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lanl · Feb 22, 2023 · 3b9c74a · 3b9c74a
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diff --git a/Documentation/sphinx-docs/source/conf.py b/Documentation/sphinx-docs/source/conf.py
@@ -70,10 +70,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'2.6, LANL, Docs: LA-UR-17-22216, Software: LA-CC-17-027'
+version = u'2.7, LANL, Docs: LA-UR-17-22216, Software: LA-CC-17-027'
 
 # The full version, including alpha/beta/rc tags.
-release = u'2.6'
+release = u'2.7'
 
 # The language for content auto-generated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -112,8 +112,8 @@
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#
-# show_authors = False
+
+show_authors = False 
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

diff --git a/Documentation/sphinx-docs/source/dfngen.rst b/Documentation/sphinx-docs/source/dfngen.rst
@@ -1,7 +1,7 @@
 .. _dfngen-chapter:
 
-dfnGen 
-######################
+dfnGen - C++ Generation Code  
+#################################
 
 dfnGen creates the discrete fracture networks using the feature rejection algorithm for meshing (FRAM). Fractures can be created stochastically or as deterministic features. 
 

diff --git a/Documentation/sphinx-docs/source/intro.rst b/Documentation/sphinx-docs/source/intro.rst
@@ -60,7 +60,18 @@ for modeling subsurface flow and transport. Computers & Geosciences, 84,
 
 Versions
 -------------------
-v2.
+
+v2.7
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Python based assignment of domain parameters, fracture families, user defined fractures
+- Interactive object interface
+- Updated for PFLOTRAN 4.0 compatability 
+- Additional bug fixes
+- Increased detail of warning and errors
+
+
+v2.6
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Hydraulic aperture of fracture based on background stress field
@@ -93,7 +104,7 @@ v2.3
 - Added PDF printing abilities
 
 
-v2.3
+v2.2
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 - pydfnWorks updated for python3
@@ -138,22 +149,23 @@ Contributors
 LANL
 ^^^^^^^
 - Jeffrey D. Hyman
-- Satish Karra
+- Matt Sweeney
 - Nataliia Makedonska
 - Carl Gable
 - Hari Viswanathan
-- Matt Sweeney
-- Shriram Srinivasan 
 - Aric Hagberg
-- Yu Chen
+- Shriram Srinivasan 
+- Aidan Stansberry 
 
 External
 ^^^^^^^^^^^^^^
+- Satish Karra (PNNL)
+- Scott Painter (ORNL)
 - Quan Bui (now at LLNL)
 - Jeremy Harrod (now at Spectra Logic)
-- Scott Painter (now at ORNL)
 - Thomas Sherman (University of Notre Dame)
 - Johannes Krotz  (Oregon State University)
+- Yu Chen 
 
 
 Copyright Information

diff --git a/Documentation/sphinx-docs/source/output.rst b/Documentation/sphinx-docs/source/output.rst
@@ -1,30 +1,19 @@
 .. _output-chapter:
 
-Output files
+Run Files
 =============
 
-dfnWorks outputs about a hundred different output files. This section describes the contents and purpose of each file.
+This section describes the contents and purpose of each file used in dfnWorks and their locations. 
 
-
-dfnGen 
---------
-
-**aperture.dat:**
-
-.. _aperture.dat:
+dfnGen - output
+------------------------
 
 **connectivity.dat:**
 
 .. _connectivity.dat:
 
 Fracture connection list. Each row corresponds to a single fracture. The integers in that row are the fractures that fracture intersects with. These are the non-zero elements of the adjacency matrix. 
 
-**convert_uge_params.txt:**
-
-.. _convert_uge_params.txt:
-
-Input file do conver_uge executable. 
-
 **DFN_output.txt:**
 
 .. _DFN_output.txt:
@@ -55,7 +44,6 @@ Abbreviated input file for DFN generator.
 
 Normal vector of each fracture in the network. 
 
-
 **params.txt:**
 
 .. _params.txt:
@@ -74,13 +62,6 @@ Fracture information output by DFNGen. Format: Fracture Number, Family number, r
 
 User defined rectangle file. 
 
-
-**radii:**
-
-.. _radii:
-
-Subdirectory containing fracture radii information. 
-
 **radii.dat:**
 
 .. _radii.dat:
@@ -101,7 +82,6 @@ Concatentated file of final radii in the DFN.
 
 Summary of rejection reasons. 
 
-
 **rejectsPerAttempt.dat:**
 
 .. _rejectsPerAttempt.dat:
@@ -135,8 +115,8 @@ Warning file output by DFNGen.
 
