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.

• 1. linux
  • 1.1. awk - manipulate text
    • 1.1.1. Separator
    • 1.1.2. awk can do math.
  • 1.2. cat - print input to standard output
  • 1.3. cd - change directories
  • 1.4. chsh - change shell
  • 1.5. cp - copy files or folders
  • 1.6. echo - Print Argument
  • 1.7. grep - search for pattern in file or folders
  • 1.8. head - read from top of file to standard output
  • 1.9. help - read documentation
  • 1.10. less - view files
  • 1.11. ls - list information about files/folders
  • 1.12. lsblk - list filesystem
  • 1.13. man - documentation for various functions
  • 1.14. mkdir - make new directories.
  • 1.15. module - load software on slurm
  • 1.16. mount - mount filesystem
  • 1.17. mv - move files/folders from one place to another.
  • 1.18. pwd - print working directory
  • 1.19. rm - delete files
  • 1.20. rsync - sync files/folders
  • 1.21. sbatch - Submit job to Slurm
  • 1.22. scancel - Cancel Slurm Jobs
  • 1.23. scp - copy files/folders over ssh
  • 1.24. sed - tranform/replace text!
  • 1.25. seq - sequence of numbers
  • 1.26. setfacl - change file/folder permissions
  • 1.27. sinfo - View information about Slurm nodes and partitions.
    • 1.27.1. Find idle partitions
  • 1.28. sort - sorts lines
  • 1.29. ssh - secure shell protocol
  • 1.30. ssh-keygen - Make SSH key
  • 1.31. tail - read from bottom of file
  • 1.32. tar - compress/uncompress files
  • 1.33. touch - Make File
  • 1.34. trap - signalled execution
  • 1.35. Reset GNOME Terminal Hotkeys
  • 1.36. Manging Multiple Compiler Versions
• apptainer
  • 1. apptainer build
  • 2. apptainer run
  • 3. apptainer shell
  • 4. apptainer instance start
    • 4.1. Instances
• Apptainer
  • Build
  • Run
• 2. ChimeraX
• 3. ffmpeg: Movies
  • 3.1. Convert ppm to png
• 4. GNU Parallel
  • 4.1. Running Parallel on HPCs
  • 4.2. Parallel Umbrella Sampling Windows for MD Simulations