pydfnworks: the dfnWorks python package
The pydfnworks package allows the user to run dfnWorks from the command line and call dfnWorks within other python scripts. Because pydfnworks is a package, users can call individual methods from the package.
pydfnworks must be installed by the user prior to running dfnworks (pydfnWorks install)
Running dfnWorks from the command line using pydfnWorks
The recommended way to run dfnWorks is using a python call on the command line, or running the script in your favorite IDE.
$ python driver.py
The script driver.py is the python control file that contains the workflow of the particular simulation. Below is a basic example taken from the 4_user_rects_example example:
from pydfnworks import *
import os
src_path = os.getcwd()
jobname = src_path + "/output"
dfnFlow_file = src_path+ '/dfn_explicit.in'
dfnTrans_file = src_path + '/PTDFN_control.dat'
DFN = DFNWORKS(jobname,
dfnFlow_file=dfnFlow_file,
dfnTrans_file=dfnTrans_file,
ncpu=8)
DFN.params['domainSize']['value'] = [1.0, 1.0, 1.0]
DFN.params['h']['value'] = 0.050
DFN.add_user_fract(shape='rect',
radii=0.6,
translation=[-0.4, 0, 0],
normal_vector=[0, 0, 1],
permeability=1.0e-12)
DFN.add_user_fract(shape='rect',
radii=1.0,
aspect_ratio=.65,
translation=[0, 0, 0],
normal_vector=[1, 0, 0],
permeability=1.0e-12)
DFN.add_user_fract(shape='rect',
radii=.6,
translation=[0.4, 0, 0.2],
normal_vector=[0, 0, 1],
permeability=2.0e-12)
DFN.add_user_fract(shape='rect',
radii=.6,
translation=[0.4, 0, -0.2],
normal_vector=[0, 0, 1],
permeability=1.0e-12)
DFN.make_working_directory(delete=True)
DFN.check_input()
DFN.print_domain_parameters()
DFN.create_network()
DFN.mesh_network()
DFN.dfn_flow()
DFN.dfn_trans()
The DFNWORKS class
Within the python script, a DFN (discrete fracture network) object is created to control the model workflow. Data and model functions are stored on this object, allowing the user to both access information about the DFN while debugging, as well as call functions for modelling everything from network generation to transport modelling. Arguments for creating the DFN object are listed below. Additional arguments and functions required to create the DFN are discussed in other sections of this manual.
Default Arguments:
from pydfnworks import *
DFN = DFNWORKS(jobname = None, #required
ncpu = 4,
dfnGen_file = None, #automatically generated
dfnFlow_file = None, #required for DFN.dfn_flow()
dfnTrans_file = None, #required for DFN.dfn_trans()
path = None,
prune_file = None,
flow_solver = 'PFLOTRAN',
inp_file = 'full_mesh.inp',
uge_file = 'full_mesh.uge',
mat_file = 'materialid.dat',
stor_file = None,
vtk_file = None,
num_nodes = None,
mesh_type = 'dfn',
cell_based_aperture = False)
jobname
Description: (Mandatory) Path of the simulation directory. Must be a valid path. The path is stored in DFN.jobname of the DFN object
Type: string
Example:
import os
src_path = os.getcwd()
jobname = src_path + "/output"
ncpu
Description: Number of processors to be used in the simulation. Stored as DFN.ncpu.
Type: integer
Example:
ncpu = 8
dfnFlow_file/dfnGen_file/dfnTrans_file
Note
dfnGen_file is depreciated, file name is automatically specified
Description: (Mandatory) Path of the input file containing run files for dfnGen, dfnFlow (PFLOTRAN/FEHM/AMANZI), and dfnTrans. This file is parsed and the paths contained within are stored as DFN.dfnGen_file, DFN.dfnFlow_file, and DFN.dfnTrans_file. The local path for the files (string after the final / are stored as DFN.local_dfnGen_file, DFN.local_dfnFlow_file, and DFN.local_dfnTrans_file.
Type: string
Example:
dfnGen_file = 'gen_4_user_rectangles.dat'
dfnFlow_file = 'dfn_explicit.in'
dfnTrans_file = 'PTDFN_control.dat'
path
Description: Path to parent directory. Useful for multiple runs using the same network with different meshing techniques, hydraulic properties, flow simulations, or pruned networks. Path is stored as DFN.path.
Type: string
Example:
path = '/dfnWorks/work/4_user_rects_example'
prune_file
Description: Path to ascii file of fractures to be retained (not removed) in the network after pruning. See the pruning example for a workflow demonstration.
Type: string
Example:
prune_file = '/dfnWorks/work/pruning_example/2_core.dat'
Note
To prune the network, include DFN.mesh_network(prune=True) in the python run file.
flow_solver
Description: Either ‘PFLOTRAN’ or ‘FEHM’
Example:
flow_solver = 'PFLOTRAN'
cell_based_aperture
Description: Toggle if the fracture apertures are cell based. If the option is included, then the workflow will assign cell-based apertures and permeabilities from the files aper_node.dat and perm_node.dat. These files consist of two columns, with a single line header value. The first column is the node number. The second column is the aperture/permeability value. See the See the in_fracture_var example for a workflow demonstration.
Type: Boolean
Example:
cell_based_aperture = True
additional arguments
Descriptions: additional arguments that have not been described here will likely not be changed by the user.
pydfnWorks : Modules
Information about the various pieces of pydfnworks is found in
pydfnGen - Network generation, meshing, and analysis
pydfnFlow - Flow simulations using PFLOTRAN and FEHM
pydfnTrans - Particle Tracking
pydfnGraph - Graph-based analysis and pipe-network simulations
Well-Package - Well simulations
Note
There are additional required arguments for network generation described in dfnGen