diff --git a/Documentation/sphinx-docs/source/conf.py b/Documentation/sphinx-docs/source/conf.py index 49f15465..2639deb3 100755 --- a/Documentation/sphinx-docs/source/conf.py +++ b/Documentation/sphinx-docs/source/conf.py @@ -80,7 +80,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: diff --git a/Documentation/sphinx-docs/source/pydfnGen.rst b/Documentation/sphinx-docs/source/pydfnGen.rst index 2bade714..f8662c40 100644 --- a/Documentation/sphinx-docs/source/pydfnGen.rst +++ b/Documentation/sphinx-docs/source/pydfnGen.rst @@ -193,12 +193,8 @@ DFM Creating a conforming DFM mesh DFN ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: pydfnworks.dfnGen.meshing.dfm +.. automodule:: pydfnworks.dfnGen.meshing.dfm.mesh_dfm :members: mesh_dfm - - - - diff --git a/docs/_modules/index.html b/docs/_modules/index.html index b359001e..f93c8af8 100644 --- a/docs/_modules/index.html +++ b/docs/_modules/index.html @@ -97,6 +97,7 @@

All modules for which code is available

  • pydfnworks.dfnGen.generation.output_report.gen_output
  • pydfnworks.dfnGen.generation.stress
  • pydfnworks.dfnGen.meshing.add_attribute_to_mesh
    • +
  • pydfnworks.dfnGen.meshing.dfm.mesh_dfm
  • pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm
  • pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn
  • pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper
    • diff --git a/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html b/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html index 2dfd51a4..32b341f0 100644 --- a/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html +++ b/docs/_modules/pydfnworks/dfnGen/meshing/mesh_dfn/mesh_dfn.html @@ -93,6 +93,7 @@

    Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn

    .. moduleauthor:: Jeffrey Hyman <jhyman@lanl.gov> """ + import os import sys import shutil @@ -119,21 +120,20 @@

    Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn

    strict=True, quiet=True): """ - - Mesh fracture network using LaGriT + Mesh fracture network using LaGriT Parameters - ------------ + ---------- self : object DFN Class uniform_mesh : bool toggle for uniform or variable mesh. Default : False min_dist : float - Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist x h + Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist * h max_dist : float - Defines the minimum distance from the intersections with resolution max_resolution x h. This value is the factor of h, distance = max_dist x h + Defines the minimum distance from the intersections with resolution max_resolution * h. This value is the factor of h, distance = max_dist * h max_resolution_factor : float - Maximum factor of the mesh resolultion (max_resolution x h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh. + Maximum factor of the mesh resolultion (max_resolution *h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh. cleanup : bool toggle to clean up directory (remove meshing files after a run). Default : True strict : bool @@ -142,11 +142,11 @@

    Source code for pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn

    Toggle to turn on/off verbose information to screen about meshing. Default is true, does not print to screen Returns - ------------ + ------- None Notes - ------------ + ------ 1. All fractures in self.prune_file must intersect at least 1 other fracture """ diff --git a/docs/_sources/pydfnGen.rst.txt b/docs/_sources/pydfnGen.rst.txt index 2bade714..f8662c40 100644 --- a/docs/_sources/pydfnGen.rst.txt +++ b/docs/_sources/pydfnGen.rst.txt @@ -193,12 +193,8 @@ DFM Creating a conforming DFM mesh DFN ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: pydfnworks.dfnGen.meshing.dfm +.. automodule:: pydfnworks.dfnGen.meshing.dfm.mesh_dfm :members: mesh_dfm - - - - diff --git a/docs/genindex.html b/docs/genindex.html index f87983f2..d8487e31 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -264,8 +264,17 @@

    M

  • map_to_continuum() (in module pydfnworks.dfnGen.meshing.udfm.map2continuum)
  • mapdfn_ecpm() (in module pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm) +
    • +
  • mesh_dfm() (in module pydfnworks.dfnGen.meshing.dfm.mesh_dfm)
  • + mesh_dfm.py + +
    • +
  • mesh_dfn.py diff --git a/docs/index_docs.html b/docs/index_docs.html index 4c3ed2f9..8cff6518 100644 --- a/docs/index_docs.html +++ b/docs/index_docs.html @@ -191,7 +191,7 @@

    Welcome to dfnWorks 2.8 documentation!DFM

    • diff --git a/docs/objects.inv b/docs/objects.inv index 7c239dc1..86779310 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 927f5868..12a362db 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -146,20 +146,31 @@

    Python Module Index

    - mesh_dfn + mesh_dfm + +     + mesh_dfm.py + meshing driver for conforming DFM + + + + mesh_dfn + +     mesh_dfn.py meshing driver for DFN + id="toggle-6" style="display: none" alt="-" /> mesh_dfn_helper - +     mesh_dfn_helper.py @@ -169,121 +180,121 @@

    Python Module Index

    p + id="toggle-7" style="display: none" alt="-" /> pydfnworks - +     pydfnworks.dfnFlow.fehm - +     pydfnworks.dfnFlow.flow - +     pydfnworks.dfnFlow.mass_balance - +     pydfnworks.dfnFlow.pflotran - +     pydfnworks.dfnGen.generation.generator - +     pydfnworks.dfnGen.generation.input_checking - +     pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions - +     pydfnworks.dfnGen.generation.output_report.gen_output - +     pydfnworks.dfnGen.generation.stress - +     pydfnworks.dfnGen.meshing.add_attribute_to_mesh - +     - pydfnworks.dfnGen.meshing.dfm + pydfnworks.dfnGen.meshing.dfm.mesh_dfm - +     pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm - +     pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn - +     pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper - +     pydfnworks.dfnGen.meshing.udfm.false_connections - +     pydfnworks.dfnGen.meshing.udfm.map2continuum - +     pydfnworks.dfnGen.meshing.udfm.upscale - +     pydfnworks.dfnGen.well_package.wells - +     pydfnworks.dfnGraph.dfn2graph - +     pydfnworks.dfnGraph.graph_flow - +     pydfnworks.dfnGraph.graph_transport - +     pydfnworks.dfnGraph.pruning - +     pydfnworks.dfnTrans.transport @@ -293,11 +304,11 @@

    Python Module Index

    u + id="toggle-8" style="display: none" alt="-" /> upscale - +     upscale.py diff --git a/docs/pydfnGen.html b/docs/pydfnGen.html index dda24fb1..3e126993 100644 --- a/docs/pydfnGen.html +++ b/docs/pydfnGen.html @@ -111,7 +111,10 @@
  • DFM
    • @@ -593,15 +596,17 @@

    Meshing - LaGriT
    mesh_network(self, uniform_mesh=False, min_dist=0.5, max_dist=10, max_resolution_factor=10, well=False, cleanup=True, strict=True, quiet=True)[source]
    -

    Mesh fracture network using LaGriT

    +
    +

    Mesh fracture network using LaGriT

    +
    Parameters:

    • self (object) – DFN Class

    • uniform_mesh (bool) – toggle for uniform or variable mesh. Default : False

      • -

    • min_dist (float) – Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist x h

      • -

    • max_dist (float) – Defines the minimum distance from the intersections with resolution max_resolution x h. This value is the factor of h, distance = max_dist x h

      • -

    • max_resolution_factor (float) – Maximum factor of the mesh resolultion (max_resolution x h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh.

      • +

    • min_dist (float) – Defines the minimum distance from the intersections with resolution h/2. This value is the factor of h, distance = min_dist * h

      • +

    • max_dist (float) – Defines the minimum distance from the intersections with resolution max_resolution * h. This value is the factor of h, distance = max_dist * h

      • +

    • max_resolution_factor (float) – Maximum factor of the mesh resolultion (max_resolution *h). Depending on the slope of the linear function and size of the fracture, this may not be realized in the mesh.

    • cleanup (bool) – toggle to clean up directory (remove meshing files after a run). Default : True

    • strict (bool) – Toggle if a few mesh errors are acceptable. default is true

    • quiet (bool) – Toggle to turn on/off verbose information to screen about meshing. Default is true, does not print to screen

      • @@ -863,8 +868,28 @@

      Authors

      DFM

      -
      -

      Creating a conforming DFM mesh DFN

      +
      +

      Creating a conforming DFM mesh DFN

      +
      +
      +mesh_dfm(self, dirname='dfm_mesh', allowed_percentage=1, cleanup=True)[source]
      +

      ” Creates a conforming mesh of a DFN using a uniform background tetrahedron mesh. The DFN must be meshed using a uniform triangular mesh. (DFN.mesh_network(uniform_mesh = True))

      +
      +
      Parameters:
      +
        +

      • dirname (string) – name of working directory. Default : dfm_mesh

        • +

      • allowed_percentage (float) – Percentage of the mesh allowed to be missing and still continue

        • +

      • cleanup (bool) – Clean up working directory. If true dep files are moved into subdirectories

        • +
      +
      +
      Return type:
      +

      None

      +
      +
      +

      Notes

      +

      The final mesh is output in exodus format. This requires that LaGriT is built against exodus.

