Using Basak.lmptab in LAMMPS

LAMMPS input files are provided for use with the table file:

• UO2.lmpstruct: structure file for single UO₂ cell, that can be read with read_data when atom_style full is used.
• equilibrate.lmpin: input file containing LAMMPS instructions. Performs 10ps of 300K NPT equilibration, creating a 4×4×4 super-cell.

Copy these files into the same directory as Basak.lmptab, the simulation can then be run using:

lammps -in equilibrate.lmpin -log equilibrate.lmpout -echo both

The section of equilibrate.lmpin which defines the potential model and makes use of the table file is as follows:

variable O equal 1
variable U equal 2

set type $O charge -1.2
set type $U charge 2.4

kspace_style pppm 1.0e-6

pair_style hybrid/overlay coul/long ${SR_CUTOFF} table linear 6500 pppm
pair_coeff * * coul/long
pair_coeff $O $O table Basak.lmptab O-O
pair_coeff $O $U table Basak.lmptab O-U
pair_coeff $U $U table Basak.lmptab U-U

Notes:

1. As LAMMPS uses ID numbers to define species the variable commands associate:
   • index 1 with variable $O
   • index 2 with $U to aid readability.

3. The set type SPECIES_ID charge lines define the charges of oxygen and uranium.

3. Uses the hybrid/overlay pair_style to combine the coul/long and table styles.

   pair_style hybrid/overlay coul/long ${SR_CUTOFF} table linear 6500 pppm
   

   • The coul/long style is used to calculate electrostatic interactions using the pppm kspace_style defined previously.

   • table linear 6500 pppm:

     • linear interpolation of table values should be used
     • all 6500 rows of the table are employed
     • corrections appropriate to the pppm kspace_style will be applied.

4. Means that electrostatic interactions should be calculated between all pairs of ions.

   pair_coeff * * coul/long
   

5. Each pair_coeff reads an interaction from the Basak.lmptab file.

   pair_coeff $O $O table Basak.lmptab O-O
   pair_coeff $O $U table Basak.lmptab O-U
   pair_coeff $U $U table Basak.lmptab U-U
   

   • The general form is:

     • pair_coeff SPECIES_A SPECIES_A table TABLE_FILENAME TABLE_KEYWORD
     • Here the SPECIES_* use the $O and $U variables defined earlier.
     • TABLE_KEYWORD - the table file contains multiple blocks, each defining a single interaction.
     • The TABLE_KEYWORD is the title of the block. The labels are of the form LABEL_A-LABEL_B albeit with the species sorted into alphabetical order.