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. Default is 'metal'. Choices: 'metal', 'real', 'lj'
            type: string
        atom_style:         # atom style for LAMMPS. Default is 'atomic'. Choices: 'atomic', 'charge', 'molecular',...
            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_Mishin2001.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. Default is 'cg'. Choices: 'cg', 'sd', 'fire', ....
            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. Default is 'none'. Choices: 'none', 'xyz', 'xy', 'yz', 'xz'.
            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

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

        ### pressure control
        press:              # external stress in GPa. Default is None if not set. Accept: float, 3-vector.
            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. Default is 'none'. Choices: 'none', 'xyz', 'xy', 'yz', 'xz'.
            type: string
        pdamp:              # damping timesteps for barostat. Default is 1000.
            type: integer
        barostat:           # barostat. Default is 'nose_hoover_chain'. Choices: 'nose_hoover_chain'
            type: string
            allowed: ['nose_hoover_chain']

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