      +
      +
      diff --git a/docs/searchindex.js b/docs/searchindex.js index c45e7b31..e4e1f15c 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["applications", "dfnflow", "dfngen", "dfntrans", "examples", "gallery", "index", "index_docs", "intro", "output", "publications", "pydfnFlow", "pydfnGen", "pydfnGraph", "pydfnTrans", "pydfnWorks-well", "pydfnworks", "setup"], "filenames": ["applications.rst", "dfnflow.rst", "dfngen.rst", "dfntrans.rst", "examples.rst", "gallery.rst", "index.rst", "index_docs.rst", "intro.rst", "output.rst", "publications.rst", "pydfnFlow.rst", "pydfnGen.rst", "pydfnGraph.rst", "pydfnTrans.rst", "pydfnWorks-well.rst", "pydfnworks.rst", "setup.rst"], "titles": ["Example Applications", "dfnFlow", "dfnGen - C++ Generation Code", "dfnTrans", "Examples", "dfnWorks Gallery", "Welcome to dfnWorks 2.8 documentation!", "Welcome to dfnWorks 2.8 documentation!", "Welcome To dfnWorks", "Run Files", "dfnWorks Publications", "pydfnworks: dfnFlow", "pydfnworks: dfnGen", "pydfnworks: dfnGraph", "pydfnworks: dfnTrans", "pydfnworks: Well Package", "pydfnworks: the dfnWorks python package", "Setting and Running up dfnWorks"], "terms": {"dfnwork": [0, 2, 4, 9, 11, 12], "provid": [0, 1, 2, 3, 4, 8, 12], "framework": [0, 8, 10], "necessari": [0, 12], "perform": [0, 2, 3, 8], "multiphas": [0, 17], "simul": [0, 1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 13, 16, 17], "flow": [0, 1, 2, 3, 4, 6, 7, 8, 10, 12, 16, 17], "reactiv": [0, 3, 8, 10, 17], "transport": [0, 2, 3, 4, 6, 7, 8, 10, 12, 16, 17], "reservoir": [0, 10], "scale": [0, 8, 10, 17], "A": [0, 2, 8, 10, 12, 13], "particular": [0, 8, 13, 16], "highlight": 0, "here": [0, 2, 4, 16], "i": [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "sequest": 0, "co": [0, 2, 8], "2": [0, 1, 2, 4, 12, 13, 16, 17], "from": [0, 2, 3, 6, 7, 8, 9, 10, 11, 13, 15], "anthropogen": 0, "sourc": [0, 6, 7, 8, 11, 12, 13, 14, 15, 17], "dispos": 0, "geolog": 0, "format": [0, 1, 9, 10, 11, 12, 13, 15, 17], "deep": 0, "salin": 0, "aquif": [0, 10], "abandon": 0, "oil": 0, "field": [0, 3, 5, 6, 7, 8, 10], "one": [0, 1, 2, 3, 4, 12, 17], "princip": 0, "method": [0, 2, 3, 6, 7, 10, 16], "under": [0, 1, 8, 10], "consider": 0, "reduc": [0, 2, 10], "footprint": 0, "atmospher": 0, "due": [0, 2, 4, 9, 10], "fossil": 0, "fuel": 0, "bachu": 0, "2002": 0, "pacala": 0, "socolow": 0, "2004": 0, "For": [0, 2, 12, 17], "safe": 0, "sustain": 0, "long": 0, "term": [0, 8, 12], "storag": 0, "prevent": 0, "leak": 0, "through": [0, 2, 3, 4, 8], "exist": [0, 12], "fault": [0, 10], "fractur": [0, 1, 3, 5, 6, 7, 8, 9, 10, 13, 16, 17], "rock": [0, 10, 12], "along": [0, 2, 4, 5], "ones": 0, "creat": [0, 1, 2, 4, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17], "dure": [0, 2, 10], "inject": [0, 10], "process": [0, 3, 6, 7, 9, 10, 15, 17], "understand": [0, 2, 10], "complex": 0, "physic": [0, 3, 10, 13], "chemic": 0, "interact": [0, 3, 8, 10], "between": [0, 2, 9, 10, 12, 17], "water": [0, 10, 11, 12, 13], "brine": 0, "vital": 0, "capabl": [0, 2, 8], "studi": [0, 8, 10, 12], "dfn": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17], "can": [0, 1, 2, 4, 8, 11, 12, 15, 16, 17], "us": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17], "potenti": 0, "migrat": 0, "cap": 0, "risk": [0, 12], "associ": 0, "propos": 0, "subsurfac": [0, 1, 8, 10, 17], "deplet": 0, "moreov": 0, "pflotran": [0, 1, 4, 6, 7, 8, 12, 15, 16], "coupl": 0, "cell": [0, 9, 11, 12, 16], "base": [0, 2, 6, 7, 8, 9, 10, 11, 16, 17], "transmiss": [0, 10, 12], "allow": [0, 3, 16, 17], "dynam": 0, "chang": [0, 4, 12, 16], "permeabl": [0, 1, 9, 10, 11, 12, 16], "miner": 0, "precipit": 0, "dissolut": 0, "tempor": 0, "evolut": [0, 10], "supercrit": [0, 10], "co2": [0, 10], "displac": [0, 12], "meter": [0, 2, 4, 12], "cube": 0, "contain": [0, 2, 4, 6, 7, 8, 9, 12, 13, 15, 16], "24": 0, "The": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 17], "initi": [0, 1, 2, 9, 13], "fulli": 0, "satur": 0, "top": [0, 2, 9, 11, 12], "left": [0, 2, 4, 9, 11], "time": [0, 1, 2, 8, 10, 12, 13], "0": [0, 1, 2, 4, 6, 7, 11, 12, 13, 16], "hour": 0, "slowli": 0, "system": [0, 10, 12], "bottom": [0, 2, 9, 11], "domain": [0, 4, 6, 7, 8, 9, 12], "total": [0, 2, 12, 13], "10": [0, 1, 2, 8, 12], "h": [0, 6, 7, 8, 9, 10, 11, 12, 13, 16], "There": [0, 2, 12, 16], "an": [0, 1, 2, 3, 4, 6, 7, 8, 10, 13, 15, 17], "flush": 0, "first": [0, 2, 4, 10, 12, 13, 16], "rate": [0, 2, 13], "decreas": 0, "hydraul": [0, 5, 6, 7, 8, 10, 16], "frack": 0, "ha": [0, 2, 4, 8, 9, 11], "access": [0, 12, 16], "hydrocarbon": 0, "trap": 0, "low": [0, 4], "media": [0, 8, 10, 17], "tight": 0, "involv": [0, 1], "high": [0, 4, 8, 17], "pressur": [0, 1, 4, 5, 11, 13], "also": [0, 2, 12, 17], "new": [0, 2, 4, 8, 10, 12], "increas": [0, 2, 8, 10, 17], "howev": [0, 2, 3, 8, 17], "fundament": 0, "why": 0, "work": [0, 2, 8, 10, 11, 12, 14, 15, 16, 17], "its": [0, 2, 8, 12], "ramif": 0, "ar": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "well": [0, 1, 2, 6, 7, 8, 10, 12, 16, 17], "understood": 0, "karra": [0, 1, 3, 8, 10], "et": [0, 10, 12, 13], "al": [0, 10, 12, 13], "2015": [0, 3, 8, 10], "gener": [0, 3, 4, 6, 7, 8, 9, 10, 16], "typic": [0, 11, 14], "product": [0, 8, 10], "site": [0, 10], "thi": [0, 1, 2, 4, 6, 7, 9, 11, 12, 16, 17], "model": [0, 8, 10, 12, 13, 16], "thei": [0, 2, 12], "found": [0, 2, 4, 8, 11, 13, 16, 17], "good": [0, 2, 8], "agreement": 0, "data": [0, 8, 10, 12, 16], "determin": [0, 2, 3, 8, 10, 12], "what": [0, 12, 13], "mechan": [0, 10, 12], "control": [0, 3, 13, 16, 17], "declin": 0, "curv": [0, 1, 10], "swedish": 0, "manag": 0, "compani": 0, "skb": 0, "undertaken": 0, "detail": [0, 1, 2, 3, 6, 7, 8, 9, 11, 12, 13, 17], "investig": 0, "granit": 0, "forsmark": 0, "sweden": 0, "host": [0, 10, 17], "spent": 0, "2011": 0, "hartlei": 0, "joyc": 0, "2013": [0, 12], "area": [0, 2, 9, 11, 12], "about": [0, 2, 3, 6, 7, 9, 11, 12, 15, 16], "120": 0, "km": 0, "north": [0, 2], "stockholm": 0, "northern": 0, "uppland": 0, "construct": [0, 2], "crystallin": [0, 10], "bedrock": 0, "depth": 0, "approxim": [0, 4, 8], "500": 0, "m": [0, 1, 2, 3, 10, 12, 13, 15, 17], "statist": [0, 2, 10], "multipl": [0, 2, 11, 16], "set": [0, 2, 4, 6, 7, 8, 11, 12, 14], "wa": [0, 8, 12], "develop": [0, 8, 17], "paramet": [0, 1, 4, 6, 7, 8, 9, 11, 13, 14, 15], "we": [0, 3, 4, 8, 12, 17], "adopt": [0, 3, 8], "subset": 0, "consist": [0, 4, 16, 17], "three": [0, 2, 3, 8, 10, 12, 13], "background": [0, 6, 7, 8], "non": [0, 2, 3, 9, 10, 13], "determinist": [0, 2], "circular": [0, 4], "whose": [0, 4, 5], "orient": [0, 6, 7, 8, 12], "follow": [0, 2, 4, 5, 8, 10, 12, 15, 17], "fisher": [0, 2, 12], "distribut": [0, 5, 6, 7, 8, 10, 12, 13, 17], "radii": [0, 5, 9, 12, 16], "sampl": [0, 1, 2, 8, 10, 12], "truncat": [0, 5, 6, 7, 10, 12], "power": [0, 2, 6, 7, 10, 12], "law": [0, 2, 6, 7, 10, 12], "estim": 0, "radiu": [0, 6, 7, 12, 15], "apertur": [0, 5, 8, 9, 10, 11, 12, 16], "relat": [0, 2, 12], "size": [0, 2, 4, 8, 10, 11, 12, 13], "cubic": [0, 4], "adler": 0, "2012": 0, "formul": 0, "uniform": [0, 2, 4, 12, 13], "each": [0, 2, 3, 4, 9, 12, 13], "vari": 0, "among": 0, "network": [0, 1, 3, 4, 6, 7, 8, 9, 10, 12, 13, 15, 16, 17], "side": [0, 2, 4, 9], "length": [0, 2, 6, 7, 9, 12, 13], "kilomet": [0, 8, 10], "dirichlet": [0, 1, 4], "boundari": [0, 1, 2, 4, 9, 11, 12, 13], "condit": [0, 1, 4, 8, 9, 11, 13], "impos": [0, 2], "1": [0, 1, 2, 6, 7, 11, 12, 13, 16, 17], "mpa": 0, "gradient": [0, 4, 9], "align": [0, 4], "vertic": [0, 2, 4, 12], "axi": [0, 2, 4], "noflow": 0, "enforc": 0, "later": [0, 8], "particl": [0, 3, 4, 5, 10, 13, 14, 15, 16], "trajectori": [0, 3, 4, 13], "p": [0, 10], "thovert": 0, "j": [0, 2, 8, 10, 12], "f": [0, 2, 10, 12], "mourzenko": 0, "v": [0, 10, 17], "porou": [0, 10, 12, 17], "oxford": 0, "univers": [0, 8], "press": 0, "unit": [0, 2, 11, 12, 13], "kingdom": 0, "": [0, 1, 2, 3, 4, 5, 8, 10, 13], "respons": [0, 10], "climat": 0, "road": 0, "map": [0, 6, 7, 8], "select": [0, 2], "transform": 0, "space": [0, 2], "phase": 0, "conver": 0, "43": 0, "87": 0, "102": 0, "l": [0, 2, 3, 8, 10, 12], "approach": [0, 2, 3, 8, 10, 13], "algorithm": [0, 2, 3, 4, 8, 10, 13, 17], "groundwat": [0, 10], "support": [0, 2, 11, 12, 13], "safeti": 0, "assess": 0, "Fors": 0, "mark": [0, 8], "hydrol": 0, "200": 0, "216": 0, "makedonska": [0, 1, 2, 3, 8, 10], "n": [0, 2, 3, 8, 10, 12], "viswanathan": [0, 8, 10], "painter": [0, 2, 3, 8, 10], "hyman": [0, 2, 8, 10, 12, 13], "effect": [0, 2, 3, 10, 11, 12], "advect": [0, 3, 10], "matrix": [0, 3, 8, 9, 10, 12, 13], "diffus": [0, 3, 8, 10, 13], "natur": [0, 4, 10], "ga": [0, 10], "resour": [0, 10], "re": [0, 2, 10, 17], "review": [0, 10, 13], "r": [0, 2, 8, 10, 12, 15, 17], "stabil": 0, "wedg": 0, "solv": [0, 3, 13, 17], "problem": [0, 3, 10], "next": [0, 12, 17], "50": [0, 2], "year": [0, 8], "current": [0, 4, 6, 7, 11, 12, 13, 14, 17], "technologi": 0, "scienc": [0, 8, 10, 12], "305": 0, "968": 0, "972": 0, "final": [0, 2, 8, 9, 12, 16, 17], "main": [0, 2, 10, 12, 17], "report": [0, 2, 8, 10, 12], "sr": 0, "project": [0, 2], "technic": 0, "tr": 0, "11": [0, 12], "01": [0, 1], "solver": [1, 8, 11, 17], "fehm": [1, 6, 7, 8, 9, 12, 16], "recommend": [1, 2, 4, 8, 16, 17], "larg": [1, 11, 17], "number": [1, 2, 9, 12, 13, 16], "o": [1, 10, 12, 16, 17], "1000": 1, "function": [1, 2, 4, 6, 7, 8, 9, 11, 12, 14, 15, 16], "call": [1, 8, 11, 12, 15, 16], "part": 1, "pydfnwork": [1, 2, 6, 7, 8], "mesh": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17], "file": [1, 4, 6, 7, 11, 13, 14, 15, 16, 17], "need": [1, 2, 12, 17], "run": [1, 2, 4, 6, 7, 8, 13], "unstructur": [1, 3], "ug": [1, 9, 16], "ex": [1, 9, 11, 15], "pleas": [1, 8, 12], "see": [1, 2, 8, 11, 12, 13, 16, 17], "user": [1, 4, 6, 7, 8, 9, 16], "manual": [1, 6, 7, 16], "http": [1, 2, 4, 8, 11, 12, 17], "www": [1, 4, 11, 17], "org": [1, 2, 4, 11, 17], "explicit": 1, "usag": [1, 10, 12], "further": 1, "exampl": [1, 6, 7, 8, 12, 15, 16, 17], "input": [1, 4, 6, 7, 8, 9, 11, 13, 14, 16], "repositori": [1, 6, 7, 8, 10], "start": [1, 2, 3, 9, 13, 17], "point": [1, 2, 9, 12, 15], "build": [1, 6, 7], "your": [1, 4, 8, 12, 16, 17], "deck": 1, "below": [1, 2, 12, 16], "refer": [1, 2, 12], "descript": [1, 2, 3, 8, 16], "jan": 1, "13": [1, 2, 12], "2014": [1, 2, 10], "nataliia": [1, 8, 10], "satish": [1, 8, 10], "lanl": [1, 6, 7, 11, 12, 17], "simulation_typ": 1, "process_model": 1, "subsurface_flow": 1, "mode": [1, 2, 10, 11, 12], "richard": 1, "end": [1, 4, 5, 9, 13], "discret": [1, 2, 3, 8, 10, 12, 13, 16], "grid": 1, "type": [1, 2, 11, 12, 13, 14, 15, 16], "unstructured_explicit": 1, "full_mesh_vol_area": [1, 9], "graviti": 1, "d0": 1, "fluid": [1, 10], "properti": [1, 2, 6, 7, 9, 10, 16], "fluid_properti": 1, "diffusion_coeffici": 1, "d": [1, 2, 8, 10, 12], "9": [1, 2], "dataset": 1, "filenam": [1, 2, 11, 12, 13, 15], "dfn_properti": [1, 9], "h5": [1, 9, 12], "materi": [1, 4, 8, 9, 10, 12], "material_properti": 1, "soil1": 1, "id": [1, 4, 9, 12, 16], "poros": [1, 12, 13], "25d0": 1, "tortuos": [1, 12], "5d0": 1, "characteristic_curv": 1, "default": [1, 2, 11, 12, 13, 16], "characterist": [1, 10], "saturation_funct": 1, "van_genuchten": 1, "alpha": [1, 2, 12], "4": [1, 2, 6, 7, 10, 12, 16], "liquid_residual_satur": 1, "1d0": 1, "max_capillary_pressur": 1, "d8": 1, "permeability_funct": 1, "mualem_vg_liq": 1, "output": [1, 6, 7, 8, 11, 12, 13, 16, 17], "option": [1, 2, 8, 12, 13, 16, 17], "05": [1, 2], "5": [1, 2, 3, 4, 6, 7, 12], "tecplot": 1, "block": [1, 8, 13], "print_primal_grid": 1, "vtk": [1, 4, 9, 11, 12, 17], "mass_flowr": 1, "mass_bal": 1, "variabl": [1, 5, 10, 12, 17], "liquid_pressur": 1, "initial_timestep_s": 1, "8": [1, 2, 4, 12, 16], "final_tim": 1, "maximum_timestep_s": 1, "steady_st": 1, "reference_pressur": 1, "1500000": 1, "region": [1, 6, 7, 8, 12], "all": [1, 2, 4, 8, 11, 12, 13, 14, 15, 17], "coordin": [1, 12, 15], "d20": 1, "inflow": [1, 4, 11, 13], "pboundary_left_w": [1, 9], "outflow": [1, 4, 11, 13], "pboundary_right_": [1, 9], "flow_condit": 1, "01325d6": 1, "d6": 1, "coupler": 1, "initial_condit": 1, "boundary_condit": 1, "stratigraphi": 1, "strata": 1, "end_subsurfac": 1, "featur": [2, 8, 10, 12], "reject": [2, 8, 9, 10], "fram": [2, 8], "stochast": [2, 4, 8, 10, 12], "implement": [2, 3, 12, 17], "methodologi": [2, 3, 8], "w": [2, 3, 8, 10], "gabl": [2, 3, 8, 10], "conform": [2, 6, 7, 8, 10, 17], "delaunai": [2, 8, 10, 17], "triangul": [2, 8, 10, 17], "dimension": [2, 3, 8, 10, 12, 13], "strategi": [2, 10], "siam": [2, 10, 13], "sci": [2, 10], "comput": [2, 3, 4, 8, 10, 11, 17], "36": 2, "a1871": 2, "a1894": 2, "si": [2, 13], "mandatori": [2, 16], "label": 2, "must": [2, 8, 12, 13, 16, 17], "present": [2, 4, 12, 17], "python": [2, 6, 7, 8, 12], "driver": [2, 6, 7, 14, 16], "script": [2, 4, 12, 16, 17], "which": [2, 3, 4, 8, 9, 11, 12, 13, 14, 17], "center": [2, 12], "origin": [2, 4, 12], "entri": 2, "span": 2, "x": [2, 4, 9, 11, 12], "east": 2, "west": 2, "second": [2, 4, 12, 16], "y": [2, 4, 9, 10, 11], "south": 2, "third": [2, 12], "z": [2, 9, 10, 11], "list": [2, 8, 9, 12, 13, 15, 16], "float": [2, 11, 12, 13, 15], "none": [2, 11, 12, 13, 14, 15, 16, 17], "valu": [2, 9, 11, 12, 13, 16], "20": 2, "minimum": [2, 4, 12], "maximum": [2, 4, 12], "direct": [2, 4, 8, 11, 13], "temporari": 2, "insert": [2, 4, 12], "outsid": 2, "after": [2, 12, 16], "complet": [2, 12], "back": [2, 9, 11], "expans": 2, "help": [2, 17], "mitig": 2, "edg": [2, 4, 13, 17], "densiti": [2, 10, 11], "param": [2, 9, 11, 12, 16], "ad": [2, 6, 7, 8], "subtract": 2, "less": 2, "than": [2, 8], "rule": 2, "thumb": 2, "least": [2, 12, 17], "largest": 2, "stratograph": 2, "If": [2, 8, 11, 12, 15, 16, 17], "height": 2, "assign": [2, 8, 12, 16], "when": [2, 12], "pydfngen": [2, 16], "neg": [2, 9, 13], "integ": [2, 9, 13, 16], "two": [2, 4, 16], "lower": 2, "upper": 2, "limit": [2, 8, 9, 13], "etc": 2, "everi": [2, 9], "entir": 2, "element": [2, 3, 9, 12], "zmin": 2, "zmax": 2, "30": 2, "40": 2, "overlap": 2, "cuboid": 2, "creation": 2, "bound": 2, "box": 2, "theses": 2, "six": 2, "minx": 2, "maxx": 2, "mini": 2, "maxi": 2, "minz": 2, "maxz": 2, "15": 2, "Will": 2, "min": 2, "max": 2, "do": [2, 3, 8, 17], "same": [2, 4, 12, 16], "face": [2, 11], "boolean": [2, 11, 12, 16], "fals": [2, 11, 12, 13, 16], "true": [2, 11, 12, 16], "ignor": [2, 13], "keep": 2, "cluster": [2, 10], "retain": [2, 8, 16], "onli": [2, 3, 11, 12, 13], "connect": [2, 9, 10, 12, 13], "correspond": [2, 4, 9, 11, 12, 13], "3": [2, 6, 7, 12, 17], "within": [2, 4, 5, 8, 16], "criteria": 2, "stop": [2, 12], "onc": 2, "accept": [2, 12], "p32": [2, 12], "have": [2, 4, 9, 11, 15, 16, 17], "been": [2, 8, 9, 16], "meet": 2, "belong": [2, 12], "request": [2, 13], "posit": [2, 12], "100": 2, "probabl": [2, 12], "occurr": 2, "add": [2, 8, 11, 12], "up": [2, 4, 6, 7, 8, 12, 13], "save": [2, 12], "order": [2, 4], "automat": [2, 12, 16, 17], "prior": [2, 4, 8, 16], "ani": [2, 8, 17], "possibl": [2, 8], "constraint": 2, "met": [2, 8], "definit": 2, "theta": [2, 12], "phi": [2, 12, 13], "degre": [2, 12], "angl": [2, 9, 12], "specifi": [2, 12, 16], "string": [2, 11, 12, 13, 14, 15, 16], "either": [2, 8, 12, 16], "radian": [2, 12], "reason": [2, 9], "unless": 2, "turn": [2, 12], "greater": 2, "cdot": 2, "sqrt": 2, "where": [2, 10, 12, 15, 17], "smaller": 2, "10th": 2, "larger": 2, "1000th": 2, "zero": [2, 9], "clear": 2, "requir": [2, 4, 6, 7, 8, 11, 12, 14, 16], "discuss": [2, 16], "off": [2, 12, 13], "result": [2, 9, 12], "coars": 2, "visual": [2, 4, 8, 10, 12, 17], "you": [2, 4, 8, 12, 17], "cannot": 2, "full": [2, 9, 13], "intent": 2, "upscal": [2, 6, 7, 10], "octre": [2, 10, 12], "udfm": [2, 6, 7, 10], "modul": [2, 6, 7, 8, 12, 17], "print": [2, 6, 7, 8], "inform": [2, 3, 6, 7, 9, 10, 11, 13, 15, 16], "screen": [2, 11, 12], "debug": [2, 16, 17], "more": [2, 8, 12, 13], "effici": [2, 10], "hit": 2, "target": [2, 12, 13], "befor": [2, 12, 17], "being": [2, 12], "equal": 2, "queue": 2, "percentag": 2, "smallest": 2, "begin": 2, "properli": 2, "resolv": [2, 3], "represent": [2, 3, 4, 5, 8, 10, 12, 13, 17], "exhaust": 2, "random": [2, 8, 10, 12], "like": [2, 16], "doubl": [2, 11, 13], "examin": 2, "check": [2, 8, 12], "prescrib": 2, "output_report": [2, 12], "No": 2, "longer": [2, 12], "should": [2, 8, 11, 12], "done": [2, 17], "mesh_network": [2, 4, 12, 16], "visual_mod": [2, 12], "want": [2, 12], "quick": 2, "standard": 2, "full_mesh": [2, 4, 9, 16], "inp": [2, 4, 9, 12, 15, 16], "reduced_mesh": [2, 12], "clock": 2, "uniqu": [2, 3], "produc": [2, 8, 9, 12], "reproduc": [2, 4, 8], "42069": 2, "dfn_output": [2, 9], "txt": [2, 4, 9, 11, 12], "isol": [2, 4, 9], "remov": [2, 4, 9, 12, 13, 15, 16], "contribut": 2, "fail": [2, 12], "still": 2, "whether": [2, 8, 12], "tripl": [2, 9], "intersect": [2, 9, 10, 12, 13, 15, 17], "even": [2, 8, 12], "dfntran": [2, 6, 7, 8, 16], "doe": [2, 3, 10, 11, 12], "cutoff": 2, "e": [2, 10, 11, 13], "g": [2, 10, 11, 13], "down": 2, "those": [2, 12], "how": [2, 17], "alwai": 2, "sequenti": [2, 10], "respect": 2, "forc": [2, 11], "sort": [2, 10], "minim": 2, "both": [2, 16], "radii_allaccept": 2, "dat": [2, 4, 9, 11, 12, 15, 16], "xradiu": 2, "yradiu": 2, "userpolygon": 2, "userrectangl": 2, "userellips": 2, "per": [2, 9], "radii_allaccepted_fam_1": 2, "distributionnumb": 2, "radii_final_fam_1": 2, "section": [2, 4, 9, 12, 16, 17], "describ": [2, 9, 16, 17], "disc": [2, 8], "shape": [2, 12, 16], "match": [2, 10], "index": [2, 9, 11, 12], "shown": [2, 5], "written": [2, 8, 11, 12, 13, 15], "dictionari": [2, 12, 15], "meant": 2, "addit": [2, 6, 7, 8], "whole": [2, 12], "intens": [2, 12], "p_": 2, "32": 2, "text": [2, 12], "surfac": [2, 4], "divid": 2, "volum": [2, 3, 8, 9, 11, 15, 17], "until": 2, "obtain": [2, 3, 4, 6, 7, 13], "desir": [2, 12, 17], "02": 2, "ellipt": [2, 4], "12": [2, 12, 16], "16": 2, "lead": 2, "challeng": [2, 3, 10], "via": [2, 10], "suggest": 2, "aspect": [2, 12], "ratio": [2, 12], "circl": 2, "twice": 2, "make": [2, 8, 12, 15], "As": [2, 12], "degrad": 2, "accuraci": 2, "von": [2, 12], "mise": [2, 12], "bf": 2, "boldsymbol": 2, "mu": [2, 12], "kappa": [2, 12], "frac": 2, "exp": [2, 6, 7, 12], "t": [2, 10, 12, 13], "pi": 2, "sinh": 2, "mean": [2, 12], "vector": [2, 5, 9, 12], "denot": 2, "transpos": 2, "commun": 2, "23": 2, "1994": 2, "157": 2, "164": 2, "andrew": 2, "wood": 2, "indic": [2, 13], "concentr": [2, 12], "around": [2, 12], "17": [2, 8], "45": [2, 12], "78": 2, "sphere": 2, "small": 2, "deviat": 2, "numer": [2, 3, 10, 13], "becom": 2, "unstabl": 2, "vec": 2, "_x": 2, "sin": 2, "_y": 2, "_z": 2, "onto": 2, "56": 2, "270": 2, "four": [2, 4, 12], "differ": [2, 10, 12, 16], "log": [2, 10, 12], "sigma": [2, 12], "ln": 2, "right": [2, 4, 8, 9, 11], "varianc": [2, 12], "underli": 2, "en": 2, "wikipedia": 2, "wiki": 2, "normal_distribut": 2, "equat": [2, 3, 12, 17], "abov": [2, 8], "convert": [2, 11, 12, 15], "609": 2, "040": 2, "r_0": 2, "r_u": 2, "expon": [2, 4], "6": [2, 4, 6, 7, 16, 17], "tpl": [2, 6, 7, 12], "lambda": 2, "25": [2, 12], "7": [2, 6, 7, 9], "527": 2, "89": 2, "singl": [2, 4, 9, 12, 16], "These": [2, 9, 15, 16, 17], "mono": 2, "dispers": [2, 3, 10], "rectangular": [2, 4], "squar": 2, "ref": 2, "includ": [2, 4, 8, 9, 12, 16], "wai": [2, 8, 16, 17], "One": [2, 12], "put": [2, 11], "convex": 2, "vertex": [2, 4, 13], "To": [2, 6, 7, 10, 12, 16, 17], "incoper": 2, "add_user_fract": [2, 12, 16], "add_user_fract_from_fil": [2, 12], "predefin": 2, "go": [2, 10, 17], "activ": 2, "read": [2, 13], "path": [2, 6, 7, 8, 10, 11, 12, 13, 14], "valid": [2, 16], "filepath": 2, "userell_input_filepath": 2, "4_user_ell_uniform": 2, "define_4_user_ellips": 2, "int": [2, 11, 12, 13], "expect": [2, 9], "line": [2, 4, 6, 7, 9, 11, 12, 14], "accord": 2, "keyword": [2, 12], "mix": [2, 10], "90": 2, "37": 2, "name": [2, 8, 11, 12, 13, 15, 16], "4_user_el": 2, "ellcoord": 2, "node": [2, 9, 12, 13, 15, 16], "x_0": 2, "y_0": 2, "z_0": 2, "x_1": 2, "y_1": 2, "z_1": 2, "ldot": 2, "x_n": 2, "y_n": 2, "z_n": 2, "clockwis": 2, "counterclockwis": 2, "planar": 2, "BY": [2, 8], "note": [2, 3, 4, 9, 11, 12, 13, 14, 15, 17], "white": 2, "matter": 2, "x1": [2, 9, 12, 15], "y1": [2, 9, 12, 15], "z1": [2, 9, 12, 15], "x2": [2, 12], "y2": [2, 12], "z2": [2, 12], "x3": 2, "y3": 2, "z3": 2, "x4": 2, "y4": 2, "z4": 2, "xn": [2, 12, 15], "yn": [2, 12, 15], "zn": [2, 12, 15], "4_user_rect": 2, "define_4_user_rect": 2, "rectcoord": 2, "user_polygon": 2, "refpolygonbycoord_input_file_path": 2, "Then": [2, 3, 12], "remain": 2, "614809755508": 2, "215302589745": 2, "14052566974": 2, "545132019741": 2, "76296408041": 2, "01135305297": 2, "46205561432": 2, "11169723114": 2, "28911258873": 2, "7422671348": 2, "903335314403": 2, "34275683413": 2, "19676496723": 2, "52840001844": 2, "54841054822": 2, "3215018603": 2, "70265907788": 2, "28455866847": 2, "968743065242": 2, "39004354883": 2, "5300049043": 2, "82257143457": 2, "169537908304": 2, "10365780918": 2, "89449659536": 2, "39229757501": 2, "47097810869": 2, "7368040684": 2, "396173810104": 2, "9199696155": 2, "76351044547": 2, "192549006049": 2, "33581920939": 2, "157462422292": 2, "76600532497": 2, "29594241204": 2, "30082072643": 2, "47978607543": 2, "64081751301": 2, "793278268371": 2, "81778296407": 2, "561983329033": 2, "45819042638": 2, "44636375172": 2, "4541413343": 2, "51825209439": 