Functions
def	create_graph (self, graph_type, inflow, outflow)

def	create_fracture_graph (inflow, outflow, topology_file="connectivity.dat", fracture_info="fracture_info.dat")

def	boundary_index (bc_name)

def	create_intersection_graph (inflow, outflow, intersection_file="intersection_list.dat", fracture_info="fracture_info.dat")

def	create_bipartite_graph (inflow, outflow, intersection_list='intersection_list.dat', fracture_info='fracture_info.dat')

def	add_fracture_source (self, G, source)

def	add_fracture_target (self, G, target)

def	k_shortest_paths (G, k, source, target, weight)

def	k_shortest_paths_backbone (self, G, k, source='s', target='t', weight=None)

def	pull_source_and_target (nodes, source='s', target='t')

def	dump_fractures (self, G, filename)

def	greedy_edge_disjoint (self, G, source='s', target='t', weight='None', k='')

def	plot_graph (self, G, source='s', target='t', output_name="dfn_graph")

def	dump_json_graph (self, G, name)

def	load_json_graph (self, name)

def	add_perm (G, fracture_info="fracture_info.dat")

def	add_area (G, fracture_info="fracture_info.dat")

def	add_weight (G)

Function Documentation

◆ add_area()

def pydfnworks.dfnGraph.dfn2graph.add_area	(	G,
		fracture_info = `"fracture_info.dat"`
	)

 Read Fracture aperture from fracture_info.dat and 
load on the edges in the graph. Graph must be intersection to node
representation

Parameters
----------
    G : NetworkX Graph
        networkX graph 
    fracture_info : str
        filename for fracture information

Returns
-------
    None

Definition at line 872 of file dfn2graph.py.

◆ add_fracture_source()

def pydfnworks.dfnGraph.dfn2graph.add_fracture_source	(	self,
		G,
		source
	)

Returns the k shortest paths in a graph 

Parameters
----------
    G : NetworkX Graph
        NetworkX Graph based on a DFN 
    source_list : list
        list of integers corresponding to fracture numbers
    remove_old_source: bool
        remove old source from the graph

Returns 
-------
    G : NetworkX Graph

Notes
-----
    bipartite graph not supported

Definition at line 365 of file dfn2graph.py.

◆ add_fracture_target()

def pydfnworks.dfnGraph.dfn2graph.add_fracture_target	(	self,
		G,
		target
	)

Returns the k shortest paths in a graph 

Parameters
----------
    G : NetworkX Graph
        NetworkX Graph based on a DFN 
    target : list
        list of integers corresponding to fracture numbers
Returns 
-------
    G : NetworkX Graph

Notes
-----
    bipartite graph not supported

Definition at line 441 of file dfn2graph.py.

◆ add_perm()

def pydfnworks.dfnGraph.dfn2graph.add_perm	(	G,
		fracture_info = `"fracture_info.dat"`
	)

 Add fracture permeability to Graph. If Graph representation is
fracture, then permeability is a node attribute. If graph representation 
is intersection, then permeability is an edge attribute


Parameters
---------- 
    G :networkX graph
        NetworkX Graph based on the DFN

    fracture_infor : str
            filename for fracture information
Returns
-------

Notes
-----

Definition at line 818 of file dfn2graph.py.

Referenced by pydfnworks.dfnGraph.dfn2graph.create_fracture_graph(), and pydfnworks.dfnGraph.dfn2graph.create_intersection_graph().

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◆ add_weight()

def pydfnworks.dfnGraph.dfn2graph.add_weight ( G )

Compute weight w = K*A/L associated with each edge 
Parameters
----------
    G : NetworkX Graph
        networkX graph 

Returns
-------
    None

Definition at line 902 of file dfn2graph.py.

◆ boundary_index()

def pydfnworks.dfnGraph.dfn2graph.boundary_index ( bc_name )

Determines boundary index in intersections_list.dat from name

Parameters
----------
    bc_name : string
        Boundary condition name

Returns
-------
    bc_index : int
        integer indexing of cube faces

Notes
-----
top = 1
bottom = 2
left = 3
front = 4
right = 5
back = 6

Definition at line 116 of file dfn2graph.py.

Referenced by pydfnworks.dfnGraph.dfn2graph.create_bipartite_graph(), and pydfnworks.dfnGraph.dfn2graph.create_intersection_graph().

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◆ create_bipartite_graph()

def pydfnworks.dfnGraph.dfn2graph.create_bipartite_graph	(	inflow,
		outflow,
		intersection_list = `'intersection_list.dat'`,
		fracture_info = `'fracture_info.dat'`
	)

Creates a bipartite graph of the DFN.
Nodes are in two sets, fractures and intersections, with edges connecting them.


