Quantum Chemistry: CHEM 210 A 2021

Python Setup

• Download Anaconda if you haven't already https://www.anaconda.com/distribution/

  • Make sure conda is installed and in your $PATH by looking at this command's output.

    conda --version

    Can check if $PATH environment variable is pointing to the spot you installed Anaconda via this command:

    echo $PATH

• Checkout this site for installing Psi4 with Anaconda http://www.psicode.org/psi4manual/1.1/conda.html

  • Before doing anything else, update conda!

    conda update --all

  • Create virtual environment for Psi4

    $ conda create -n Psi4env python=3.7 psi4 psi4-rt -c psi4

  • Now can use this environment with the command

      (base) $ conda activate Psi4env

    and deactivate it with

       (Psi4env) $ conda deactivate

  • To add other packages (e.g. matplotlib) within your new virtual environment issue this command

       (Psi4env) $ conda install matplotlib

    The bare bones Psi4 environment may not have some packages we will use so this may be required if Spyder cannot find the module.

• If you use an IDE like Spyder, then you need to install Spyder within your virtual environment.

  • So activate your environment like above and then install Spyder

      (Psi4env) $ conda install spyder

  • Now still within your virtual environment invoke spyder.

       (Psi4env) $ spyder

    Now you will be working inside of the Spyder IDE and have everything that's in the Psi4 environment!

• Another useful IDE and voted number 1 for python is Pycharm. This IDE has a larger learning curve and that usually means it will benefit you in the long run if you adopt this as your main editor. I know most professionals in industry swear by it and I am pretty sure the professional version is free for students!

  • https://www.jetbrains.com/pycharm/promo/anaconda/
  • Here is an example setting up a virtual environment in Pycharm https://medium.com/infinity-aka-aseem/how-to-setup-pycharm-with-an-anaconda-virtual-environment-already-created-fb927bacbe61

Unix Setup

• You MUST install Xcode! It will give you all the developer programs you will need in the terminal. https://apps.apple.com/us/app/xcode/id497799835?mt=12
• Package managers are extremely helpful and for Mac OS we will use MacPorts. https://www.macports.org/install.php.
• Installing Molden via MacPorts

  $ sudo port install molden

Windows Setup (Requires Windows 10)

• First, setup Windows Subsystem Linux (WSL) to get the Linux bash shell by following this site: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/
• Second, setup an X-server so we can use Molden. For Windows there is a program called Xming; follow this site for setup steps: https://www.howtogeek.com/261575/how-to-run-graphical-linux-desktop-applications-from-windows-10s-bash-shell/
  • Run this command to set your enviroment to always launch the X-server correctly:

  $ echo "export DISPLAY=:0" >> ~/.bashrc

Now we have a Windows developer setup!

• Now lets download Molden and install: http://cheminf.cmbi.ru.nl/molden/molden.html
  1. Go to your new linux bash prompt.
  2. Find the downloaded Molden .tar file
  3. Untar the file

  $ tar -xvf molden_file_name.tar

4. Go inside molden folder

  $ cd molden_file_name

5. Type the command

  $ make molden

6. Now type the command

  $ make install

If you get errors in this process, please let me know.

• To get Psi4 working, we found a channel for Psi4 on Windows https://anaconda.org/raimis/psi4. So just need to issue this command in your Psi4 environment:

 (Psi4env) $ conda install -c raimis psi4

Psi4

• http://www.psicode.org/psi4manual/1.2/index.html

Slack

• Say what's up! https://join.slack.com/t/chem210a-2021/shared_invite/zt-khicv6bp-7CEgrwKfG2~M~W5dMOShiQ

Useful Unix/Linux Terminal Commands

• I found this website that mentions some of the most used commands so have a look! https://learntocodewith.me/command-line/unix-command-cheat-sheet/