Running LAMMPS with lammps_helper

lammps_helper provides two things to help run LAMMPS simulations from python. One to help create LAMMPS input files and one to run them. I suggest you use an IPython environment such as Jupyter Lab.

Creating LAMMPS input files:

At the beginning of your Jupyter Lab notebook, use this code:

import lammps_helper as lh

ip = get_ipython()
ip.register_magics(lh.lammps_magics)

Then you can write LAMMPS files in your notebook and export them rather than writing them separately. Using the %%writetemplate cell magic, any python variables in your LAMMPS code will be replaced by their values during export. For example:

temperature = 300
output_base_name = f'my_lammps_output_{temperature}K'
simulation_steps = 20000
list_element_names = 'Pb I N C H'

%%writetemplate in.my_lammps_input_file

# This is a LAMMPS input file

units      real
dimension  3
boundary   p p p
atom_style full

pair_style      lj/cut 12.500
bond_style harmonic
angle_style harmonic
dihedral_style charmm

read_data data.my_lammps_data_file

thermo_style custom step temp etotal spcpu cpuremain

# equillibrate at temperature
fix fix_npt_equilibrate all npt temp {temperature} {temperature} 100 iso 1.0 1.0 500
dump dump_trajectory_equilibrate all dcd 100 {output_base_name}_equilibration.dcd
dump_modify dump_trajectory_equilibrate unwrap yes
run {simulation_steps}

# dump the system to check geometry
write_dump all xyz {output_base_name}_after_equilibrate.xyz modify element {list_element_names}

unfix fix_npt_equilibrate
undump dump_trajectory_equilibrate

# write restart file after equilibration
write_restart {output_base_name}_after_equilibrate.restart

Will create a file named in.my_lammps_input_file that will run a simulation at 300 K for 20000 timesteps and the data files created by LAMMPS will share a common naming scheme that includes the temperature.

Running LAMMPS

To run your input file in LAMMPS, do this

lh.run_lammps('in.my_lammps_input_file', f'log_{output_base_name}_equilibrate.lammps')

This simply issues the lmp_serial command. You may add variables here as well. See run_lammps() for more info. You will get output like this

Running calculation...
Writing to log_my_lammps_output_300K_equilibrate.lammps.
Calculation started at 08-06-20 16:10:45
Calculation complete at 08-06-20 16:10:45 in 0:00:00.076904.