More Notes !!

Notes I wish I had showed me when I started

This collection was an attempt to consolidated my experiences in computational chemistry. Entering the field with no background in mathematics or computers, a lot was learned through trial and error. Despite these shortcomings, I am forever grateful to the exceptional guidance and continued support of Dr. Genwei Zhang, Dr. Zheng Pei, Dr. Xiaoliang Pan, and Dr. Yihan Shao.

I hope many of you will find this information useful in your future endeavors.

• linux
  • awk - manipulate text
    • Separator
    • awk can do math.
  • cat - print input to standard output
  • cd - change directories
  • chsh - change shell
  • cp - copy files or folders
  • echo - Print Argument
  • grep - search for pattern in file or folders
  • head - read from top of file to standard output
  • help - read documentation
  • less - view files
  • ls - list information about files/folders
  • lsblk - list filesystem
  • man - documentation for various functions
  • mkdir - make new directories.
  • module - load software on slurm
  • mount - mount filesystem
  • mv - move files/folders from one place to another.
  • pwd - print working directory
  • rm - delete files
  • rsync - sync files/folders
  • sbatch - Submit job to Slurm
  • scancel - Cancel Slurm Jobs
  • scp - copy files/folders over ssh
  • sed - tranform/replace text!
  • seq - sequence of numbers
  • setfacl - change file/folder permissions
  • sinfo - View information about Slurm nodes and partitions.
    • Find idle partitions
  • sort - sorts lines
  • ssh - secure shell protocol
  • ssh-keygen - Make SSH key
  • tail - read from bottom of file
  • tar - compress/uncompress files
  • touch - Make File
  • trap - signalled execution
  • Reset GNOME Terminal Hotkeys
  • Manging Multiple Compiler Versions
• apptainer
  • apptainer build
  • apptainer run
  • apptainer shell
  • apptainer instance start
    • Instances
• Apptainer
  • Build
  • Run
• ChimeraX
• ffmpeg: Movies
  • Convert ppm to png
• GNU Parallel
  • Running Parallel on HPCs
  • Parallel Umbrella Sampling Windows for MD Simulations