Parameters
----------
    inflow : str
        name of inflow boundary
    outflow : str
        name of outflow boundary
    intersection_list: str
         filename of intersections generated from DFN
    fracture_infor : str
            filename for fracture information

Returns
-------
    B : NetworkX Graph

Notes
-----
See Hyman et al. 2018 "Identifying Backbones in Three-Dimensional Discrete Fracture Networks: A Bipartite Graph-Based Approach" SIAM Multiscale Modeling and Simulation for more details

Definition at line 272 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.boundary_index().

Referenced by pydfnworks.dfnGraph.dfn2graph.create_graph().

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◆ create_fracture_graph()

def pydfnworks.dfnGraph.dfn2graph.create_fracture_graph	(	inflow,
		outflow,
		topology_file = `"connectivity.dat"`,
		fracture_info = `"fracture_info.dat"`
	)

 Create a graph based on topology of network. Fractures
are represented as nodes and if two fractures intersect 
there is an edge between them in the graph. 

Source and Target node are added to the graph. 

Parameters
----------
    inflow : string
        Name of inflow boundary (connect to source)
    outflow : string
        Name of outflow boundary (connect to target)
    topology_file : string
        Name of adjacency matrix file for a DFN default=connectivity.dat  
    fracture_infor : str
            filename for fracture information

Returns
-------
    G : NetworkX Graph
        NetworkX Graph where vertices in the graph correspond to fractures and edges indicated two fractures intersect  

Notes
-----

Definition at line 53 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.add_perm().

Referenced by pydfnworks.dfnGraph.dfn2graph.create_graph().

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◆ create_graph()

def pydfnworks.dfnGraph.dfn2graph.create_graph	(	self,
		graph_type,
		inflow,
		outflow
	)

Header function to create a graph based on a DFN

Parameters
----------
    self : object
        DFN Class object 
    graph_type : string
        Option for what graph representation of the DFN is requested. Currently supported are fracture, intersection, and bipartitie 
    inflow : string
        Name of inflow boundary (connect to source)
    outflow : string
        Name of outflow boundary (connect to target)

Returns
-------
    G : NetworkX Graph
        Graph based on DFN 

Notes
-----

Definition at line 17 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.create_bipartite_graph(), pydfnworks.dfnGraph.dfn2graph.create_fracture_graph(), and pydfnworks.dfnGraph.dfn2graph.create_intersection_graph().

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◆ create_intersection_graph()

def pydfnworks.dfnGraph.dfn2graph.create_intersection_graph	(	inflow,
		outflow,
		intersection_file = `"intersection_list.dat"`,
		fracture_info = `"fracture_info.dat"`
	)

 Create a graph based on topology of network.
Edges are represented as nodes and if two intersections
are on the same fracture, there is an edge between them in the graph. 

Source and Target node are added to the graph. 

Parameters
----------
    inflow : string
        Name of inflow boundary
    outflow : string
        Name of outflow boundary
    intersection_file : string
         File containing intersection information
         File Format:
         fracture 1, fracture 2, x center, y center, z center, intersection length

    fracture_infor : str
            filename for fracture information
Returns
-------
    G : NetworkX Graph
        Vertices have attributes x,y,z location and length. Edges has attribute length

Notes
-----
Aperture and Perm on edges can be added using add_app and add_perm functions

Definition at line 154 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.add_perm(), and pydfnworks.dfnGraph.dfn2graph.boundary_index().

Referenced by pydfnworks.dfnGraph.dfn2graph.create_graph().

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◆ dump_fractures()

def pydfnworks.dfnGraph.dfn2graph.dump_fractures	(	self,
		G,
		filename
	)

Write fracture numbers assocaited with the graph G out into an ASCII file inputs

Parameters
----------
    self : object
        DFN Class
    G : NetworkX graph
        NetworkX Graph based on the DFN
    filename : string
        Output filename 

Returns
-------

Notes
-----

Definition at line 615 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.pull_source_and_target().

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◆ dump_json_graph()

def pydfnworks.dfnGraph.dfn2graph.dump_json_graph	(	self,
		G,
		name
	)

Write graph out in json format

Parameters
---------- 
    self : object 
        DFN Class
    G :networkX graph
        NetworkX Graph based on the DFN
    name : string
         Name of output file (no .json)

Returns
-------

Notes
-----

Definition at line 769 of file dfn2graph.py.

