From 448df773ad9e4bb4d3f8283b1f89e8c6726101b8 Mon Sep 17 00:00:00 2001
From: Jeffrey Hyman <you@ejhyman@lanl.gov>
Date: Mon, 30 Oct 2023 14:56:19 -0400
Subject: [PATCH] upload html

---
 docs/_modules/index.html    |   6 +-
 docs/_sources/index.rst.txt |  28 +++
 docs/applications.html      |   6 +-
 docs/dfnflow.html           |   6 +-
 docs/dfngen.html            |   6 +-
 docs/dfntrans.html          |   6 +-
 docs/examples.html          |   6 +-
 docs/gallery.html           |   6 +-
 docs/genindex.html          |   6 +-
 docs/index.html             | 365 ++++++++++++++++++++++++++++++++++++
 docs/intro.html             |  10 +-
 docs/objects.inv            | Bin 5915 -> 5909 bytes
 docs/output.html            |   6 +-
 docs/publications.html      |   6 +-
 docs/py-modindex.html       |   6 +-
 docs/pydfnFlow.html         |   6 +-
 docs/pydfnGen.html          |   6 +-
 docs/pydfnGraph.html        |   6 +-
 docs/pydfnTrans.html        |   6 +-
 docs/pydfnWorks-well.html   |   6 +-
 docs/pydfnworks.html        |   6 +-
 docs/search.html            |   6 +-
 docs/searchindex.js         |   2 +-
 docs/setup.html             |   6 +-
 24 files changed, 456 insertions(+), 63 deletions(-)
 create mode 100644 docs/_sources/index.rst.txt
 create mode 100644 docs/index.html

diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 79e1777d..9f492ae4 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -28,7 +28,7 @@
 
           
           
-          <a href="../index_docs.html" class="icon icon-home">
+          <a href="../index.html" class="icon icon-home">
             dfnWorks
               <img src="../_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -68,14 +68,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../index_docs.html">dfnWorks</a>
+          <a href="../index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Overview: module code</li>
       <li class="wy-breadcrumbs-aside">
       </li>
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
new file mode 100644
index 00000000..4a5576d9
--- /dev/null
+++ b/docs/_sources/index.rst.txt
@@ -0,0 +1,28 @@
+.. dfnWorks documentation master file, created by Satish Karra Oct 6, 2016
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to dfnWorks 2.7 documentation!
+=======================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 3
+
+   intro
+   applications
+   setup
+   examples 
+   pydfnworks
+   pydfnGen
+   pydfnFlow
+   pydfnTrans
+   pydfnGraph
+   pydfnWorks-well
+   dfngen
+   dfnflow
+   dfntrans
+   output
+   publications
+   gallery
diff --git a/docs/applications.html b/docs/applications.html
index 55ab3cdf..b839da82 100644
--- a/docs/applications.html
+++ b/docs/applications.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -76,14 +76,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Example Applications</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/applications.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/dfnflow.html b/docs/dfnflow.html
index 3d3048eb..b55b86d5 100644
--- a/docs/dfnflow.html
+++ b/docs/dfnflow.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -71,14 +71,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">dfnFlow</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/dfnflow.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/dfngen.html b/docs/dfngen.html
index 034dc308..472c6ad2 100644
--- a/docs/dfngen.html
+++ b/docs/dfngen.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -194,14 +194,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">dfnGen - C++ Generation Code</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/dfngen.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/dfntrans.html b/docs/dfntrans.html
index 214a7fc1..d6f92804 100644
--- a/docs/dfntrans.html
+++ b/docs/dfntrans.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -74,14 +74,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">dfnTrans</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/dfntrans.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/examples.html b/docs/examples.html
index b49db5b1..264c27a6 100644
--- a/docs/examples.html
+++ b/docs/examples.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -78,14 +78,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Examples</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/examples.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/gallery.html b/docs/gallery.html
index 2f62466e..5877fb24 100644
--- a/docs/gallery.html
+++ b/docs/gallery.html
@@ -30,7 +30,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -70,14 +70,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">dfnWorks Gallery</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/gallery.rst.txt" rel="nofollow"> View page source</a>
diff --git a/docs/genindex.html b/docs/genindex.html
index 6d114127..86659593 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -28,7 +28,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
             dfnWorks
               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
           </a>
