3. 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.

• 3.1. linux
  • 3.1.1. awk - manipulate text
    • 3.1.1.1. Separator
    • 3.1.1.2. awk can do math.
  • 3.1.2. cat - print input to standard output
  • 3.1.3. cd - change directories
  • 3.1.4. chsh - change shell
  • 3.1.5. cp - copy files or folders
    • 3.1.5.1. Copy Folders with cp -r
  • 3.1.6. echo - Print Argument
  • 3.1.7. grep - search for pattern in file or folders
  • 3.1.8. head - read from top of file to standard output
  • 3.1.9. help - read documentation
  • 3.1.10. less - view files
  • 3.1.11. ls - list information about files/folders
  • 3.1.12. lsblk - list filesystem
  • 3.1.13. man - documentation for various functions
  • 3.1.14. mkdir - make new directories.
  • 3.1.15. module - load software on slurm
  • 3.1.16. mount - mount filesystem
  • 3.1.17. mv - move files/folders from one place to another.
    • 3.1.17.1. Move/Rename Files and Folders
  • 3.1.18. pwd - print working directory
  • 3.1.19. rm - delete files
    • 3.1.19.1. Deleting Multiple Files
    • 3.1.19.2. Deleting Folders
  • 3.1.20. rsync - sync files/folders
  • 3.1.21. sbatch - Submit job to Slurm
  • 3.1.22. scancel - Cancel Slurm Jobs
  • 3.1.23. scp - copy files/folders over ssh
  • 3.1.24. sed - tranform/replace text!
  • 3.1.25. seq - sequence of numbers
  • 3.1.26. setfacl - change file/folder permissions
  • 3.1.27. sinfo - View information about Slurm nodes and partitions.
    • 3.1.27.1. Find idle partitions
  • 3.1.28. sort - sorts lines
  • 3.1.29. ssh - secure shell protocol
  • 3.1.30. ssh-keygen - Make SSH key
  • 3.1.31. tail - read from bottom of file
  • 3.1.32. tar - compress/uncompress files
  • 3.1.33. touch - Make File
  • 3.1.34. trap - signalled execution
  • 3.1.35. Reset GNOME Terminal Hotkeys
  • 3.1.36. Manging Multiple Compiler Versions
• 3.2. apptainer
  • 3.2.1. apptainer build
  • 3.2.2. apptainer run
  • 3.2.3. apptainer shell
  • 3.2.4. apptainer instance start
    • 3.2.4.1. Instances
• 3.3. Apptainer
  • 3.3.1. Build
  • 3.3.2. Run
• 3.4. ChimeraX
• 3.5. ffmpeg: Movies
  • 3.5.1. Convert ppm to png
• 3.6. GNU Parallel
  • 3.6.1. Running Parallel on HPCs
  • 3.6.2. Parallel Umbrella Sampling Windows for MD Simulations