", false], [19, "module-arbdmodel.mesh_process_surface", false], [20, "module-arbdmodel.mesh_process_volume", false], [21, "module-arbdmodel.mesh_rigidbody", false], [22, "module-arbdmodel.simplearbd", false], [23, "module-arbdmodel.structure_from_pdb", false], [24, "module-arbdmodel.structure_rigidbody", false], [26, "module-arbdmodel.shape_cg", false], [27, "module-arbdmodel.engine", false], [29, "module-arbdmodel.parmed_bd", false], [30, "module-arbdmodel.binary_manager", false], [31, "module-arbdmodel.coords", false], [32, "module-arbdmodel.grid", false], [34, "module-arbdmodel.logger", false], [35, "module-arbdmodel.version", false]], "monomer_index_to_contour() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.monomer_index_to_contour", false], [15, "id12", false]], "monomer_length (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.monomer_length", false]], "monomers_per_bead_group (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.monomers_per_bead_group", false]], "mpipibeads (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiBeads", false]], "mpipimodel (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiModel", false]], "mpipinonbonded (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiNonbonded", false]], "namdengine (class in arbdmodel.engine)": [[27, "arbdmodel.engine.NamdEngine", false]], "neighborhood_average() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.neighborhood_average", false]], "nt (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.nt", false]], "nullpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.NullPotential", false]], "num_bead_groups (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.num_bead_groups", false]], "num_heavy_cluster (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster", false]], "num_heavy_cluster (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.num_heavy_cluster", false]], "num_monomers (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.num_monomers", false]], "num_steps (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.num_steps", false]], "num_steps (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.num_steps", false]], "onckbeads (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckBeads", false]], "onckmodel (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckModel", false]], "oncknonbonded (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded", false]], "other() (connection method)": [[15, "arbdmodel.polymer.Connection.other", false]], "output_period (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.output_period", false]], "output_period (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.output_period", false]], "p (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.p", false]], "pairdistributiondof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.PairDistributionDof", false]], "pairlist_distance (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.pairlist_distance", false]], "parent (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Parent", false]], "parmed_structure (parmedarbd attribute)": [[29, "arbdmodel.parmed_bd.ParmedArbd.parmed_structure", false]], "parmedarbd (class in arbdmodel.parmed_bd)": [[29, "arbdmodel.parmed_bd.ParmedArbd", false]], "parse_output() (hydroprorunner method)": [[27, "arbdmodel.engine.HydroProRunner.parse_output", false]], "particletype (class in arbdmodel.core_objects)": 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"arbdmodel.polymer.PolymerModel", false]], "polymersection (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerSection", false]], "position_spline_params (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.position_spline_params", false]], "potential (abstractibipotential attribute)": [[6, "arbdmodel.ibi.AbstractIBIpotential.potential", false]], "potential() (abstractibipotential method)": [[6, "id0", false], [6, "id4", false]], "potential() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.potential", false], [8, "id1", false]], "potential() (boundarypotential method)": [[8, "arbdmodel.interactions.BoundaryPotential.potential", false]], "potential() (halfharmonic method)": [[8, "arbdmodel.interactions.HalfHarmonic.potential", false]], "potential() (harmonicbond method)": [[8, "arbdmodel.interactions.HarmonicBond.potential", false]], "potential() (harmonicbondedpotential method)": [[8, 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"arbdmodel.sim_config.SimConf.combine", false]], "compute_volume() (angledof method)": [[6, "arbdmodel.ibi.AngleDof.compute_volume", false]], "compute_volume() (bonddof method)": [[6, "arbdmodel.ibi.BondDof.compute_volume", false]], "compute_volume() (degreeoffreedom method)": [[6, "arbdmodel.ibi.DegreeOfFreedom.compute_volume", false]], "compute_volume() (pairdistributiondof method)": [[6, "arbdmodel.ibi.PairDistributionDof.compute_volume", false]], "compute_volume() (radiusdof method)": [[6, "arbdmodel.ibi.RadiusDof.compute_volume", false]], "concentration_to_debye_length() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length", false]], "connectableelement (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.ConnectableElement", false]], "connection (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Connection", false]], "constant_force() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.constant_force", false]], "contour_to_monomer_index() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_monomer_index", false]], "contour_to_orientation() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_orientation", false]], "contour_to_position() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_position", false]], "contour_to_tangent() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_tangent", false]], "convert_sod_to_mg() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg", false]], "convolve_kernel_truncate() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.convolve_kernel_truncate", false]], "create_bounding_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.create_bounding_grid", false]], "create_dual_topology() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology", false]], "create_dual_topology_model() (parmedarbd class method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model", false]], "create_engine() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_engine", false]], "create_model() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_model", false]], "create_null() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.Create_null", false]], "debye_length (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.debye_length", false]], "debye_length (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.debye_length", false]], "default_binary (arbdengine property)": [[27, "arbdmodel.engine.ArbdEngine.default_binary", false]], "default_binary (namdengine property)": [[27, "arbdmodel.engine.NamdEngine.default_binary", false]], "default_binary (simengine property)": [[27, "arbdmodel.engine.SimEngine.default_binary", false]], "defaultsimconf (class in arbdmodel.sim_config)": [[4, "arbdmodel.sim_config.DefaultSimConf", false]], "degreeoffreedom (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DegreeOfFreedom", false]], "delete() (connection method)": [[15, "arbdmodel.polymer.Connection.delete", false]], "diffusiverigidbodytype (class