@@ -68,14 +68,14 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index_docs.html">dfnWorks</a>
+          <a href="index.html">dfnWorks</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index_docs.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Index</li>
       <li class="wy-breadcrumbs-aside">
       </li>
diff --git a/docs/index.html b/docs/index.html
new file mode 100644
index 00000000..827981d2
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,365 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Welcome to dfnWorks 2.7 documentation! &mdash; dfnWorks 2.7 documentation</title>
+      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=ab527d87"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Welcome To dfnWorks" href="intro.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="#" class="icon icon-home">
+            dfnWorks
+              <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
+          </a>
+              <div class="version">
+                2.7, LANL, Docs: LA-UR-17-22216, Software: LA-CC-17-027
+              </div>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="intro.html">Welcome To dfnWorks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="applications.html">Example Applications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="setup.html">Setting and Running up dfnWorks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnworks.html">pydfnworks: the dfnWorks python package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnGen.html">pydfnworks: dfnGen</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnFlow.html">pydfnworks: dfnFlow</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnTrans.html">pydfnworks: dfnTrans</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnGraph.html">pydfnworks: dfnGraph</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnWorks-well.html">pydfnworks: Well Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dfngen.html">dfnGen - C++ Generation Code</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dfnflow.html">dfnFlow</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dfntrans.html">dfnTrans</a></li>
+<li class="toctree-l1"><a class="reference internal" href="output.html">Run Files</a></li>
+<li class="toctree-l1"><a class="reference internal" href="publications.html">dfnWorks Publications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="gallery.html">dfnWorks Gallery</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="#">dfnWorks</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="#" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Welcome to dfnWorks 2.7 documentation!</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="welcome-to-dfnworks-2-7-documentation">
+<h1>Welcome to dfnWorks 2.7 documentation!<a class="headerlink" href="#welcome-to-dfnworks-2-7-documentation" title="Link to this heading"></a></h1>
+<p>Contents:</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="intro.html">Welcome To dfnWorks</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#obtaining-dfnworks">Obtaining dfnWorks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#citing-dfnworks">Citing dfnWorks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#versions">Versions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-7">v2.7</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-6">v2.6</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-5">v2.5</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-4">v2.4</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-3">v2.3</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-2">v2.2</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-1">v2.1</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#v2-0">v2.0</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#about-this-manual">About this  manual</a></li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#contact">Contact</a></li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#contributors">Contributors</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#lanl">LANL</a></li>
+<li class="toctree-l3"><a class="reference internal" href="intro.html#external">External</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="intro.html#copyright-information">Copyright Information</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="applications.html">Example Applications</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="applications.html#carbon-dioxide-sequestration">Carbon dioxide sequestration</a></li>