2, "66719739398": 2, "0912558548": 2, "1739128129": 2, "74246641127": 2, "809628560699": 2, "56729801834": 2, "10664963232": 2, "17895163585": 2, "75834169562": 2, "23742727251": 2, "80010131269": 2, "26666449977": 2, "40228077595": 2, "45665913893": 2, "23685468994": 2, "54844410108": 2, "5749811435": 2, "06272440502": 2, "61045433532": 2, "565188057474": 2, "92263630123": 2, "27643915621": 2, "710166484812": 2, "89865208954": 2, "42113429321": 2, "22497133918": 2, "00482133497": 2, "61970921408": 2, "322281059007": 2, "27249031626": 2, "91468659533": 2, "549550927249": 2, "19700291895": 2, "3154355331": 2, "64584005023": 2, "20544838483": 2, "98437001886": 2, "31745142962": 2, "22589362057": 2, "804792681255": 2, "91861492809": 2, "70593999999": 2, "29639431251": 2, "25224389054": 2, "10094407568": 2, "6562865987": 2, "03245087974": 2, "992518232701": 2, "50612429324": 2, "10741842947": 2, "384249987443": 2, "93387033715": 2, "43323157864": 2, "222868762162": 2, "860529584164": 2, "81903344627": 2, "38212753352": 2, "499362646346": 2, "03882643837": 2, "4905528176": 2, "349200223043": 2, "9638588789": 2, "8673209588": 2, "22305329999": 2, "63804581282": 2, "39564264412": 2, "56312416852": 2, "08462835745": 2, "41898893677": 2, "65124788861": 2, "11909954775": 2, "10520773081": 2, "8645938936": 2, "89290711889": 2, "80872562941": 2, "11160312936": 2, "39770554375": 2, "19173173493": 2, "34506895229": 2, "42895858094": 2, "20485792137": 2, "85177752427": 2, "81351205493": 2, "99702019362": 2, "0853427250495": 2, "66597219167": 2, "50868187563": 2, "289753327606": 2, "588931258258": 2, "08441961571": 2, "88990150472": 2, "64805531643": 2, "34094328974": 2, "922507014307": 2, "71519798881": 2, "85778630995": 2, "841071899053": 2, "310044679731": 2, "25820816606": 2, "26426496474": 2, "84566856205": 2, "49988903618": 2, "94418542615": 2, "40633923745": 2, "44125563949": 2, "48254521057": 2, "07783735953": 2, "94508200102": 2, "5639802392": 2, "05259419185": 2, "54466008318": 2, "14078724661": 2, "483028953749": 2, "30297907019": 2, "4608669326": 2, "04369954706": 2, "36161304612": 2, "18143095055": 2, "610312831185": 2, "21771261931": 2, "80909183961": 2, "814183043594": 2, "47247873318": 2, "26469088948": 2, "29432736239": 2, "44327042469": 2, "867130728085": 2, "96307141873": 2, "14719749191": 2, "564917036364": 2, "42867426252": 2, "75769541671": 2, "19257780773": 2, "00417817281": 2, "50292931657": 2, "648176891617": 2, "475965761662": 2, "53213764385": 2, "74938298608": 2, "14470985076": 2, "82821050463": 2, "27165416308": 2, "97370232204": 2, "13046740212": 2, "01807341608": 2, "962283071202": 2, "35725325459": 2, "83562647916": 2, "23286105726": 2, "12746635144": 2, "40616097581": 2, "67958113114": 2, "45759785589": 2, "34398137987": 2, "64526675756": 2, "polgyon": 2, "solut": [3, 4, 8, 9, 10, 11, 12], "dfnflow": [3, 6, 7, 8, 16], "dfngen": [3, 6, 7, 8, 16], "lagrangian": [3, 8], "repres": [3, 10, 12], "conserv": 3, "collect": 3, "indivis": 3, "passiv": 3, "tracer": 3, "track": [3, 4, 10, 13, 15, 16], "wealth": 3, "local": [3, 16, 17], "b": [3, 10, 12], "suffer": 3, "inher": 3, "c": [3, 6, 7, 8, 10, 17], "intrins": [3, 8], "parallel": [3, 8, 10, 17], "fashion": [3, 8], "anoth": [3, 11, 14], "pose": 3, "aris": [3, 8], "qualiti": [3, 8], "phenomena": 3, "interest": 3, "mass": [3, 12], "so": [3, 4, 8, 17], "galerkin": 3, "finit": [3, 8, 13, 17], "code": [3, 4, 6, 7, 8, 15, 17], "reconstruct": 3, "veloc": [3, 4, 5, 13], "darci": 3, "flux": [3, 13], "pathlin": [3, 4, 5, 8], "It": [3, 17], "import": [3, 16, 17], "itself": [3, 8], "longitudin": 3, "sorption": 3, "other": [3, 8, 12, 16], "retent": 3, "easili": 3, "incorpor": 3, "post": 3, "bui": [3, 8, 10], "q": [3, 10], "geoscienc": [3, 8, 10], "19": [3, 8], "1123": 3, "1137": 3, "doxygen": [3, 6, 7], "few": [4, 12], "folder": [4, 17], "focu": 4, "document": [4, 8, 17], "confirm": 4, "correctli": 4, "carri": 4, "out": [4, 8, 9, 11, 12, 13], "imag": [4, 13, 17], "render": 4, "paraview": 4, "free": [4, 8], "simplest": 4, "proce": [4, 12], "directori": [4, 6, 7, 8, 9, 11, 12, 14, 15, 16], "subdirectori": [4, 9, 12], "command": [4, 6, 7, 11, 12, 14, 17], "Be": 4, "sure": [4, 12], "test_output_fil": 4, "locat": [4, 9, 12, 13], "test": [4, 6, 7], "case": [4, 10], "defin": [4, 6, 7, 8, 9, 12], "color": [4, 5, 13], "overlaid": 4, "load": 4, "job": [4, 12], "red": [4, 13], "appli": [4, 10, 12], "blue": [4, 13], "parsed_vtk": [4, 9], "dfn_explicit": [4, 9, 16], "001": [4, 9, 12], "uniformli": 4, "inlet": [4, 13], "exit": [4, 12], "horizont": 4, "might": 4, "exactli": 4, "magnitud": 4, "part_": 4, "4_user_rectangl": 4, "traj": 4, "extract": [4, 6, 7], "tube": 4, "filter": 4, "clariti": 4, "In": [4, 10], "ellips": [4, 6, 7, 12], "resolut": [4, 10, 11, 12, 15, 17], "argument": [4, 6, 7, 11, 12, 14], "slope": [4, 12], "run_explicit": 4, "py": [4, 12, 16, 17], "famili": [4, 6, 7, 8, 9, 17], "1m": 4, "50m": 4, "10m": 4, "gen_exponential_dist": 4, "modifi": [4, 8], "card": [4, 11, 12], "5m": 4, "15m": 4, "core": 4, "dead": [4, 5], "identifi": [4, 9, 10, 13, 15], "networkx": [4, 13, 17], "github": [4, 6, 7, 8], "io": [4, 17], "sub": [4, 15, 17], "207": 4, "79": 4, "topologi": [4, 10], "compos": 5, "powerlaw": 5, "contour": 5, "graph": [5, 6, 7, 8, 10, 16], "intern": [5, 10, 12], "purpl": 5, "content": [6, 7, 9], "cite": [6, 7], "version": [6, 7, 12, 17], "v2": [6, 7, 12], "contact": [6, 7], "contributor": [6, 7], "extern": [6, 7], "copyright": [6, 7], "applic": [6, 7, 8, 10], "carbon": [6, 7], "dioxid": [6, 7], "sequestr": [6, 7, 8], "shale": [6, 7, 10], "energi": [6, 7, 8, 10], "nuclear": [6, 7, 8, 10], "wast": [6, 7, 8, 10], "docker": [6, 7, 8], "nativ": [6, 7], "clone": [6, 7], "dnfwork": [6, 7], "fix": [6, 7, 8], "lagrit": [6, 7, 8, 11], "petsc": [6, 7], "instal": [6, 7, 16], "4_user_defined_rect": [6, 7], "4_user_defined_ell_uniform": [6, 7], "exponenti": [6, 7], "prune": [6, 7, 16], "packag": [6, 7, 8, 17], "class": [6, 7, 11, 12, 13, 14, 15, 17], "jobnam": [6, 7, 12], "ncpu": [6, 7, 11], "dfnflow_fil": [6, 7], "dfngen_fil": [6, 7], "dfntrans_fil": [6, 7], "prune_fil": [6, 7, 12], "flow_solv": [6, 7, 11], "cell_based_apertur": [6, 7], "analysi": [6, 7, 10, 13, 16], "modif": [6, 7, 8], "stress": [6, 7, 8, 10], "primari": [6, 7, 10, 11, 13, 14], "helper": [6, 7], "mapdfn_ecpm": [6, 7, 12], "dfm": [6, 7], "create_dfn_flow_link": [6, 7, 11], "dfn_flow": [6, 7, 11, 16], "set_flow_solv": [6, 7, 11], "lagrit2pflotran": [6, 7, 11], "parse_pflotran_vtk_python": [6, 7, 11], "pflotran_cleanup": [6, 7, 11], "write_perms_and_correct_volumes_area": [6, 7, 11], "zone2ex": [6, 7, 11], "correct_stor_fil": [6, 7, 11], "effective_perm": [6, 7, 11], "check_dfn_trans_run_fil": [6, 7, 14], "copy_dfn_trans_fil": [6, 7, 14], "create_dfn_trans_link": [6, 7, 14], "dfn_tran": [6, 7, 14, 16], "run_dfn_tran": [6, 7, 14], "dfngraph": [6, 7, 8], "add_fracture_sourc": [6, 7, 13], "add_fracture_target": [6, 7, 13], "create_graph": [6, 7, 13], "dump_fractur": [6, 7, 13], "dump_json_graph": [6, 7, 13], "load_json_graph": [6, 7, 13], "plot_graph": [6, 7, 13], "greedy_edge_disjoint": [6, 7, 13], "k_shortest_paths_backbon": [6, 7, 13], "run_graph_flow": [6, 7, 13], "run_graph_transport": [6, 7, 13], "cleanup_wel": [6, 7, 15], "combine_well_boundary_zon": [6, 7, 15], "find_well_intersection_point": [6, 7, 15], "tag_well_in_mesh": [6, 7, 15], "domains": [6, 7, 16], "domainsizeincreas": [6, 7], "numoflay": [6, 7], "layer": [6, 7, 12], "numofregion": [6, 7], "ignoreboundaryfac": [6, 7], "boundaryfac": [6, 7], "stopcondit": [6, 7, 12], "npoli": [6, 7], "famprob": [6, 7], "orientationopt": [6, 7, 12], "angleopt": [6, 7], "disablefram": [6, 7], "printrejectreason": [6, 7], "rejectsperfractur": [6, 7], "radiilistincreas": [6, 7], "visualizationmod": [6, 7], "seed": [6, 7], "keeponlylargestclust": [6, 7], "keepisolatedfractur": [6, 7], "tripleintersect": [6, 7], "removefractureslessthan": [6, 7], "insertuserrectanglesfirst": [6, 7], "forcelargefractur": [6, 7], "outputallradii": [6, 7], "outputacceptedradiiperfamili": [6, 7], "outputfinalradiiperfamili": [6, 7], "rectangl": [6, 7, 9, 12], "polygon": [6, 7, 9, 12], "public": [6, 7, 8], "galleri": [6, 7], "suit": 8, "lo": [8, 17], "alamo": [8, 17], "nation": [8, 10, 12, 17], "laboratori": [8, 12, 17], "rang": 8, "millimet": 8, "combin": [8, 15], "toolbox": [8, 17], "suitabl": [8, 17], "util": 8, "massiv": [8, 17], "workflow": [8, 11, 12, 16], "highli": [8, 17], "variou": [8, 16], "tool": [8, 17], "aim": 8, "seamless": 8, "scientif": [8, 10], "download": [8, 17], "com": [8, 17], "hub": [8, 17], "ees16": [8, 17], "84": 8, "bibtex": 8, "articl": 8, "hyman2015dfnwork": 8, "titl": 8, "author": 8, "jeffrei": [8, 10, 12], "carl": [8, 10], "scott": [8, 10], "hari": [8, 10], "journal": [8, 10, 12], "page": [8, 10], "publish": 8, "elsevi": 8, "poisson": [8, 10], "v3": 8, "ecpm": [8, 12], "bug": 8, "tdrw": [8, 13], "object": [8, 11, 12, 13, 14, 15, 16], "interfac": 8, "updat": 8, "compat": 8, "warn": [8, 9, 12], "error": [8, 12], "trend": [8, 12], "plung": [8, 12], "dip": [8, 12], "strike": [8, 12], "techniqu": [8, 16], "expand": [8, 15], "pdf": [8, 12], "abil": 8, "python3": 8, "pipe": [8, 13, 16], "dfn2graph": 8, "streamlin": 8, "rout": 8, "walk": 8, "much": 8, "faster": [8, 17], "mathematica": 8, "successfulli": 8, "350": 8, "000": [8, 9], "compris": 8, "short": 8, "tutori": 8, "prepar": 8, "some": [8, 12], "email": 8, "gov": [8, 11, 12], "question": 8, "let": [8, 12], "u": 8, "know": 8, "ll": 8, "matt": 8, "sweenei": [8, 10, 12], "aric": [8, 10], "hagberg": [8, 10], "shriram": [8, 10], "srinivasan": [8, 10], "aidan": [8, 12], "stansberri": 8, "pnnl": 8, "ornl": 8, "quan": 8, "now": 8, "llnl": 8, "jeremi": 8, "harrod": 8, "spectra": 8, "logic": 8, "thoma": 8, "sherman": [8, 10], "notr": 8, "dame": 8, "johann": 8, "krotz": [8, 10], "oregon": 8, "state": [8, 9, 10, 11, 13], "yu": 8, "chen": [8, 10], "la": 8, "ur": 8, "22216": 8, "softwar": [8, 17], "cc": 8, "027": 8, "2018": [8, 10, 13], "triad": 8, "secur": [8, 10], "llc": 8, "reserv": 8, "program": [8, 12], "govern": 8, "contract": 8, "89233218cna000001": 8, "oper": 8, "depart": 8, "administr": 8, "grant": 8, "act": 8, "behalf": 8, "nonexclus": 8, "paid": 8, "irrevoc": 8, "worldwid": 8, "licens": 8, "deriv": 8, "copi": [8, 11, 14], "publicli": 8, "displai": 8, "permit": 8, "neither": 8, "THE": 8, "nor": 8, "warranti": 8, "express": 8, "OR": 8, "impli": 8, "assum": [8, 11, 12], "liabil": 8, "FOR": 8, "OF": 8, "clearli": 8, "confus": 8, "avail": [8, 17], "addition": 8, "redistribut": 8, "gnu": 8, "foundat": 8, "accordingli": 8, "hope": 8, "without": [8, 12], "merchant": 8, "fit": 8, "purpos": [8, 9], "binari": [8, 9], "form": 8, "notic": 8, "disclaim": 8, "mai": [8, 12], "endors": 8, "promot": 8, "specif": 8, "permiss": 8, "AND": 8, "AS": 8, "BUT": 8, "NOT": 8, "TO": 8, "IN": 8, "NO": 8, "event": 8, "shall": 8, "BE": 8, "liabl": 8, "indirect": 8, "incident": 8, "special": 8, "exemplari": 8, "consequenti": 8, "damag": 8, "procur": 8, "substitut": 8, "servic": 8, "loss": 8, "profit": 8, "busi": 8, "interrupt": 8, "caus": 8, "ON": 8, "theori": [8, 10], "strict": [8, 12], "tort": 8, "neglig": 8, "otherwis": 8, "IF": 8, "advis": 8, "SUCH": 8, "row": 9, "adjac": 9, "input_gener": 9, "input_generator_clean": 9, "abbrevi": 9, "normal_vector": [9, 12, 16], "normal": [9, 12], "visualmod": 9, "dud": 9, "dimens": 9, "poly_info": 9, "rotat": [9, 12], "rotateln": 9, "x0": [9, 15], "y0": [9, 15], "z0": [9, 15], "user_rect": 9, "concatent": 9, "radii_fin": 9, "summari": [9, 12], "rejectsperattempt": 9, "attempt": 9, "translat": [9, 12, 16], "centriod": 9, "triple_point": 9, "warningfiledfngen": 9, "intersection_list": 9, "fracture1": 9, "fracture2": 9, "bound_zon": 9, "lgi": 9, "dump": [9, 11, 12, 13], "zone": [9, 10, 11, 15], "boundary_output": 9, "finalmesh": 9, "brief": 9, "av": [9, 15], "lg": 9, "correct": [9, 11, 12], "convert_ug": 9, "full_mesh_viz": 9, "lagrit_log": 9, "individu": [9, 11, 12, 13, 16], "logx3dgen": 9, "outx3dgen": 9, "mgli": 9, "poli": [9, 12], "contiain": 9, "tri_fractur": 9, "stor": [9, 11], "user_funct": 9, "coarsen": 9, "rescal": 9, "cellinfo": [9, 11], "steadi": [9, 10, 11, 13], "ma": 9, "_dfn_explicit": 9, "attribut": [9, 15], "materialid": [9, 16], "perm": 9, "pboundary_back_n": 9, "pboundary_bottom": 9, "pboundary_front_": 9, "front": [9, 11], "pboundary_top": 9, "middleton": 10, "carei": 10, "currier": 10, "kang": 10, "jimenez": 10, "mart\u0131nez": 10, "porter": 10, "aqueou": 10, "opportun": 10, "influenc": 10, "resourc": [10, 12], "research": [10, 12], "rougier": 10, "zhou": 10, "discoveri": 10, "while": [10, 12, 15, 16, 17], "chapter": 10, "71": 10, "88": 10, "ac": 10, "2016": [10, 12], "mallei": 10, "jim\u00e9nez": 10, "mart\u00ednez": 10, "jw": 10, "ml": 10, "frash": 10, "multi": [10, 17], "phil": 10, "tran": 10, "soc": 10, "aldrich": 10, "woodr": 10, "hamann": 10, "ieee": 10, "transact": 10, "graphic": 10, "2017": [10, 13], "evalu": 10, "advanc": 10, "correl": [10, 12], "implic": [10, 12], "spars": [10, 12, 13], "djidjev": 10, "learn": 10, "predict": [10, 13], "propag": 10, "symposium": 10, "workshop": 10, "ipdpsw": 10, "mohd": 10, "yusof": 10, "passag": [10, 13], "reduct": [10, 13], "phy": 10, "rev": 10, "96": 10, "013304": 10, "jul": 10, "hadgu": 10, "k": [10, 12, 13], "klise": 10, "wang": 10, "compar": 10, "equival": [10, 12], "continuum": [10, 12, 17], "far": 10, "hypothet": 10, "hydrologi": 10, "romano": 10, "valocchi": 10, "battaglia": 10, "bigi": 10, "majella": 10, "mountain": 10, "itali": 10, "procedia": 10, "125": [10, 12], "556": 10, "560": 10, "valera": 10, "guo": 10, "kelli": 10, "matz": 10, "cantu": 10, "percu": 10, "machin": [10, 17], "mudunuru": 10, "geophys": [10, 12], "invers": 10, "character": 10, "mine": [10, 12], "asa": 10, "william": 10, "esteban": 10, "lei": 10, "discontinu": 10, "percol": 10, "jimen\u00e9z": 10, "nonlinear": 10, "interplai": 10, "structur": 10, "heterogen": 10, "mont": 10, "carlo": 10, "osthu": 10, "moor": 10, "hunter": 10, "quantifi": 10, "topolog": 10, "uncertainti": [10, 12], "robust": 10, "fidel": 10, "preserv": 10, "dave": 10, "gowri": 10, "backbon": [10, 13], "net": 10, "bipartit": [10, 13], "multiscal": [10, 13], "lukasczyk": 10, "garth": 10, "leitt": 10, "ahren": 10, "queri": 10, "search": 10, "explor": 10, "ensembl": 10, "engin": [10, 12], "bolster": 10, "impact": [10, 12], "behavior": 10, "2019": 10, "dentz": 10, "link": 10, "geophi": 10, "sol": 10, "ea": 10, "pathwai": 10, "kwickli": 10, "birdsel": 10, "confer": 10, "proceed": 10, "topopah": 10, "spring": 10, "pahut": 10, "mesa": 10, "2nd": 10, "pawar": 10, "merg": 10, "With": [10, 17], "3d": 10, "novel": 10, "frampton": 10, "zou": 10, "disconnect": 10, "textur": 10, "stauffer": 10, "caprock": 10, "rajaram": 10, "insight": 10, "breakthrough": 10, "letter": 10, "emerg": 10, "stabl": 10, "refin": [10, 12], "mediacomput": 10, "panda": 10, "probabilist": 10, "subnetwork": 10, "quantif": 10, "2020": [10, 12], "carneval": 10, "tartarello": 10, "geologi": 10, "cawi": 10, "identif": 10, "geosci": 10, "guthri": 10, "role": 10, "pham": 10, "parashar": 10, "sund": 10, "pohlmann": 10, "solid": [10, 12], "earth": [10, 12], "channel": 10, "preferenti": 10, "e2020wr027986": 10, "calibr": 10, "nevada": 10, "usa": 10, "hydrogeol": 10, "transient": [10, 11], "liangchao": 10, "vladimir": 10, "cvetkov": 10, "infer": 10, "pump": 10, "han": 10, "anomal": 10, "2021": 10, "sole": 10, "mari": 10, "vassallo": 10, "rapid": 10, "forecast": 10, "histori": 10, "unconvent": 10, "bridg": 10, "ambient": 10, "ushijima": 10, "mwesigwa": 10, "safro": 10, "multilevel": 10, "partit": 10, "mathemat": 10, "yingtao": 10, "hu": 10, "wenji": 10, "xu": 10, "liangtong": 10, "zhan": 10, "yunmin": 10, "hydromechan": 10, "cement": 10, "lithospher": 10, "2022": 10, "restrepo": 10, "disk": 10, "self": [11, 12, 13, 14, 15], "symlink": [11, 12, 14], "absolut": [11, 14, 17], "return": [11, 12, 13, 14, 15], "dump_vtk": 11, "portion": [11, 12], "bool": [11, 12, 13], "write": [11, 12, 13], "therein": [11, 13], "sovler": 11, "boundary_cell_area": 11, "take": [11, 12], "grid_vtk_fil": 11, "cell_data": 11, "point_data": 11, "local_dfnflow_fil": [11, 16], "inp2vtk_python": [11, 12], "restart": 11, "restart_fil": 11, "checkpoint": 11, "execut": [11, 12, 14, 17], "index_start": 11, "index_finish": 11, "concaten": 11, "delet": [11, 12, 16], "them": [11, 17], "pick": 11, "darcyvel": 11, "loop": 11, "over": [11, 13], "perm_fil": 11, "aper_fil": 11, "uge_fil": [11, 16], "correct_ug": 11, "zone_fil": 11, "plane": [11, 13], "rel": 11, "account": [11, 12], "inflow_pressur": 11, "outflow_pressur": 11, "boundary_fil": 11, "pascal": 11, "pboundary_left": 11, "local_jobname_effective_perm": 11, "20c": 11, "add_fracture_famili": 12, "family_numb": 12, "number_of_point": 12, "beta_distribut": 12, "beta": 12, "log_mean": 12, "log_std": 12, "exp_mean": 12, "constant": 12, "min_radiu": 12, "max_radiu": 12, "hy_vari": 12, "hy_funct": 12, "hy_param": 12, "rect": [12, 16], "ell": 12, "dein": 12, "log_norm": 12, "fracutr": 12, "probabili": 12, "th": 12, "eboundari": 12, "distribtuion": 12, "2pi": 12, "specfi": 12, "ebeta": 12, "fo": 12, "relationship": 12, "semi": 12, "syntax": 12, "popul": 12, "html": 12, "aspect_ratio": [12, 16], "angle_opt": 12, "orientation_opt": 12, "trend_plung": 12, "dip_strik": 12, "number_of_vertic": 12, "user_defined_": 12, "choic": 12, "orien": 12, "tramsmiss": 12, "attach": 12, "awar": 12, "0e": [12, 16], "npolygon": 12, "by_coord": 12, "arrai": 12, "src": [12, 17], "src_path": [12, 16], "1e": 12, "print_user_fracture_inform": 12, "frac_numb": 12, "fracture_numb": 12, "print_domain_paramet": [12, 16], "print_al": 12, "print_family_inform": 12, "termin": 12, "check_input": [12, 16], "from_fil": 12, "clean": 12, "own": 12, "separ": 12, "newlin": 12, "kei": 12, "colon": 12, "ie": 12, "place": [12, 17], "comment": 12, "On": [12, 17], "noth": 12, "rais": 12, "continu": 12, "past": 12, "maintain": 12, "futur": 12, "create_network": [12, 16], "succeed": 12, "dfn_gen": 12, "wrapper": 12, "make_working_directori": [12, 16], "dfngen_mesh": 12, "made": [12, 13], "overrid": 12, "routin": [12, 15], "grab_polygon_data": 12, "flag": 12, "store_polygon_data": 12, "store": [12, 16], "np": 12, "alreadi": [12, 17], "prompt": 12, "overwrit": 12, "gen_output": 12, "synopsi": 12, "moduleauthor": 12, "jhyman": 12, "verbos": 12, "output_dir": 12, "dfngen_output_report": 12, "plot": 12, "family_": 12, "toggl": [12, 16], "amount": 12, "progress": 12, "_output_report": 12, "perfectli": 12, "log_": 12, "mathcal": 12, "strength": 12, "independ": 12, "ident": 12, "cor": 12, "semicorrel": 12, "speci": 12, "fi": 12, "fourth": 12, "assumpt": 12, "variat": 12, "stress_based_apertur": 12, "sigma_mat": 12, "friction_angl": 12, "dilation_angl": 12, "critical_shear_displac": 12, "003": 12, "shear_modulu": 12, "10000000000": 12, "min_b": 12, "shear_stiff": 12, "400000000000": 12, "tensor": 12, "calcul": 12, "bandi": 12, "pa": [12, 13], "friction": 12, "dilat": 12, "critic": 12, "shear": 12, "modulu": 12, "stiff": 12, "matthew": 12, "ryan": 12, "e2020jb019754": 12, "baghbanan": 12, "alireza": 12, "lanru": 12, "jing": 12, "2008": 12, "1320": 12, "1334": 12, "zhao": 12, "zhihong": 12, "comparison": 12, "geotechn": 12, "110": 12, "123": 12, "uniform_mesh": 12, "min_dist": 12, "max_dist": 12, "max_resolution_factor": 12, "cleanup": 12, "quiet": 12, "distanc": 12, "factor": 12, "max_resolut": 12, "resolult": 12, "depend": 12, "linear": 12, "realiz": 12, "create_mesh_link": 12, "inp2gmv": 12, "inp_fil": [12, 16], "gmv": 12, "viewer": 12, "str": [12, 13], "attribur": 12, "librari": 12, "run_lagrit_script": 12, "lagrit_fil": 12, "output_fil": 12, "failur": 12, "success": 12, "add_variable_to_mesh": 12, "variable_fil": 12, "mesh_file_in": 12, "mesh_file_out": 12, "node_bas": 12, "column": [12, 16], "map_to_continuum": 12, "orl": 12, "dir_nam": 12, "level": 12, "octree_dfn": 12, "fracx": 12, "mat_perm": 12, "mat_por": 12, "map2continuum": 12, "perm_fehm": 12, "rock_fehm": 12, "mesh_perm": 12, "permeabilit": 12, "mesh_poros": 12, "check_false_connect": 12, "fmc_filnam": 12, "pickl": 12, "num_false_connect": 12, "num_cell_fals": 12, "voronoi": [12, 17], "false_connect": 12, "tupl": 12, "thu": 12, "mapdfn2pflotran": 12, "mapdfn": 12, "version2": 12, "medium": 12, "edit": 12, "nx": 12, "ny": 12, "nz": 12, "k_background": 12, "bulk_por": 12, "h5origin": 12, "hardwir": 12, "numpi": [12, 17], "h5py": [12, 17], "date": 12, "07": 12, "18": 12, "sand": 12, "sand2018": 12, "7605": 12, "matrix_perm": 12, "matrix_poros": [12, 13], "cell_siz": 12, "matrix_on": 12, "tortuosity_factor": 12, "lump_diag_term": 12, "correction_factor": 12, "stairstep": 12, "edfm": 12, "emili": 12, "stein": 12, "ergiamb": 12, "sandia": 12, "8844": 12, "teresa": 12, "porton": 12, "tporton": 12, "rosi": 12, "leon": 12, "2023": 12, "integr": 12, "source_list": 13, "remove_old_sourc": 13, "old": 13, "graph_typ": 13, "header": [13, 16], "bipartiti": 13, "assocait": 13, "ascii": [13, 16], "json": 13, "output_nam": 13, "dfn_graph": 13, "png": 13, "black": 13, "weight": 13, "greedi": 13, "find": 13, "disjoint": 13, "subgraph": 13, "mm": 13, "shortest": 13, "pressure_in": 13, "pressure_out": 13, "fluid_viscos": 13, "00089": 13, "driven": 