Mineral Physics Tutorial for the CIDER 2018 Meeting, Santa Barbara, CA

by Dan Shim (Arizona State University)

Purpose of the tutorial

In the mineral physics tutorial at CIDER 2018, we will demonstrate typical data analysis for equation of state (EOS). We then discuss ways to estimate and propagate uncertainties for better use of EOS data.

Here I explain the necessary computer setups for the tutorial.

General guide

The tutorial materials will be provided in a VirtualMachine file. The installation instruction here is for installing the tutorial materials in the VirtualMachine file. Therefore, if you obtain the VirtualMachine file, you do not need to install the materials separately following this instruction.

However, you may use this instruction to run the tutorial materials directly in your host OS system rather than through Virtual Machine. Advantages for this approach include: the code will be executed much faster and you can continue enjoying python + jupyter setup for your data analysis in the future.

Note that the instruction here is NOT tested for Windows OS. There should be some slight but important differences. Please contact Dan Shim for questions.

Pre-requisite

Anaconda for python 3.6 version

You need to have the Anaconda distribution of python installed in your VirtualMachine or your local hard drive. If not installed already, please download the version above and install.

Note that Graphical installer is easier if you have Mac OSX (and windows I believe). For Linux, I found that the command line option works better.

Update anaconda

Once you finish the Anaconda installation, you may update the Anaconda meta package.

1. Run terminal.app or console.

2. Run anaconda base or root environment (Note that you do not need to type the commands below. You may just copy and paste in the terminal and then press the return key. This applies to all other commands below).

   source activate base

3. Run the following.

   conda update --all

   Update will take a few minutes.

Pytheos

The tutorial materials require the pytheos module. You can install it simply by:

pip install pytheos

Pytheos Jupyter Notebook examples

Tutorial materials are in jupyter notebook. In the instruction below, we will install the jupyter notebook files.

1. Under your home folder, make a new directory and move to the directory

   cd ~
   mkdir EOS_tutorial1
   cd EOS_tutorial1

2. Install pytheos tutorial (don't forget the period at the end of the command below).

   git clone https://github.com/SHDShim/pytheos.git .

Data analysis examples

We also use the data analysis presented in Ye et al. (2017) JGR in the tutorial. They are provided in jupyter notebook files.

1. Go back to your home folder, make a separate folder, and move to the folder.

   cd ~
   mkdir EOS_tutorial2
   cd EOS_tutorial2

2. Install the jupyter notebook files (don't forget the period at the end of the command below).

   git clone https://github.com/SHDShim/cider2018_tutorial.git .

Now you are all set!

Reference

Mineral physics tutorial for CIDER2018 @ GitHub

Pytheos @ Github

Pytheos documentation @ Github

Y. Ye, V. Prakapenka, Y. Meng, and S.‐H. Shim (2017) Intercomparison of the gold, platinum, and MgO pressure scales up to 140 GPa and 2500 K. Journal of Geophysical Research