A LAMMPS fix for parameterizing Tersoff potentials. Optional Coulombic and Lennard-Jones contributions are available for the range outside the Tersoff cutoffs. This fix works for the December 7th, 2015 version of LAMMPs which can be downloaded here.

1. If you don't have an SSH key, generate one like this:

   ssh-keygen -t rsa -b 4096 -C "your_email@example.com"  #Creates an ssh key, using your GitHub e-mail as a label
   

   When prompted to "Enter a file in which to save the key," press Enter If asked to Overwrite, enter 'y' At the prompt, type a secure passphrase Retype your secure passphrase

   • Add the SSH key to your GitHub account

     gedit ~/.ssh/id_rsa.pub

   In the top right corner of any GitHub page in your browser, click on your profile photo, the click 'Settings' In the user settings sidebar, click 'SSH keys' Click 'New SSH key' In the "Title" field, add a descriptive label for the new key Copy and Paste the contents from the 'id_rsa.pub' file into the "Key" field Click 'Add SSH key'

   • Load your keys into your SSH agent

      eval "$(ssh-agent -s)"
      
      ssh-add
     

   Enter passphrase

   • Test your SSH connection

     ssh -T git@github.com

   You should see the message "Hi 'username'! You've successfully authenicated, but GitHub does not provide shell access."

2. From the lammps source folder, download the repository from github:

   git init
   
   git remote add origin git@github.com:jminuse/lammps-min-params.git
   
   git fetch
   
   git checkout -t origin/master
   

   "git checkout -t origin/master" may give the error "Untracked working tree file 'FILE_NAME_HERE' would be overwritten by merge."

   In this case, the simplest option is to delete the offending file, then repeat

   rm FILE_NAME_HERE
   
   git checkout -t origin/master 
   

   until "Untracked working tree file" is replaced by a message like "Branch master set up to track remote branch master from origin."

3. Make the new version of lammps by running

   make serial
   

4. You're done! Now each time you sit down to work, just update your local copy via:

   git pull
   

   And when you save your changes:

   git add -u
   
   git commit -m "Comment about the changes"
   
   git push
   

   This will make your changes appear to others when they use "git pull" later.

1. Build example structures for yoru system in Avogadro (including any OPLS bonds)

2. Optimize with orca (e.g. Opt B98-D3 def2-TZVP)

3. Analyze at higher level (e.g. SP RI-B2PLYP D3BJ def2-TZVP)

4. Put molecule file system.cml in orca output directory

5. Run python run_min_params.py RUN_NAME. The output parameters will start to appear in lammps/RUN_NAME_best.tersoff.

6. When error is reasonable (e.g. below 10%) cp lammps/RUN_NAME_best.tersoff lammps/md_input.tersoff. This allows you to run an annealing job with these parameters using python run_normal.py RUN_NAME_2

7. See what went wrong and adjust parameter guess (lammps/input.tersoff), bounds, or data set. Frames from view lammps/RUN_NAME_2 can be used as example structures.