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Obtaining Codes

We use two molecular simulation programs in our group. The first is an in-house, CHARMM-based code developed mainly by Dr. Knotts and his colleague Dr. Nitin Rathore. It is called "thecode." The other is LAMMPS. LAMMPS is developed by Sandia National Labs. One of the main researchers over LAMMPS is BYU alumnus Paul Crozier who obtained his PhD under Dr. Rowley.

Obtaining LAMMPS

Download the newest stable release of LAMMPS using one of two methods.
- Navigate here and click on "Download" under the table entry "LAMMPS Stable Release".
- Run wget https://download.lammps.org/tars/lammps-stable.tar.gz from a shell (command line)
Copy the .tar file to the supercomputer (if needed)
- For details on transferring files, see Basic Bash Commands page that highlights the scp command.
Extract the files using tar -xzvf lammps-stable.tar.gz
Copy the Knotts Group additions for Go-like surface model (a folder called USER-KNOTTS) to lammps-DayMonthYear/src/ directory.
- USER-KNOTTS is available at ~/groups/fslg_ksg/
- USER-KNOTTS is also available on https://github.com/thomasknotts/USER-KNOTTS.
  - git clone https://github.com/thomasknotts/USER-KNOTTS.git

Obtaining thecode

The best way to obtain thecode is through CVS. CVS is version control system that keeps track of the changes made to the program, allows multiple users to make changes to the code, and ensures each user has an up-to-date version.

The repository for CVS in our group is housed on watt. To load "thecode" onto your watt account:
$ cvs -d /export/home/cvsroot checkout thecode

If logged into another computer (like the supercomputer), you can obtain thecode by:
$ cvs -d username-on-watt@watt.et.byu.edu:/export/home/cvsroot checkout thecode

To determine if your checked out version of thecode is different than the repository execute within "thecode" folder:
$ cvs diff

To update a checked out version of thecode, move into thecode folder and execute:
$ cvs update