in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.DiffusiveRigidBodyType", false]], "dihedraldof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DihedralDof", false]], "dimensions_from_structure() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.dimensions_from_structure", false]], "dimensions_from_structure() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.dimensions_from_structure", false]], "display() (citation method)": [[35, "arbdmodel.version.Citation.display", false]], "dnamodel (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaModel", false]], "dnastrandbeads (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads", false]], "duplicate() (group method)": [[1, "arbdmodel.core_objects.Group.duplicate", false]], "duplicate() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.duplicate", false]], "duplicate() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.duplicate", false]], "excludedattributes (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.excludedAttributes", false]], "extend() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.extend", false]], "extend() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.extend", false]], "filename() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.filename", false], [6, "id1", false]], "filename() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.filename", false], [8, "id0", false]], "filename() (harmonicbondedpotential method)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.filename", false]], "filename() (nullpotential method)": [[8, "arbdmodel.interactions.NullPotential.filename", false]], "filename() (shapecgnonbonded method)": [[26, "arbdmodel.shape_cg.ShapeCGNonbonded.filename", false]], "filename() (wlcskpotential method)": [[8, "arbdmodel.interactions.WLCSKPotential.filename", false]], "fill_nans() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.fill_nans", false]], "find_shape_based_sites() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.find_shape_based_sites", false]], "fjcbeadsfrompolymer (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcBeadsFromPolymer", false]], "fjcmodel (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcModel", false]], "from_protein_list() (shapecgmodel class method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.from_protein_list", false]], "gaussian_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.gaussian_kernel", false]], "generate_beads() (polymermodel method)": [[15, "arbdmodel.polymer.PolymerModel.generate_beads", false]], "generate_beads() (salimodel method)": [[16, "arbdmodel.sali_polymer_model.SaliModel.generate_beads", false]], "generate_charge_distribution() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution", false]], "generate_coordinates() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_coordinates", false]], "generate_electrostatic_map() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map", false]], "generate_potential_grid() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid", false]], "generate_potential_grid() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid", false]], "generate_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.generate_protein", false]], "generate_random_protein_positions() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions", false]], "generate_spanning_vectors() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_spanning_vectors", false]], "generate_vdw_maps() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps", false]], "get_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_angles", false]], "get_attached_particles() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles", false]], "get_attached_particles() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles", false]], "get_binary() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.get_binary", false]], "get_bond_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bond_angles", false]], "get_bonds() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bonds", false]], "get_center() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.get_center", false]], "get_center() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_center", false]], "get_center() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_center", false]], "get_center() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_center", false]], "get_cg_distribution() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution", false], [6, "id2", false]], "get_coarse_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein", false]], "get_coarse_types() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types", false]], "get_collapsed_position() (transformable method)": [[1, "arbdmodel.core_objects.Transformable.get_collapsed_position", false]], "get_connected_location() (location method)": [[15, "arbdmodel.polymer.Location.get_connected_location", false]], "get_connections() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_connections", false]], "get_connections_and_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_connections_and_locations", false]], "get_contour_sorted_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations", false]], "get_default_conf() (arbdengine method)": [[27, "arbdmodel.engine.ArbdEngine.get_default_conf", false]], "get_default_conf() (namdengine method)": [[27, "arbdmodel.engine.NamdEngine.get_default_conf", false]], "get_default_conf() (simengine method)": [[27, "arbdmodel.engine.SimEngine.get_default_conf", false]], "get_dihedrals() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_dihedrals", false]], "get_exclusions() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_exclusions", false]], "get_grid_files() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files", false]], "get_impropers() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_impropers", false]], "get_location_at() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_location_at", false]], "get_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_locations", false]], "get_monomer_index() (location method)": [[15, "arbdmodel.polymer.Location.get_monomer_index", false]], "get_original_recursively() (clone method)": [[1, "arbdmodel.core_objects.Clone.get_original_recursively", false]], "get_particle_assignments() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.get_particle_assignments", false]], "get_product_potentials() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_product_potentials", false]], "get_protein_types() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.get_protein_types", false]], "get_resource_path() (in module arbdmodel.logger)": [[34, "arbdmodel.logger.get_resource_path", false]], "get_restraints() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.get_restraints", false]], "get_restraints() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_restraints", false]], "get_restraints() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.get_restraints", false]], "get_restraints() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.get_restraints", false]], "get_slice_enclosing_smaller_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.get_slice_enclosing_smaller_grid", false]], "get_target_distribution() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.get_target_distribution", false], [6, "id3", false]], "get_values() (degreeoffreedom method)": [[6, "arbdmodel.ibi.DegreeOfFreedom.get_values", false]], "get_values() (pairdistributiondof method)": [[6, "arbdmodel.ibi.PairDistributionDof.get_values", false]], "get_vector_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_vector_angles", false]], "get_version() (in