Schema for LAMMPS input¤
The schema to configure the LAMMPS input file to perform atomistic simulations.
The sections of the schema are:
-
Define the atomic structure.
structure(dict): Define the atomic structure.
-
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/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
extra_settings: # list of custom lines to be added in the setting section. Default is None.
type: list
### custom keys, only for some specific workflows
auto_atom_names: # auto assign atoms in `pair_coeff` lines. Default is False.
type: boolean
file_potentials: # list of potential files (relative to run_dir). E.g., ["SiC.tersoff"]
type: list
optimize: ###ANCHOR Parameters to run optimization the structure
type: dict
allow_unknown: False
schema:
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 box 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 # allơ extra parameters that are not defined in the schema.
schema:
output_script: # path to the output script. Default is 'run.lammps'
type: string
Example config 1:¤
structure:
pair_style: ["e3gnn"]
pair_coeff: ['* * ../copy_model/model_02/deployed_serial.pt Mo S']
read_data: conf.lmpdata
pbc: [1, 1, 1]
md:
dt: 0.001
thermostat: nose_hoover_chain
barostat: nose_hoover_chain
tdamp: 100
pdamp: 1000
equil_steps: 20000
traj_freq: 5
num_frames: 20
mask: [1, 1, 1]
deform_limit: 0.9
temp: 1
press: 0
ensemble: NPT
extra:
output_script: iter_0013/01_md/md_00000_id0_0_t1_s0.0/cli_lammps.lmp