+<li class="toctree-l2"><a class="reference internal" href="applications.html#shale-energy-extraction">Shale energy extraction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="applications.html#nuclear-waste-repository">Nuclear waste repository</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="setup.html">Setting and Running up dfnWorks</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="setup.html#docker">Docker</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#running-the-dfnworks-container">Running the dfnWorks container</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="setup.html#native-build-from-github-repository">Native build from github repository</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#clone-the-dnfworks-repository">Clone the dnfWorks repository</a></li>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#fix-paths-in-test-directory">Fix paths in test directory</a></li>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#set-the-lagrit-petsc-pflotran-python-and-fehm-paths">Set the LagriT, PETSC, PFLOTRAN, Python, and FEHM paths</a></li>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#installing-pydfnworks">Installing pydfnworks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="setup.html#installation-requirements-for-native-build">Installation Requirements for Native Build</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#user-defined-rects">4_user_defined_rects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#user-defined-ell-uniform">4_user_defined_ell_uniform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#exp-exponentially-distributed-fracture-lengths">exp: Exponentially Distributed fracture lengths</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#tpl-truncated-power-law">TPL: Truncated Power-Law</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#graph-based-pruning">Graph-based pruning</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnworks.html">pydfnworks: the dfnWorks python package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnworks.html#running-dfnworks-from-the-command-line-using-pydfnworks">Running dfnWorks from the command line using pydfnWorks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnworks.html#the-dfnworks-class">The DFNWORKS class</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#jobname">jobname</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#ncpu">ncpu</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#dfnflow-file-dfngen-file-dfntrans-file">dfnFlow_file/dfnGen_file/dfnTrans_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#path">path</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#prune-file">prune_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#flow-solver">flow_solver</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#cell-based-aperture">cell_based_aperture</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnworks.html#additional-arguments">additional arguments</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnworks.html#pydfnworks-modules">pydfnWorks : Modules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnworks.html#detailed-doxygen-documentation">Detailed Doxygen Documentation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnGen.html">pydfnworks: dfnGen</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnGen.html#dfngen">dfnGen</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#adding-fracture-families">Adding Fracture Families</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#adding-user-fractures">Adding User Fractures</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#adding-user-fractures-from-a-file">Adding User Fractures From a File</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#print-parameter-information">Print Parameter Information</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#processing-generator-input">Processing Generator Input</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.generation.generator">Running the Generator</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.generation.output_report.gen_output">Analysis of Generated DFN</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#additional-information-on-the-modification-of-hydraulic-properties-of-the-dfn">Additional Information on the Modification of Hydraulic Properties of the DFN</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.generation.stress">Modification of hydraulic properties of the DFN based on background stress field</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnGen.html#meshing-lagrit">Meshing - LaGriT</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mesh_dfn">Primary DFN meshing driver</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.mesh_dfn_helper">Meshing helper methods</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnGen.html#udfm">UDFM</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGen.html#module-pydfnworks.dfnGen.meshing.udfm.map2continuum">Creating an upscaled mesh of the DFN</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnFlow.html">pydfnworks: dfnFlow</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnFlow.html#module-pydfnworks.dfnFlow.flow">Running Flow : General</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.flow.create_dfn_flow_links"><code class="docutils literal notranslate"><span class="pre">create_dfn_flow_links()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.flow.dfn_flow"><code class="docutils literal notranslate"><span class="pre">dfn_flow()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.flow.set_flow_solver"><code class="docutils literal notranslate"><span class="pre">set_flow_solver()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnFlow.html#module-pydfnworks.dfnFlow.pflotran">Running