module arbdmodel.version)": [[35, "arbdmodel.version.get_version", false]], "getparticletypesandcounts() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.getParticleTypesAndCounts", false]], "group (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Group", false]], "groupsite (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.GroupSite", false]], "halfharmonic (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HalfHarmonic", false]], "harmonicangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicAngle", false]], "harmonicbond (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBond", false]], "harmonicbondedpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBondedPotential", false]], "harmonicdihedral (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicDihedral", false]], "harmonicvectorangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicVectorAngle", false]], "hpsbeads (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsBeads", false]], "hpsmodel (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsModel", false]], "hpsnonbonded (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsNonbonded", false]], "hydroprorunner (class in arbdmodel.engine)": [[27, "arbdmodel.engine.HydroProRunner", false]], "ibiangle (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIAngle", false]], "ibibond (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIBond", false]], "ibidihedral (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIDihedral", false]], "ibinonbonded (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBINonbonded", false]], "index() (parent method)": [[1, "arbdmodel.core_objects.Parent.index", false]], "initialize_binary_paths() (in module arbdmodel.binary_manager)": [[30, "arbdmodel.binary_manager.initialize_binary_paths", false]], "insert() (parent method)": [[1, "arbdmodel.core_objects.Parent.insert", false]], "insert_monomers() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.insert_monomers", false]], "is_dirty() (in module arbdmodel.version)": [[35, "arbdmodel.version.is_dirty", false]], "is_same_type() (particletype method)": [[1, "arbdmodel.core_objects.ParticleType.is_same_type", false]], "isotropic_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.isotropic_kernel", false]], "items() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.items", false]], "iterate_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.iterate_connections_and_locations", false]], "khbeads (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhBeads", false]], "khmodel (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhModel", false]], "khnonbonded (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded", false]], "kscale (harmonicangle property)": [[8, "arbdmodel.interactions.HarmonicAngle.kscale", false]], "kscale (harmonicbond property)": [[8, "arbdmodel.interactions.HarmonicBond.kscale", false]], "kscale (harmonicbondedpotential property)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.kscale", false]], "kscale (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.kscale", false]], "kscale (harmonicvectorangle property)": [[8, "arbdmodel.interactions.HarmonicVectorAngle.kscale", false]], "lennardjones (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.LennardJones", false]], "linearbond (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.LinearBond", false]], "load_structure() (parmedarbd method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.load_structure", false]], "load_target_ibi_distributions() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.load_target_IBI_distributions", false]], "loadgrid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.loadGrid", false]], "location (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Location", false]], "main() (in module arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.main", false]], "max_force (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.max_force", false]], "max_force (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.max_force", false]], "max_force (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.max_force", false]], "max_potential (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.max_potential", false]], "meshprocessor (class in arbdmodel.mesh_process_volume)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor", false]], "meshrigidbodytype (class in arbdmodel.mesh_rigidbody)": [[21, "arbdmodel.mesh_rigidbody.MeshRigidBodyType", false]], "micron_to_angstrom (meshprocessor attribute)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM", false]], "micron_to_angstrom (surfacemeshprocessor attribute)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM", false]], "minimizermsd() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.minimizeRmsd", false]], "module": [[1, "module-arbdmodel.core_objects", false], [3, "module-arbdmodel.model", false], [4, "module-arbdmodel.sim_config", false], [6, "module-arbdmodel.ibi", false], [8, "module-arbdmodel.interactions", false], [9, "module-arbdmodel.fjc_polymer_model", false], [10, "module-arbdmodel.hps_polymer_model", false], [12, "module-arbdmodel.kh_polymer_model", false], [13, "module-arbdmodel.mpipi_polymer", false], [14, "module-arbdmodel.onck_polymer_model", false], [15, "module-arbdmodel.polymer", false], [16, "module-arbdmodel.sali_polymer_model", false], [17, "module-arbdmodel.ssdna_two_bead", false], [19, "module-arbdmodel.mesh_process_surface", false], [20, "module-arbdmodel.mesh_process_volume", false], [21, "module-arbdmodel.mesh_rigidbody", false], [22, "module-arbdmodel.simplearbd", false], [23, "module-arbdmodel.structure_from_pdb", false], [24, "module-arbdmodel.structure_rigidbody", false], [26, "module-arbdmodel.shape_cg", false], [27, "module-arbdmodel.engine", false], [29, "module-arbdmodel.parmed_bd", false], [30, "module-arbdmodel.binary_manager", false], [31, "module-arbdmodel.coords", false], [32, "module-arbdmodel.grid", false], [34, "module-arbdmodel.logger", false], [35, "module-arbdmodel.version", false]], "monomer_index_to_contour() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.monomer_index_to_contour", false]], "monomers_per_bead_group (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.monomers_per_bead_group", false]], "mpipibeads (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiBeads", false]], "mpipimodel (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiModel", false]], "mpipinonbonded (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiNonbonded", false]], "namdengine (class in arbdmodel.engine)": [[27, "arbdmodel.engine.NamdEngine", false]], "neighborhood_average() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.neighborhood_average", false]], "nt (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.nt", false]], "nullpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.NullPotential", false]], "num_bead_groups (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.num_bead_groups", false]], "onckbeads (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckBeads", false]], "onckmodel (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckModel", false]], "oncknonbonded (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded", false]], "other() (connection method)": [[15, "arbdmodel.polymer.Connection.other", false]], "p (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.p", false]], "pairdistributiondof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.PairDistributionDof", false]], "parent (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Parent", false]], "parmed_structure (parmedarbd attribute)": [[29, "arbdmodel.parmed_bd.ParmedArbd.parmed_structure", false]], "parmedarbd (class in arbdmodel.parmed_bd)": [[29, "arbdmodel.parmed_bd.ParmedArbd", false]], "parse_output() (hydroprorunner method)": [[27, "arbdmodel.engine.HydroProRunner.parse_output", false]], "particletype (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.ParticleType", false]], "pdbmodel (class in arbdmodel.model)": [[3, "arbdmodel.model.PdbModel", false]], "peptide_bond (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.peptide_bond", false]], "periodic (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.periodic", false]], "periodic (abstractpotential property)": [[8, "id1", false]], "periodic (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.periodic", false]], "periodic (ibidihedral property)": [[6, "arbdmodel.ibi.IBIDihedral.periodic", false]], "pointparticle (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.PointParticle", false]], "polymer (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.polymer", false]], "polymerbeads (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerBeads", false]], "polymergroup (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerGroup", false]], "polymermodel (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerModel", false]], "polymersection (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerSection", false]], "potential (abstractibipotential attribute)": [[6, "arbdmodel.ibi.AbstractIBIpotential.potential", false]], "potential() (abstractibipotential method)": [[6, "id0", false], [6, "id4", false]], "potential() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.potential", false], [8, "id2", false]], "potential() (boundarypotential method)": [[8, "arbdmodel.interactions.BoundaryPotential.potential", false]], "potential() (halfharmonic method)": [[8, "arbdmodel.interactions.HalfHarmonic.potential", false]], "potential() (harmonicbond method)": [[8, "arbdmodel.interactions.HarmonicBond.potential", false]], "potential() (harmonicbondedpotential method)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.potential", false]], 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+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
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-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
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+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
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diff --git a/_build/html/tutorials/2-polymer-objects/2-polymer-objects.html b/_build/html/tutorials/2-polymer-objects/2-polymer-objects.html
index b3de9a33cdf0660c803e5fa00fcfcefb0bcd8b97..3d8d5d4787fc7a44146eba25a6c041484b32a013 100644
--- a/_build/html/tutorials/2-polymer-objects/2-polymer-objects.html
+++ b/_build/html/tutorials/2-polymer-objects/2-polymer-objects.html
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
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-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html b/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html
index 5c584943c69a5ca1f1a7c18776938b956f7d5049..26b98f93959b4966baa134fc9013a3ac399d6d34 100644
--- a/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html
+++ b/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html
@@ -32,19 +32,19 @@
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-    <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
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-    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
   
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@@ -61,9 +61,9 @@
     <script src="../../_static/copybutton.js?v=f281be69"></script>
     <script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
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-    <script src="../../_static/js/hoverxref.js"></script>
-    <script src="../../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../../_static/js/micromodal.min.js"></script>
+    <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
     <script>let toggleOpenOnPrint = 'true';</script>
@@ -445,6 +445,20 @@ document.write(`
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
+<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
+<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">line</span> <span class="mi">4</span>
+<span class="g g-Whitespace">      </span><span class="mi">2</span> <span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="ne">----&gt; </span><span class="mi">4</span> <span class="kn">from</span><span class="w"> </span><span class="nn">arbdmodel</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdEngine</span>
+<span class="g g-Whitespace">      </span><span class="mi">5</span> <span class="kn">from</span><span class="w"> </span><span class="nn">arbdmodel.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">readArbdCoords</span>
+<span class="g g-Whitespace">      </span><span class="mi">6</span> <span class="kn">from</span><span class="w"> </span><span class="nn">arbdmodel.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerSection</span>
+
+<span class="ne">ModuleNotFoundError</span>: No module named &#39;arbdmodel&#39;
+</pre></div>
+</div>
+</div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -498,53 +512,6 @@ document.write(`
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
-<span class="ne">TypeError</span><span class="g g-Whitespace">                                 </span>Traceback (most recent call last)
-<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">line</span> <span class="mi">17</span>
-<span class="g g-Whitespace">     </span><span class="mi">13</span> <span class="n">debye_length</span> <span class="o">=</span> <span class="mi">10</span>
-<span class="g g-Whitespace">     </span><span class="mi">15</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span> <span class="o">=</span> <span class="n">create_arbd_polymer_objects</span><span class="p">()</span>
-<span class="ne">---&gt; </span><span class="mi">17</span> <span class="n">model</span> <span class="o">=</span> <span class="n">NupModel</span><span class="p">(</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">18</span>                   <span class="n">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">19</span>                   <span class="n">temperature</span><span class="o">=</span><span class="n">temperature</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">20</span>                   <span class="n">damping_coefficient</span> <span class="o">=</span> <span class="mi">50000</span><span class="p">,</span> <span class="c1"># units of 1/ns</span>
-<span class="g g-Whitespace">     </span><span class="mi">21</span>                   <span class="n">decomp_period</span> <span class="o">=</span> <span class="n">decomp_period</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">22</span>                   <span class="n">pairlist_distance</span> <span class="o">=</span> <span class="mi">50</span><span class="o">+</span><span class="n">skin_depth</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">23</span>                   <span class="n">dimensions</span> <span class="o">=</span> <span class="n">dimensions</span>
-<span class="g g-Whitespace">     </span><span class="mi">24</span>                   <span class="p">)</span>