13, "outlet": 13, "gtild": 13, "acycl": 13, "volumetr": 13, "travel": 13, "nparticl": 13, "partime_fil": 13, "frac_id_fil": 13, "hdf5": 13, "initial_posit": 13, "dump_traj": 13, "tdrw_flag": 13, "matrix_diffus": 13, "fracture_spac": 13, "control_plan": 13, "cp_filenam": 13, "given": 13, "graph_flow": 13, "dump_flag": 13, "ensur": 14, "execuatebl": 14, "move": 15, "well_data": 15, "well_coord": 15, "allboundari": 15, "higher": 15, "run_find_well_intersection_point": 15, "subroutin": 15, "redund": 15, "polylin": 15, "well_": 15, "_line": 15, "_volum": 15, "becaus": 16, "favorit": 16, "basic": 16, "taken": 16, "4_user_rects_exampl": 16, "getcwd": 16, "ptdfn_control": 16, "050": 16, "65": 16, "everyth": 16, "mat_fil": 16, "stor_fil": 16, "vtk_file": 16, "num_nod": 16, "mesh_typ": 16, "processor": 16, "depreci": 16, "amanzi": 16, "pars": 16, "local_dfngen_fil": 16, "local_dfntrans_fil": 16, "gen_4_user_rectangl": 16, "parent": 16, "demonstr": 16, "pruning_exampl": 16, "2_core": 16, "aper_nod": 16, "perm_nod": 16, "in_fracture_var": 16, "piec": 16, "pydfnflow": 16, "pydfntran": 16, "pydfngraph": 16, "easiest": 17, "get": 17, "our": 17, "visit": 17, "pull": 17, "dockerhub": 17, "latest": 17, "ti": 17, "exchang": 17, "mount": 17, "local_fold": 17, "expos": 17, "maco": 17, "instruct": 17, "setup": 17, "instead": 17, "git": 17, "pathnam": 17, "throughout": 17, "fix_path": 17, "cd": 17, "bin": 17, "dfnworks_path": 17, "petsc_dir": 17, "petsc_arch": 17, "environment": 17, "pflotran_ex": 17, "python_ex": 17, "lagrit_ex": 17, "vi": 17, "environ": 17, "home": 17, "usernam": 17, "altern": 17, "dfnworksrc": 17, "arch": 17, "darwin": 17, "anaconda3": 17, "fehm_ex": 17, "xfehm_v3": 17, "compli": 17, "bdist_wheel": 17, "pip": 17, "dist": 17, "py3": 17, "whl": 17, "releas": 17, "enabl": 17, "quantiti": 17, "mac": 17, "unix": 17, "ubuntu": 17, "anaconda": 17, "scipi": 17, "matplotlib": 17, "multiprocess": 17, "argpars": 17, "shutil": 17, "sy": 17, "subprocess": 17, "glob": 17, "fpdf": 17, "coincid": 17, "triangl": 17, "partial": 17, "differenti": 17, "multicompon": 17, "design": 17, "leadership": 17, "supercomput": 17, "workstat": 17, "laptop": 17, "open": 17, "cross": 17, "platform": 17, "bottleneck": 17, "step": 17, "greatli": 17, "speed": 17, "visualis": 17, "xmf": 17, "veri": 17}, "objects": {"false_connections": [[12, 0, 0, "-", "py"]], "graph_transport": [[13, 0, 0, "-", "py"]], "map2continuum": [[12, 0, 0, "-", "py"]], "mesh_dfn": [[12, 0, 0, "-", "py"]], "mesh_dfn_helper": [[12, 0, 0, "-", "py"]], "pydfnworks.dfnFlow": [[11, 0, 0, "-", "fehm"], [11, 0, 0, "-", "flow"], [11, 0, 0, "-", "mass_balance"], [11, 0, 0, "-", "pflotran"]], "pydfnworks.dfnFlow.fehm": [[11, 1, 1, "", "correct_stor_file"], [11, 1, 1, "", "fehm"]], "pydfnworks.dfnFlow.flow": [[11, 1, 1, "", "create_dfn_flow_links"], [11, 1, 1, "", "dfn_flow"], [11, 1, 1, "", "set_flow_solver"]], "pydfnworks.dfnFlow.mass_balance": [[11, 1, 1, "", "effective_perm"]], "pydfnworks.dfnFlow.pflotran": [[11, 1, 1, "", "lagrit2pflotran"], [11, 1, 1, "", "parse_pflotran_vtk_python"], [11, 1, 1, "", "pflotran"], [11, 1, 1, "", "pflotran_cleanup"], [11, 1, 1, "", "write_perms_and_correct_volumes_areas"], [11, 1, 1, "", "zone2ex"]], "pydfnworks.dfnGen.generation": [[12, 0, 0, "-", "generator"], [12, 0, 0, "-", "input_checking"], [12, 0, 0, "-", "stress"]], "pydfnworks.dfnGen.generation.generator": [[12, 1, 1, "", "create_network"], [12, 1, 1, "", "dfn_gen"], [12, 1, 1, "", "grab_polygon_data"], [12, 1, 1, "", "make_working_directory"]], "pydfnworks.dfnGen.generation.input_checking": [[12, 1, 1, "", "print_domain_parameters"], [12, 1, 1, "", "print_family_information"], [12, 0, 0, "-", "user_defined_fracture_functions"]], "pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions": [[12, 1, 1, "", "print_user_fracture_information"]], "pydfnworks.dfnGen.generation.output_report": [[12, 0, 0, "-", "gen_output"]], "pydfnworks.dfnGen.generation.output_report.gen_output": [[12, 1, 1, "", "output_report"]], "pydfnworks.dfnGen.generation.stress": [[12, 1, 1, "", "stress_based_apertures"]], "pydfnworks.dfnGen.meshing": [[12, 0, 0, "-", "add_attribute_to_mesh"], [12, 0, 0, "-", "dfm"]], "pydfnworks.dfnGen.meshing.add_attribute_to_mesh": [[12, 1, 1, "", "add_variable_to_mesh"]], "pydfnworks.dfnGen.meshing.mapdfn_ecpm": [[12, 0, 0, "-", "mapdfn_ecpm"]], "pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm": [[12, 1, 1, "", "mapdfn_ecpm"]], "pydfnworks.dfnGen.meshing.mesh_dfn": [[12, 0, 0, "-", "mesh_dfn"], [12, 0, 0, "-", "mesh_dfn_helper"]], "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn": [[12, 1, 1, "", "mesh_network"]], "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper": [[12, 1, 1, "", "create_mesh_links"], [12, 1, 1, "", "inp2gmv"], [12, 1, 1, "", "inp2vtk_python"], [12, 1, 1, "", "run_lagrit_script"]], "pydfnworks.dfnGen.meshing.udfm": [[12, 0, 0, "-", "false_connections"], [12, 0, 0, "-", "map2continuum"], [12, 0, 0, "-", "upscale"]], "pydfnworks.dfnGen.meshing.udfm.false_connections": [[12, 1, 1, "", "check_false_connections"]], "pydfnworks.dfnGen.meshing.udfm.map2continuum": [[12, 1, 1, "", "map_to_continuum"]], "pydfnworks.dfnGen.meshing.udfm.upscale": [[12, 1, 1, "", "upscale"]], "pydfnworks.dfnGen.well_package": [[15, 0, 0, "-", "wells"]], "pydfnworks.dfnGen.well_package.wells": [[15, 1, 1, "", "cleanup_wells"], [15, 1, 1, "", "combine_well_boundary_zones"], [15, 1, 1, "", "find_well_intersection_points"], [15, 1, 1, "", "tag_well_in_mesh"]], "pydfnworks.dfnGraph": [[13, 0, 0, "-", "dfn2graph"], [13, 0, 0, "-", "graph_flow"], [13, 0, 0, "-", "graph_transport"], [13, 0, 0, "-", "pruning"]], "pydfnworks.dfnGraph.dfn2graph": [[13, 1, 1, "", "add_fracture_source"], [13, 1, 1, "", "add_fracture_target"], [13, 1, 1, "", "create_graph"], [13, 1, 1, "", "dump_fractures"], [13, 1, 1, "", "dump_json_graph"], [13, 1, 1, "", "load_json_graph"], [13, 1, 1, "", "plot_graph"]], "pydfnworks.dfnGraph.graph_flow": [[13, 1, 1, "", "run_graph_flow"]], "pydfnworks.dfnGraph.graph_transport": [[13, 1, 1, "", "run_graph_transport"]], "pydfnworks.dfnGraph.pruning": [[13, 1, 1, "", "greedy_edge_disjoint"], [13, 1, 1, "", "k_shortest_paths_backbone"]], "pydfnworks.dfnTrans": [[14, 0, 0, "-", "transport"]], "pydfnworks.dfnTrans.transport": [[14, 1, 1, "", "check_dfn_trans_run_files"], [14, 1, 1, "", "copy_dfn_trans_files"], [14, 1, 1, "", "create_dfn_trans_links"], [14, 1, 1, "", "dfn_trans"], [14, 1, 1, "", "run_dfn_trans"]], "upscale": [[12, 0, 0, "-", "py"]]}, "objtypes": {"0": "py:module", "1": "py:function"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"]}, "titleterms": {"exampl": [0, 2, 4], "applic": 0, "carbon": 0, "dioxid": 0, "sequestr": 0, "shale": 0, "energi": 0, "extract": 0, "nuclear": 0, "wast": 0, "repositori": [0, 17], "dfnflow": [1, 11], "dfngen": [2, 9, 12], "c": 2, "gener": [2, 11, 12, 13], "code": 2, "domain": 2, "paramet": [2, 12], "domains": 2, "domainsizeincreas": 2, "numoflay": 2, "layer": 2, "numofregion": 2, "region": 2, "ignoreboundaryfac": 2, "boundaryfac": 2, "network": 2, "stopcondit": 2, "npoli": 2, "famprob": 2, "orientationopt": 2, "angleopt": 2, "h": 2, "disablefram": 2, "printrejectreason": 2, "rejectsperfractur": 2, "radiilistincreas": 2, "visualizationmod": 2, "seed": 2, "keeponlylargestclust": 2, "keepisolatedfractur": 2, "tripleintersect": 2, "removefractureslessthan": 2, "insertuserrectanglesfirst": 2, "forcelargefractur": 2, "output": [2, 9], "outputallradii": 2, "outputacceptedradiiperfamili": 2, "outputfinalradiiperfamili": 2, "fractur": [2, 4, 12], "famili": [2, 12], "ellips": 2, "nfamel": 2, "elay": 2, "eregion": 2, "e_p32target": 2, "enumpoint": 2, "easpect": 2, "orient": 2, "ekappa": 2, "spheric": 2, "coordin": 2, "etheta": 2, "ephi": 2, "trend": 2, "plung": 2, "etrend": 2, "eplung": 2, "dip": 2, "strike": 2, "estrik": 2, "edip": 2, "In": 2, "plane": 2, "rotat": 2, "ebetadistribut": 2, "ebeta": 2, "radiu": 2, "distribut": [2, 4], "edistr": 2, "lognorm": 2, "elogmean": 2, "esd": 2, "elogmin": 2, "elogmax": 2, "truncat": [2, 4], "powerlaw": 2, "ealpha": 2, "emin": 2, "emax": 2, "exponenti": [2, 4], "eexpmean": 2, "eexpmin": 2, "eexpmax": 2, "constant": 2, "econst": 2, "rectangl": 2, "nfamrect": 2, "rlayer": 2, "rregion": 2, "r_p32target": 2, "raspect": 2, "rkappa": 2, "rtheta": 2, "rphi": 2, "rtrend": 2, "rplung": 2, "rstrike": 2, "rdip": 2, "rbetadistribut": 2, "rbeta": 2, "rdistr": 2, "rlogmean": 2, "rsd": 2, "rlogmin": 2, "rlogmax": 2, "ralpha": 2, "rmin": 2, "rmax": 2, "rexpmean": 2, "rexpmin": 2, "rexpmax": 2, "rconst": 2, "user": [2, 12], "defin": 2, "userellipsesonoff": 2, "userell_input_file_path": 2, "nuserel": 2, "number_of_vertic": 2, "radii": 2, "aspect_ratio": 2, "beta": 2, "translat": 2, "userorientationopt": 2, "normal": 2, "trend_plung": 2, "dip_strik": 2, "input": [2, 12], "userellbycoord": 2, "ellbycoord_input_file_path": 2, "nellips": 2, "nnode": 2, "By": 2, "userrectanglesonoff": 2, "userrect_input_file_path": 2, "nuserrect": 2, "userrecbycoord": 2, "rectbycoord_input_file_path": 2, "nrectangl": 2, "polygon": 2, "userpolygonbycoord": 2, "polygonbycoord_input_file_path": 2, "file": [2, 9, 12], "format": 2, "npolygon": 2, "sourc": 2, "document": [2, 3, 6, 7, 16], "doxygen": [2, 16], "dfntran": [3, 14], "4_user_defined_rect": 4, "4_user_defined_ell_uniform": 4, "exp": 4, "length": 4, "tpl": 4, "power": 4, "law": 4, "graph": [4, 13], "base": [4, 12, 13], "prune": 4, "dfnwork": [5, 6, 7, 8, 10, 15, 16, 17], "galleri": 5, "welcom": [6, 7, 8], "2": [6, 7, 8], "8": [6, 7, 8], "To": 8, "obtain": 8, "cite": 8, "version": 8, "v2": 8, "current": 8, "7": 8, "6": 8, "5": 8, "4": 8, "3": 8, "1": 8, "0": 8, "about": 8, "thi": 8, "manual": 8, "contact": 8, "contributor": 8, "lanl": 8, "extern": 8, "copyright": 8, "inform": [8, 12], "run": [9, 11, 12, 14, 16, 17], "lagrit": [9, 12, 17], "pflotran": [9, 11, 17], "public": 10, "pydfnwork": [11, 12, 13, 14, 15, 16, 17], "flow": [11, 13], "fehm": [11, 17], "process": [11, 12], "ad": 12, "from": [12, 16, 17], "print": 12, "analysi": 12, "dfn": 12, "addit": [12, 16], "modif": 12, "hydraul": 12, "properti": 12, "background": 12, "stress": 12, "field": 12, "mesh": 12, "primari": 12, "driver": 12, "helper": 12, "method": 12, "udfm": 12, "creat": 12, "an": 12, "upscal": 12, "map": 12, "author": 12, "dfm": 12, "conform": 12, "dfngraph": 13, "function": 13, "transport": [13, 14], "simul": 14, "well": 15, "packag": [15, 16], "python": [16, 17], "command": 16, "line": 16, "us": 16, "The": 16, "class": 16, "jobnam": 16, "ncpu": 16, "dfnflow_fil": 16, "dfngen_fil": 16, "dfntrans_fil": 16, "path": [16, 17], "prune_fil": 16, "flow_solv": 16, "cell_based_apertur": 16, "argument": 16, "modul": 16, "detail": 16, "set": 17, "up": 17, "docker": 17, "contain": 17, "nativ": 17, "build": 17, "github": 17, "clone": 17, "dnfwork": 17, "fix": 17, "test": 17, "directori": 17, "petsc": 17, "instal": 17, "requir": 17, "oper": 17, "system": 17, "cmake": 17, "paraview": 17}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Example Applications": [[0, "example-applications"]], "Carbon dioxide sequestration": [[0, "carbon-dioxide-sequestration"]], "Shale energy extraction": [[0, "shale-energy-extraction"]], "Nuclear waste repository": [[0, "nuclear-waste-repository"]], "dfnFlow": [[1, "dfnflow"]], "dfnGen - C++ Generation Code": [[2, "dfngen-c-generation-code"]], "Domain Parameters": [[2, "domain-parameters"]], "domainSize": [[2, "domainsize"]], "domainSizeIncrease": [[2, "domainsizeincrease"]], "numOfLayers": [[2, "numoflayers"]], "layers": [[2, "layers"]], "numOfRegions": [[2, "numofregions"]], "regions": [[2, "regions"]], "ignoreBoundaryFaces": [[2, "ignoreboundaryfaces"]], "boundaryFaces": [[2, "boundaryfaces"]], "General Network Generation Parameters": [[2, "general-network-generation-parameters"]], "stopCondition": [[2, "stopcondition"]], "nPoly": [[2, "npoly"]], "famProb": [[2, "famprob"]], "orientationOption": [[2, "orientationoption"]], "angleOption": [[2, "angleoption"]], "h": [[2, "h"]], "disableFram": [[2, "disablefram"]], "printRejectReasons": [[2, "printrejectreasons"]], "rejectsPerFracture": [[2, "rejectsperfracture"]], "radiiListIncrease": [[2, "radiilistincrease"]], "visualizationMode": [[2, "visualizationmode"]], "seed": [[2, "seed"]], "keepOnlyLargestCluster": [[2, "keeponlylargestcluster"]], "keepIsolatedFractures": [[2, "keepisolatedfractures"]], "tripleIntersections": [[2, "tripleintersections"]], "removeFracturesLessThan": [[2, "removefractureslessthan"]], "insertUserRectanglesFirst": [[2, "insertuserrectanglesfirst"]], "forceLargeFractures": [[2, "forcelargefractures"]], "General Network Output Parameters": [[2, "general-network-output-parameters"]], "outputAllRadii": [[2, "outputallradii"]], "outputAcceptedRadiiPerFamily": [[2, "outputacceptedradiiperfamily"]], "outputFinalRadiiPerFamily": [[2, "outputfinalradiiperfamily"]], "Fracture Family Generation Parameters: Ellipse": [[2, "fracture-family-generation-parameters-ellipse"]], "Ellipse: General Parameters": [[2, "ellipse-general-parameters"]], "nFamEll": [[2, "nfamell"]], "eLayer": [[2, "elayer"]], "eRegion": [[2, "eregion"]], "e_p32Targets": [[2, "e-p32targets"]], "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, "rectangle-constant"]], "rconst": [[2, "rconst"]], "User Defined Fracture Generation Parameters": [[2, "user-defined-fracture-generation-parameters"]], "User Defined Ellipses": [[2, "user-defined-ellipses"]], "userEllipsesOnOff": [[2, "userellipsesonoff"]], "UserEll_Input_File_Path": [[2, "userell-input-file-path"]], "General user defined ellipses parameters": [[2, "general-user-defined-ellipses-parameters"]], "nUserEll": [[2, "nuserell"]], "Number_of_Vertices": [[2, "number-of-vertices"]], "Radii": [[2, "radii"]], "Aspect_Ratio": [[2, "aspect-ratio"]], "AngleOption (User Defined Fracture)": [[2, "angleoption-user-defined-fracture"]], "Beta": [[2, "beta"]], "Translation": [[2, "translation"]], "userOrientationOption": [[2, "userorientationoption"]], "Normal": [[2, "normal"]], "Trend_Plunge": [[2, "trend-plunge"]], "Dip_Strike": [[2, "dip-strike"]], "General Ellipse Input Example": [[2, "general-ellipse-input-example"]], "userEllByCoord": [[2, "userellbycoord"]], "EllByCoord_Input_File_Path": [[2, "ellbycoord-input-file-path"]], "User defined ellipses by coordinate parameters": [[2, "user-defined-ellipses-by-coordinate-parameters"]], "nEllipses": [[2, "nellipses"]], "nNodes": [[2, "nnodes"]], "Coordinates": [[2, "coordinates"]], "Ellipse By Coordinate Example": [[2, "ellipse-by-coordinate-example"]], "User Defined Rectangles": [[2, "user-defined-rectangles"]], "userRectanglesOnOff": [[2, "userrectanglesonoff"]], "UserRect_Input_File_Path": [[2, "userrect-input-file-path"]], "General user defined rectangles parameters": [[2, "general-user-defined-rectangles-parameters"]], "nUserRect": [[2, "nuserrect"]], "General Rectangle Input Example": [[2, "general-rectangle-input-example"]], "userRecByCoord": [[2, "userrecbycoord"]], "RectByCoord_Input_File_Path": [[2, "rectbycoord-input-file-path"]], "User defined rectangles by coordinate parameters": [[2, "user-defined-rectangles-by-coordinate-parameters"]], "nRectangles": [[2, "nrectangles"]], "Rectangle By Coordinate Example": [[2, "rectangle-by-coordinate-example"]], "Polygons": [[2, "polygons"]], "userPolygonByCoord": [[2, "userpolygonbycoord"]], "PolygonByCoord_Input_File_Path:": [[2, "polygonbycoord-input-file-path"]], "Polygon file format": [[2, "polygon-file-format"]], "nPolygons": [[2, "npolygons"]], "Source Code Documentation (Doxygen)": [[2, "source-code-documentation-doxygen"]], "dfnTrans": [[3, "dfntrans"]], "Documentation": [[3, "documentation"]], "Examples": [[4, "examples"]], "4_user_defined_rects": [[4, "user-defined-rects"]], "4_user_defined_ell_uniform": [[4, "user-defined-ell-uniform"]], "exp: Exponentially Distributed fracture lengths": [[4, "exp-exponentially-distributed-fracture-lengths"]], "TPL: Truncated Power-Law": [[4, "tpl-truncated-power-law"]], "Graph-based pruning": [[4, "graph-based-pruning"]], "dfnWorks Gallery": [[5, "dfnworks-gallery"]], "Welcome to dfnWorks 2.8 documentation!": [[6, "welcome-to-dfnworks-2-8-documentation"], [7, "welcome-to-dfnworks-2-8-documentation"]], "Welcome To dfnWorks": [[8, "welcome-to-dfnworks"]], "Obtaining dfnWorks": [[8, "obtaining-dfnworks"]], "Citing dfnWorks": [[8, "citing-dfnworks"]], "Versions": [[8, "versions"]], "v2.8 - Current": [[8, "v2-8-current"]], "v2.7": [[8, "v2-7"]], "v2.6": [[8, "v2-6"]], "v2.5": [[8, "v2-5"]], "v2.4": [[8, "v2-4"]], "v2.3": [[8, "v2-3"]], "v2.2": [[8, "v2-2"]], "v2.1": [[8, "v2-1"]], "v2.0": [[8, "v2-0"]], "About this manual": [[8, "about-this-manual"]], "Contact": [[8, "contact"]], "Contributors": [[8, "contributors"]], "LANL": [[8, "lanl"]], "External": [[8, "external"]], "Copyright Information": [[8, "copyright-information"]], "Run Files": [[9, "run-files"]], "dfnGen - output": [[9, "dfngen-output"]], "LaGrit - Output": [[9, "lagrit-output"]], "PFLOTRAN - output": [[9, "pflotran-output"]], "dfnWorks Publications": [[10, "dfnworks-publications"]], "pydfnworks: dfnFlow": [[11, "pydfnworks-dfnflow"]], "Running Flow : General": [[11, "module-pydfnworks.dfnFlow.flow"]], "Running Flow: PFLOTRAN": [[11, "module-pydfnworks.dfnFlow.pflotran"]], "Running Flow: FEHM": [[11, "module-pydfnworks.dfnFlow.fehm"]], "Processing Flow": [[11, "module-pydfnworks.dfnFlow.mass_balance"]], "pydfnworks: dfnGen": [[12, "pydfnworks-dfngen"]], "dfnGen": [[12, "dfngen"]], "Adding Fracture Families": [[12, "adding-fracture-families"]], "Adding User Fractures": [[12, "adding-user-fractures"]], "Adding User Fractures From a File": [[12, "adding-user-fractures-from-a-file"]], "Print Parameter Information": [[12, "print-parameter-information"]], "Processing Generator Input": [[12, "processing-generator-input"]], "Running the Generator": [[12, "module-pydfnworks.dfnGen.generation.generator"]], "Analysis of Generated DFN": [[12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"]], "Additional Information on the Modification of Hydraulic Properties of the DFN": [[12, "additional-information-on-the-modification-of-hydraulic-properties-of-the-dfn"]], "Modification of hydraulic properties of the DFN based on background stress field": [[12, "module-pydfnworks.dfnGen.generation.stress"]], "Meshing - LaGriT": [[12, "meshing-lagrit"]], "Primary DFN meshing driver": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"]], "Meshing helper methods": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"]], "UDFM": [[12, "udfm"]], "Creating an upscaled mesh of the DFN (UDFM)": [[12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "Map-DFN upscaling": [[12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"]], "Authors": [[12, "authors"]], "DFM": [[12, "dfm"]], "Creating a conforming DFM mesh DFN": [[12, "module-pydfnworks.dfnGen.meshing.dfm"]], "pydfnworks: dfnGraph": [[13, "pydfnworks-dfngraph"]], "General Graph Functions": [[13, "module-pydfnworks.dfnGraph.dfn2graph"]], "Graph-Based Flow and Transport": [[13, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks: dfnTrans": [[14, "pydfnworks-dfntrans"]], "Running Transport Simulations": [[14, "module-pydfnworks.dfnTrans.transport"]], "pydfnworks: Well Package": [[15, "pydfnworks-well-package"]], "dfnWorks - Well Package": [[15, "module-pydfnworks.dfnGen.well_package.wells"]], "pydfnworks: the dfnWorks python package": [[16, "pydfnworks-the-dfnworks-python-package"]], "Running dfnWorks from the command line using pydfnWorks": [[16, "running-dfnworks-from-the-command-line-using-pydfnworks"]], "The DFNWORKS class": [[16, "the-dfnworks-class"]], "jobname": [[16, "jobname"]], "ncpu": [[16, "ncpu"]], "dfnFlow_file/dfnGen_file/dfnTrans_file": [[16, "dfnflow-file-dfngen-file-dfntrans-file"]], "path": [[16, "path"]], "prune_file": [[16, "prune-file"]], "flow_solver": [[16, "flow-solver"]], "cell_based_aperture": [[16, "cell-based-aperture"]], "additional arguments": [[16, "additional-arguments"]], "pydfnWorks : Modules": [[16, "pydfnworks-modules"]], "Detailed Doxygen Documentation": [[16, "detailed-doxygen-documentation"]], "Setting and Running up dfnWorks": [[17, "setting-and-running-up-dfnworks"]], "Docker": [[17, "docker"]], "Running the dfnWorks container": [[17, "running-the-dfnworks-container"]], "Native build from github repository": [[17, "native-build-from-github-repository"]], "Clone the dnfWorks repository": [[17, "clone-the-dnfworks-repository"]], "Fix paths in test directory": [[17, "fix-paths-in-test-directory"]], "Set the LagriT, PETSC, PFLOTRAN, Python, and FEHM paths": [[17, "set-the-lagrit-petsc-pflotran-python-and-fehm-paths"]], "Installing pydfnworks": [[17, "installing-pydfnworks"]], "Installation Requirements for Native Build": [[17, "installation-requirements-for-native-build"]], "Operating Systems": [[17, "operating-systems"]], "Python": [[17, "python"]], "LaGriT": [[17, "lagrit"]], "PFLOTRAN": [[17, "pflotran"]], "FEHM": [[17, "fehm"]], "CMake": [[17, "cmake"]], "Paraview": [[17, "paraview"]]}, "indexentries": {"correct_stor_file() (in module pydfnworks.dfnflow.fehm)": [[11, "pydfnworks.dfnFlow.fehm.correct_stor_file"]], "create_dfn_flow_links() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.create_dfn_flow_links"]], "dfn_flow() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.dfn_flow"]], "effective_perm() (in