◆ greedy_edge_disjoint()

def pydfnworks.dfnGraph.dfn2graph.greedy_edge_disjoint	(	self,
		G,
		source = `'s'`,
		target = `'t'`,
		weight = `'None'`,
		k = `''`
	)

Greedy Algorithm to find edge disjoint subgraph from s to t. 
See Hyman et al. 2018 SIAM MMS

Parameters
----------
    self : object 
        DFN Class Object
    G : NetworkX graph
        NetworkX Graph based on the DFN
    source : node 
        Starting node
    target : node
        Ending node
    weight : string
        Edge weight used for finding the shortest path
    k : int
        Number of edge disjoint paths requested

Returns
-------
    H : NetworkX Graph
        Subgraph of G made up of the k shortest of all edge-disjoint paths from source to target

Notes
-----
    1. Edge weights must be numerical and non-negative.
    2. See Hyman et al. 2018 "Identifying Backbones in Three-Dimensional Discrete Fracture Networks: A Bipartite Graph-Based Approach" SIAM Multiscale Modeling and Simulation for more details

Definition at line 654 of file dfn2graph.py.

◆ k_shortest_paths()

def pydfnworks.dfnGraph.dfn2graph.k_shortest_paths	(	G,
		k,
		source,
		target,
		weight
	)

Returns the k shortest paths in a graph 

Parameters
----------
    G : NetworkX Graph
        NetworkX Graph based on a DFN 
    k : int
        Number of requested paths
    source : node 
        Starting node
    target : node
        Ending node
    weight : string
        Edge weight used for finding the shortest path

Returns 
-------
    paths : sets of nodes
        a list of lists of nodes in the k shortest paths

Notes
-----
Edge weights must be numerical and non-negative

Definition at line 514 of file dfn2graph.py.

Referenced by pydfnworks.dfnGraph.dfn2graph.k_shortest_paths_backbone().

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◆ k_shortest_paths_backbone()

def pydfnworks.dfnGraph.dfn2graph.k_shortest_paths_backbone	(	self,
		G,
		k,
		source = `'s'`,
		target = `'t'`,
		weight = `None`
	)

Returns the subgraph made up of the k shortest paths in a graph 

Parameters
----------
    G : NetworkX Graph
        NetworkX Graph based on a DFN 
    k : int
        Number of requested paths
    source : node 
        Starting node
    target : node
        Ending node
    weight : string
        Edge weight used for finding the shortest path

Returns 
-------
    H : NetworkX Graph
        Subgraph of G made up of the k shortest paths 

Notes
-----
    See Hyman et al. 2017 "Predictions of first passage times in sparse discrete fracture networks using graph-based reductions" Physical Review E for more details

Definition at line 543 of file dfn2graph.py.

References pydfnworks.dfnGraph.dfn2graph.k_shortest_paths().

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◆ load_json_graph()

def pydfnworks.dfnGraph.dfn2graph.load_json_graph	(	self,
		name
	)

 Read in graph from json format

Parameters
---------- 
    self : object 
        DFN Class
    name : string
         Name of input file (no .json)

Returns
-------
    G :networkX graph
        NetworkX Graph based on the DFN

Definition at line 795 of file dfn2graph.py.

◆ plot_graph()

def pydfnworks.dfnGraph.dfn2graph.plot_graph	(	self,
		G,
		source = `'s'`,
		target = `'t'`,
		output_name = `"dfn_graph"`
	)

 Create a png of a graph with source nodes colored blue, target red, and all over nodes black

Parameters
---------- 
    G : NetworkX graph
        NetworkX Graph based on the DFN
    source : node 
        Starting node
    target : node
        Ending node
    output_name : string
        Name of output file (no .png)

Returns
-------

Notes
-----
Image is written to output_name.png

Definition at line 714 of file dfn2graph.py.

◆ pull_source_and_target()

def pydfnworks.dfnGraph.dfn2graph.pull_source_and_target	(	nodes,
		source = `'s'`,
		target = `'t'`
	)

Removes source and target from list of nodes, useful for dumping subnetworks to file for remeshing

Parameters
----------
    nodes :list 
        List of nodes in the graph
    source : node 
        Starting node
    target : node
        Ending node
Returns
-------
    nodes : list
        List of nodes with source and target nodes removed

Notes
-----

Definition at line 587 of file dfn2graph.py.

Referenced by pydfnworks.dfnGraph.dfn2graph.dump_fractures().

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Functions

Function Documentation

◆ add_area()

◆ add_fracture_source()

◆ add_fracture_target()

◆ add_perm()

◆ add_weight()

◆ boundary_index()

◆ create_bipartite_graph()

◆ create_fracture_graph()

◆ create_graph()

◆ create_intersection_graph()

◆ dump_fractures()

◆ dump_json_graph()

◆ greedy_edge_disjoint()

◆ k_shortest_paths()

◆ k_shortest_paths_backbone()

◆ load_json_graph()

◆ plot_graph()

◆ pull_source_and_target()