-<span class="g g-Whitespace">     </span><span class="mi">25</span> <span class="n">engine</span> <span class="o">=</span> <span class="n">ArbdEngine</span><span class="p">(</span> <span class="n">integrator</span> <span class="o">=</span> <span class="s1">&#39;Langevin&#39;</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">26</span>                      <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e7</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">27</span>                      <span class="n">output_period</span><span class="o">=</span><span class="mf">1e4</span><span class="p">,</span>
-<span class="g g-Whitespace">     </span><span class="mi">28</span>                      <span class="n">gpu</span> <span class="o">=</span> <span class="mi">0</span>
-<span class="g g-Whitespace">     </span><span class="mi">29</span>                     <span class="p">)</span>
-<span class="g g-Whitespace">     </span><span class="mi">30</span> <span class="n">directory</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;1-one_bead_per_res-</span><span class="si">{</span><span class="n">model_name</span><span class="si">}</span><span class="s1">&#39;</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239,</span> in <span class="ni">HpsModel.__init__</span><span class="nt">(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)</span>
-<span class="g g-Whitespace">    </span><span class="mi">236</span> <span class="k">if</span> <span class="n">sequences</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-<span class="g g-Whitespace">    </span><span class="mi">237</span>     <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">&quot;HpsModel must be provided a sequences argument&quot;</span><span class="p">)</span>
-<span class="ne">--&gt; </span><span class="mi">239</span> <span class="n">PolymerModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> <span class="n">monomers_per_bead_group</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">241</span><span class="w"> </span><span class="sd">&quot;&quot;&quot; Update type diffusion coefficients &quot;&quot;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">242</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span> <span class="o">=</span> <span class="n">all_types</span> <span class="o">=</span> <span class="p">[</span><span class="n">t</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">t</span> <span class="ow">in</span> <span class="n">_types</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703,</span> in <span class="ni">PolymerModel.__init__</span><span class="nt">(self, polymers, sequences, monomers_per_bead_group, **kwargs)</span>
-<span class="g g-Whitespace">    </span><span class="mi">701</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequences</span> <span class="o">=</span> <span class="n">sequences</span>
-<span class="g g-Whitespace">    </span><span class="mi">702</span> <span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span> <span class="o">=</span> <span class="n">monomers_per_bead_group</span>
-<span class="ne">--&gt; </span><span class="mi">703</span> <span class="n">ArbdModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">[],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">705</span><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate beads &quot;&quot;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">706</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231,</span> in <span class="ni">ArbdModel.__init__</span><span class="nt">(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)</span>
-<span class="g g-Whitespace">    </span><span class="mi">228</span>     <span class="n">cell_origin</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
-<span class="g g-Whitespace">    </span><span class="mi">230</span> <span class="c1"># Initialize parent class</span>
-<span class="ne">--&gt; </span><span class="mi">231</span> <span class="n">PdbModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="p">,</span>
-<span class="g g-Whitespace">    </span><span class="mi">232</span>                  <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">235</span> <span class="c1"># Store origin which might be different from cell_origin</span>
-<span class="g g-Whitespace">    </span><span class="mi">236</span> <span class="bp">self</span><span class="o">.</span><span class="n">origin</span> <span class="o">=</span> <span class="n">cell_origin</span>
-
-<span class="ne">TypeError</span>: __init__() takes from 1 to 4 positional arguments but 6 were given
-</pre></div>
-</div>
-</div>
 </div>
 </section>
 <section id="step-2-setting-up-a-coarser-model">
diff --git a/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html b/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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     <script>let toggleOpenOnPrint = 'true';</script>
@@ -428,6 +428,20 @@ document.write(`
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
+<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
+<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span>
+<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="c1">## Create a function to construct the DNA model (we&#39;ll repeat this a few times)</span>
+<span class="ne">----&gt; </span><span class="mi">2</span> <span class="kn">from</span><span class="w"> </span><span class="nn">arbdmodel.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerSection</span>
+<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="kn">from</span><span class="w"> </span><span class="nn">arbdmodel.ssdna_two_bead</span><span class="w"> </span><span class="kn">import</span> <span class="n">DnaModel</span><span class="p">,</span> <span class="n">_P</span><span class="p">,</span> <span class="n">_B</span> 
+<span class="g g-Whitespace">      </span><span class="mi">5</span> <span class="k">def</span><span class="w"> </span><span class="nf">make_dna_model</span><span class="p">():</span>
+<span class="g g-Whitespace">      </span><span class="mi">6</span>     <span class="c1">## Create spline-based polymer</span>
+
+<span class="ne">ModuleNotFoundError</span>: No module named &#39;arbdmodel&#39;
+</pre></div>
+</div>
+</div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -440,52 +454,6 @@ document.write(`
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
-<span class="ne">TypeError</span><span class="g g-Whitespace">                                 </span>Traceback (most recent call last)
-<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span>
-<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="c1">## Optionally simulate the DNA-only model to see how it performs and behaves</span>
-<span class="ne">----&gt; </span><span class="mi">2</span> <span class="n">model</span> <span class="o">=</span> <span class="n">make_dna_model</span><span class="p">()</span>
-<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="n">model</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">output_name</span><span class="o">=</span><span class="s1">&#39;run&#39;</span><span class="p">,</span>
-<span class="g g-Whitespace">      </span><span class="mi">4</span>                <span class="n">directory</span><span class="o">=</span><span class="s1">&#39;trombone-no_ssb&#39;</span><span class="p">,</span>
-<span class="g g-Whitespace">      </span><span class="mi">5</span>                <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e5</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="mf">1e3</span><span class="p">,</span>