module pydfnworks.dfnflow.mass_balance)": [[11, "pydfnworks.dfnFlow.mass_balance.effective_perm"]], "fehm() (in module pydfnworks.dfnflow.fehm)": [[11, "pydfnworks.dfnFlow.fehm.fehm"]], "lagrit2pflotran() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.lagrit2pflotran"]], "module": [[11, "module-pydfnworks.dfnFlow.fehm"], [11, "module-pydfnworks.dfnFlow.flow"], [11, "module-pydfnworks.dfnFlow.mass_balance"], [11, "module-pydfnworks.dfnFlow.pflotran"], [12, "module-false_connections.py"], [12, "module-map2continuum.py"], [12, "module-mesh_dfn.py"], [12, "module-mesh_dfn_helper.py"], [12, "module-pydfnworks.dfnGen.generation.generator"], [12, "module-pydfnworks.dfnGen.generation.input_checking"], [12, "module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"], [12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"], [12, "module-pydfnworks.dfnGen.generation.stress"], [12, "module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"], [12, "module-pydfnworks.dfnGen.meshing.dfm"], [12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"], [12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"], [12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"], [12, "module-pydfnworks.dfnGen.meshing.udfm.false_connections"], [12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"], [12, "module-pydfnworks.dfnGen.meshing.udfm.upscale"], [12, "module-upscale.py"], [13, "module-graph_transport.py"], [13, "module-pydfnworks.dfnGraph.dfn2graph"], [13, "module-pydfnworks.dfnGraph.graph_flow"], [13, "module-pydfnworks.dfnGraph.graph_transport"], [13, "module-pydfnworks.dfnGraph.pruning"], [14, "module-pydfnworks.dfnTrans.transport"], [15, "module-pydfnworks.dfnGen.well_package.wells"]], "parse_pflotran_vtk_python() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.parse_pflotran_vtk_python"]], "pflotran() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.pflotran"]], "pflotran_cleanup() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.pflotran_cleanup"]], "pydfnworks.dfnflow.fehm": [[11, "module-pydfnworks.dfnFlow.fehm"]], "pydfnworks.dfnflow.flow": [[11, "module-pydfnworks.dfnFlow.flow"]], "pydfnworks.dfnflow.mass_balance": [[11, "module-pydfnworks.dfnFlow.mass_balance"]], "pydfnworks.dfnflow.pflotran": [[11, "module-pydfnworks.dfnFlow.pflotran"]], "set_flow_solver() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.set_flow_solver"]], "write_perms_and_correct_volumes_areas() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.write_perms_and_correct_volumes_areas"]], "zone2ex() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.zone2ex"]], "add_variable_to_mesh() (in module pydfnworks.dfngen.meshing.add_attribute_to_mesh)": [[12, "pydfnworks.dfnGen.meshing.add_attribute_to_mesh.add_variable_to_mesh"]], "check_false_connections() (in module pydfnworks.dfngen.meshing.udfm.false_connections)": [[12, "pydfnworks.dfnGen.meshing.udfm.false_connections.check_false_connections"]], "create_mesh_links() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.create_mesh_links"]], "create_network() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.create_network"]], "dfn_gen() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.dfn_gen"]], "false_connections.py": [[12, "module-false_connections.py"]], "grab_polygon_data() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.grab_polygon_data"]], "inp2gmv() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.inp2gmv"]], "inp2vtk_python() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.inp2vtk_python"]], "make_working_directory() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.make_working_directory"]], "map2continuum.py": [[12, "module-map2continuum.py"]], "map_to_continuum() (in module pydfnworks.dfngen.meshing.udfm.map2continuum)": [[12, "pydfnworks.dfnGen.meshing.udfm.map2continuum.map_to_continuum"]], "mapdfn_ecpm() (in module pydfnworks.dfngen.meshing.mapdfn_ecpm.mapdfn_ecpm)": [[12, "pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm.mapdfn_ecpm"]], "mesh_dfn.py": [[12, "module-mesh_dfn.py"]], "mesh_dfn_helper.py": [[12, "module-mesh_dfn_helper.py"]], "mesh_network() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn.mesh_network"]], "output_report() (in module pydfnworks.dfngen.generation.output_report.gen_output)": [[12, "pydfnworks.dfnGen.generation.output_report.gen_output.output_report"]], "print_domain_parameters() (in module pydfnworks.dfngen.generation.input_checking)": [[12, "pydfnworks.dfnGen.generation.input_checking.print_domain_parameters"]], "print_family_information() (in module pydfnworks.dfngen.generation.input_checking)": [[12, "pydfnworks.dfnGen.generation.input_checking.print_family_information"]], "print_user_fracture_information() (in module pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions)": [[12, "pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions.print_user_fracture_information"]], "pydfnworks.dfngen.generation.generator": [[12, "module-pydfnworks.dfnGen.generation.generator"]], "pydfnworks.dfngen.generation.input_checking": [[12, "module-pydfnworks.dfnGen.generation.input_checking"]], "pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions": [[12, "module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"]], "pydfnworks.dfngen.generation.output_report.gen_output": [[12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"]], "pydfnworks.dfngen.generation.stress": [[12, "module-pydfnworks.dfnGen.generation.stress"]], "pydfnworks.dfngen.meshing.add_attribute_to_mesh": [[12, "module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"]], "pydfnworks.dfngen.meshing.dfm": [[12, "module-pydfnworks.dfnGen.meshing.dfm"]], "pydfnworks.dfngen.meshing.mapdfn_ecpm.mapdfn_ecpm": [[12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"]], "pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"]], "pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"]], "pydfnworks.dfngen.meshing.udfm.false_connections": [[12, "module-pydfnworks.dfnGen.meshing.udfm.false_connections"]], "pydfnworks.dfngen.meshing.udfm.map2continuum": [[12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "pydfnworks.dfngen.meshing.udfm.upscale": [[12, "module-pydfnworks.dfnGen.meshing.udfm.upscale"]], "run_lagrit_script() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.run_lagrit_script"]], "stress_based_apertures() (in module pydfnworks.dfngen.generation.stress)": [[12, "pydfnworks.dfnGen.generation.stress.stress_based_apertures"]], "upscale() (in module pydfnworks.dfngen.meshing.udfm.upscale)": [[12, "pydfnworks.dfnGen.meshing.udfm.upscale.upscale"]], "upscale.py": [[12, "module-upscale.py"]], "add_fracture_source() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.add_fracture_source"]], "add_fracture_target() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.add_fracture_target"]], "create_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.create_graph"]], "dump_fractures() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.dump_fractures"]], "dump_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.dump_json_graph"]], "graph_transport.py": [[13, "module-graph_transport.py"]], "greedy_edge_disjoint() (in module pydfnworks.dfngraph.pruning)": [[13, "pydfnworks.dfnGraph.pruning.greedy_edge_disjoint"]], "k_shortest_paths_backbone() (in module pydfnworks.dfngraph.pruning)": [[13, "pydfnworks.dfnGraph.pruning.k_shortest_paths_backbone"]], "load_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.load_json_graph"]], "plot_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.plot_graph"]], "pydfnworks.dfngraph.dfn2graph": [[13, "module-pydfnworks.dfnGraph.dfn2graph"]], "pydfnworks.dfngraph.graph_flow": [[13, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks.dfngraph.graph_transport": [[13, "module-pydfnworks.dfnGraph.graph_transport"]], "pydfnworks.dfngraph.pruning": [[13, "module-pydfnworks.dfnGraph.pruning"]], "run_graph_flow() (in module pydfnworks.dfngraph.graph_flow)": [[13, "pydfnworks.dfnGraph.graph_flow.run_graph_flow"]], "run_graph_transport() (in module pydfnworks.dfngraph.graph_transport)": [[13, "pydfnworks.dfnGraph.graph_transport.run_graph_transport"]], "check_dfn_trans_run_files() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.check_dfn_trans_run_files"]], "copy_dfn_trans_files() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.copy_dfn_trans_files"]], "create_dfn_trans_links() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.create_dfn_trans_links"]], "dfn_trans() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.dfn_trans"]], "pydfnworks.dfntrans.transport": [[14, "module-pydfnworks.dfnTrans.transport"]], "run_dfn_trans() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.run_dfn_trans"]], "cleanup_wells() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.cleanup_wells"]], "combine_well_boundary_zones() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.combine_well_boundary_zones"]], "find_well_intersection_points() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.find_well_intersection_points"]], "pydfnworks.dfngen.well_package.wells": [[15, "module-pydfnworks.dfnGen.well_package.wells"]], "tag_well_in_mesh() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.tag_well_in_mesh"]]}}) \ No newline at end of file +Search.setIndex({"docnames": ["applications", "dfnflow", "dfngen", "dfntrans", "examples", "gallery", "index", "index_docs", "intro", "output", "publications", "pydfnFlow", "pydfnGen", "pydfnGraph", "pydfnTrans", "pydfnWorks-well", "pydfnworks", "setup"], "filenames": ["applications.rst", "dfnflow.rst", "dfngen.rst", "dfntrans.rst", "examples.rst", "gallery.rst", "index.rst", "index_docs.rst", "intro.rst", "output.rst", "publications.rst", "pydfnFlow.rst", "pydfnGen.rst", "pydfnGraph.rst", "pydfnTrans.rst", "pydfnWorks-well.rst", "pydfnworks.rst", "setup.rst"], "titles": ["Example Applications", "dfnFlow", "dfnGen - C++ Generation Code", "dfnTrans", "Examples", "dfnWorks Gallery", "Welcome to dfnWorks 2.8 documentation!", "Welcome to dfnWorks 2.8 documentation!", "Welcome To dfnWorks", "Run Files", "dfnWorks Publications", "pydfnworks: dfnFlow", "pydfnworks: dfnGen", "pydfnworks: dfnGraph", "pydfnworks: dfnTrans", "pydfnworks: Well Package", "pydfnworks: the dfnWorks python package", "Setting and Running up dfnWorks"], "terms": {"dfnwork": [0, 2, 4, 9, 11, 12], "provid": [0, 1, 2, 3, 4, 8, 12], "framework": [0, 8, 10], "necessari": [0, 12], "perform": [0, 2, 3, 8], "multiphas": [0, 17], "simul": [0, 1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 13, 16, 17], "flow": [0, 1, 2, 3, 4, 6, 7, 8, 10, 12, 16, 17], "reactiv": [0, 3, 8, 10, 17], "transport": [0, 2, 3, 4, 6, 7, 8, 10, 12, 16, 17], "reservoir": [0, 10], "scale": [0, 8, 10, 17], "A": [0, 2, 8, 10, 12, 13], "particular": [0, 8, 13, 16], "highlight": 0, "here": [0, 2, 4, 16], "i": [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "sequest": 0, "co": [0, 2, 8], "2": [0, 1, 2, 4, 12, 13, 16, 17], "from": [0, 2, 3, 6, 7, 8, 9, 10, 11, 13, 15], "anthropogen": 0, "sourc": [0, 6, 7, 8, 11, 12, 13, 14, 15, 17], "dispos": 0, "geolog": 0, "format": [0, 1, 9, 10, 11, 12, 13, 15, 17], "deep": 0, "salin": 0, "aquif": [0, 10], "abandon": 0, "oil": 0, "field": [0, 3, 5, 6, 7, 8, 10], "one": [0, 1, 2, 3, 4, 12, 17], "princip": 0, "method": [0, 2, 3, 6, 7, 10, 16], "under": [0, 1, 8, 10], "consider": 0, "reduc": [0, 2, 10], "footprint": 0, "atmospher": 0, "due": [0, 2, 4, 9, 10], "fossil": 0, "fuel": 0, "bachu": 0, "2002": 0, "pacala": 0, "socolow": 0, "2004": 0, "For": [0, 2, 12, 17], "safe": 0, "sustain": 0, "long": 0, "term": [0, 8, 12], "storag": 0, "prevent": 0, "leak": 0, "through": [0, 2, 3, 4, 8], "exist": [0, 12], "fault": [0, 10], "fractur": [0, 1, 3, 5, 6, 7, 8, 9, 10, 13, 16, 17], "rock": [0, 10, 12], "along": [0, 2, 4, 5], "ones": 0, "creat": [0, 1, 2, 4, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17], "dure": [0, 2, 10], "inject": [0, 10], "process": [0, 3, 6, 7, 9, 10, 15, 17], "understand": [0, 2, 10], "complex": 0, "physic": [0, 3, 10, 13], "chemic": 0, "interact": [0, 3, 8, 10], "between": [0, 2, 9, 10, 12, 17], "water": [0, 10, 11, 12, 13], "brine": 0, "vital": 0, "capabl": [0, 2, 8], "studi": [0, 8, 10, 12], "dfn": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17], "can": [0, 1, 2, 4, 8, 11, 12, 15, 16, 17], "us": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17], "potenti": 0, "migrat": 0, "cap": 0, "risk": [0, 12], "associ": 0, "propos": 0, "subsurfac": [0, 1, 8, 10, 17], "deplet": 0, "moreov": 0, "pflotran": [0, 1, 4, 6, 7, 8, 12, 15, 16], "coupl": 0, "cell": [0, 9, 11, 12, 16], "base": [0, 2, 6, 7, 8, 9, 10, 11, 16, 17], "transmiss": [0, 10, 12], "allow": [0, 3, 12, 16, 17], "dynam": 0, "chang": [0, 4, 12, 16], "permeabl": [0, 1, 9, 10, 11, 12, 16], "miner": 0, "precipit": 0, "dissolut": 0, "tempor": 0, "evolut": [0, 10], "supercrit": [0, 10], "co2": [0, 10], "displac": [0, 12], "meter": [0, 2, 4, 12], "cube": 0, "contain": [0, 2, 4, 6, 7, 8, 9, 12, 13, 15, 16], "24": 0, "The": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 17], "initi": [0, 1, 2, 9, 13], "fulli": 0, "satur": 0, "top": [0, 2, 9, 11, 12], "left": [0, 2, 4, 9, 11], "time": [0, 1, 2, 8, 10, 12, 13], "0": [0, 1, 2, 4, 6, 7, 11, 12, 13, 16], "hour": 0, "slowli": 0, "system": [0, 10, 12], "bottom": [0, 2, 9, 11], "domain": [0, 4, 6, 7, 8, 9, 12], "total": [0, 2, 12, 13], "10": [0, 1, 2, 8, 12], "h": [0, 6, 7, 8, 9, 10, 11, 12, 13, 16], "There": [0, 2, 12, 16], "an": [0, 1, 2, 3, 4, 6, 7, 8, 10, 13, 15, 17], "flush": 0, "first": [0, 2, 4, 10, 12, 13, 16], "rate": [0, 2, 13], "decreas": 0, "hydraul": [0, 5, 6, 7, 8, 10, 16], "frack": 0, "ha": [0, 2, 4, 8, 9, 11], "access": [0, 12, 16], "hydrocarbon": 0, "trap": 0, "low": [0, 4], "media": [0, 8, 10, 17], "tight": 0, "involv": [0, 1], "high": [0, 4, 8, 17], "pressur": [0, 1, 4, 5, 11, 13], "also": [0, 2, 12, 17], "new": [0, 2, 4, 8, 10, 12], "increas": [0, 2, 8, 10, 17], "howev": [0, 2, 3, 8, 17], "fundament": 0, "why": 0, "work": [0, 2, 8, 10, 11, 12, 14, 15, 16, 17], "its": [0, 2, 8, 12], "ramif": 0, "ar": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17], "well": [0, 1, 2, 6, 7, 8, 10, 12, 16, 17], "understood": 0, "karra": [0, 1, 3, 8, 10], "et": [0, 10, 12, 13], "al": [0, 10, 12, 13], "2015": [0, 3, 8, 10], "gener": [0, 3, 4, 6, 7, 8, 9, 10, 16], "typic": [0, 11, 14], "product": [0, 8, 10], "site": [0, 10], "thi": [0, 1, 2, 4, 6, 7, 9, 11, 12, 16, 17], "model": [0, 8, 10, 12, 13, 16], "thei": [0, 2, 12], "found": [0, 2, 4, 8, 11, 13, 16, 17], "good": [0, 2, 8], "agreement": 0, "data": [0, 8, 10, 12, 16], "determin": [0, 2, 3, 8, 10, 12], "what": [0, 12, 13], "mechan": [0, 10, 12], "control": [0, 3, 13, 16, 17], "declin": 0, "curv": [0, 1, 10], "swedish": 0, "manag": 0, "compani": 0, "skb": 0, "undertaken": 0, "detail": [0, 1, 2, 3, 6, 7, 8, 9, 11, 12, 13, 17], "investig": 0, "granit": 0, "forsmark": 0, "sweden": 0, "host": [0, 10, 17], "spent": 0, "2011": 0, "hartlei": 0, "joyc": 0, "2013": [0, 12], "area": [0, 2, 9, 11, 12], "about": [0, 2, 3, 6, 7, 9, 11, 12, 15, 16], "120": 0, "km": 0, "north": [0, 2], "stockholm": 0, "northern": 0, "uppland": 0, "construct": [0, 2], "crystallin": [0, 10], "bedrock": 0, "depth": 0, "approxim": [0, 4, 8], "500": 0, "m": [0, 1, 2, 3, 10, 12, 13, 15, 17], "statist": [0, 2, 10], "multipl": [0, 2, 11, 16], "set": [0, 2, 4, 6, 7, 8, 11, 12, 14], "wa": [0, 8, 12], "develop": [0, 8, 17], "paramet": [0, 1, 4, 6, 7, 8, 9, 11, 13, 14, 15], "we": [0, 3, 4, 8, 12, 17], "adopt": [0, 3, 8], "subset": 0, "consist": [0, 4, 16, 17], "three": [0, 2, 3, 8, 10, 12, 13], "background": [0, 6, 7, 8], "non": [0, 2, 3, 9, 10, 13], "determinist": [0, 2], "circular": [0, 4], "whose": [0, 4, 5], "orient": [0, 6, 7, 8, 12], "follow": [0, 2, 4, 5, 8, 10, 12, 15, 17], "fisher": [0, 2, 12], "distribut": [0, 5, 6, 7, 8, 10, 12, 13, 17], "radii": [0, 5, 9, 12, 16], "sampl": [0, 1, 2, 8, 10, 12], "truncat": [0, 5, 6, 7, 10, 12], "power": [0, 2, 6, 7, 10, 12], "law": [0, 2, 6, 7, 10, 12], "estim": 0, "radiu": [0, 6, 7, 12, 15], "apertur": [0, 5, 8, 9, 10, 11, 12, 16], "relat": [0, 2, 12], "size": [0, 2, 4, 8, 10, 11, 12, 13], "cubic": [0, 4], "adler": 0, "2012": 0, "formul": 0, "uniform": [0, 2, 4, 12, 13], "each": [0, 2, 3, 4, 9, 12, 13], "vari": 0, "among": 0, "network": [0, 1, 3, 4, 6, 7, 8, 9, 10, 12, 13, 15, 16, 17], "side": [0, 2, 4, 9], "length": [0, 2, 6, 7, 9, 12, 13], "kilomet": [0, 8, 10], "dirichlet": [0, 1, 4], "boundari": [0, 1, 2, 4, 9, 11, 12, 13], "condit": [0, 1, 4, 8, 9, 11, 13], "impos": [0, 2], "1": [0, 1, 2, 6, 7, 11, 12, 13, 16, 17], "mpa": 0, "gradient": [0, 4, 9], "align": [0, 4], "vertic": [0, 2, 4, 12], "axi": [0, 2, 4], "noflow": 0, "enforc": 0, "later": [0, 8], "particl": [0, 3, 4, 5, 10, 13, 14, 15, 16], "trajectori": [0, 3, 4, 13], "p": [0, 10], "thovert": 0, "j": [0, 2, 8, 10, 12], "f": [0, 2, 10, 12], "mourzenko": 0, "v": [0, 10, 17], "porou": [0, 10, 12, 17], "oxford": 0, "univers": [0, 8], "press": 0, "unit": [0, 2, 11, 12, 13], "kingdom": 0, "": [0, 1, 2, 3, 4, 5, 8, 10, 13], "respons": [0, 10], "climat": 0, "road": 0, "map": [0, 6, 7, 8], "select": [0, 2], "transform": 0, "space": [0, 2], "phase": 0, "conver": 0, "43": 0, "87": 0, "102": 0, "l": [0, 2, 3, 8, 10, 12], "approach": [0, 2, 3, 8, 10, 13], "algorithm": [0, 2, 3, 4, 8, 10, 13, 17], "groundwat": [0, 10], "support": [0, 2, 11, 12, 13], "safeti": 0, "assess": 0, "Fors": 0, "mark": [0, 8], "hydrol": 0, "200": 0, "216": 0, "makedonska": [0, 1, 2, 3, 8, 10], "n": [0, 2, 3, 8, 10, 12], "viswanathan": [0, 8, 10], "painter": [0, 2, 3, 8, 10], "hyman": [0, 2, 8, 10, 12, 13], "effect": [0, 2, 3, 10, 11, 12], "advect": [0, 3, 10], "matrix": [0, 3, 8, 9, 10, 12, 13], "diffus": [0, 3, 8, 10, 13], "natur": [0, 4, 10], "ga": [0, 10], "resour": [0, 10], "re": [0, 2, 10, 17], "review": [0, 10, 13], "r": [0, 2, 8, 10, 12, 15, 17], "stabil": 0, "wedg": 0, "solv": [0, 3, 13, 17], "problem": [0, 3, 10], "next": [0, 12, 17], "50": [0, 2], "year": [0, 8], "current": [0, 4, 6, 7, 11, 12, 13, 14, 17], "technologi": 0, "scienc": [0, 8, 10, 12], "305": 0, "968": 0, "972": 0, "final": [0, 2, 8, 9, 12, 16, 17], "main": [0, 2, 10, 12, 17], "report": [0, 2, 8, 10, 12], "sr": 0, "project": [0, 2], "technic": 0, "tr": 0, "11": [0, 12], "01": [0, 1], "solver": [1, 8, 11, 17], "fehm": [1, 6, 7, 8, 9, 12, 16], "recommend": [1, 2, 4, 8, 16, 17], "larg": [1, 11, 17], "number": [1, 2, 9, 12, 13, 16], "o": [1, 10, 12, 16, 17], "1000": 1, "function": [1, 2, 4, 6, 7, 8, 9, 11, 12, 14, 15, 16], "call": [1, 8, 11, 12, 15, 16], "part": 1, "pydfnwork": [1, 2, 6, 7, 8], "mesh": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17], "file": [1, 4, 6, 7, 11, 13, 14, 15, 16, 17], "need": [1, 2, 12, 17], "run": [1, 2, 4, 6, 7, 8, 13], "unstructur": [1, 3], "ug": [1, 9, 16], "ex": [1, 9, 11, 15], "pleas": [1, 8, 12], "see": [1, 2, 8, 11, 12, 13, 16, 17], "user": [1, 4, 6, 7, 8, 9, 16], "manual": [1, 6, 7, 16], "http": [1, 2, 4, 8, 11, 12, 17], "www": [1, 4, 11, 17], "org": [1, 2, 4, 11, 17], "explicit": 1, "usag": [1, 10, 12], "further": 1, "exampl": [1, 6, 7, 8, 12, 15, 16, 17], "input": [1, 4, 6, 7, 8, 9, 11, 13, 14, 16], "repositori": [1, 6, 7, 8, 10], "start": [1, 2, 3, 9, 13, 17], "point": [1, 2, 9, 12, 15], "build": [1, 6, 7], "your": [1, 4, 8, 12, 16, 17], "deck": 1, "below": [1, 2, 12, 16], "refer": [1, 2, 12], "descript": [1, 2, 3, 8, 16], "jan": 1, "13": [1, 2, 12], "2014": [1, 2, 10], "nataliia": [1, 8, 10], "satish": [1, 8, 10], "lanl": [1, 6, 7, 11, 12, 17], "simulation_typ": 1, "process_model": 1, "subsurface_flow": 1, "mode": [1, 2, 10, 11, 12], "richard": 1, "end": [1, 4, 5, 9, 13], "discret": [1, 2, 3, 8, 10, 12, 13, 16], "grid": 1, "type": [1, 2, 11, 12, 13, 14, 15, 16], "unstructured_explicit": 1, "full_mesh_vol_area": [1, 9], "graviti": 1, "d0": 1, "fluid": [1, 10], "properti": [1, 2, 6, 7, 9, 10, 16], "fluid_properti": 1, "diffusion_coeffici": 1, "d": [1, 2, 8, 10, 12], "9": [1, 2], "dataset": 1, "filenam": [1, 2, 11, 12, 13, 15], "dfn_properti": [1, 9], "h5": [1, 9, 12], "materi": [1, 4, 8, 9, 10, 12], "material_properti": 1, "soil1": 1, "id": [1, 4, 9, 12, 16], "poros": [1, 12, 13], "25d0": 1, "tortuos": [1, 12], "5d0": 1, "characteristic_curv": 1, "default": [1, 2, 11, 12, 13, 16], "characterist": [1, 10], "saturation_funct": 1, "van_genuchten": 1, "alpha": [1, 2, 12], "4": [1, 2, 6, 7, 10, 12, 16], "liquid_residual_satur": 1, "1d0": 1, "max_capillary_pressur": 1, "d8": 1, "permeability_funct": 1, "mualem_vg_liq": 1, "output": [1, 6, 7, 8, 11, 12, 13, 16, 17], "option": [1, 2, 8, 12, 13, 16, 17], "05": [1, 2], "5": [1, 2, 3, 4, 6, 7, 12], "tecplot": 1, "block": [1, 8, 13], "print_primal_grid": 1, "vtk": [1, 4, 9, 11, 12, 17], "mass_flowr": 1, "mass_bal": 1, "variabl": [1, 5, 10, 12, 17], "liquid_pressur": 1, "initial_timestep_s": 1, "8": [1, 2, 4, 12, 16], "final_tim": 1, "maximum_timestep_s": 1, "steady_st": 1, "reference_pressur": 1, "1500000": 1, "region": [1, 6, 7, 8, 12], "all": [1, 2, 4, 8, 11, 12, 13, 14, 15, 17], "coordin": [1, 12, 15], "d20": 1, "inflow": [1, 4, 11, 13], "pboundary_left_w": [1, 9], "outflow": [1, 4, 11, 13], "pboundary_right_": [1, 9], "flow_condit": 1, "01325d6": 1, "d6": 1, "coupler": 1, "initial_condit": 1, "boundary_condit": 1, "stratigraphi": 