 List of intersections between fractures. Format is fracture1 fracture2 x y z length. Negative numbers correspond to intersections with boundaries.
 
-LaGrit 
----------
+LaGrit - Output
+------------------
 
 **bound_zones.lgi:**
 
@@ -228,8 +208,8 @@ FEHM stor file. Information about cell volume and area.
 Function used by LaGriT for meshing. Defines coarsening gradient. 
 
 
-PFLOTRAN 
-----------
+PFLOTRAN - output 
+--------------------
 
 Fracture based aperture value for the DFN. Used to rescale volumes in full_mesh_vol_area.uge. 
 
@@ -338,69 +318,69 @@ Boundary file for right of the domain used by PFLOTRAN.
 
 Boundary file for top of the domain used by PFLOTRAN. 
 
-dfnTrans 
--------------
+.. dfnTrans  
+.. -------------
 
-**allboundaries.zone:**
+.. **allboundaries.zone:**
 
-.. _allboundaries.zone:
+.. .. _allboundaries.zone:
 
-Concatenated file of all zone files. 
+.. Concatenated file of all zone files. 
 
-**darcyvel.dat:**
+.. **darcyvel.dat:**
 
-.. _darcyvel.dat:
+.. .. _darcyvel.dat:
 
-Concatenated file of darcy velocities output by PFLOTRAN. 
+.. Concatenated file of darcy velocities output by PFLOTRAN. 
 
-**dfnTrans_output_dir:**
+.. **dfnTrans_output_dir:**
 
-.. _dfnTrans_output_dir:
+.. .. _dfnTrans_output_dir:
 
-Outpur directory from DFNTrans. Particle travel times, trajectories, and reconstructed Velocities are in this directory. 
+.. Outpur directory from DFNTrans. Particle travel times, trajectories, and reconstructed Velocities are in this directory. 
 
-**PTDFN_control.dat:**
+.. **PTDFN_control.dat:**
 
-.. _PTDFN_control.dat:
+.. .. _PTDFN_control.dat:
 
-Input file for DFNTrans. 
+.. Input file for DFNTrans. 
 
-**pboundary_back_n.zone:**
+.. **pboundary_back_n.zone:**
 
-.. _pboundary_back_s.zone:
+.. .. _pboundary_back_s.zone:
 
-Boundary zone file for the back of the domain. Normal vector (0,1,0) +- pi/2 
+.. Boundary zone file for the back of the domain. Normal vector (0,1,0) +- pi/2 
 
-**pboundary_bottom.zone:**
+.. **pboundary_bottom.zone:**
 
-.. _pboundary_bottom.zone:
+.. .. _pboundary_bottom.zone:
 
-Boundary zone file for the bottom of the domain. Normal vector (0,0,-1) +- pi/2 
+.. Boundary zone file for the bottom of the domain. Normal vector (0,0,-1) +- pi/2 
 
-**pboundary_front_s.zone:**
+.. **pboundary_front_s.zone:**
 
-.. _pboundary_front_n.zone:
+.. .. _pboundary_front_n.zone:
 
-Boundary zone file for the front of the domain. Normal vector (0,-1,0) +- pi/2 
+.. Boundary zone file for the front of the domain. Normal vector (0,-1,0) +- pi/2 
 
 
-**pboundary_left_w.zone:**
+.. **pboundary_left_w.zone:**
 
-.. _pboundary_left_w.zone:
+.. .. _pboundary_left_w.zone:
 
-Boundary zone file for the left side of the domain. Normal vector (-1,0,0) +- pi/2 
+.. Boundary zone file for the left side of the domain. Normal vector (-1,0,0) +- pi/2 
 
 
-**pboundary_right_e.zone:**
+.. **pboundary_right_e.zone:**
 
-.. _pboundary_right_e.zone:
+.. .. _pboundary_right_e.zone:
 
 
-Boundary zone file for the bottom of the domain. Normal  vector (1,0,0) +- pi/2 
+.. Boundary zone file for the bottom of the domain. Normal  vector (1,0,0) +- pi/2 
 
-**pboundary_top.zone:**
+.. **pboundary_top.zone:**
 
-.. _pboundary_top.zone:
+.. .. _pboundary_top.zone:
 
-Boundary zone file for the top of the domain. Normal vector (0,0,1) +- pi/2 
+.. Boundary zone file for the top of the domain. Normal vector (0,0,1) +- pi/2 
 
diff --git a/Documentation/sphinx-docs/source/publications.rst b/Documentation/sphinx-docs/source/publications.rst
@@ -102,7 +102,7 @@ The following are publications that use *dfnWorks*:
 
 #. `\S. Srinivasan, D. O’Malley, J. D. Hyman, s. Karra, H. S. Viswanathan, and G. Srinivasan Transient flow modeling in fractured media using graphs. (2020) Physical Review E.  <https://journals.aps.org/pre/accepted/c6078R6bFb11881299011174b59f5a96a29a879a7#abstract>`_.
 
