clean-up

Author: MuellerSeb

README.md

@@ -3,33 +3,26 @@
 
 # Overview
 
-This project aims to use realizations of heterogeneous hydraulic conductivity with a binary inclusion structures for numerical subsurface flow and transport simulations. 
-Code is available to (i) generate and (ii) visualize random conductivity structures of binary inclusions. Furthermore, routines are provided (iii) to perform flow and transport simulations making use of the FEM-solver OpenGeoSys and (iv) to post-process results. 
+This project aims to use realizations of heterogeneous hydraulic conductivity with a binary inclusion structures for numerical subsurface flow and transport simulations.
+Code is available to (i) generate and (ii) visualize random conductivity structures of binary inclusions. Furthermore, routines are provided (iii) to perform flow and transport simulations making use of the FEM-solver OpenGeoSys and (iv) to post-process results.
 
 ## Structure
 
-The project is organized as follows
-    • README.md - description of the project 
-    • data/ - folder for data used in the project 
-    • results/ 
-    • src/ - folder containing the Python scripts of the project:	
-
-Please try to organize your example in the given Structure
-- `README.md` - description of the project 
-- `data/` - folder for data used in the project 
-- `results/` - folder with simulation results and plots 
-- `src/` - folder containing the Python scripts of the project:	
-  + 01_plot_binary_inclusions.py
-  + 02_run_sim.py
-  + 03_run_ensemble.py
-  + binary_inclusions.py
-  + sim_processing.py
+The project is organized as follows:
+
+- `README.md` - description of the project
+- `results/` - folder with simulation results and plots
+- `src/` - folder containing the Python scripts of the project:
+  + `01_plot_binary_inclusions.py` - generate and visualize inclusion structures
+  + `02_run_sim.py` - run OGS 5 simulation on inclusion structures according to MADE setting
+  + `03_run_ensemble.py` - run OGS 5 ensemble of transport simulations
+  + `binary_inclusions.py` - package containing inclusing structure classes
+  + `sim_processing.py` - package containing post-processing routines
 
 ## Python environment
 
 To make the example reproducible, we provide the following files:
 - `requirements.txt` - requirements for [pip](https://pip.pypa.io/en/stable/user_guide/#requirements-files) to install all needed packages
-- `spec-file.txt` - specification file to create the original [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments)
 
 ## Contact
 

requirements.txt

@@ -1,6 +1,3 @@
-numpy 
-matplotlib
+ogs5py==1.1.1
 scipy
-copy
-gstools==1.2.1
-ogs5py
+matplotlib

spec-file.txt

@@ -1,10 +1,9 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 Script to create and visualize random binary inclusion structures:
     - simple inclusion structure
     - block inclusion structure
-Fields are by default in 2D for visualization. 
+Fields are by default in 2D for visualization.
 
 Structures in 3D and different block arrangement can be created by modifying
 setting parameters, particular dim and/or axis
@@ -23,10 +22,10 @@
 ### Simple binary inclusion structure ###
 #########################################
 
-### initialize simple binary inclusion structure with specified settings 
-### as instance of the class Simple_Binary_Inclusions                    
+### initialize simple binary inclusion structure with specified settings
+### as instance of the class Simple_Binary_Inclusions
 BI = bi.Simple_Binary_Inclusions(
-    dim=2,          # dimesionality of structure    
+    dim=2,          # dimesionality of structure
     k_bulk=1e-5,    # bulk conductivity value
     k_incl=1e-3,    # conductivity value of inclusions
     nx=8,           # number of units in x-direction
@@ -54,12 +53,12 @@
 ### Two block binary inclusion structure ###
 ############################################
 
-### initialize block binary inclusion structure with specified settings 
+### initialize block binary inclusion structure with specified settings
 ### as instance of the class Block_Binary_Inclusions
 BIB = bi.Block_Binary_Inclusions(
-    dim=2,                  # dimesionality of structure    
+    dim=2,                  # dimesionality of structure
     axis=0,                 # direction of multiple blocks (0=x, 1=z, 2=y)
-    k_bulk=[1e-5, 1e-3],    # bulk-conductivity value in each block 
+    k_bulk=[1e-5, 1e-3],    # bulk-conductivity value in each block
     k_incl=[1e-3, 1e-5],    # conductivity values of inclusions in each block
     nn=[4, 18],             # number of units within each block (now x-dir)
     ll=[10, 10],            # unit lengths within blocks (now x-dir)

src/01_plot_binary_inclusions.py

@@ -1,19 +1,18 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 Subsurface flow and tranport simulation in a random binary inclusion structure
 with the FEM solver of the groundwater flow equation and advection-dispersion-
 equation OpenGeoSys.
 
-This script allows to perform a 2D simulation according to the flow and transport 
-situation of the MADE-1 tracer tests (Columbus, Mississippi) in a 2D setting 
-with a binary inclusion structure of hydraulic conductivity. 
+This script allows to perform a 2D simulation according to the flow and transport
+situation of the MADE-1 tracer tests (Columbus, Mississippi) in a 2D setting
+with a binary inclusion structure of hydraulic conductivity.
 