1, "strata": 1, "end_subsurfac": 1, "featur": [2, 8, 10, 12], "reject": [2, 8, 9, 10], "fram": [2, 8], "stochast": [2, 4, 8, 10, 12], "implement": [2, 3, 12, 17], "methodologi": [2, 3, 8], "w": [2, 3, 8, 10], "gabl": [2, 3, 8, 10], "conform": [2, 6, 7, 8, 10, 17], "delaunai": [2, 8, 10, 17], "triangul": [2, 8, 10, 17], "dimension": [2, 3, 8, 10, 12, 13], "strategi": [2, 10], "siam": [2, 10, 13], "sci": [2, 10], "comput": [2, 3, 4, 8, 10, 11, 17], "36": 2, "a1871": 2, "a1894": 2, "si": [2, 13], "mandatori": [2, 16], "label": 2, "must": [2, 8, 12, 13, 16, 17], "present": [2, 4, 12, 17], "python": [2, 6, 7, 8, 12], "driver": [2, 6, 7, 14, 16], "script": [2, 4, 12, 16, 17], "which": [2, 3, 4, 8, 9, 11, 12, 13, 14, 17], "center": [2, 12], "origin": [2, 4, 12], "entri": 2, "span": 2, "x": [2, 4, 9, 11, 12], "east": 2, "west": 2, "second": [2, 4, 12, 16], "y": [2, 4, 9, 10, 11], "south": 2, "third": [2, 12], "z": [2, 9, 10, 11], "list": [2, 8, 9, 12, 13, 15, 16], "float": [2, 11, 12, 13, 15], "none": [2, 11, 12, 13, 14, 15, 16, 17], "valu": [2, 9, 11, 12, 13, 16], "20": 2, "minimum": [2, 4, 12], "maximum": [2, 4, 12], "direct": [2, 4, 8, 11, 13], "temporari": 2, "insert": [2, 4, 12], "outsid": 2, "after": [2, 12, 16], "complet": [2, 12], "back": [2, 9, 11], "expans": 2, "help": [2, 17], "mitig": 2, "edg": [2, 4, 13, 17], "densiti": [2, 10, 11], "param": [2, 9, 11, 12, 16], "ad": [2, 6, 7, 8], "subtract": 2, "less": 2, "than": [2, 8], "rule": 2, "thumb": 2, "least": [2, 12, 17], "largest": 2, "stratograph": 2, "If": [2, 8, 11, 12, 15, 16, 17], "height": 2, "assign": [2, 8, 12, 16], "when": [2, 12], "pydfngen": [2, 16], "neg": [2, 9, 13], "integ": [2, 9, 13, 16], "two": [2, 4, 16], "lower": 2, "upper": 2, "limit": [2, 8, 9, 13], "etc": 2, "everi": [2, 9], "entir": 2, "element": [2, 3, 9, 12], "zmin": 2, "zmax": 2, "30": 2, "40": 2, "overlap": 2, "cuboid": 2, "creation": 2, "bound": 2, "box": 2, "theses": 2, "six": 2, "minx": 2, "maxx": 2, "mini": 2, "maxi": 2, "minz": 2, "maxz": 2, "15": 2, "Will": 2, "min": 2, "max": 2, "do": [2, 3, 8, 17], "same": [2, 4, 12, 16], "face": [2, 11], "boolean": [2, 11, 12, 16], "fals": [2, 11, 12, 13, 16], "true": [2, 11, 12, 16], "ignor": [2, 13], "keep": 2, "cluster": [2, 10], "retain": [2, 8, 16], "onli": [2, 3, 11, 12, 13], "connect": [2, 9, 10, 12, 13], "correspond": [2, 4, 9, 11, 12, 13], "3": [2, 6, 7, 12, 17], "within": [2, 4, 5, 8, 16], "criteria": 2, "stop": [2, 12], "onc": 2, "accept": [2, 12], "p32": [2, 12], "have": [2, 4, 9, 11, 15, 16, 17], "been": [2, 8, 9, 16], "meet": 2, "belong": [2, 12], "request": [2, 13], "posit": [2, 12], "100": 2, "probabl": [2, 12], "occurr": 2, "add": [2, 8, 11, 12], "up": [2, 4, 6, 7, 8, 12, 13], "save": [2, 12], "order": [2, 4], "automat": [2, 12, 16, 17], "prior": [2, 4, 8, 16], "ani": [2, 8, 17], "possibl": [2, 8], "constraint": 2, "met": [2, 8], "definit": 2, "theta": [2, 12], "phi": [2, 12, 13], "degre": [2, 12], "angl": [2, 9, 12], "specifi": [2, 12, 16], "string": [2, 11, 12, 13, 14, 15, 16], "either": [2, 8, 12, 16], "radian": [2, 12], "reason": [2, 9], "unless": 2, "turn": [2, 12], "greater": 2, "cdot": 2, "sqrt": 2, "where": [2, 10, 12, 15, 17], "smaller": 2, "10th": 2, "larger": 2, "1000th": 2, "zero": [2, 9], "clear": 2, "requir": [2, 4, 6, 7, 8, 11, 12, 14, 16], "discuss": [2, 16], "off": [2, 12, 13], "result": [2, 9, 12], "coars": 2, "visual": [2, 4, 8, 10, 12, 17], "you": [2, 4, 8, 12, 17], "cannot": 2, "full": [2, 9, 13], "intent": 2, "upscal": [2, 6, 7, 10], "octre": [2, 10, 12], "udfm": [2, 6, 7, 10], "modul": [2, 6, 7, 8, 12, 17], "print": [2, 6, 7, 8], "inform": [2, 3, 6, 7, 9, 10, 11, 13, 15, 16], "screen": [2, 11, 12], "debug": [2, 16, 17], "more": [2, 8, 12, 13], "effici": [2, 10], "hit": 2, "target": [2, 12, 13], "befor": [2, 12, 17], "being": [2, 12], "equal": 2, "queue": 2, "percentag": [2, 12], "smallest": 2, "begin": 2, "properli": 2, "resolv": [2, 3], "represent": [2, 3, 4, 5, 8, 10, 12, 13, 17], "exhaust": 2, "random": [2, 8, 10, 12], "like": [2, 16], "doubl": [2, 11, 13], "examin": 2, "check": [2, 8, 12], "prescrib": 2, "output_report": [2, 12], "No": 2, "longer": [2, 12], "should": [2, 8, 11, 12], "done": [2, 17], "mesh_network": [2, 4, 12, 16], "visual_mod": [2, 12], "want": [2, 12], "quick": 2, "standard": 2, "full_mesh": [2, 4, 9, 16], "inp": [2, 4, 9, 12, 15, 16], "reduced_mesh": [2, 12], "clock": 2, "uniqu": [2, 3], "produc": [2, 8, 9, 12], "reproduc": [2, 4, 8], "42069": 2, "dfn_output": [2, 9], "txt": [2, 4, 9, 11, 12], "isol": [2, 4, 9], "remov": [2, 4, 9, 12, 13, 15, 16], "contribut": 2, "fail": [2, 12], "still": [2, 12], "whether": [2, 8, 12], "tripl": [2, 9], "intersect": [2, 9, 10, 12, 13, 15, 17], "even": [2, 8, 12], "dfntran": [2, 6, 7, 8, 16], "doe": [2, 3, 10, 11, 12], "cutoff": 2, "e": [2, 10, 11, 13], "g": [2, 10, 11, 13], "down": 2, "those": [2, 12], "how": [2, 17], "alwai": 2, "sequenti": [2, 10], "respect": 2, "forc": [2, 11], "sort": [2, 10], "minim": 2, "both": [2, 16], "radii_allaccept": 2, "dat": [2, 4, 9, 11, 12, 15, 16], "xradiu": 2, "yradiu": 2, "userpolygon": 2, "userrectangl": 2, "userellips": 2, "per": [2, 9], "radii_allaccepted_fam_1": 2, "distributionnumb": 2, "radii_final_fam_1": 2, "section": [2, 4, 9, 12, 16, 17], "describ": [2, 9, 16, 17], "disc": [2, 8], "shape": [2, 12, 16], "match": [2, 10], "index": [2, 9, 11, 12], "shown": [2, 5], "written": [2, 8, 11, 12, 13, 15], "dictionari": [2, 12, 15], "meant": 2, "addit": [2, 6, 7, 8], "whole": [2, 12], "intens": [2, 12], "p_": 2, "32": 2, "text": [2, 12], "surfac": [2, 4], "divid": 2, "volum": [2, 3, 8, 9, 11, 15, 17], "until": 2, "obtain": [2, 3, 4, 6, 7, 13], "desir": [2, 12, 17], "02": 2, "ellipt": [2, 4], "12": [2, 12, 16], "16": 2, "lead": 2, "challeng": [2, 3, 10], "via": [2, 10], "suggest": 2, "aspect": [2, 12], "ratio": [2, 12], "circl": 2, "twice": 2, "make": [2, 8, 12, 15], "As": [2, 12], "degrad": 2, "accuraci": 2, "von": [2, 12], "mise": [2, 12], "bf": 2, "boldsymbol": 2, "mu": [2, 12], "kappa": [2, 12], "frac": 2, "exp": [2, 6, 7, 12], "t": [2, 10, 12, 13], "pi": 2, "sinh": 2, "mean": [2, 12], "vector": [2, 5, 9, 12], "denot": 2, "transpos": 2, "commun": 2, "23": 2, "1994": 2, "157": 2, "164": 2, "andrew": 2, "wood": 2, "indic": [2, 13], "concentr": [2, 12], "around": [2, 12], "17": [2, 8], "45": [2, 12], "78": 2, "sphere": 2, "small": 2, "deviat": 2, "numer": [2, 3, 10, 13], "becom": 2, "unstabl": 2, "vec": 2, "_x": 2, "sin": 2, "_y": 2, "_z": 2, "onto": 2, "56": 2, "270": 2, "four": [2, 4, 12], "differ": [2, 10, 12, 16], "log": [2, 10, 12], "sigma": [2, 12], "ln": 2, "right": [2, 4, 8, 9, 11], "varianc": [2, 12], "underli": 2, "en": 2, "wikipedia": 2, "wiki": 2, "normal_distribut": 2, "equat": [2, 3, 12, 17], "abov": [2, 8], "convert": [2, 11, 12, 15], "609": 2, "040": 2, "r_0": 2, "r_u": 2, "expon": [2, 4], "6": [2, 4, 6, 7, 16, 17], "tpl": [2, 6, 7, 12], "lambda": 2, "25": [2, 12], "7": [2, 6, 7, 9], "527": 2, "89": 2, "singl": [2, 4, 9, 12, 16], "These": [2, 9, 15, 16, 17], "mono": 2, "dispers": [2, 3, 10], "rectangular": [2, 4], "squar": 2, "ref": 2, "includ": [2, 4, 8, 9, 12, 16], "wai": [2, 8, 16, 17], "One": [2, 12], "put": [2, 11], "convex": 2, "vertex": [2, 4, 13], "To": [2, 6, 7, 10, 12, 16, 17], "incoper": 2, "add_user_fract": [2, 12, 16], "add_user_fract_from_fil": [2, 12], "predefin": 2, "go": [2, 10, 17], "activ": 2, "read": [2, 13], "path": [2, 6, 7, 8, 10, 11, 12, 13, 14], "valid": [2, 16], "filepath": 2, "userell_input_filepath": 2, "4_user_ell_uniform": 2, "define_4_user_ellips": 2, "int": [2, 11, 12, 13], "expect": [2, 9], "line": [2, 4, 6, 7, 9, 11, 12, 14], "accord": 2, "keyword": [2, 12], "mix": [2, 10], "90": 2, "37": 2, "name": [2, 8, 11, 12, 13, 15, 16], "4_user_el": 2, "ellcoord": 2, "node": [2, 9, 12, 13, 15, 16], "x_0": 2, "y_0": 2, "z_0": 2, "x_1": 2, "y_1": 2, "z_1": 2, "ldot": 2, "x_n": 2, "y_n": 2, "z_n": 2, "clockwis": 2, "counterclockwis": 2, "planar": 2, "BY": [2, 8], "note": [2, 3, 4, 9, 11, 12, 13, 14, 15, 17], "white": 2, "matter": 2, "x1": [2, 9, 12, 15], "y1": [2, 9, 12, 15], "z1": [2, 9, 12, 15], "x2": [2, 12], "y2": [2, 12], "z2": [2, 12], "x3": 2, "y3": 2, "z3": 2, "x4": 2, "y4": 2, "z4": 2, "xn": [2, 12, 15], "yn": [2, 12, 15], "zn": [2, 12, 15], "4_user_rect": 2, "define_4_user_rect": 2, "rectcoord": 2, "user_polygon": 2, "refpolygonbycoord_input_file_path": 2, "Then": [2, 3, 12], "remain": 2, "614809755508": 2, "215302589745": 2, "14052566974": 2, "545132019741": 2, "76296408041": 2, "01135305297": 2, "46205561432": 2, "11169723114": 2, "28911258873": 2, "7422671348": 2, "903335314403": 2, "34275683413": 2, "19676496723": 2, "52840001844": 2, "54841054822": 2, "3215018603": 2, "70265907788": 2, "28455866847": 2, "968743065242": 2, "39004354883": 2, "5300049043": 2, "82257143457": 2, "169537908304": 2, "10365780918": 2, "89449659536": 2, "39229757501": 2, "47097810869": 2, "7368040684": 2, "396173810104": 2, "9199696155": 2, "76351044547": 2, "192549006049": 2, "33581920939": 2, "157462422292": 2, "76600532497": 2, "29594241204": 2, "30082072643": 2, "47978607543": 2, "64081751301": 2, "793278268371": 2, "81778296407": 2, "561983329033": 2, "45819042638": 2, "44636375172": 2, "4541413343": 2, "51825209439": 2, "66719739398": 2, "0912558548": 2, "1739128129": 2, "74246641127": 2, "809628560699": 2, "56729801834": 2, "10664963232": 2, "17895163585": 2, "75834169562": 2, "23742727251": 2, "80010131269": 2, "26666449977": 2, "40228077595": 2, "45665913893": 2, "23685468994": 2, "54844410108": 2, "5749811435": 2, "06272440502": 2, "61045433532": 2, "565188057474": 2, "92263630123": 2, "27643915621": 2, "710166484812": 2, "89865208954": 2, "42113429321": 2, "22497133918": 2, "00482133497": 2, "61970921408": 2, "322281059007": 2, "27249031626": 2, "91468659533": 2, "549550927249": 2, "19700291895": 2, "3154355331": 2, "64584005023": 2, "20544838483": 2, "98437001886": 2, "31745142962": 2, "22589362057": 2, "804792681255": 2, "91861492809": 2, "70593999999": 2, "29639431251": 2, "25224389054": 2, "10094407568": 2, "6562865987": 2, "03245087974": 2, "992518232701": 2, "50612429324": 2, "10741842947": 2, "384249987443": 2, "93387033715": 2, "43323157864": 2, "222868762162": 2, "860529584164": 2, "81903344627": 2, "38212753352": 2, "499362646346": 2, "03882643837": 2, "4905528176": 2, "349200223043": 2, "9638588789": 2, "8673209588": 2, "22305329999": 2, "63804581282": 2, "39564264412": 2, "56312416852": 2, "08462835745": 2, "41898893677": 2, "65124788861": 2, "11909954775": 2, "10520773081": 2, "8645938936": 2, "89290711889": 2, "80872562941": 2, "11160312936": 2, "39770554375": 2, "19173173493": 2, "34506895229": 2, "42895858094": 2, "20485792137": 2, "85177752427": 2, "81351205493": 2, "99702019362": 2, "0853427250495": 2, "66597219167": 2, "50868187563": 2, "289753327606": 2, "588931258258": 2, "08441961571": 2, "88990150472": 2, "64805531643": 2, "34094328974": 2, "922507014307": 2, "71519798881": 2, "85778630995": 2, "841071899053": 2, "310044679731": 2, "25820816606": 2, "26426496474": 2, "84566856205": 2, "49988903618": 2, "94418542615": 2, "40633923745": 2, "44125563949": 2, "48254521057": 2, "07783735953": 2, "94508200102": 2, "5639802392": 2, "05259419185": 2, "54466008318": 2, "14078724661": 2, "483028953749": 2, "30297907019": 2, "4608669326": 2, "04369954706": 2, "36161304612": 2, "18143095055": 2, "610312831185": 2, "21771261931": 2, "80909183961": 2, "814183043594": 2, "47247873318": 2, "26469088948": 2, "29432736239": 2, "44327042469": 2, "867130728085": 2, "96307141873": 2, "14719749191": 2, "564917036364": 2, "42867426252": 2, "75769541671": 2, "19257780773": 2, "00417817281": 2, "50292931657": 2, "648176891617": 2, "475965761662": 2, "53213764385": 2, "74938298608": 2, "14470985076": 2, "82821050463": 2, "27165416308": 2, "97370232204": 2, "13046740212": 2, "01807341608": 2, "962283071202": 2, "35725325459": 2, "83562647916": 2, "23286105726": 2, "12746635144": 2, "40616097581": 2, "67958113114": 2, "45759785589": 2, "34398137987": 2, "64526675756": 2, "polgyon": 2, "solut": [3, 4, 8, 9, 10, 11, 12], "dfnflow": [3, 6, 7, 8, 16], "dfngen": [3, 6, 7, 8, 16], "lagrangian": [3, 8], "repres": [3, 10, 12], "conserv": 3, "collect": 3, "indivis": 3, "passiv": 3, "tracer": 3, "track": [3, 4, 10, 13, 15, 16], "wealth": 3, "local": [3, 16, 17], "b": [3, 10, 12], "suffer": 3, "inher": 3, "c": [3, 6, 7, 8, 10, 17], "intrins": [3, 8], "parallel": [3, 8, 10, 17], "fashion": [3, 8], "anoth": [3, 11, 14], "pose": 3, "aris": [3, 8], "qualiti": [3, 8], "phenomena": 3, "interest": 3, "mass": [3, 12], "so": [3, 4, 8, 17], "galerkin": 3, "finit": [3, 8, 13, 17], "code": [3, 4, 6, 7, 8, 15, 17], "reconstruct": 3, "veloc": [3, 4, 5, 13], "darci": 3, "flux": [3, 13], "pathlin": [3, 4, 5, 8], "It": [3, 17], "import": [3, 16, 17], "itself": [3, 8], "longitudin": 3, "sorption": 3, "other": [3, 8, 12, 16], "retent": 3, "easili": 3, "incorpor": 3, "post": 3, "bui": [3, 8, 10], "q": [3, 10], "geoscienc": [3, 8, 10], "19": [3, 8], "1123": 3, "1137": 3, "doxygen": [3, 6, 7], "few": [4, 12], "folder": [4, 17], "focu": 4, "document": [4, 8, 17], "confirm": 4, "correctli": 4, "carri": 4, "out": [4, 8, 9, 11, 12, 13], "imag": [4, 13, 17], "render": 4, "paraview": 4, "free": [4, 8], "simplest": 4, "proce": [4, 12], "directori": [4, 6, 7, 8, 9, 11, 12, 14, 15, 16], "subdirectori": [4, 9, 12], "command": [4, 6, 7, 11, 12, 14, 17], "Be": 4, "sure": [4, 12], "test_output_fil": 4, "locat": [4, 9, 12, 13], "test": [4, 6, 7], "case": [4, 10], "defin": [4, 6, 7, 8, 9, 12], "color": [4, 5, 13], "overlaid": 4, "load": 4, "job": [4, 12], "red": [4, 13], "appli": [4, 10, 12], "blue": [4, 13], "parsed_vtk": [4, 9], "dfn_explicit": [4, 9, 16], "001": [4, 9, 12], "uniformli": 4, "inlet": [4, 13], "exit": [4, 12], "horizont": 4, "might": 4, "exactli": 4, "magnitud": 4, "part_": 4, "4_user_rectangl": 4, "traj": 4, "extract": [4, 6, 7], "tube": 4, "filter": 4, "clariti": 4, "In": [4, 10], "ellips": [4, 6, 7, 12], "resolut": [4, 10, 11, 12, 15, 17], "argument": [4, 6, 7, 11, 12, 14], "slope": [4, 12], "run_explicit": 4, "py": [4, 12, 16, 17], "famili": [4, 6, 7, 8, 9, 17], "1m": 4, "50m": 4, "10m": 4, "gen_exponential_dist": 4, "modifi": [4, 8], "card": [4, 11, 12], "5m": 4, "15m": 4, "core": 4, "dead": [4, 5], "identifi": [4, 9, 10, 13, 15], "networkx": [4, 13, 17], "github": [4, 6, 7, 8], "io": [4, 17], "sub": [4, 15, 17], "207": 4, "79": 4, "topologi": [4, 10], "compos": 5, "powerlaw": 5, "contour": 5, "graph": [5, 6, 7, 8, 10, 16], "intern": [5, 10, 12], "purpl": 5, "content": [6, 7, 9], "cite": [6, 7], "version": [6, 7, 12, 17], "v2": [6, 7, 12], "contact": [6, 7], "contributor": [6, 7], "extern": [6, 7], "copyright": [6, 7], "applic": [6, 7, 8, 10], "carbon": [6, 7], "dioxid": [6, 7], "sequestr": [6, 7, 8], "shale": [6, 7, 10], "energi": [6, 7, 8, 10], "nuclear": [6, 7, 8, 10], "wast": [6, 7, 8, 10], "docker": [6, 7, 8], "nativ": [6, 7], "clone": [6, 7], "dnfwork": [6, 7], "fix": [6, 7, 8], "lagrit": [6, 7, 8, 11], "petsc": [6, 7], "instal": [6, 7, 16], "4_user_defined_rect": [6, 7], "4_user_defined_ell_uniform": [6, 7], "exponenti": [6, 7], "prune": [6, 7, 16], "packag": [6, 7, 8, 17], "class": [6, 7, 11, 12, 13, 14, 15, 17], "jobnam": [6, 7, 12], "ncpu": [6, 7, 11], "dfnflow_fil": [6, 7], "dfngen_fil": [6, 7], "dfntrans_fil": [6, 7], "prune_fil": [6, 7, 12], "flow_solv": [6, 7, 11], "cell_based_apertur": [6, 7], "analysi": [6, 7, 10, 13, 16], "modif": [6, 7, 8], "stress": [6, 7, 8, 10], "primari": [6, 7, 10, 11, 13, 14], "helper": [6, 7], "mapdfn_ecpm": [6, 7, 12], "dfm": [6, 7], "create_dfn_flow_link": [6, 7, 11], "dfn_flow": [6, 7, 11, 16], "set_flow_solv": [6, 7, 11], "lagrit2pflotran": [6, 7, 11], "parse_pflotran_vtk_python": [6, 7, 11], "pflotran_cleanup": [6, 7, 11], "write_perms_and_correct_volumes_area": [6, 7, 11], "zone2ex": [6, 7, 11], "correct_stor_fil": [6, 7, 11], "effective_perm": [6, 7, 11], "check_dfn_trans_run_fil": [6, 7, 14], "copy_dfn_trans_fil": [6, 7, 14], "create_dfn_trans_link": [6, 7, 14], "dfn_tran": [6, 7, 14, 16], "run_dfn_tran": [6, 7, 14], "dfngraph": [6, 7, 8], "add_fracture_sourc": [6, 7, 13], "add_fracture_target": [6, 7, 13], "create_graph": [6, 7, 13], "dump_fractur": [6, 7, 13], "dump_json_graph": [6, 7, 13], "load_json_graph": [6, 7, 13], "plot_graph": [6, 7, 13], "greedy_edge_disjoint": [6, 7, 13], "k_shortest_paths_backbon": [6, 7, 13], "run_graph_flow": [6, 7, 13], "run_graph_transport": [6, 7, 13], "cleanup_wel": [6, 7, 15], "combine_well_boundary_zon": [6, 7, 15], "find_well_intersection_point": [6, 7, 15], "tag_well_in_mesh": [6, 7, 15], "domains": [6, 7, 16], "domainsizeincreas": [6, 7], "numoflay": [6, 7], "layer": [6, 7, 12], "numofregion": [6, 7], "ignoreboundaryfac": [6, 7], "boundaryfac": [6, 7], "stopcondit": [6, 7, 12], "npoli": [6, 7], "famprob": [6, 7], "orientationopt": [6, 7, 12], "angleopt": [6, 7], "disablefram": [6, 7], "printrejectreason": [6, 7], "rejectsperfractur": [6, 7], "radiilistincreas": [6, 7], "visualizationmod": [6, 7], "seed": [6, 7], "keeponlylargestclust": [6, 7], "keepisolatedfractur": [6, 7], "tripleintersect": [6, 7], "removefractureslessthan": [6, 7], "insertuserrectanglesfirst": [6, 7], "forcelargefractur": [6, 7], "outputallradii": [6, 7], "outputacceptedradiiperfamili": [6, 7], "outputfinalradiiperfamili": [6, 7], "rectangl": [6, 7, 9, 12], "polygon": [6, 7, 9, 12], "public": [6, 7, 8], "galleri": [6, 7], "suit": 8, "lo": [8, 17], "alamo": [8, 17], "nation": [8, 10, 12, 17], "laboratori": [8, 12, 17], "rang": 8, "millimet": 8, "combin": [8, 15], "toolbox": [8, 17], "suitabl": [8, 17], "util": 8, "massiv": [8, 17], "workflow": [8, 11, 12, 16], "highli": [8, 17], "variou": [8, 16], "tool": [8, 17], "aim": 8, "seamless": 8, "scientif": [8, 10], "download": [8, 17], "com": [8, 17], "hub": [8, 17], "ees16": [8, 17], "84": 8, "bibtex": 8, "articl": 8, "hyman2015dfnwork": 8, "titl": 8, "author": 8, "jeffrei": [8, 10, 12], "carl": [8, 10], "scott": [8, 10], "hari": [8, 10], "journal": [8, 10, 12], "page": [8, 10], "publish": 8, "elsevi": 8, "poisson": [8, 10], "v3": 8, "ecpm": [8, 12], "bug": 8, "tdrw": [8, 13], "object": [8, 11, 12, 13, 14, 15, 16], "interfac": 8, "updat": 8, "compat": 8, "warn": [8, 9, 12], "error": [8, 12], "trend": [8, 12], "plung": [8, 12], "dip": [8, 12], "strike": [8, 12], "techniqu": [8, 16], "expand": [8, 15], "pdf": [8, 12], "abil": 8, "python3": 8, "pipe": [8, 13, 16], "dfn2graph": 8, "streamlin": 8, "rout": 8, "walk": 8, "much": 8, "faster": [8, 17], "mathematica": 8, "successfulli": 8, "350": 8, "000": [8, 9], "compris": 8, "short": 8, "tutori": 8, "prepar": 8, "some": [8, 12], "email": 8, "gov": [8, 11, 12], "question": 8, "let": [8, 12], "u": 8, "know": 8, "ll": 8, "matt": 8, "sweenei": [8, 10, 12], "aric": [8, 10], "hagberg": [8, 10], "shriram": [8, 10], "srinivasan": [8, 10], "aidan": [8, 12], "stansberri": 8, "pnnl": 8, "ornl": 8, "quan": 8, "now": 8, "llnl": 8, "jeremi": 8, "harrod": 8, "spectra": 8, "logic": 8, "thoma": 8, "sherman": [8, 10], "notr": 8, "dame": 8, "johann": 8, "krotz": [8, 10], "oregon": 8, "state": [8, 9, 10, 11, 13], "yu": 8, "chen": [8, 10], "la": 8, "ur": 8, "22216": 8, "softwar": [8, 17], "cc": 8, "027": 8, "2018": [8, 10, 13], "triad": 8, "secur": [8, 10], "llc": 8, "reserv": 8, "program": [8, 12], "govern": 8, "contract": 8, "89233218cna000001": 8, "oper": 8, "depart": 8, "administr": 8, "grant": 8, "act": 8, "behalf": 8, "nonexclus": 8, "paid": 8, "irrevoc": 8, "worldwid": 8, "licens": 8, "deriv": 8, "copi": [8, 11, 14], "publicli": 8, "displai": 8, "permit": 8, "neither": 8, "THE": 8, "nor": 8, "warranti": 8, "express": 8, "OR": 8, "impli": 8, "assum": [8, 11, 12], "liabil": 8, "FOR": 8, "OF": 8, "clearli": 8, "confus": 8, "avail": [8, 17], "addition": 8, "redistribut": 8, "gnu": 8, "foundat": 8, "accordingli": 8, "hope": 8, "without": [8, 12], "merchant": 8, "fit": 8, "purpos": [8, 9], "binari": [8, 9], "form": 8, "notic": 8, "disclaim": 8, "mai": [8, 12], "endors": 8, "promot": 8, "specif": 8, "permiss": 8, "AND": 8, "AS": 8, "BUT": 8, "NOT": 8, "TO": 8, "IN": 8, "NO": 8, "event": 8, "shall": 8, "BE": 8, "liabl": 8, "indirect": 8, "incident": 8, "special": 8, "exemplari": 8, "consequenti": 8, "damag": 8, "procur": 8, "substitut": 8, "servic": 8, "loss": 8, "profit": 8, "busi": 8, "interrupt": 8, "caus": 8, "ON": 8, "theori": [8, 10], "strict": [8, 12], "tort": 8, "neglig": 8, "otherwis": 8, "IF": 8, "advis": 8, "SUCH": 8, "row": 9, "adjac": 9, "input_gener": 9, "input_generator_clean": 9, "abbrevi": 9, "normal_vector": [9, 12, 16], "normal": [9, 12], "visualmod": 9, "dud": 9, "dimens": 9, "poly_info": 9, "rotat": [9, 12], "rotateln": 9, "x0": [9, 15], "y0": [9, 15], "z0": [9, 15], "user_rect": 9, "concatent": 9, "radii_fin": 9, "summari": [9, 12], "rejectsperattempt": 9, "attempt": 9, "translat": [9, 12, 16], "centriod": 9, "triple_point": 9, "warningfiledfngen": 9, "intersection_list": 9, "fracture1": 9, "fracture2": 9, "bound_zon": 9, "lgi": 9, "dump": [9, 11, 12, 13], "zone": [9, 10, 11, 15], "boundary_output": 9, "finalmesh": 9, "brief": 9, "av": [9, 15], "lg": 9, "correct": [9, 11, 12], "convert_ug": 9, "full_mesh_viz": 9, "lagrit_log": 9, "individu": [9, 11, 12, 13, 16], "logx3dgen": 9, "outx3dgen": 9, "mgli": 9, "poli": [9, 12], "contiain": 9, "tri_fractur": 