spark-brc/apexmf_wf

Optimization workflows for AMRS models

apexmf

apexmf is a set of python modules for APEX-MODFLOW model (Bailey et al., 2021) parameter estimation and uncertainty analysis with the open-source suite PEST (Doherty 2010a and 2010b, and Doherty and other, 2010).

Uncertainty Analysis for AMRS model

Get data and jupyter notebooks

You essentially have 2 options:

Easy way

• Download the data zip file
• Unzip apexmf_tutorials-main.zip to a prefered location.

Hard way (Dev mode)

• You will need to install Git if you don't have it installed already. Downloads are available at [the link](https://git-scm.com/download). On windows, be sure to select the option that installs command-line tools

• For Git, you will need to set up SSH keys to work with Github. To do so:

  • Go to GitHub.com and set up an account
  • On Windows, open Git Bash (on Mac/Linux, just open a terminal) and set up ssh keys if you haven't already. To do this, simply type ssh-keygen in git bash/terminal and accept all defaults (important note - when prompted for an optional passphrase, just hit return.)

• Follow the instructions to set up the SSH keys with your GitHub account.

• Clone the materials from GitHub.

  • Open a git bash shell from the start menu (or, on a Mac/Linux, open a terminal)
  • Navigate to the folder you made to put the course materials
  • Clone the materials by executing the following in the git bash or terminal window:

git clone https://github.com/spark-brc/apexmf_tutorials.git

Installation

To execute jupyter notebook, we need the Miniconda environment.

1. Miniconda Python:

• If you don't already have conda installed, please download Miniconda for your operating system from https://conda.io/en/latest/miniconda.html (choose the latest version for your operating system, 64-bit). You should not need elevated rights to install this.
• Run the installer and select "only my user" when prompted. This will allow you to work with your python installation directly.

2. Set Environment and install libraries:

• After installation, go to the START menu and select "Miniconda Prompt" to open a DOS box.
• Type the following command:

conda install -c conda-forge mamba

• Using the cd command in the Miniconda DOS box, navigate to the location where you have environment.yml the file and type:

mamba env create -f environment.yml

and hit ENTER.

After your virtual environment setup is complete, change the environment to apexmf_tut:

conda activate apexmf_tut

• Launch jupyter notebook

jupyter notebook

A browser window with a Jupyter notebook instance should open. Yay!

Brief overview of the API

from apexmf import apexmf_pst_utils

>>> wd = "User-APEX-MODFLOW working directory"
>>> APEX_wd = "User-APEX working directory"
>>> apexmf_pst_utils.init_setup(wd, APEX_wd)

'apex.parm.xlsx' file copied ... passed
'beopest64.exe' file copied ... passed
'i64pest.exe' file copied ... passed
'i64pwtadj1.exe' file copied ... passed
'forward_run.py' file copied ... passed