For all examples:

It is highly recommended to run this in a virtual environment. (Though it is not completely necessary.)

You can do so after you have installed anaconda:

conda create -n autotutorial python=3.10

conda activate autotutorial

After an environment is chosen (base or the one above), you must set some tutorial paths and variables.

export TUTORIAL_PATH=/path/to/automation

• linux:

export PYTHONPATH=$PYTHONPATH:$TUTORIAL_PATH/tools

• max/ios:

export PYTHONPATH="${PYTHONPATH}:$TUTORIAL_PATH/tools"

For VASP examples:

install required packages:

pip install ase pip install pymatgen

You will need to set your pymatgen vasp pseudopotential directory. You may do so by makeing a file in your home's config folder. Check first to make sure you have a config folder:

ls ~/.config

If nothing shows up, then run

mkdir ~/.config

Once this folder is made, you may open up a pmgrc.yaml file there:

vi ~/.config/.pmgrc.yaml

enter this into the first line, replacing /path/to/ with your own path to our automation tutorial folder. Do NOT enter the variable for the tutorial path here.

PMG_VASP_PSP_DIR: /path/to/automation/POT_PAW_PBE_52

IMPORTANT NOTE: you will have to ask james for this folder because he cannot post it on github! Shoot him an email in advance if at all possible to request.

for QE examples

Install QE v. 7.0 or later. See james for help if stuck! You only need to do these steps if you have QE installed and/or want to run QE DFT calculations.

First, add quantum espresso executables to your path

• linux

export PATH=$PATH:/path/to/qe-7.1/bin

• mac/ios

export PATH="${PATH}:/path/to/qe-7.1/bin"

Second, set the variable: $ESPRESSO_PSEUDO

• linux

export ESPRESSO_PSEUDO=$TUTORIAL_PATH/qe_pseudos

• mac/ios

export ESPRESSO_PSEUDO="$TUTORIAL_PATH/qe_pseudos"

For FitSNAP examples

! IF FitSNAP is not already installed, get an installation This requires the use of conda for these examples.

Step 0: Install anaconda if you have not already.

Step 1: install dependencies (lammps first)

conda install lammps

pip install numpy scipy scikit-learn virtualenv psutil pandas tabulate mpi4py Cython

Step 2: download FitSNAP somewhere convenient

git clone https://github.com/FitSNAP/FitSNAP.git

Step 3: Set the required environmental variables

FITSNAP_DIR=\path\to\FitSNAP

export PYTHONPATH=$FITSNAP_DIR:$LAMMPS_DIR/python:$PYTHONPATH