-#. `\Liangchao Zou and Vladimir Cvetkovic. Inference of Transmissivity in Crystalline Rock Using Flow Logs Under Steady‐State Pumping: Impact of Multiscale Heterogeneity. Water Resources Research (2020) <https://doi.org/10.1029/2020WR027254>`_.
+#. `\Liangchao Zou and Vladimir Cvetkovic. Inference of Transmissivity in Crystalline Rock Using Flow Logs Under Steady‐State Pumping: Impact of Multiscale Heterogeneity. Water Resources Research (2020) <https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020WR027254>`_.
 
 #. `\P. K. Kang, J. D. Hyman, W. S. Han, & M. Dentz, Anomalous Transport in Three‐Dimensional Discrete Fracture Networks: Interplay between Aperture Heterogeneity and Injection Modes. Water Resources Research (2020) <https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020WR027378>`_.
 
@@ -115,7 +115,7 @@ The following are publications that use *dfnWorks*:
 
 #. `J. D. Hyman, M. R. Sweeney, L. P. Frash, J. W. Carey, and H. S. Viswanathan. Scale‐Bridging in Three‐Dimensional Fracture Networks: Characterizing the Effects of Variable Fracture Apertures on Network‐Scale Flow Channelization. Geophysical Research Letters (2021) <https://doi.org/10.1029/2021GL094400>`_.
 
-#. `Liangchao Zou and Vladimir Cvetkovic. Evaluation of Flow‐Log Data From Crystalline Rocks With Steady‐State Pumping and Ambient Flow. Geophysical Research Letters (2021) < https://doi.org/10.1029/2021GL092741>`_.
+#. `Liangchao Zou and Vladimir Cvetkovic. Evaluation of Flow‐Log Data From Crystalline Rocks With Steady‐State Pumping and Ambient Flow. Geophysical Research Letters (2021) <https://doi.org/10.1029/2021GL092741>`_.
 
 #. `H. Ushijima-Mwesigwa, J. D. Hyman, A. Hagberg, I. Safro, S. Karra, C. W. Gable, M. R. Sweeney, and G. Srinivasan. Multilevel graph partitioning for three-dimensional discrete fracture network flow simulations. Mathematical Geosciences (2021) <https://link.springer.com/article/10.1007/s11004-021-09944-y>`_.
 

diff --git a/Documentation/sphinx-docs/source/pydfnGen.rst b/Documentation/sphinx-docs/source/pydfnGen.rst
@@ -12,6 +12,7 @@ Adding Fracture Families
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. automodule:: pydfnworks.dfnGen.generation.input_checking
     :members: add_fracture_family
+    :noindex:
 
 Example:
 
@@ -42,8 +43,7 @@ Adding User Fractures
 
 .. automodule:: pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions
     :members: add_user_fract
-
-
+    :noindex:
 
 Example:
 
@@ -62,6 +62,7 @@ Adding User Fractures From a File
 
 .. automodule:: pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions
     :members: add_user_fract_from_file
+    :noindex:
 
 Example:
 
@@ -88,7 +89,8 @@ Processing Generator Input
 
 .. automodule:: pydfnworks.dfnGen.generation.input_checking
     :members: check_input
-
+    :noindex:
+
 Running the Generator
 ^^^^^^^^^^^^^^^^^^^^^^
 .. automodule:: pydfnworks.dfnGen.generation.generator

diff --git a/Documentation/sphinx-docs/source/pydfnGraph.rst b/Documentation/sphinx-docs/source/pydfnGraph.rst
@@ -8,7 +8,14 @@ DFN Class functions used in graph analysis and pipe-network simulations
 General Graph Functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 .. automodule:: pydfnworks.dfnGraph.dfn2graph
-    :members: create_graph, k_shortest_paths_backbone, dump_json_graph, load_json_graph, plot_graph, greedy_edge_disjoint, dump_fractures, add_fracture_source, add_fracture_target
+    :members: create_graph, dump_json_graph, load_json_graph, plot_graph, dump_fractures, add_fracture_source, add_fracture_target
+
+.. automodule:: pydfnworks.dfnGraph.pruning
+    :members:  k_shortest_paths_backbone, greedy_edge_disjoint
+
+
+
+
 
 Graph-Based Flow and Transport
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^