-<span class="g g-Whitespace">      </span><span class="mi">6</span> <span class="p">)</span>
-
-<span class="nn">Cell In[3], line 23,</span> in <span class="ni">make_dna_model</span><span class="nt">()</span>
-<span class="g g-Whitespace">     </span><span class="mi">20</span> <span class="n">_P</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">(</span><span class="n">replisome_grid</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span>       <span class="c1"># scale it up by a big factor</span>
-<span class="g g-Whitespace">     </span><span class="mi">21</span> <span class="n">_B</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">(</span><span class="n">replisome_grid</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span>
-<span class="ne">---&gt; </span><span class="mi">23</span> <span class="n">model</span> <span class="o">=</span> <span class="n">DnaModel</span><span class="p">([</span><span class="n">a</span><span class="p">],</span> <span class="n">dimensions</span><span class="o">=</span><span class="p">(</span><span class="mi">3000</span><span class="p">,</span><span class="mi">3000</span><span class="p">,</span><span class="mi">3000</span><span class="p">),</span>
-<span class="g g-Whitespace">     </span><span class="mi">24</span>                  <span class="n">timestep</span> <span class="o">=</span> <span class="mf">20e-6</span>
-<span class="g g-Whitespace">     </span><span class="mi">25</span>                  <span class="p">)</span>
-<span class="g g-Whitespace">     </span><span class="mi">27</span> <span class="c1">## Restrain DNA ends</span>
-<span class="g g-Whitespace">     </span><span class="mi">28</span> <span class="n">end1</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">strands</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164,</span> in <span class="ni">DnaModel.__init__</span><span class="nt">(self, polymers, sequences, DEBUG, **kwargs)</span>
-<span class="g g-Whitespace">    </span><span class="mi">161</span> <span class="k">if</span> <span class="s1">&#39;timestep&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;timestep&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">20e-6</span>
-<span class="g g-Whitespace">    </span><span class="mi">162</span> <span class="k">if</span> <span class="s1">&#39;cutoff&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;cutoff&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">35</span>
-<span class="ne">--&gt; </span><span class="mi">164</span> <span class="n">PolymerModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> <span class="n">monomers_per_bead_group</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">165</span> <span class="bp">self</span><span class="o">.</span><span class="n">strands</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="c1"># make a nice alias</span>
-<span class="g g-Whitespace">    </span><span class="mi">167</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span> <span class="n">TabulatedNonbonded</span><span class="p">(</span><span class="n">get_resource_path</span><span class="p">(</span><span class="s1">&#39;two_bead_model/NBBB.dat&#39;</span><span class="p">)),</span> <span class="n">typeA</span><span class="o">=</span><span class="n">_B</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">_B</span> <span class="p">)</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703,</span> in <span class="ni">PolymerModel.__init__</span><span class="nt">(self, polymers, sequences, monomers_per_bead_group, **kwargs)</span>
-<span class="g g-Whitespace">    </span><span class="mi">701</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequences</span> <span class="o">=</span> <span class="n">sequences</span>
-<span class="g g-Whitespace">    </span><span class="mi">702</span> <span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span> <span class="o">=</span> <span class="n">monomers_per_bead_group</span>
-<span class="ne">--&gt; </span><span class="mi">703</span> <span class="n">ArbdModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">[],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">705</span><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate beads &quot;&quot;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">706</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span>
-
-<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231,</span> in <span class="ni">ArbdModel.__init__</span><span class="nt">(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)</span>
-<span class="g g-Whitespace">    </span><span class="mi">228</span>     <span class="n">cell_origin</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
-<span class="g g-Whitespace">    </span><span class="mi">230</span> <span class="c1"># Initialize parent class</span>
-<span class="ne">--&gt; </span><span class="mi">231</span> <span class="n">PdbModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="p">,</span>
-<span class="g g-Whitespace">    </span><span class="mi">232</span>                  <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">235</span> <span class="c1"># Store origin which might be different from cell_origin</span>
-<span class="g g-Whitespace">    </span><span class="mi">236</span> <span class="bp">self</span><span class="o">.</span><span class="n">origin</span> <span class="o">=</span> <span class="n">cell_origin</span>
-
-<span class="ne">TypeError</span>: __init__() takes from 1 to 4 positional arguments but 6 were given
-</pre></div>
-</div>
-</div>
 </div>
 <p>You can load this trajectory in VMD to inspect as usual. You should also load <code class="docutils literal notranslate"><span class="pre">grids/replisome.dx</span></code> or <code class="docutils literal notranslate"><span class="pre">replisome.{psf,pdb}</span></code> so you can see the DNA in the context of the replication machinery. Also, please note that the ssDNA model used here represents poly(dT), so it is unable to base pair or form secondary structure, which is the main reason why cells need SSB proteins.</p>
 <section id="adding-single-stranded-dna-binding-protein">
diff --git a/_build/html/tutorials/index.html b/_build/html/tutorials/index.html
index ca6e43ab44959352cc6f49fa55e552c34a6398e8..b0d12f1c34c48e97bf6659d4b33e255e28373fb7 100644
--- a/_build/html/tutorials/index.html
+++ b/_build/html/tutorials/index.html
@@ -32,19 +32,19 @@
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../_static/tabs.css?v=4c969af8" />
-    <link rel="stylesheet" type="text/css" href="../_static/proof.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/proof.css?v=b4b7a797" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-examples.css?v=e236af4b" />
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-    <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css?v=7bc2f056" />
+    <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css?v=37217874" />
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+    <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+    <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+    <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+    <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css?v=d7bf34ee" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
   
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
     <script src="../_static/copybutton.js?v=f281be69"></script>
     <script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