9, "stor": [9, 11], "user_funct": 9, "coarsen": 9, "rescal": 9, "cellinfo": [9, 11], "steadi": [9, 10, 11, 13], "ma": 9, "_dfn_explicit": 9, "attribut": [9, 15], "materialid": [9, 16], "perm": 9, "pboundary_back_n": 9, "pboundary_bottom": 9, "pboundary_front_": 9, "front": [9, 11], "pboundary_top": 9, "middleton": 10, "carei": 10, "currier": 10, "kang": 10, "jimenez": 10, "mart\u0131nez": 10, "porter": 10, "aqueou": 10, "opportun": 10, "influenc": 10, "resourc": [10, 12], "research": [10, 12], "rougier": 10, "zhou": 10, "discoveri": 10, "while": [10, 12, 15, 16, 17], "chapter": 10, "71": 10, "88": 10, "ac": 10, "2016": [10, 12], "mallei": 10, "jim\u00e9nez": 10, "mart\u00ednez": 10, "jw": 10, "ml": 10, "frash": 10, "multi": [10, 17], "phil": 10, "tran": 10, "soc": 10, "aldrich": 10, "woodr": 10, "hamann": 10, "ieee": 10, "transact": 10, "graphic": 10, "2017": [10, 13], "evalu": 10, "advanc": 10, "correl": [10, 12], "implic": [10, 12], "spars": [10, 12, 13], "djidjev": 10, "learn": 10, "predict": [10, 13], "propag": 10, "symposium": 10, "workshop": 10, "ipdpsw": 10, "mohd": 10, "yusof": 10, "passag": [10, 13], "reduct": [10, 13], "phy": 10, "rev": 10, "96": 10, "013304": 10, "jul": 10, "hadgu": 10, "k": [10, 12, 13], "klise": 10, "wang": 10, "compar": 10, "equival": [10, 12], "continuum": [10, 12, 17], "far": 10, "hypothet": 10, "hydrologi": 10, "romano": 10, "valocchi": 10, "battaglia": 10, "bigi": 10, "majella": 10, "mountain": 10, "itali": 10, "procedia": 10, "125": [10, 12], "556": 10, "560": 10, "valera": 10, "guo": 10, "kelli": 10, "matz": 10, "cantu": 10, "percu": 10, "machin": [10, 17], "mudunuru": 10, "geophys": [10, 12], "invers": 10, "character": 10, "mine": [10, 12], "asa": 10, "william": 10, "esteban": 10, "lei": 10, "discontinu": 10, "percol": 10, "jimen\u00e9z": 10, "nonlinear": 10, "interplai": 10, "structur": 10, "heterogen": 10, "mont": 10, "carlo": 10, "osthu": 10, "moor": 10, "hunter": 10, "quantifi": 10, "topolog": 10, "uncertainti": [10, 12], "robust": 10, "fidel": 10, "preserv": 10, "dave": 10, "gowri": 10, "backbon": [10, 13], "net": 10, "bipartit": [10, 13], "multiscal": [10, 13], "lukasczyk": 10, "garth": 10, "leitt": 10, "ahren": 10, "queri": 10, "search": 10, "explor": 10, "ensembl": 10, "engin": [10, 12], "bolster": 10, "impact": [10, 12], "behavior": 10, "2019": 10, "dentz": 10, "link": 10, "geophi": 10, "sol": 10, "ea": 10, "pathwai": 10, "kwickli": 10, "birdsel": 10, "confer": 10, "proceed": 10, "topopah": 10, "spring": 10, "pahut": 10, "mesa": 10, "2nd": 10, "pawar": 10, "merg": 10, "With": [10, 17], "3d": 10, "novel": 10, "frampton": 10, "zou": 10, "disconnect": 10, "textur": 10, "stauffer": 10, "caprock": 10, "rajaram": 10, "insight": 10, "breakthrough": 10, "letter": 10, "emerg": 10, "stabl": 10, "refin": [10, 12], "mediacomput": 10, "panda": 10, "probabilist": 10, "subnetwork": 10, "quantif": 10, "2020": [10, 12], "carneval": 10, "tartarello": 10, "geologi": 10, "cawi": 10, "identif": 10, "geosci": 10, "guthri": 10, "role": 10, "pham": 10, "parashar": 10, "sund": 10, "pohlmann": 10, "solid": [10, 12], "earth": [10, 12], "channel": 10, "preferenti": 10, "e2020wr027986": 10, "calibr": 10, "nevada": 10, "usa": 10, "hydrogeol": 10, "transient": [10, 11], "liangchao": 10, "vladimir": 10, "cvetkov": 10, "infer": 10, "pump": 10, "han": 10, "anomal": 10, "2021": 10, "sole": 10, "mari": 10, "vassallo": 10, "rapid": 10, "forecast": 10, "histori": 10, "unconvent": 10, "bridg": 10, "ambient": 10, "ushijima": 10, "mwesigwa": 10, "safro": 10, "multilevel": 10, "partit": 10, "mathemat": 10, "yingtao": 10, "hu": 10, "wenji": 10, "xu": 10, "liangtong": 10, "zhan": 10, "yunmin": 10, "hydromechan": 10, "cement": 10, "lithospher": 10, "2022": 10, "restrepo": 10, "disk": 10, "self": [11, 12, 13, 14, 15], "symlink": [11, 12, 14], "absolut": [11, 14, 17], "return": [11, 12, 13, 14, 15], "dump_vtk": 11, "portion": [11, 12], "bool": [11, 12, 13], "write": [11, 12, 13], "therein": [11, 13], "sovler": 11, "boundary_cell_area": 11, "take": [11, 12], "grid_vtk_fil": 11, "cell_data": 11, "point_data": 11, "local_dfnflow_fil": [11, 16], "inp2vtk_python": [11, 12], "restart": 11, "restart_fil": 11, "checkpoint": 11, "execut": [11, 12, 14, 17], "index_start": 11, "index_finish": 11, "concaten": 11, "delet": [11, 12, 16], "them": [11, 17], "pick": 11, "darcyvel": 11, "loop": 11, "over": [11, 13], "perm_fil": 11, "aper_fil": 11, "uge_fil": [11, 16], "correct_ug": 11, "zone_fil": 11, "plane": [11, 13], "rel": 11, "account": [11, 12], "inflow_pressur": 11, "outflow_pressur": 11, "boundary_fil": 11, "pascal": 11, "pboundary_left": 11, "local_jobname_effective_perm": 11, "20c": 11, "add_fracture_famili": 12, "family_numb": 12, "number_of_point": 12, "beta_distribut": 12, "beta": 12, "log_mean": 12, "log_std": 12, "exp_mean": 12, "constant": 12, "min_radiu": 12, "max_radiu": 12, "hy_vari": 12, "hy_funct": 12, "hy_param": 12, "rect": [12, 16], "ell": 12, "dein": 12, "log_norm": 12, "fracutr": 12, "probabili": 12, "th": 12, "eboundari": 12, "distribtuion": 12, "2pi": 12, "specfi": 12, "ebeta": 12, "fo": 12, "relationship": 12, "semi": 12, "syntax": 12, "popul": 12, "html": 12, "aspect_ratio": [12, 16], "angle_opt": 12, "orientation_opt": 12, "trend_plung": 12, "dip_strik": 12, "number_of_vertic": 12, "user_defined_": 12, "choic": 12, "orien": 12, "tramsmiss": 12, "attach": 12, "awar": 12, "0e": [12, 16], "npolygon": 12, "by_coord": 12, "arrai": 12, "src": [12, 17], "src_path": [12, 16], "1e": 12, "print_user_fracture_inform": 12, "frac_numb": 12, "fracture_numb": 12, "print_domain_paramet": [12, 16], "print_al": 12, "print_family_inform": 12, "termin": 12, "check_input": [12, 16], "from_fil": 12, "clean": 12, "own": 12, "separ": 12, "newlin": 12, "kei": 12, "colon": 12, "ie": 12, "place": [12, 17], "comment": 12, "On": [12, 17], "noth": 12, "rais": 12, "continu": 12, "past": 12, "maintain": 12, "futur": 12, "create_network": [12, 16], "succeed": 12, "dfn_gen": 12, "wrapper": 12, "make_working_directori": [12, 16], "dfngen_mesh": 12, "made": [12, 13], "overrid": 12, "routin": [12, 15], "grab_polygon_data": 12, "flag": 12, "store_polygon_data": 12, "store": [12, 16], "np": 12, "alreadi": [12, 17], "prompt": 12, "overwrit": 12, "gen_output": 12, "synopsi": 12, "moduleauthor": 12, "jhyman": 12, "verbos": 12, "output_dir": 12, "dfngen_output_report": 12, "plot": 12, "family_": 12, "toggl": [12, 16], "amount": 12, "progress": 12, "_output_report": 12, "perfectli": 12, "log_": 12, "mathcal": 12, "strength": 12, "independ": 12, "ident": 12, "cor": 12, "semicorrel": 12, "speci": 12, "fi": 12, "fourth": 12, "assumpt": 12, "variat": 12, "stress_based_apertur": 12, "sigma_mat": 12, "friction_angl": 12, "dilation_angl": 12, "critical_shear_displac": 12, "003": 12, "shear_modulu": 12, "10000000000": 12, "min_b": 12, "shear_stiff": 12, "400000000000": 12, "tensor": 12, "calcul": 12, "bandi": 12, "pa": [12, 13], "friction": 12, "dilat": 12, "critic": 12, "shear": 12, "modulu": 12, "stiff": 12, "matthew": 12, "ryan": 12, "e2020jb019754": 12, "baghbanan": 12, "alireza": 12, "lanru": 12, "jing": 12, "2008": 12, "1320": 12, "1334": 12, "zhao": 12, "zhihong": 12, "comparison": 12, "geotechn": 12, "110": 12, "123": 12, "uniform_mesh": 12, "min_dist": 12, "max_dist": 12, "max_resolution_factor": 12, "cleanup": 12, "quiet": 12, "distanc": 12, "factor": 12, "max_resolut": 12, "resolult": 12, "depend": 12, "linear": 12, "realiz": 12, "create_mesh_link": 12, "inp2gmv": 12, "inp_fil": [12, 16], "gmv": 12, "viewer": 12, "str": [12, 13], "attribur": 12, "librari": 12, "run_lagrit_script": 12, "lagrit_fil": 12, "output_fil": 12, "failur": 12, "success": 12, "add_variable_to_mesh": 12, "variable_fil": 12, "mesh_file_in": 12, "mesh_file_out": 12, "node_bas": 12, "column": [12, 16], "map_to_continuum": 12, "orl": 12, "dir_nam": 12, "level": 12, "octree_dfn": 12, "fracx": 12, "mat_perm": 12, "mat_por": 12, "map2continuum": 12, "perm_fehm": 12, "rock_fehm": 12, "mesh_perm": 12, "permeabilit": 12, "mesh_poros": 12, "check_false_connect": 12, "fmc_filnam": 12, "pickl": 12, "num_false_connect": 12, "num_cell_fals": 12, "voronoi": [12, 17], "false_connect": 12, "tupl": 12, "thu": 12, "mapdfn2pflotran": 12, "mapdfn": 12, "version2": 12, "medium": 12, "edit": 12, "nx": 12, "ny": 12, "nz": 12, "k_background": 12, "bulk_por": 12, "h5origin": 12, "hardwir": 12, "numpi": [12, 17], "h5py": [12, 17], "date": 12, "07": 12, "18": 12, "sand": 12, "sand2018": 12, "7605": 12, "matrix_perm": 12, "matrix_poros": [12, 13], "cell_siz": 12, "matrix_on": 12, "tortuosity_factor": 12, "lump_diag_term": 12, "correction_factor": 12, "stairstep": 12, "edfm": 12, "emili": 12, "stein": 12, "ergiamb": 12, "sandia": 12, "8844": 12, "teresa": 12, "porton": 12, "tporton": 12, "rosi": 12, "leon": 12, "2023": 12, "integr": 12, "mesh_dfm": 12, "dirnam": 12, "dfm_mesh": 12, "allowed_percentag": 12, "tetrahedron": 12, "triangular": 12, "miss": 12, "dep": 12, "move": [12, 15], "exodu": 12, "built": 12, "against": 12, "source_list": 13, "remove_old_sourc": 13, "old": 13, "graph_typ": 13, "header": [13, 16], "bipartiti": 13, "assocait": 13, "ascii": [13, 16], "json": 13, "output_nam": 13, "dfn_graph": 13, "png": 13, "black": 13, "weight": 13, "greedi": 13, "find": 13, "disjoint": 13, "subgraph": 13, "mm": 13, "shortest": 13, "pressure_in": 13, "pressure_out": 13, "fluid_viscos": 13, "00089": 13, "driven": 13, "outlet": 13, "gtild": 13, "acycl": 13, "volumetr": 13, "travel": 13, "nparticl": 13, "partime_fil": 13, "frac_id_fil": 13, "hdf5": 13, "initial_posit": 13, "dump_traj": 13, "tdrw_flag": 13, "matrix_diffus": 13, "fracture_spac": 13, "control_plan": 13, "cp_filenam": 13, "given": 13, "graph_flow": 13, "dump_flag": 13, "ensur": 14, "execuatebl": 14, "well_data": 15, "well_coord": 15, "allboundari": 15, "higher": 15, "run_find_well_intersection_point": 15, "subroutin": 15, "redund": 15, "polylin": 15, "well_": 15, "_line": 15, "_volum": 15, "becaus": 16, "favorit": 16, "basic": 16, "taken": 16, "4_user_rects_exampl": 16, "getcwd": 16, "ptdfn_control": 16, "050": 16, "65": 16, "everyth": 16, "mat_fil": 16, "stor_fil": 16, "vtk_file": 16, "num_nod": 16, "mesh_typ": 16, "processor": 16, "depreci": 16, "amanzi": 16, "pars": 16, "local_dfngen_fil": 16, "local_dfntrans_fil": 16, "gen_4_user_rectangl": 16, "parent": 16, "demonstr": 16, "pruning_exampl": 16, "2_core": 16, "aper_nod": 16, "perm_nod": 16, "in_fracture_var": 16, "piec": 16, "pydfnflow": 16, "pydfntran": 16, "pydfngraph": 16, "easiest": 17, "get": 17, "our": 17, "visit": 17, "pull": 17, "dockerhub": 17, "latest": 17, "ti": 17, "exchang": 17, "mount": 17, "local_fold": 17, "expos": 17, "maco": 17, "instruct": 17, "setup": 17, "instead": 17, "git": 17, "pathnam": 17, "throughout": 17, "fix_path": 17, "cd": 17, "bin": 17, "dfnworks_path": 17, "petsc_dir": 17, "petsc_arch": 17, "environment": 17, "pflotran_ex": 17, "python_ex": 17, "lagrit_ex": 17, "vi": 17, "environ": 17, "home": 17, "usernam": 17, "altern": 17, "dfnworksrc": 17, "arch": 17, "darwin": 17, "anaconda3": 17, "fehm_ex": 17, "xfehm_v3": 17, "compli": 17, "bdist_wheel": 17, "pip": 17, "dist": 17, "py3": 17, "whl": 17, "releas": 17, "enabl": 17, "quantiti": 17, "mac": 17, "unix": 17, "ubuntu": 17, "anaconda": 17, "scipi": 17, "matplotlib": 17, "multiprocess": 17, "argpars": 17, "shutil": 17, "sy": 17, "subprocess": 17, "glob": 17, "fpdf": 17, "coincid": 17, "triangl": 17, "partial": 17, "differenti": 17, "multicompon": 17, "design": 17, "leadership": 17, "supercomput": 17, "workstat": 17, "laptop": 17, "open": 17, "cross": 17, "platform": 17, "bottleneck": 17, "step": 17, "greatli": 17, "speed": 17, "visualis": 17, "xmf": 17, "veri": 17}, "objects": {"false_connections": [[12, 0, 0, "-", "py"]], "graph_transport": [[13, 0, 0, "-", "py"]], "map2continuum": [[12, 0, 0, "-", "py"]], "mesh_dfm": [[12, 0, 0, "-", "py"]], "mesh_dfn": [[12, 0, 0, "-", "py"]], "mesh_dfn_helper": [[12, 0, 0, "-", "py"]], "pydfnworks.dfnFlow": [[11, 0, 0, "-", "fehm"], [11, 0, 0, "-", "flow"], [11, 0, 0, "-", "mass_balance"], [11, 0, 0, "-", "pflotran"]], "pydfnworks.dfnFlow.fehm": [[11, 1, 1, "", "correct_stor_file"], [11, 1, 1, "", "fehm"]], "pydfnworks.dfnFlow.flow": [[11, 1, 1, "", "create_dfn_flow_links"], [11, 1, 1, "", "dfn_flow"], [11, 1, 1, "", "set_flow_solver"]], "pydfnworks.dfnFlow.mass_balance": [[11, 1, 1, "", "effective_perm"]], "pydfnworks.dfnFlow.pflotran": [[11, 1, 1, "", "lagrit2pflotran"], [11, 1, 1, "", "parse_pflotran_vtk_python"], [11, 1, 1, "", "pflotran"], [11, 1, 1, "", "pflotran_cleanup"], [11, 1, 1, "", "write_perms_and_correct_volumes_areas"], [11, 1, 1, "", "zone2ex"]], "pydfnworks.dfnGen.generation": [[12, 0, 0, "-", "generator"], [12, 0, 0, "-", "input_checking"], [12, 0, 0, "-", "stress"]], "pydfnworks.dfnGen.generation.generator": [[12, 1, 1, "", "create_network"], [12, 1, 1, "", "dfn_gen"], [12, 1, 1, "", "grab_polygon_data"], [12, 1, 1, "", "make_working_directory"]], "pydfnworks.dfnGen.generation.input_checking": [[12, 1, 1, "", "print_domain_parameters"], [12, 1, 1, "", "print_family_information"], [12, 0, 0, "-", "user_defined_fracture_functions"]], "pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions": [[12, 1, 1, "", "print_user_fracture_information"]], "pydfnworks.dfnGen.generation.output_report": [[12, 0, 0, "-", "gen_output"]], "pydfnworks.dfnGen.generation.output_report.gen_output": [[12, 1, 1, "", "output_report"]], "pydfnworks.dfnGen.generation.stress": [[12, 1, 1, "", "stress_based_apertures"]], "pydfnworks.dfnGen.meshing": [[12, 0, 0, "-", "add_attribute_to_mesh"]], "pydfnworks.dfnGen.meshing.add_attribute_to_mesh": [[12, 1, 1, "", "add_variable_to_mesh"]], "pydfnworks.dfnGen.meshing.dfm": [[12, 0, 0, "-", "mesh_dfm"]], "pydfnworks.dfnGen.meshing.dfm.mesh_dfm": [[12, 1, 1, "", "mesh_dfm"]], "pydfnworks.dfnGen.meshing.mapdfn_ecpm": [[12, 0, 0, "-", "mapdfn_ecpm"]], "pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm": [[12, 1, 1, "", "mapdfn_ecpm"]], "pydfnworks.dfnGen.meshing.mesh_dfn": [[12, 0, 0, "-", "mesh_dfn"], [12, 0, 0, "-", "mesh_dfn_helper"]], "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn": [[12, 1, 1, "", "mesh_network"]], "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper": [[12, 1, 1, "", "create_mesh_links"], [12, 1, 1, "", "inp2gmv"], [12, 1, 1, "", "inp2vtk_python"], [12, 1, 1, "", "run_lagrit_script"]], "pydfnworks.dfnGen.meshing.udfm": [[12, 0, 0, "-", "false_connections"], [12, 0, 0, "-", "map2continuum"], [12, 0, 0, "-", "upscale"]], "pydfnworks.dfnGen.meshing.udfm.false_connections": [[12, 1, 1, "", "check_false_connections"]], "pydfnworks.dfnGen.meshing.udfm.map2continuum": [[12, 1, 1, "", "map_to_continuum"]], "pydfnworks.dfnGen.meshing.udfm.upscale": [[12, 1, 1, "", "upscale"]], "pydfnworks.dfnGen.well_package": [[15, 0, 0, "-", "wells"]], "pydfnworks.dfnGen.well_package.wells": [[15, 1, 1, "", "cleanup_wells"], [15, 1, 1, "", "combine_well_boundary_zones"], [15, 1, 1, "", "find_well_intersection_points"], [15, 1, 1, "", "tag_well_in_mesh"]], "pydfnworks.dfnGraph": [[13, 0, 0, "-", "dfn2graph"], [13, 0, 0, "-", "graph_flow"], [13, 0, 0, "-", "graph_transport"], [13, 0, 0, "-", "pruning"]], "pydfnworks.dfnGraph.dfn2graph": [[13, 1, 1, "", "add_fracture_source"], [13, 1, 1, "", "add_fracture_target"], [13, 1, 1, "", "create_graph"], [13, 1, 1, "", "dump_fractures"], [13, 1, 1, "", "dump_json_graph"], [13, 1, 1, "", "load_json_graph"], [13, 1, 1, "", "plot_graph"]], "pydfnworks.dfnGraph.graph_flow": [[13, 1, 1, "", "run_graph_flow"]], "pydfnworks.dfnGraph.graph_transport": [[13, 1, 1, "", "run_graph_transport"]], "pydfnworks.dfnGraph.pruning": [[13, 1, 1, "", "greedy_edge_disjoint"], [13, 1, 1, "", "k_shortest_paths_backbone"]], "pydfnworks.dfnTrans": [[14, 0, 0, "-", "transport"]], "pydfnworks.dfnTrans.transport": [[14, 1, 1, "", "check_dfn_trans_run_files"], [14, 1, 1, "", "copy_dfn_trans_files"], [14, 1, 1, "", "create_dfn_trans_links"], [14, 1, 1, "", "dfn_trans"], [14, 1, 1, "", "run_dfn_trans"]], "upscale": [[12, 0, 0, "-", "py"]]}, "objtypes": {"0": "py:module", "1": "py:function"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"]}, "titleterms": {"exampl": [0, 2, 4], "applic": 0, "carbon": 0, "dioxid": 0, "sequestr": 0, "shale": 0, "energi": 0, "extract": 0, "nuclear": 0, "wast": 0, "repositori": [0, 17], "dfnflow": [1, 11], "dfngen": [2, 9, 12], "c": 2, "gener": [2, 11, 12, 13], "code": 2, "domain": 2, "paramet": [2, 12], "domains": 2, "domainsizeincreas": 2, "numoflay": 2, "layer": 2, "numofregion": 2, "region": 2, "ignoreboundaryfac": 2, "boundaryfac": 2, "network": 2, "stopcondit": 2, "npoli": 2, "famprob": 2, "orientationopt": 2, "angleopt": 2, "h": 2, "disablefram": 2, "printrejectreason": 2, "rejectsperfractur": 2, "radiilistincreas": 2, "visualizationmod": 2, "seed": 2, "keeponlylargestclust": 2, "keepisolatedfractur": 2, "tripleintersect": 2, "removefractureslessthan": 2, "insertuserrectanglesfirst": 2, "forcelargefractur": 2, "output": [2, 9], "outputallradii": 2, "outputacceptedradiiperfamili": 2, "outputfinalradiiperfamili": 2, "fractur": [2, 4, 12], "famili": [2, 12], "ellips": 2, "nfamel": 2, "elay": 2, "eregion": 2, "e_p32target": 2, "enumpoint": 2, "easpect": 2, "orient": 2, "ekappa": 2, "spheric": 2, "coordin": 2, "etheta": 2, "ephi": 2, "trend": 2, "plung": 2, "etrend": 2, "eplung": 2, "dip": 2, "strike": 2, "estrik": 2, "edip": 2, "In": 2, "plane": 2, "rotat": 2, "ebetadistribut": 2, "ebeta": 2, "radiu": 2, "distribut": [2, 4], "edistr": 2, "lognorm": 2, "elogmean": 2, "esd": 2, "elogmin": 2, "elogmax": 2, "truncat": [2, 4], "powerlaw": 2, "ealpha": 2, "emin": 2, "emax": 2, "exponenti": [2, 4], "eexpmean": 2, "eexpmin": 2, "eexpmax": 2, "constant": 2, "econst": 2, "rectangl": 2, "nfamrect": 2, "rlayer": 2, "rregion": 2, "r_p32target": 2, "raspect": 2, "rkappa": 2, "rtheta": 2, "rphi": 2, "rtrend": 2, "rplung": 2, "rstrike": 2, "rdip": 2, "rbetadistribut": 2, "rbeta": 2, "rdistr": 2, "rlogmean": 2, "rsd": 2, "rlogmin": 2, "rlogmax": 2, "ralpha": 2, "rmin": 2, "rmax": 2, "rexpmean": 2, "rexpmin": 2, "rexpmax": 2, "rconst": 2, "user": [2, 12], "defin": 2, "userellipsesonoff": 2, "userell_input_file_path": 2, "nuserel": 2, "number_of_vertic": 2, "radii": 2, "aspect_ratio": 2, "beta": 2, "translat": 2, "userorientationopt": 2, "normal": 2, "trend_plung": 2, "dip_strik": 2, "input": [2, 12], "userellbycoord": 2, "ellbycoord_input_file_path": 2, "nellips": 2, "nnode": 2, "By": 2, "userrectanglesonoff": 2, "userrect_input_file_path": 2, "nuserrect": 2, "userrecbycoord": 2, "rectbycoord_input_file_path": 2, "nrectangl": 2, "polygon": 2, "userpolygonbycoord": 2, "polygonbycoord_input_file_path": 2, "file": [2, 9, 12], "format": 2, "npolygon": 2, "sourc": 2, "document": [2, 3, 6, 7, 16], "doxygen": [2, 16], "dfntran": [3, 14], "4_user_defined_rect": 4, "4_user_defined_ell_uniform": 4, "exp": 4, "length": 4, "tpl": 4, "power": 4, "law": 4, "graph": [4, 13], "base": [4, 12, 13], "prune": 4, "dfnwork": [5, 6, 7, 8, 10, 15, 16, 17], "galleri": 5, "welcom": [6, 7, 8], "2": [6, 7, 8], "8": [6, 7, 8], "To": 8, "obtain": 8, "cite": 8, "version": 8, "v2": 8, "current": 8, "7": 8, "6": 8, "5": 8, "4": 8, "3": 8, "1": 8, "0": 8, "about": 8, "thi": 8, "manual": 8, "contact": 8, "contributor": 8, "lanl": 8, "extern": 8, "copyright": 8, "inform": [8, 12], "run": [9, 11, 12, 14, 16, 17], "lagrit": [9, 12, 17], "pflotran": [9, 11, 17], "public": 10, "pydfnwork": [11, 12, 13, 14, 15, 16, 17], "flow": [11, 13], "fehm": [11, 17], "process": [11, 12], "ad": 12, "from": [12, 16, 17], "print": 12, "analysi": 12, "dfn": 12, "addit": [12, 16], "modif": 12, "hydraul": 12, "properti": 12, "background": 12, "stress": 12, "field": 12, "mesh": 12, "primari": 12, "driver": 12, "helper": 12, "method": 12, "udfm": 12, "creat": 12, "an": 12, "upscal": 12, "map": 12, "author": 12, "dfm": 12, "conform": 12, "dfngraph": 13, "function": 13, "transport": [13, 14], "simul": 14, "well": 15, "packag": [15, 16], "python": [16, 17], "command": 16, "line": 16, "us": 16, "The": 16, "class": 16, "jobnam": 16, "ncpu": 16, "dfnflow_fil": 16, "dfngen_fil": 16, "dfntrans_fil": 16, "path": [16, 17], "prune_fil": 16, "flow_solv": 16, "cell_based_apertur": 16, "argument": 16, "modul": 16, "detail": 16, "set": 17, "up": 17, "docker": 17, "contain": 17, "nativ": 17, "build": 17, "github": 17, "clone": 17, "dnfwork": 17, "fix": 17, "test": 17, "directori": 17, "petsc": 17, "instal": 17, "requir": 17, "oper": 17, "system": 17, "cmake": 17, "paraview": 17}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"Example Applications": [[0, "example-applications"]], "Carbon dioxide sequestration": [[0, "carbon-dioxide-sequestration"]], "Shale energy extraction": [[0, "shale-energy-extraction"]], "Nuclear waste repository": [[0, "nuclear-waste-repository"]], "dfnFlow": [[1, "dfnflow"]], "dfnGen - C++ Generation Code": [[2, "dfngen-c-generation-code"]], "Domain Parameters": [[2, "domain-parameters"]], "domainSize": [[2, "domainsize"]], "domainSizeIncrease": [[2, "domainsizeincrease"]], "numOfLayers": [[2, "numoflayers"]], "layers": [[2, "layers"]], "numOfRegions": [[2, "numofregions"]], "regions": [[2, "regions"]], "ignoreBoundaryFaces": [[2, "ignoreboundaryfaces"]], "boundaryFaces": [[2, "boundaryfaces"]], "General Network Generation