Flow: PFLOTRAN</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.lagrit2pflotran"><code class="docutils literal notranslate"><span class="pre">lagrit2pflotran()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.parse_pflotran_vtk_python"><code class="docutils literal notranslate"><span class="pre">parse_pflotran_vtk_python()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.pflotran"><code class="docutils literal notranslate"><span class="pre">pflotran()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.pflotran_cleanup"><code class="docutils literal notranslate"><span class="pre">pflotran_cleanup()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.write_perms_and_correct_volumes_areas"><code class="docutils literal notranslate"><span class="pre">write_perms_and_correct_volumes_areas()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.pflotran.zone2ex"><code class="docutils literal notranslate"><span class="pre">zone2ex()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnFlow.html#module-pydfnworks.dfnFlow.fehm">Running Flow: FEHM</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.fehm.correct_stor_file"><code class="docutils literal notranslate"><span class="pre">correct_stor_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.fehm.fehm"><code class="docutils literal notranslate"><span class="pre">fehm()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnFlow.html#module-pydfnworks.dfnFlow.mass_balance">Processing Flow</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnFlow.html#pydfnworks.dfnFlow.mass_balance.effective_perm"><code class="docutils literal notranslate"><span class="pre">effective_perm()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnTrans.html">pydfnworks: dfnTrans</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnTrans.html#module-pydfnworks.dfnTrans.transport">Running Transport Simulations</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnTrans.html#pydfnworks.dfnTrans.transport.check_dfn_trans_run_files"><code class="docutils literal notranslate"><span class="pre">check_dfn_trans_run_files()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnTrans.html#pydfnworks.dfnTrans.transport.copy_dfn_trans_files"><code class="docutils literal notranslate"><span class="pre">copy_dfn_trans_files()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnTrans.html#pydfnworks.dfnTrans.transport.create_dfn_trans_links"><code class="docutils literal notranslate"><span class="pre">create_dfn_trans_links()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnTrans.html#pydfnworks.dfnTrans.transport.dfn_trans"><code class="docutils literal notranslate"><span class="pre">dfn_trans()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnTrans.html#pydfnworks.dfnTrans.transport.run_dfn_trans"><code class="docutils literal notranslate"><span class="pre">run_dfn_trans()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnGraph.html">pydfnworks: dfnGraph</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnGraph.html#module-pydfnworks.dfnGraph.dfn2graph">General Graph Functions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.add_fracture_source"><code class="docutils literal notranslate"><span class="pre">add_fracture_source()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.add_fracture_target"><code class="docutils literal notranslate"><span class="pre">add_fracture_target()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.create_graph"><code class="docutils literal notranslate"><span class="pre">create_graph()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.dump_fractures"><code class="docutils literal notranslate"><span class="pre">dump_fractures()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.dump_json_graph"><code class="docutils literal notranslate"><span class="pre">dump_json_graph()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.load_json_graph"><code class="docutils literal notranslate"><span class="pre">load_json_graph()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.dfn2graph.plot_graph"><code class="docutils literal notranslate"><span class="pre">plot_graph()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.pruning.greedy_edge_disjoint"><code class="docutils literal notranslate"><span class="pre">greedy_edge_disjoint()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.pruning.k_shortest_paths_backbone"><code class="docutils literal notranslate"><span class="pre">k_shortest_paths_backbone()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="pydfnGraph.html#module-pydfnworks.dfnGraph.graph_flow">Graph-Based Flow and Transport</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.graph_flow.run_graph_flow"><code class="docutils literal notranslate"><span class="pre">run_graph_flow()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnGraph.html#pydfnworks.dfnGraph.graph_transport.run_graph_transport"><code class="docutils literal notranslate"><span class="pre">run_graph_transport()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pydfnWorks-well.html">pydfnworks: Well