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Schema for LAMMPS input

The schema to configure the LAMMPS input file to perform atomistic simulations.

The sections of the schema are:

  1. Define the atomic structure.

    • structure (dict): Define the atomic structure.

  2. Define the simulation

    • md (dict): Define parameters for the molecular dynamics simulation.
    • optimize (dict): Define parameters for the optimization.

Schema:

### Schema for YAML configuration to generate LAMMPS input script
### Similar to [ASE's schema](https://thangckt.github.io/alff_doc/schema/config_ase/), except the key `calc` is removed.

structure:                ### ANCHOR: Define atomic structure
  type: dict
  required: True
  schema:
    read_data:            # the path to the *.lammps_data file as initial structure
      type: string
    read_restart:         # the path to the *.lammps_restart file as initial structure
      type: string
    pbc:                  # set periodic bounday condition. Default [1, 1, 1]
      type: list
    units:                # units for LAMMPS. Choices: 'metal', 'real', 'lj'. Default is 'metal'
      type: string
    atom_style:           # atom style for LAMMPS. Choices: 'atomic', 'charge', 'molecular',... Default is 'atomic'
      type: string
    dimension:            # dimension of the simulation. Default is 3
      type: integer
    pair_style:           # pair style for LAMMPS. Default is ['eam/alloy']
      type: list
    pair_coeff:           # pair coefficients for LAMMPS. Default is ['* * Cu.eam.alloy  Cu']
      type: list


optimize:                 ### ANCHOR: Parameters to run optimization the structure
  type: dict
  schema:
    fmax:                 # force convergence criteria. Default is 0.05 eV/Ang
      type: float
    mask:                 # 1x6 array of booleans: 1 for relax, 0 for fixed; indicating which of the six independent components of the strain are relaxed. Default is: pbc + [1,1,1]
      type: list
    max_steps:            # maximum number of steps for optimization. Default is 10000
      type: integer

    min_style:            # minimization style supported by LAMMPS. Choices: 'cg', 'sd', 'fire',... Default is 'cg'
      type: string
    etol:                 # energy convergence criteria. Default is 1.0e-9 eV
      type: float
    ftol:                 # force convergence criteria. Default is 1.0e-9 eV/Ang
      type: float
    maxiter:              # maximum number of iterations for minimization. Default is 100000
      type: integer
    maxeval:              # maximum number of evaluations for minimization. Default is 100000
      type: integer
    dmax:                 # maximum displacement for each step. Default is 0.01 Ang
      type: float
    press:                # control stress. Default is [None, None, None]
      type: [list, float, boolean]
    mask:                 # 1x3 array of booleans: 1 for relax, 0 for fixed; indicating which of the three independent components of the stress are relaxed. Default is [1,1,1]
      type: list
    couple:               # couple the stress and strain. Choices: 'none', 'xyz', 'xy', 'yz', 'xz'. Default is 'none'
      type: string


md:                       ### ANCHOR: Parameters to run AIMD/MD simulation. Supported: NVE, NVT, NPT
                          ## NVT with thermostat: 'langevin', 'nose_hoover_chain'
                          ## NPT with: - 'nose_hoover_chain' barostat + 'langevin' thermostat
                          #            - 'nose_hoover_chain' barostat + 'nose_hoover_chain' thermostat
  type: dict
  schema:
    ensemble:             # ensemble name. Choices: NVE, NVT, NPT. Default is NVE
      type: string
    dt:                   # timestep in fs. Default is 0.001 ps
      type: float
    traj_freq:            # dump frames every `traj_freq` steps. Default is 1.
      type: integer
    num_frames:           # number of frames to be collected. Then total MD nsteps = (num_frames * traj_freq)
      type: integer
    equil_steps:          # number of equilibration steps before running production. Default is 0.
      type: integer

    plumed_file:          # path to the plumed file. Default is None.
      type: string
    thermo_freq:          # frequency to print thermodynamic properties. Default is 5000 steps.
      type: integer
    first_minimize:       # whether to perform a first minimization before running MD. Default is False.
      type: boolean

    ### temperature control
    temp:                 # temperature in K. Default is 300 K
      type: float
    tdamp:                # damping timesteps for thermostat. Default is 100.
      type: integer
    thermostat:           # thermostat. Choices: 'langevin', 'nose_hoover_chain'. Default is 'nose_hoover_chain'.
      type: string
      allowed: ['langevin', 'nose_hoover_chain']

    ### pressure control
    press:                # external stress in GPa. Accept: float, 3-vector. Default is None.
      type: [list, float, boolean]
    mask:                 # periodic dimensions to relax. Set to (1,1,1) to allow fully flexible box. Set to (1,1,0) to disallow elongations along the z-axis, etc. Default is [1,1,1]
      type: list
    couple:               # couple the stress and strain. Choices: 'none', 'xyz', 'xy', 'yz', 'xz'. Default is 'none'
      type: string
    pdamp:                # damping timesteps for barostat. Default is 1000.
      type: integer
    barostat:             # barostat. Choices: 'nose_hoover_chain'. Default is 'nose_hoover_chain'
      type: string
      allowed: ['nose_hoover_chain']
    deform_limit:         # Maximum **fractional change** allowed for any box dimension. The simulation stops if $abs(L - L0) / L0 > deform_limit$ in any of x, y, or z dim. Default is None.
      type: [float]

extra:                    ### ANCHOR: Extra parameters
  type: dict
  allow_unknown: True
  schema:
    output_script:        # path to the output script. Default is 'run.lammps'
      type: string