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-    <script src="../_static/js/tooltipster.bundle.min.js"></script>
-    <script src="../_static/js/micromodal.min.js"></script>
+    <script src="../_static/js/hoverxref.js?v=c95ade4f"></script>
+    <script src="../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+    <script src="../_static/js/micromodal.min.js?v=04d6302d"></script>
     <script>let toggleHintShow = 'Click to show';</script>
     <script>let toggleHintHide = 'Click to hide';</script>
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diff --git a/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb b/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb
index 58c67d2d3f42c51868457fa061e9497f26ff77e0..1e9dfbb3f35260482bc87450150beae4c3d5ff39 100644
--- a/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb
+++ b/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb
@@ -20,7 +20,19 @@
    "execution_count": 1,
    "id": "0076eb69",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'arbdmodel'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 4\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mnumpy\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mas\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mnp\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mpathlib\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m Path\n\u001b[0;32m----> 4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01marbdmodel\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ArbdEngine\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01marbdmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcoords\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m readArbdCoords\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01marbdmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpolymer\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m PolymerSection\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'arbdmodel'"
+     ]
+    }
+   ],
    "source": [
     "## Usually this script would be put in it's own python file so it can be imported into multiple other scripts\n",
     "import numpy as np\n",
@@ -98,25 +110,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "fa9b96ae",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "TypeError",
-     "evalue": "__init__() takes from 1 to 4 positional arguments but 6 were given",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[2], line 17\u001b[0m\n\u001b[1;32m     13\u001b[0m debye_length \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m10\u001b[39m\n\u001b[1;32m     15\u001b[0m polymers, sequences \u001b[38;5;241m=\u001b[39m create_arbd_polymer_objects()\n\u001b[0;32m---> 17\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mNupModel\u001b[49m\u001b[43m(\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     18\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mdebye_length\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdebye_length\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     19\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mtemperature\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtemperature\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     20\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mdamping_coefficient\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m50000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# units of 1/ns\u001b[39;49;00m\n\u001b[1;32m     21\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mdecomp_period\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdecomp_period\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     22\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mpairlist_distance\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m50\u001b[39;49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43mskin_depth\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     23\u001b[0m \u001b[43m                  \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\n\u001b[1;32m     24\u001b[0m \u001b[43m                  \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     25\u001b[0m engine \u001b[38;5;241m=\u001b[39m ArbdEngine( integrator \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mLangevin\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     26\u001b[0m                      num_steps\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e7\u001b[39m,\n\u001b[1;32m     27\u001b[0m                      output_period\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e4\u001b[39m,\n\u001b[1;32m     28\u001b[0m                      gpu \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m     29\u001b[0m                     )\n\u001b[1;32m     30\u001b[0m directory \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m1-one_bead_per_res-\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmodel_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239\u001b[0m, in \u001b[0;36mHpsModel.__init__\u001b[0;34m(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)\u001b[0m\n\u001b[1;32m    236\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sequences \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m    237\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mNotImplementedError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHpsModel must be provided a sequences argument\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 239\u001b[0m \u001b[43mPolymerModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmonomers_per_bead_group\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    241\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Update type diffusion coefficients \"\"\"\u001b[39;00m\n\u001b[1;32m    242\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtypes \u001b[38;5;241m=\u001b[39m all_types \u001b[38;5;241m=\u001b[39m [t \u001b[38;5;28;01mfor\u001b[39;00m key,t \u001b[38;5;129;01min\u001b[39;00m _types\u001b[38;5;241m.\u001b[39mitems()]\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703\u001b[0m, in \u001b[0;36mPolymerModel.__init__\u001b[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)\u001b[0m\n\u001b[1;32m    701\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequences \u001b[38;5;241m=\u001b[39m sequences\n\u001b[1;32m    702\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmonomers_per_bead_group \u001b[38;5;241m=\u001b[39m monomers_per_bead_group\n\u001b[0;32m--> 703\u001b[0m \u001b[43mArbdModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    705\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Generate beads \"\"\"\u001b[39;00m\n\u001b[1;32m    706\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_beads()\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231\u001b[0m, in \u001b[0;36mArbdModel.__init__\u001b[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)\u001b[0m\n\u001b[1;32m    228\u001b[0m     cell_origin \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m    230\u001b[0m \u001b[38;5;66;03m# Initialize parent class\u001b[39;00m\n\u001b[0;32m--> 231\u001b[0m \u001b[43mPdbModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mchildren\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_duplicate_bonded_terms\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    232\u001b[0m \u001b[43m                 \u001b[49m\u001b[43mcell_vectors\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcell_origin\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    235\u001b[0m \u001b[38;5;66;03m# Store origin which might be different from cell_origin\u001b[39;00m\n\u001b[1;32m    236\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39morigin \u001b[38;5;241m=\u001b[39m cell_origin\n",