Package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pydfnWorks-well.html#module-pydfnworks.dfnGen.well_package.wells">dfnWorks - Well Package</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pydfnWorks-well.html#pydfnworks.dfnGen.well_package.wells.cleanup_wells"><code class="docutils literal notranslate"><span class="pre">cleanup_wells()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnWorks-well.html#pydfnworks.dfnGen.well_package.wells.combine_well_boundary_zones"><code class="docutils literal notranslate"><span class="pre">combine_well_boundary_zones()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnWorks-well.html#pydfnworks.dfnGen.well_package.wells.find_well_intersection_points"><code class="docutils literal notranslate"><span class="pre">find_well_intersection_points()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="pydfnWorks-well.html#pydfnworks.dfnGen.well_package.wells.tag_well_in_mesh"><code class="docutils literal notranslate"><span class="pre">tag_well_in_mesh()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="dfngen.html">dfnGen - C++ Generation Code</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#domain-parameters">Domain Parameters</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#domainsize">domainSize</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#domainsizeincrease">domainSizeIncrease</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#numoflayers">numOfLayers</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#layers">layers</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#numofregions">numOfRegions</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#regions">regions</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#ignoreboundaryfaces">ignoreBoundaryFaces</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#boundaryfaces">boundaryFaces</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#general-network-generation-parameters">General Network Generation Parameters</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#stopcondition">stopCondition</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#npoly">nPoly</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#famprob">famProb</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#orientationoption">orientationOption</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#angleoption">angleOption</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#h">h</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#disablefram">disableFram</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#printrejectreasons">printRejectReasons</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#rejectsperfracture">rejectsPerFracture</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#radiilistincrease">radiiListIncrease</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#visualizationmode">visualizationMode</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#seed">seed</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#keeponlylargestcluster">keepOnlyLargestCluster</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#keepisolatedfractures">keepIsolatedFractures</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#tripleintersections">tripleIntersections</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#removefractureslessthan">removeFracturesLessThan</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#insertuserrectanglesfirst">insertUserRectanglesFirst</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#forcelargefractures">forceLargeFractures</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#general-network-output-parameters">General Network Output Parameters</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#outputallradii">outputAllRadii</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#outputacceptedradiiperfamily">outputAcceptedRadiiPerFamily</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#outputfinalradiiperfamily">outputFinalRadiiPerFamily</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#fracture-family-generation-parameters-ellipse">Fracture Family Generation Parameters: Ellipse</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#ellipse-general-parameters">Ellipse: General Parameters</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#ellipse-fracture-orientation">Ellipse: Fracture Orientation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#ellipse-fracture-radius-distributions">Ellipse: Fracture Radius Distributions</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#fracture-family-generation-parameters-rectangle">Fracture Family Generation Parameters: Rectangle</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#rectangle-general-parameters">Rectangle: General Parameters</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#rectangle-fracture-orientation">Rectangle: Fracture Orientation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#rectangle-fracture-radius-distributions">Rectangle: Fracture Radius Distributions</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#user-defined-fracture-generation-parameters">User Defined Fracture Generation Parameters</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#user-defined-ellipses">User Defined Ellipses</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#user-defined-rectangles">User Defined Rectangles</a></li>
