Purpose

The guide for installing LAMMPS relies on a basic knowledge of Linux and it's command line interface. You won't need any advanced knowledge to complete an install, but it is nice to know a few basic commands.

You can press up arrow to scroll through a list of previously entered commands.

Change Directory

cd

This changes directory, much like in windows. There are a few shortcuts that can be nice to know. We always start a linux session in the home directory, to get back here any time use

cd ~/

This can be followed by a known file path, for example

cd ~/lammps/

This command, and indeed most, will autocorrect on tab. This makes traversing directories much quicker.

you can traverse up one director by entering

cd ..

much like in Windows ./ represents current directory and ../ is the directory above the current.

Print Working Directory

pwd

This simply outputs the current working directory.

List

ls

This will list the current directory's contents. The colours mean different file / folder types. White is a file, blue is a directory, and red is a tar.gz archive for example.

ls -l

This will show more details about a file including its read/write permissions, group and owner

Modify this with

ls -l -h

To see human readable file sizes

ls -l -h ~/lammps/
or
ls -lh ~/lammps/

Will list the contents of the /home/<username>/lammps directory regardless of current directory.

View / edit file contents

cat filename

This can be useful just to see a text file or config file, usually if you want to edit it you will need to use a text editor. Ubuntu ships with Nano. 

Be aware that large files could take a very long time to cat and it is an operation that cannot be interrupted. Use ls -lh to see file sizes before using cat on a file if you suspect it may be large. 

You can also use the less command, to get a paginated output. 

less filename

this will allow you to use the arrows and page buttons to scroll the file. 

For a full text editor run:

nano /filename

This will likely ask for sudo permissions to create files or edit them, depending on the directory. See the section on sudo for more.

You do not need to be in a directory to act on it, for example, if I know there is a file in my home folder I want to look at or edit I can enter the full file path as the argument even though my current directory is something else

pwd
/home/daniel/Lammps/fftw-3.3.8
sudo nano ~/folder/filename.txt/

This will still open the file for editing and allow you to save it even though the working directory is elsewhere. This works for almost any command that by default operates in your current directory.

Sudo

Sudo basically means "do as admin" this will request the sudo pass, which would usually be the password you set up at the beginning. In most cases apps will need to be installed with sudo.

sudo apt install neofetch

if you run a command and get permission denied you can run

sudo !!

to run the last command entered as sudo.

Sudo usually won't ask for a password every time, there is a short cooldown on requests after which the pass will be requested again.

Manual

This command is very useful for discovering options and possible flags for commands. It displays the manual page for a given command. This will explain all possible inputs to a given command.

man ls

This will show the manual page for the given command. A useful variation if you are just unsure what a command is meant to do is 

man -f ls

This will list the man pages that match the command entered along with the command's description. To get more info on how to effectively use the manual, type 

man man