-      "\u001b[0;31mTypeError\u001b[0m: __init__() takes from 1 to 4 positional arguments but 6 were given"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "\n",
     "temperature = 298.15\n",
diff --git a/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb b/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb
index 20719e83926af27591ea663fbcb0d2ca0b516b1c..efa305dc3df78354e95d5bedcdbbb621beb1bbd9 100644
--- a/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb
+++ b/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb
@@ -50,7 +50,19 @@
    "execution_count": 3,
    "id": "6818145a",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'arbdmodel'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m## Create a function to construct the DNA model (we'll repeat this a few times)\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01marbdmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpolymer\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m PolymerSection\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01marbdmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mssdna_two_bead\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m DnaModel, _P, _B \n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21mmake_dna_model\u001b[39m():\n\u001b[1;32m      6\u001b[0m     \u001b[38;5;66;03m## Create spline-based polymer\u001b[39;00m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'arbdmodel'"
+     ]
+    }
+   ],
    "source": [
     "## Create a function to construct the DNA model (we'll repeat this a few times)\n",
     "from arbdmodel.polymer import PolymerSection\n",
@@ -90,26 +102,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "d74b1f0c",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "TypeError",
-     "evalue": "__init__() takes from 1 to 4 positional arguments but 6 were given",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m## Optionally simulate the DNA-only model to see how it performs and behaves\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mmake_dna_model\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      3\u001b[0m model\u001b[38;5;241m.\u001b[39msimulate(output_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m      4\u001b[0m                directory\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtrombone-no_ssb\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m      5\u001b[0m                num_steps\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e5\u001b[39m, output_period\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e3\u001b[39m,\n\u001b[1;32m      6\u001b[0m )\n",
-      "Cell \u001b[0;32mIn[3], line 23\u001b[0m, in \u001b[0;36mmake_dna_model\u001b[0;34m()\u001b[0m\n\u001b[1;32m     20\u001b[0m _P\u001b[38;5;241m.\u001b[39mgrid \u001b[38;5;241m=\u001b[39m (replisome_grid, \u001b[38;5;241m500\u001b[39m)       \u001b[38;5;66;03m# scale it up by a big factor\u001b[39;00m\n\u001b[1;32m     21\u001b[0m _B\u001b[38;5;241m.\u001b[39mgrid \u001b[38;5;241m=\u001b[39m (replisome_grid, \u001b[38;5;241m500\u001b[39m)\n\u001b[0;32m---> 23\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mDnaModel\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[43ma\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     24\u001b[0m \u001b[43m                 \u001b[49m\u001b[43mtimestep\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m20e-6\u001b[39;49m\n\u001b[1;32m     25\u001b[0m \u001b[43m                 \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     27\u001b[0m \u001b[38;5;66;03m## Restrain DNA ends\u001b[39;00m\n\u001b[1;32m     28\u001b[0m end1 \u001b[38;5;241m=\u001b[39m model\u001b[38;5;241m.\u001b[39mstrands[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mchildren[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mchildren[\u001b[38;5;241m0\u001b[39m]\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164\u001b[0m, in \u001b[0;36mDnaModel.__init__\u001b[0;34m(self, polymers, sequences, DEBUG, **kwargs)\u001b[0m\n\u001b[1;32m    161\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtimestep\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m kwargs: kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtimestep\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m20e-6\u001b[39m\n\u001b[1;32m    162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcutoff\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m kwargs: kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcutoff\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m35\u001b[39m\n\u001b[0;32m--> 164\u001b[0m \u001b[43mPolymerModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmonomers_per_bead_group\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    165\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstrands \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mchildren \u001b[38;5;66;03m# make a nice alias\u001b[39;00m\n\u001b[1;32m    167\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_nonbonded_interaction( TabulatedNonbonded(get_resource_path(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtwo_bead_model/NBBB.dat\u001b[39m\u001b[38;5;124m'\u001b[39m)), typeA\u001b[38;5;241m=\u001b[39m_B, typeB\u001b[38;5;241m=\u001b[39m_B )\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:703\u001b[0m, in \u001b[0;36mPolymerModel.__init__\u001b[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)\u001b[0m\n\u001b[1;32m    701\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequences \u001b[38;5;241m=\u001b[39m sequences\n\u001b[1;32m    702\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmonomers_per_bead_group \u001b[38;5;241m=\u001b[39m monomers_per_bead_group\n\u001b[0;32m--> 703\u001b[0m \u001b[43mArbdModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    705\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Generate beads \"\"\"\u001b[39;00m\n\u001b[1;32m    706\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_beads()\n",
-      "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231\u001b[0m, in \u001b[0;36mArbdModel.__init__\u001b[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)\u001b[0m\n\u001b[1;32m    228\u001b[0m     cell_origin \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m    230\u001b[0m \u001b[38;5;66;03m# Initialize parent class\u001b[39;00m\n\u001b[0;32m--> 231\u001b[0m \u001b[43mPdbModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mchildren\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_duplicate_bonded_terms\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    232\u001b[0m \u001b[43m                 \u001b[49m\u001b[43mcell_vectors\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcell_origin\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    235\u001b[0m \u001b[38;5;66;03m# Store origin which might be different from cell_origin\u001b[39;00m\n\u001b[1;32m    236\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39morigin \u001b[38;5;241m=\u001b[39m cell_origin\n",
-      "\u001b[0;31mTypeError\u001b[0m: __init__() takes from 1 to 4 positional arguments but 6 were given"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "## Optionally simulate the DNA-only model to see how it performs and behaves\n",
     "model = make_dna_model()\n",