+<li class="toctree-l3"><a class="reference internal" href="dfngen.html#polygons">Polygons</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="dfngen.html#source-code-documentation-doxygen">Source Code Documentation (Doxygen)</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="dfnflow.html">dfnFlow</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dfntrans.html">dfnTrans</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="dfntrans.html#documentation">Documentation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="output.html">Run Files</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="output.html#dfngen-output">dfnGen - output</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html#lagrit-output">LaGrit - Output</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html#pflotran-output">PFLOTRAN - output</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="publications.html">dfnWorks Publications</a></li>
+<li class="toctree-l1"><a class="reference internal" href="gallery.html">dfnWorks Gallery</a></li>
+</ul>
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diff --git a/docs/objects.inv b/docs/objects.inv
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+          <a href="index.html" class="icon icon-home">
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diff --git a/docs/publications.html b/docs/publications.html
index 02f8bdb6..9a4dbf5e 100644
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+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index bdb35004..9b914949 100644
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+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
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diff --git a/docs/pydfnFlow.html b/docs/pydfnFlow.html
index 523487bf..b8ad7db4 100644
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+          <a href="index.html" class="icon icon-home">
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+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
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diff --git a/docs/pydfnGen.html b/docs/pydfnGen.html
index 8e101917..8fb5dce3 100644
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+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
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diff --git a/docs/pydfnGraph.html b/docs/pydfnGraph.html
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diff --git a/docs/pydfnTrans.html b/docs/pydfnTrans.html
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\ No newline at end of file
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"enumPoints": [[2, "enumpoints"]], "easpect": [[2, "easpect"]], "Ellipse: Fracture Orientation": [[2, "ellipse-fracture-orientation"]], "ekappa": [[2, "ekappa"]], "Ellipse: Spherical Coordinates": [[2, "ellipse-spherical-coordinates"]], "etheta": [[2, "etheta"]], "ephi": [[2, "ephi"]], "Ellipse: Trend & Plunge": [[2, "ellipse-trend-plunge"]], "etrend": [[2, "etrend"]], "eplunge": [[2, "eplunge"]], "Ellipse: Dip & Strike": [[2, "ellipse-dip-strike"]], "estrike": [[2, "estrike"]], "edip": [[2, "edip"]], "Ellipse: In Plane Rotation": [[2, "ellipse-in-plane-rotation"]], "ebetaDistribution": [[2, "ebetadistribution"]], "ebeta": [[2, "ebeta"]], "Ellipse: Fracture Radius Distributions": [[2, "ellipse-fracture-radius-distributions"]], "edistr": [[2, "edistr"]], "Ellipse: Lognormal Distribution": [[2, "ellipse-lognormal-distribution"]], "eLogMean": [[2, "elogmean"]], "esd": [[2, "esd"]], "eLogMin": [[2, "elogmin"]], "eLogMax": [[2, "elogmax"]], "Ellipse: Truncated Powerlaw Distribution": [[2, "ellipse-truncated-powerlaw-distribution"]], "ealpha": [[2, "ealpha"]], "emin": [[2, "emin"]], "emax": [[2, "emax"]], "Ellipse: Exponential Distribution": [[2, "ellipse-exponential-distribution"]], "eExpMean": [[2, "eexpmean"]], "eExpMin": [[2, "eexpmin"]], "eExpMax": [[2, "eexpmax"]], "Ellipse: Constant": [[2, "ellipse-constant"]], "econst": [[2, "econst"]], "Fracture Family Generation Parameters: Rectangle": [[2, "fracture-family-generation-parameters-rectangle"]], "Rectangle: General Parameters": [[2, "rectangle-general-parameters"]], "nFamRect": [[2, "nfamrect"]], "rLayer": [[2, "rlayer"]], "rRegion": [[2, "rregion"]], "r_p32Targets": [[2, "r-p32targets"]], "raspect": [[2, "raspect"]], "Rectangle: Fracture Orientation": [[2, "rectangle-fracture-orientation"]], "rkappa": [[2, "rkappa"]], "Rectangle: Spherical Coordinates": [[2, "rectangle-spherical-coordinates"]], "rtheta": [[2, "rtheta"]], "rphi": [[2, "rphi"]], "Rectangle: Trend & Plunge": [[2, "rectangle-trend-plunge"]], "rtrend": [[2, "rtrend"]], "rplunge": [[2, "rplunge"]], "Rectangle: Dip & Strike": [[2, "rectangle-dip-strike"]], "rstrike": [[2, "rstrike"]], "rdip": [[2, "rdip"]], "Rectangle: In Plane Rotation": [[2, "rectangle-in-plane-rotation"]], "rbetaDistribution": [[2, "rbetadistribution"]], "rbeta": [[2, "rbeta"]], "Rectangle: Fracture Radius Distributions": [[2, "rectangle-fracture-radius-distributions"]], "rdistr": [[2, "rdistr"]], "Rectangle: Lognormal Distribution": [[2, "rectangle-lognormal-distribution"]], "rLogMean": [[2, "rlogmean"]], "rsd": [[2, "rsd"]], "rLogMin": [[2, "rlogmin"]], "rLogMax": [[2, "rlogmax"]], "Rectangle: Truncated Powerlaw Distribution": [[2, "rectangle-truncated-powerlaw-distribution"]], "ralpha": [[2, "ralpha"]], "rmin": [[2, "rmin"]], "rmax": [[2, "rmax"]], "Rectangle: Exponential Distribution": [[2, "rectangle-exponential-distribution"]], "rExpMean": [[2, "rexpmean"]], "rExpMin": [[2, "rexpmin"]], "rExpMax": [[2, "rexpmax"]], "Rectangle: Constant": [[2, 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background stress field": [[11, "module-pydfnworks.dfnGen.generation.stress"]], "Meshing - LaGriT": [[11, "meshing-lagrit"]], "Primary DFN meshing driver": [[11, "module-pydfnworks.dfnGen.meshing.mesh_dfn"]], "Meshing helper methods": [[11, "module-pydfnworks.dfnGen.meshing.mesh_dfn_helper"]], "UDFM": [[11, "udfm"]], "Creating an upscaled mesh of the DFN": [[11, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "pydfnworks: dfnGraph": [[12, "pydfnworks-dfngraph"]], "General Graph Functions": [[12, "module-pydfnworks.dfnGraph.dfn2graph"]], "Graph-Based Flow and Transport": [[12, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks: dfnTrans": [[13, "pydfnworks-dfntrans"]], "Running Transport Simulations": [[13, "module-pydfnworks.dfnTrans.transport"]], "pydfnworks: Well Package": [[14, "pydfnworks-well-package"]], "dfnWorks - Well Package": [[14, "module-pydfnworks.dfnGen.well_package.wells"]], "pydfnworks: the dfnWorks python package": [[15, "pydfnworks-the-dfnworks-python-package"]], "Running dfnWorks from the command line using pydfnWorks": [[15, "running-dfnworks-from-the-command-line-using-pydfnworks"]], "The DFNWORKS class": [[15, "the-dfnworks-class"]], "jobname": [[15, "jobname"]], "ncpu": [[15, "ncpu"]], "dfnFlow_file/dfnGen_file/dfnTrans_file": [[15, "dfnflow-file-dfngen-file-dfntrans-file"]], "path": [[15, "path"]], "prune_file": [[15, "prune-file"]], "flow_solver": [[15, "flow-solver"]], "cell_based_aperture": [[15, "cell-based-aperture"]], "additional arguments": [[15, "additional-arguments"]], "pydfnWorks : Modules": [[15, "pydfnworks-modules"]], "Detailed Doxygen Documentation": [[15, "detailed-doxygen-documentation"]], "Setting and Running up dfnWorks": [[16, "setting-and-running-up-dfnworks"]], "Docker": [[16, "docker"]], "Running the dfnWorks container": [[16, "running-the-dfnworks-container"]], "Native build from github repository": [[16, "native-build-from-github-repository"]], "Clone the dnfWorks 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[[10, "pydfnworks.dfnFlow.pflotran.pflotran_cleanup"]], "pydfnworks.dfnflow.fehm": [[10, "module-pydfnworks.dfnFlow.fehm"]], "pydfnworks.dfnflow.flow": [[10, "module-pydfnworks.dfnFlow.flow"]], "pydfnworks.dfnflow.mass_balance": [[10, "module-pydfnworks.dfnFlow.mass_balance"]], "pydfnworks.dfnflow.pflotran": [[10, "module-pydfnworks.dfnFlow.pflotran"]], "set_flow_solver() (in module pydfnworks.dfnflow.flow)": [[10, "pydfnworks.dfnFlow.flow.set_flow_solver"]], "write_perms_and_correct_volumes_areas() (in module pydfnworks.dfnflow.pflotran)": [[10, "pydfnworks.dfnFlow.pflotran.write_perms_and_correct_volumes_areas"]], "zone2ex() (in module pydfnworks.dfnflow.pflotran)": [[10, "pydfnworks.dfnFlow.pflotran.zone2ex"]], "add_variable_to_mesh() (in module pydfnworks.dfngen.meshing.add_attribute_to_mesh)": [[11, "pydfnworks.dfnGen.meshing.add_attribute_to_mesh.add_variable_to_mesh"]], "check_false_connections() (in module pydfnworks.dfngen.meshing.udfm.false_connections)": [[11, 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pydfnworks.dfngen.generation.generator)": [[11, "pydfnworks.dfnGen.generation.generator.make_working_directory"]], "map2continuum.py": [[11, "module-map2continuum.py"]], "map_to_continuum() (in module pydfnworks.dfngen.meshing.udfm.map2continuum)": [[11, "pydfnworks.dfnGen.meshing.udfm.map2continuum.map_to_continuum"]], "mesh_dfn.py": [[11, "module-mesh_dfn.py"]], "mesh_dfn_helper.py": [[11, "module-mesh_dfn_helper.py"]], "mesh_network() (in module pydfnworks.dfngen.meshing.mesh_dfn)": [[11, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_network"]], "output_report() (in module pydfnworks.dfngen.generation.output_report.gen_output)": [[11, "pydfnworks.dfnGen.generation.output_report.gen_output.output_report"]], "print_domain_parameters() (in module pydfnworks.dfngen.generation.input_checking)": [[11, "pydfnworks.dfnGen.generation.input_checking.print_domain_parameters"]], "print_family_information() (in module pydfnworks.dfngen.generation.input_checking)": [[11, "pydfnworks.dfnGen.generation.input_checking.print_family_information"]], "print_user_fracture_information() (in module pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions)": [[11, "pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions.print_user_fracture_information"]], "pydfnworks.dfngen.generation.generator": [[11, "module-pydfnworks.dfnGen.generation.generator"]], "pydfnworks.dfngen.generation.input_checking": [[11, "module-pydfnworks.dfnGen.generation.input_checking"]], "pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions": [[11, "module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"]], "pydfnworks.dfngen.generation.output_report.gen_output": [[11, "module-pydfnworks.dfnGen.generation.output_report.gen_output"]], "pydfnworks.dfngen.generation.stress": [[11, "module-pydfnworks.dfnGen.generation.stress"]], "pydfnworks.dfngen.meshing.add_attribute_to_mesh": [[11, "module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"]], "pydfnworks.dfngen.meshing.mesh_dfn": [[11, "module-pydfnworks.dfnGen.meshing.mesh_dfn"]], "pydfnworks.dfngen.meshing.mesh_dfn_helper": [[11, "module-pydfnworks.dfnGen.meshing.mesh_dfn_helper"]], "pydfnworks.dfngen.meshing.udfm.false_connections": [[11, "module-pydfnworks.dfnGen.meshing.udfm.false_connections"]], "pydfnworks.dfngen.meshing.udfm.map2continuum": [[11, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "pydfnworks.dfngen.meshing.udfm.upscale": [[11, "module-pydfnworks.dfnGen.meshing.udfm.upscale"]], "run_lagrit_script() (in module pydfnworks.dfngen.meshing.mesh_dfn_helper)": [[11, "pydfnworks.dfnGen.meshing.mesh_dfn_helper.run_lagrit_script"]], "stress_based_apertures() (in module pydfnworks.dfngen.generation.stress)": [[11, "pydfnworks.dfnGen.generation.stress.stress_based_apertures"]], "upscale() (in module pydfnworks.dfngen.meshing.udfm.upscale)": [[11, "pydfnworks.dfnGen.meshing.udfm.upscale.upscale"]], "upscale.py": [[11, "module-upscale.py"]], "add_fracture_source() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.add_fracture_source"]], "add_fracture_target() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.add_fracture_target"]], "create_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.create_graph"]], "dump_fractures() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.dump_fractures"]], "dump_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.dump_json_graph"]], "graph_transport.py": [[12, "module-graph_transport.py"]], "greedy_edge_disjoint() (in module pydfnworks.dfngraph.pruning)": [[12, "pydfnworks.dfnGraph.pruning.greedy_edge_disjoint"]], "k_shortest_paths_backbone() (in module pydfnworks.dfngraph.pruning)": [[12, "pydfnworks.dfnGraph.pruning.k_shortest_paths_backbone"]], "load_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.load_json_graph"]], "plot_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[12, "pydfnworks.dfnGraph.dfn2graph.plot_graph"]], "pydfnworks.dfngraph.dfn2graph": [[12, "module-pydfnworks.dfnGraph.dfn2graph"]], "pydfnworks.dfngraph.graph_flow": [[12, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks.dfngraph.graph_transport": [[12, "module-pydfnworks.dfnGraph.graph_transport"]], "pydfnworks.dfngraph.pruning": [[12, "module-pydfnworks.dfnGraph.pruning"]], "run_graph_flow() (in module pydfnworks.dfngraph.graph_flow)": [[12, "pydfnworks.dfnGraph.graph_flow.run_graph_flow"]], "run_graph_transport() (in module pydfnworks.dfngraph.graph_transport)": [[12, "pydfnworks.dfnGraph.graph_transport.run_graph_transport"]], "check_dfn_trans_run_files() (in module pydfnworks.dfntrans.transport)": [[13, "pydfnworks.dfnTrans.transport.check_dfn_trans_run_files"]], "copy_dfn_trans_files() (in module pydfnworks.dfntrans.transport)": [[13, "pydfnworks.dfnTrans.transport.copy_dfn_trans_files"]], "create_dfn_trans_links() (in module pydfnworks.dfntrans.transport)": [[13, "pydfnworks.dfnTrans.transport.create_dfn_trans_links"]], "dfn_trans() (in module pydfnworks.dfntrans.transport)": [[13, "pydfnworks.dfnTrans.transport.dfn_trans"]], "pydfnworks.dfntrans.transport": [[13, "module-pydfnworks.dfnTrans.transport"]], "run_dfn_trans() (in module pydfnworks.dfntrans.transport)": [[13, "pydfnworks.dfnTrans.transport.run_dfn_trans"]], "cleanup_wells() (in module pydfnworks.dfngen.well_package.wells)": [[14, "pydfnworks.dfnGen.well_package.wells.cleanup_wells"]], "combine_well_boundary_zones() (in module pydfnworks.dfngen.well_package.wells)": [[14, "pydfnworks.dfnGen.well_package.wells.combine_well_boundary_zones"]], "find_well_intersection_points() (in module pydfnworks.dfngen.well_package.wells)": [[14, "pydfnworks.dfnGen.well_package.wells.find_well_intersection_points"]], "pydfnworks.dfngen.well_package.wells": [[14, "module-pydfnworks.dfnGen.well_package.wells"]], "tag_well_in_mesh() (in module pydfnworks.dfngen.well_package.wells)": [[14, "pydfnworks.dfnGen.well_package.wells.tag_well_in_mesh"]]}})
\ No newline at end of file
diff --git a/docs/setup.html b/docs/setup.html
index 7ed3de2e..f7527b7b 100644
--- a/docs/setup.html
+++ b/docs/setup.html
@@ -31,7 +31,7 @@
 
           
           
-          <a href="index_docs.html" class="icon icon-home">
+          <a href="index.html" class="icon icon-home">
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               <img src="_static/dfnworks_logo.png" class="logo" alt="Logo"/>
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@@ -94,14 +94,14 @@
 
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