Parameters": [[2, "general-network-generation-parameters"]], "stopCondition": [[2, "stopcondition"]], "nPoly": [[2, "npoly"]], "famProb": [[2, "famprob"]], "orientationOption": [[2, "orientationoption"]], "angleOption": [[2, "angleoption"]], "h": [[2, "h"]], "disableFram": [[2, "disablefram"]], "printRejectReasons": [[2, "printrejectreasons"]], "rejectsPerFracture": [[2, "rejectsperfracture"]], "radiiListIncrease": [[2, "radiilistincrease"]], "visualizationMode": [[2, "visualizationmode"]], "seed": [[2, "seed"]], "keepOnlyLargestCluster": [[2, "keeponlylargestcluster"]], "keepIsolatedFractures": [[2, "keepisolatedfractures"]], "tripleIntersections": [[2, "tripleintersections"]], "removeFracturesLessThan": [[2, "removefractureslessthan"]], "insertUserRectanglesFirst": [[2, "insertuserrectanglesfirst"]], "forceLargeFractures": [[2, "forcelargefractures"]], "General Network Output Parameters": [[2, "general-network-output-parameters"]], "outputAllRadii": [[2, "outputallradii"]], "outputAcceptedRadiiPerFamily": [[2, "outputacceptedradiiperfamily"]], "outputFinalRadiiPerFamily": [[2, "outputfinalradiiperfamily"]], "Fracture Family Generation Parameters: Ellipse": [[2, "fracture-family-generation-parameters-ellipse"]], "Ellipse: General Parameters": [[2, "ellipse-general-parameters"]], "nFamEll": [[2, "nfamell"]], "eLayer": [[2, "elayer"]], "eRegion": [[2, "eregion"]], "e_p32Targets": [[2, "e-p32targets"]], "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, "rectangle-constant"]], "rconst": [[2, "rconst"]], "User Defined Fracture Generation Parameters": [[2, "user-defined-fracture-generation-parameters"]], "User Defined Ellipses": [[2, "user-defined-ellipses"]], "userEllipsesOnOff": [[2, "userellipsesonoff"]], "UserEll_Input_File_Path": [[2, "userell-input-file-path"]], "General user defined ellipses parameters": [[2, "general-user-defined-ellipses-parameters"]], "nUserEll": [[2, "nuserell"]], "Number_of_Vertices": [[2, "number-of-vertices"]], "Radii": [[2, "radii"]], "Aspect_Ratio": [[2, "aspect-ratio"]], "AngleOption (User Defined Fracture)": [[2, "angleoption-user-defined-fracture"]], "Beta": [[2, "beta"]], "Translation": [[2, "translation"]], "userOrientationOption": [[2, "userorientationoption"]], "Normal": [[2, "normal"]], "Trend_Plunge": [[2, "trend-plunge"]], "Dip_Strike": [[2, "dip-strike"]], "General Ellipse Input Example": [[2, "general-ellipse-input-example"]], "userEllByCoord": [[2, "userellbycoord"]], "EllByCoord_Input_File_Path": [[2, "ellbycoord-input-file-path"]], "User defined ellipses by coordinate parameters": [[2, "user-defined-ellipses-by-coordinate-parameters"]], "nEllipses": [[2, "nellipses"]], "nNodes": [[2, "nnodes"]], "Coordinates": [[2, "coordinates"]], "Ellipse By Coordinate Example": [[2, "ellipse-by-coordinate-example"]], "User Defined Rectangles": [[2, "user-defined-rectangles"]], "userRectanglesOnOff": [[2, "userrectanglesonoff"]], "UserRect_Input_File_Path": [[2, "userrect-input-file-path"]], "General user defined rectangles parameters": [[2, "general-user-defined-rectangles-parameters"]], "nUserRect": [[2, "nuserrect"]], "General Rectangle Input Example": [[2, "general-rectangle-input-example"]], "userRecByCoord": [[2, "userrecbycoord"]], "RectByCoord_Input_File_Path": [[2, "rectbycoord-input-file-path"]], "User defined rectangles by coordinate parameters": [[2, "user-defined-rectangles-by-coordinate-parameters"]], "nRectangles": [[2, "nrectangles"]], "Rectangle By Coordinate Example": [[2, "rectangle-by-coordinate-example"]], "Polygons": [[2, "polygons"]], "userPolygonByCoord": [[2, "userpolygonbycoord"]], "PolygonByCoord_Input_File_Path:": [[2, "polygonbycoord-input-file-path"]], "Polygon file format": [[2, "polygon-file-format"]], "nPolygons": [[2, "npolygons"]], "Source Code Documentation (Doxygen)": [[2, "source-code-documentation-doxygen"]], "dfnTrans": [[3, "dfntrans"]], "Documentation": [[3, "documentation"]], "Examples": [[4, "examples"]], "4_user_defined_rects": [[4, "user-defined-rects"]], "4_user_defined_ell_uniform": [[4, "user-defined-ell-uniform"]], "exp: Exponentially Distributed fracture lengths": [[4, "exp-exponentially-distributed-fracture-lengths"]], "TPL: Truncated Power-Law": [[4, "tpl-truncated-power-law"]], "Graph-based pruning": [[4, "graph-based-pruning"]], "dfnWorks Gallery": [[5, "dfnworks-gallery"]], "Welcome to dfnWorks 2.8 documentation!": [[6, "welcome-to-dfnworks-2-8-documentation"], [7, "welcome-to-dfnworks-2-8-documentation"]], "Welcome To dfnWorks": [[8, "welcome-to-dfnworks"]], "Obtaining dfnWorks": [[8, "obtaining-dfnworks"]], "Citing dfnWorks": [[8, "citing-dfnworks"]], "Versions": [[8, "versions"]], "v2.8 - Current": [[8, "v2-8-current"]], "v2.7": [[8, "v2-7"]], "v2.6": [[8, "v2-6"]], "v2.5": [[8, "v2-5"]], "v2.4": [[8, "v2-4"]], "v2.3": [[8, "v2-3"]], "v2.2": [[8, "v2-2"]], "v2.1": [[8, "v2-1"]], "v2.0": [[8, "v2-0"]], "About this manual": [[8, "about-this-manual"]], "Contact": [[8, "contact"]], "Contributors": [[8, "contributors"]], "LANL": [[8, "lanl"]], "External": [[8, "external"]], "Copyright Information": [[8, "copyright-information"]], "Run Files": [[9, "run-files"]], "dfnGen - output": [[9, "dfngen-output"]], "LaGrit - Output": [[9, "lagrit-output"]], "PFLOTRAN - output": [[9, "pflotran-output"]], "dfnWorks Publications": [[10, "dfnworks-publications"]], "pydfnworks: dfnFlow": [[11, "pydfnworks-dfnflow"]], "Running Flow : General": [[11, "module-pydfnworks.dfnFlow.flow"]], "Running Flow: PFLOTRAN": [[11, "module-pydfnworks.dfnFlow.pflotran"]], "Running Flow: FEHM": [[11, "module-pydfnworks.dfnFlow.fehm"]], "Processing Flow": [[11, "module-pydfnworks.dfnFlow.mass_balance"]], "pydfnworks: dfnGen": [[12, "pydfnworks-dfngen"]], "dfnGen": [[12, "dfngen"]], "Adding Fracture Families": [[12, "adding-fracture-families"]], "Adding User Fractures": [[12, "adding-user-fractures"]], "Adding User Fractures From a File": [[12, "adding-user-fractures-from-a-file"]], "Print Parameter Information": [[12, "print-parameter-information"]], "Processing Generator Input": [[12, "processing-generator-input"]], "Running the Generator": [[12, "module-pydfnworks.dfnGen.generation.generator"]], "Analysis of Generated DFN": [[12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"]], "Additional Information on the Modification of Hydraulic Properties of the DFN": [[12, "additional-information-on-the-modification-of-hydraulic-properties-of-the-dfn"]], "Modification of hydraulic properties of the DFN based on background stress field": [[12, "module-pydfnworks.dfnGen.generation.stress"]], "Meshing - LaGriT": [[12, "meshing-lagrit"]], "Primary DFN meshing driver": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"]], "Meshing helper methods": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"]], "UDFM": [[12, "udfm"]], "Creating an upscaled mesh of the DFN (UDFM)": [[12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "Map-DFN upscaling": [[12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"]], "Authors": [[12, "authors"]], "DFM": [[12, "dfm"]], "Creating a conforming DFM mesh DFN": [[12, "module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm"]], "pydfnworks: dfnGraph": [[13, "pydfnworks-dfngraph"]], "General Graph Functions": [[13, "module-pydfnworks.dfnGraph.dfn2graph"]], "Graph-Based Flow and Transport": [[13, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks: dfnTrans": [[14, "pydfnworks-dfntrans"]], "Running Transport Simulations": [[14, "module-pydfnworks.dfnTrans.transport"]], "pydfnworks: Well Package": [[15, "pydfnworks-well-package"]], "dfnWorks - Well Package": [[15, "module-pydfnworks.dfnGen.well_package.wells"]], "pydfnworks: the dfnWorks python package": [[16, "pydfnworks-the-dfnworks-python-package"]], "Running dfnWorks from the command line using pydfnWorks": [[16, "running-dfnworks-from-the-command-line-using-pydfnworks"]], "The DFNWORKS class": [[16, "the-dfnworks-class"]], "jobname": [[16, "jobname"]], "ncpu": [[16, "ncpu"]], "dfnFlow_file/dfnGen_file/dfnTrans_file": [[16, "dfnflow-file-dfngen-file-dfntrans-file"]], "path": [[16, "path"]], "prune_file": [[16, "prune-file"]], "flow_solver": [[16, "flow-solver"]], "cell_based_aperture": [[16, "cell-based-aperture"]], "additional arguments": [[16, "additional-arguments"]], "pydfnWorks : Modules": [[16, "pydfnworks-modules"]], "Detailed Doxygen Documentation": [[16, "detailed-doxygen-documentation"]], "Setting and Running up dfnWorks": [[17, "setting-and-running-up-dfnworks"]], "Docker": [[17, "docker"]], "Running the dfnWorks container": [[17, "running-the-dfnworks-container"]], "Native build from github repository": [[17, "native-build-from-github-repository"]], "Clone the dnfWorks repository": [[17, "clone-the-dnfworks-repository"]], "Fix paths in test directory": [[17, "fix-paths-in-test-directory"]], "Set the LagriT, PETSC, PFLOTRAN, Python, and FEHM paths": [[17, "set-the-lagrit-petsc-pflotran-python-and-fehm-paths"]], "Installing pydfnworks": [[17, "installing-pydfnworks"]], "Installation Requirements for Native Build": [[17, "installation-requirements-for-native-build"]], "Operating Systems": [[17, "operating-systems"]], "Python": [[17, "python"]], "LaGriT": [[17, "lagrit"]], "PFLOTRAN": [[17, "pflotran"]], "FEHM": [[17, "fehm"]], "CMake": [[17, "cmake"]], "Paraview": [[17, "paraview"]]}, "indexentries": {"correct_stor_file() (in module pydfnworks.dfnflow.fehm)": [[11, "pydfnworks.dfnFlow.fehm.correct_stor_file"]], "create_dfn_flow_links() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.create_dfn_flow_links"]], "dfn_flow() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.dfn_flow"]], "effective_perm() (in module pydfnworks.dfnflow.mass_balance)": [[11, "pydfnworks.dfnFlow.mass_balance.effective_perm"]], "fehm() (in module pydfnworks.dfnflow.fehm)": [[11, "pydfnworks.dfnFlow.fehm.fehm"]], "lagrit2pflotran() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.lagrit2pflotran"]], "module": [[11, "module-pydfnworks.dfnFlow.fehm"], [11, "module-pydfnworks.dfnFlow.flow"], [11, "module-pydfnworks.dfnFlow.mass_balance"], [11, "module-pydfnworks.dfnFlow.pflotran"], [12, "module-false_connections.py"], [12, "module-map2continuum.py"], [12, "module-mesh_dfm.py"], [12, "module-mesh_dfn.py"], [12, "module-mesh_dfn_helper.py"], [12, "module-pydfnworks.dfnGen.generation.generator"], [12, "module-pydfnworks.dfnGen.generation.input_checking"], [12, "module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"], [12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"], [12, "module-pydfnworks.dfnGen.generation.stress"], [12, "module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"], [12, "module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm"], [12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"], [12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"], [12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"], [12, "module-pydfnworks.dfnGen.meshing.udfm.false_connections"], [12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"], [12, "module-pydfnworks.dfnGen.meshing.udfm.upscale"], [12, "module-upscale.py"], [13, "module-graph_transport.py"], [13, "module-pydfnworks.dfnGraph.dfn2graph"], [13, "module-pydfnworks.dfnGraph.graph_flow"], [13, "module-pydfnworks.dfnGraph.graph_transport"], [13, "module-pydfnworks.dfnGraph.pruning"], [14, "module-pydfnworks.dfnTrans.transport"], [15, "module-pydfnworks.dfnGen.well_package.wells"]], "parse_pflotran_vtk_python() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.parse_pflotran_vtk_python"]], "pflotran() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.pflotran"]], "pflotran_cleanup() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.pflotran_cleanup"]], "pydfnworks.dfnflow.fehm": [[11, "module-pydfnworks.dfnFlow.fehm"]], "pydfnworks.dfnflow.flow": [[11, "module-pydfnworks.dfnFlow.flow"]], "pydfnworks.dfnflow.mass_balance": [[11, "module-pydfnworks.dfnFlow.mass_balance"]], "pydfnworks.dfnflow.pflotran": [[11, "module-pydfnworks.dfnFlow.pflotran"]], "set_flow_solver() (in module pydfnworks.dfnflow.flow)": [[11, "pydfnworks.dfnFlow.flow.set_flow_solver"]], "write_perms_and_correct_volumes_areas() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.write_perms_and_correct_volumes_areas"]], "zone2ex() (in module pydfnworks.dfnflow.pflotran)": [[11, "pydfnworks.dfnFlow.pflotran.zone2ex"]], "add_variable_to_mesh() (in module pydfnworks.dfngen.meshing.add_attribute_to_mesh)": [[12, "pydfnworks.dfnGen.meshing.add_attribute_to_mesh.add_variable_to_mesh"]], "check_false_connections() (in module pydfnworks.dfngen.meshing.udfm.false_connections)": [[12, "pydfnworks.dfnGen.meshing.udfm.false_connections.check_false_connections"]], "create_mesh_links() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.create_mesh_links"]], "create_network() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.create_network"]], "dfn_gen() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.dfn_gen"]], "false_connections.py": [[12, "module-false_connections.py"]], "grab_polygon_data() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.grab_polygon_data"]], "inp2gmv() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.inp2gmv"]], "inp2vtk_python() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.inp2vtk_python"]], "make_working_directory() (in module pydfnworks.dfngen.generation.generator)": [[12, "pydfnworks.dfnGen.generation.generator.make_working_directory"]], "map2continuum.py": [[12, "module-map2continuum.py"]], "map_to_continuum() (in module pydfnworks.dfngen.meshing.udfm.map2continuum)": [[12, "pydfnworks.dfnGen.meshing.udfm.map2continuum.map_to_continuum"]], "mapdfn_ecpm() (in module pydfnworks.dfngen.meshing.mapdfn_ecpm.mapdfn_ecpm)": [[12, "pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm.mapdfn_ecpm"]], "mesh_dfm() (in module pydfnworks.dfngen.meshing.dfm.mesh_dfm)": [[12, "pydfnworks.dfnGen.meshing.dfm.mesh_dfm.mesh_dfm"]], "mesh_dfm.py": [[12, "module-mesh_dfm.py"]], "mesh_dfn.py": [[12, "module-mesh_dfn.py"]], "mesh_dfn_helper.py": [[12, "module-mesh_dfn_helper.py"]], "mesh_network() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn.mesh_network"]], "output_report() (in module pydfnworks.dfngen.generation.output_report.gen_output)": [[12, "pydfnworks.dfnGen.generation.output_report.gen_output.output_report"]], "print_domain_parameters() (in module pydfnworks.dfngen.generation.input_checking)": [[12, "pydfnworks.dfnGen.generation.input_checking.print_domain_parameters"]], "print_family_information() (in module pydfnworks.dfngen.generation.input_checking)": [[12, "pydfnworks.dfnGen.generation.input_checking.print_family_information"]], "print_user_fracture_information() (in module pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions)": [[12, "pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions.print_user_fracture_information"]], "pydfnworks.dfngen.generation.generator": [[12, "module-pydfnworks.dfnGen.generation.generator"]], "pydfnworks.dfngen.generation.input_checking": [[12, "module-pydfnworks.dfnGen.generation.input_checking"]], "pydfnworks.dfngen.generation.input_checking.user_defined_fracture_functions": [[12, "module-pydfnworks.dfnGen.generation.input_checking.user_defined_fracture_functions"]], "pydfnworks.dfngen.generation.output_report.gen_output": [[12, "module-pydfnworks.dfnGen.generation.output_report.gen_output"]], "pydfnworks.dfngen.generation.stress": [[12, "module-pydfnworks.dfnGen.generation.stress"]], "pydfnworks.dfngen.meshing.add_attribute_to_mesh": [[12, "module-pydfnworks.dfnGen.meshing.add_attribute_to_mesh"]], "pydfnworks.dfngen.meshing.dfm.mesh_dfm": [[12, "module-pydfnworks.dfnGen.meshing.dfm.mesh_dfm"]], "pydfnworks.dfngen.meshing.mapdfn_ecpm.mapdfn_ecpm": [[12, "module-pydfnworks.dfnGen.meshing.mapdfn_ecpm.mapdfn_ecpm"]], "pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn"]], "pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper": [[12, "module-pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper"]], "pydfnworks.dfngen.meshing.udfm.false_connections": [[12, "module-pydfnworks.dfnGen.meshing.udfm.false_connections"]], "pydfnworks.dfngen.meshing.udfm.map2continuum": [[12, "module-pydfnworks.dfnGen.meshing.udfm.map2continuum"]], "pydfnworks.dfngen.meshing.udfm.upscale": [[12, "module-pydfnworks.dfnGen.meshing.udfm.upscale"]], "run_lagrit_script() (in module pydfnworks.dfngen.meshing.mesh_dfn.mesh_dfn_helper)": [[12, "pydfnworks.dfnGen.meshing.mesh_dfn.mesh_dfn_helper.run_lagrit_script"]], "stress_based_apertures() (in module pydfnworks.dfngen.generation.stress)": [[12, "pydfnworks.dfnGen.generation.stress.stress_based_apertures"]], "upscale() (in module pydfnworks.dfngen.meshing.udfm.upscale)": [[12, "pydfnworks.dfnGen.meshing.udfm.upscale.upscale"]], "upscale.py": [[12, "module-upscale.py"]], "add_fracture_source() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.add_fracture_source"]], "add_fracture_target() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.add_fracture_target"]], "create_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.create_graph"]], "dump_fractures() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.dump_fractures"]], "dump_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.dump_json_graph"]], "graph_transport.py": [[13, "module-graph_transport.py"]], "greedy_edge_disjoint() (in module pydfnworks.dfngraph.pruning)": [[13, "pydfnworks.dfnGraph.pruning.greedy_edge_disjoint"]], "k_shortest_paths_backbone() (in module pydfnworks.dfngraph.pruning)": [[13, "pydfnworks.dfnGraph.pruning.k_shortest_paths_backbone"]], "load_json_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.load_json_graph"]], "plot_graph() (in module pydfnworks.dfngraph.dfn2graph)": [[13, "pydfnworks.dfnGraph.dfn2graph.plot_graph"]], "pydfnworks.dfngraph.dfn2graph": [[13, "module-pydfnworks.dfnGraph.dfn2graph"]], "pydfnworks.dfngraph.graph_flow": [[13, "module-pydfnworks.dfnGraph.graph_flow"]], "pydfnworks.dfngraph.graph_transport": [[13, "module-pydfnworks.dfnGraph.graph_transport"]], "pydfnworks.dfngraph.pruning": [[13, "module-pydfnworks.dfnGraph.pruning"]], "run_graph_flow() (in module pydfnworks.dfngraph.graph_flow)": [[13, "pydfnworks.dfnGraph.graph_flow.run_graph_flow"]], "run_graph_transport() (in module pydfnworks.dfngraph.graph_transport)": [[13, "pydfnworks.dfnGraph.graph_transport.run_graph_transport"]], "check_dfn_trans_run_files() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.check_dfn_trans_run_files"]], "copy_dfn_trans_files() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.copy_dfn_trans_files"]], "create_dfn_trans_links() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.create_dfn_trans_links"]], "dfn_trans() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.dfn_trans"]], "pydfnworks.dfntrans.transport": [[14, "module-pydfnworks.dfnTrans.transport"]], "run_dfn_trans() (in module pydfnworks.dfntrans.transport)": [[14, "pydfnworks.dfnTrans.transport.run_dfn_trans"]], "cleanup_wells() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.cleanup_wells"]], "combine_well_boundary_zones() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.combine_well_boundary_zones"]], "find_well_intersection_points() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.find_well_intersection_points"]], "pydfnworks.dfngen.well_package.wells": [[15, "module-pydfnworks.dfnGen.well_package.wells"]], "tag_well_in_mesh() (in module pydfnworks.dfngen.well_package.wells)": [[15, "pydfnworks.dfnGen.well_package.wells.tag_well_in_mesh"]]}}) \ No newline at end of file diff --git a/pydfnworks/pydfnworks.egg-info/SOURCES.txt b/pydfnworks/pydfnworks.egg-info/SOURCES.txt index 21e48dec..617886d2 100644 --- a/pydfnworks/pydfnworks.egg-info/SOURCES.txt +++ b/pydfnworks/pydfnworks.egg-info/SOURCES.txt @@ -84,6 +84,7 @@ pydfnworks/dfnGraph/__init__.py pydfnworks/dfnGraph/bipartite_graph.py pydfnworks/dfnGraph/dfn2graph.py pydfnworks/dfnGraph/fracture_graph.py +pydfnworks/dfnGraph/graphConversions.py pydfnworks/dfnGraph/graph_attributes.py pydfnworks/dfnGraph/graph_conversions.py pydfnworks/dfnGraph/graph_flow.py @@ -92,6 +93,7 @@ pydfnworks/dfnGraph/graph_transport.py pydfnworks/dfnGraph/intersection_graph.py pydfnworks/dfnGraph/particle_class.py pydfnworks/dfnGraph/particle_io.py +pydfnworks/dfnGraph/projection.py pydfnworks/dfnGraph/pruning.py pydfnworks/dfnTrans/__init__.py pydfnworks/dfnTrans/transport.py diff --git a/pydfnworks/pydfnworks/dfnGen/meshing/dfm/mesh_dfm.py b/pydfnworks/pydfnworks/dfnGen/meshing/dfm/mesh_dfm.py index 12bb8df2..5cb3d7a6 100644 --- a/pydfnworks/pydfnworks/dfnGen/meshing/dfm/mesh_dfm.py +++ b/pydfnworks/pydfnworks/dfnGen/meshing/dfm/mesh_dfm.py @@ -758,11 +758,10 @@ def mesh_dfm(self, dirname = "dfm_mesh", allowed_percentage = 1, cleanup = True) Parameters ------------------ - self : DFN Object dirname : string name of working directory. Default : dfm_mesh - percentage : float - + allowed_percentage : float + Percentage of the mesh allowed to be missing and still continue cleanup : bool Clean up working directory. If true dep files are moved into subdirectories @@ -772,7 +771,7 @@ def mesh_dfm(self, dirname = "dfm_mesh", allowed_percentage = 1, cleanup = True) Notes -------------- - None + The final mesh is output in exodus format. This requires that LaGriT is built against exodus. """