-Simulation are performed with the FEM solver OpenGeoSys (OGS5) for subsurface 
-flow and transport controlled via the API ogs5py: Initialization of the project, 
-writing files, simulation run and reading of simulation results. Setting-addapted 
+Simulation are performed with the FEM solver OpenGeoSys (OGS5) for subsurface
+flow and transport controlled via the API ogs5py: Initialization of the project,
+writing files, simulation run and reading of simulation results. Setting-addapted
 conductivity fields are generated with the script binary_inclusions.
- 
+
 @author: A. Zech
 Licence MIT, A.Zech, 2020
 """
@@ -115,21 +114,21 @@
 sim.gli.add_polyline(points=[2, 3], name="top")
 sim.gli.add_polyline(points=[1, 2], name="right")
 sim.gli.add_polyline(
-    points=[[0, domain["z_0"] + 5.2, 0], [0, domain["z_0"] + 5.8, 0]], 
+    points=[[0, domain["z_0"] + 5.2, 0], [0, domain["z_0"] + 5.8, 0]],
     name="source"
 )
 sim.gli.swap_axis("y", "z")
 
 ### -----------------------  properties------------------------------------- #
 sim.mfp.add_block(  # FLUID_PROPERTIES
-    FLUID_TYPE="LIQUID", 
-    PCS_TYPE="HEAD", 
-    DENSITY=[1, 1000.0], 
+    FLUID_TYPE="LIQUID",
+    PCS_TYPE="HEAD",
+    DENSITY=[1, 1000.0],
     VISCOSITY=[1, 0.001]
 )
 sim.mcp.add_block(
-        NAME="CONCENTRATION1", 
-        MOBILE=1, 
+        NAME="CONCENTRATION1",
+        MOBILE=1,
         DIFFUSION=[1, 1.0e-08]
         )
 sim.msp.add_block(DENSITY=[1, 2000])
@@ -142,14 +141,13 @@
     STORAGE="1 {}".format(storage),
     MASS_DISPERSION=[1, dispersivity_long, dispersivity_trans],
 )
-# sim.mmp.update_block(PERMEABILITY_TENSOR=['ISOTROPIC', '1e-6']) # for homogeneous K-distribution
 
 ### --------------------heterogeneous K: binary structure ------------------ #
 
 sim.mpd.add(name="conductivity")
 sim.mpd.add_block(
-    MSH_TYPE="GROUNDWATER_FLOW", 
-    MMP_TYPE="PERMEABILITY", 
+    MSH_TYPE="GROUNDWATER_FLOW",
+    MMP_TYPE="PERMEABILITY",
     DIS_TYPE="ELEMENT"
 )
 
@@ -269,7 +267,7 @@
 print("Write Tranport Simulation files to directory: {}".format(sim.task_root))
 sim.write_input()
 
-sim.msh.export_mesh(# export binary conductivity structure for vtk-visualization
+sim.msh.export_mesh(  # export binary conductivity structure for vtk-visualization
     filepath="{}/conductivity.vtu".format(sim.task_root),
     file_format="vtk",
     cell_data_by_id={"transmissivity": BI.kk_mesh},
@@ -284,7 +282,7 @@
 if success:
     print("Simulation finished successfully.")
     it_out = -1
-    
+
     out = sim.readvtk()
     times = out[""]["TIME"]
     points = out[""]["DATA"][1]["points"]
@@ -301,8 +299,7 @@
     ax = fig.add_subplot(1, 1, 1)
     colormap = plt.get_cmap("bone_r")
 
-#    ixmax = int(100 / domain["dx"])  # limit plot in x-direction to 80m
-    ixmax = int(200 / domain["dx"])  # limit plot in x-direction to 80m
+    ixmax = int(200 / domain["dx"])
     ax.contourf(
         xmesh[:, :ixmax],
         zmesh[:, :ixmax],

src/02_run_sim.py

@@ -1,8 +1,7 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Script to run an ensemble of subsurface flow and transport simulations with 
-OpenGeoSys (via the API ogs5py) on random binary inclusion structures of 
+Script to run an ensemble of subsurface flow and transport simulations with
+OpenGeoSys (via the API ogs5py) on random binary inclusion structures of
 hydraulic conductivity.
 
 @author: A. Zech
@@ -111,37 +110,37 @@
     sim.gli.add_polyline(points=[2, 3], name="top")
     sim.gli.add_polyline(points=[1, 2], name="right")
     sim.gli.add_polyline(
-        points=[[0, domain["z_0"] + 5.2, 0], [0, domain["z_0"] + 5.8, 0]], 
+        points=[[0, domain["z_0"] + 5.2, 0], [0, domain["z_0"] + 5.8, 0]],
         name="source"
     )
     sim.gli.swap_axis("y", "z")
 
     ### -----------------------  properties------------------------------------- #
     sim.mfp.add_block(  # FLUID_PROPERTIES
-        FLUID_TYPE="LIQUID", 
-        PCS_TYPE="HEAD", 
-        DENSITY=[1, 1000.0], 
+        FLUID_TYPE="LIQUID",
+        PCS_TYPE="HEAD",
+        DENSITY=[1, 1000.0],
         VISCOSITY=[1, 0.001]
     )
     sim.mcp.add_block(
-            NAME="CONCENTRATION1", 
-            MOBILE=1, 
+            NAME="CONCENTRATION1",
+            MOBILE=1,
             DIFFUSION=[1, 1.0e-08]
     )
     sim.msp.add_block(DENSITY=[1, 2000])
 
     ### --------------------heterogeneous K: binary structure ------------------ #
     BI.structure(seed=20201012 + sim_id)
     BI.structure2mesh(
-            sim.msh.centroids_flat, 
-            x0=domain["x_0"], 
+            sim.msh.centroids_flat,
+            x0=domain["x_0"],
             z0=domain["z_0"]
     )
 
     sim.mpd.add(name="conductivity")
     sim.mpd.add_block(
-        MSH_TYPE="GROUNDWATER_FLOW", 
-        MMP_TYPE="PERMEABILITY", 
+        MSH_TYPE="GROUNDWATER_FLOW",
+        MMP_TYPE="PERMEABILITY",
         DIS_TYPE="ELEMENT"
     )
     sim.mpd.update_block(DATA=zip(range(len(BI.kk_mesh)), BI.kk_mesh))