Schema for ASE input¶
The schema to configure the ASE input file to perform atomistic simulations.
The sections of the schema are:
-
Define the atomic structure.
structure(dict): Define the atomic structure.
-
Define the calculator with following keys.
gpaw_calc(dict): Define the GPAW calculator.dftd3_calc(dict): Define the DFTD3 calculator for Van der Waals correctionase_calc(dict): Define a custom ASE calculator.
-
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 run CLI script
structure: ### ANCHOR: Define atomic structure
type: dict
required: True
schema:
from_extxyz: # the path to the EXTXYZ file for input structure
type: string
required: True
pbc: # set periodic bounday condition. This will overwrite the PBC in the EXTXYZ file. eg. [1, 1, 1]
type: [list, boolean]
calc: ### SECTION Parameters of calculators
type: dict
required: True
schema:
gpaw: ### ANCHOR: GPAW calculator. Accept all GPAW parameters: https://gpaw.readthedocs.io/documentation/basic.html
type: dict
allow_unknown: True
schema:
mode: # calculation mode. Default is "fd".
type: dict
schema:
name: # name of the mode. Choices: "fd", "lcao", "pw".
type: string
ecut: # energy cutoff in eV for plane wave mode. Default is 500 eV
type: float
xc: # exchange-correlation functional
type: string
kpts: # if not set `kpts`, then only Gamma-point is used
type: dict
convergence: # convergence criteria
type: dict
occupations: # occupation method. Default is "fermi-dirac"
type: dict
txt: # output file name. Default is "gpaw_out.txt"
type: string
symmetry: # use symmetry.
type: string
parallel: # parallelization
type: dict
dftd3: ### ANCHOR: DFT-D3 calculator for Van der Waals correction
type: dict
schema:
damping: # use DFT-D3 damping. Default is "d3zero" (zero-damping). Choices: "d3bj","d3zero","d3bjm","d3zerom","d3op".
type: string
### ANCHOR: Define ASE's calculator by two ways: using 'pyfile' or 'pyscript'.
py_file: # python file that defines ASE's calculator. Python script must return the variable `calc`.
type: string
py_script: # list[str] of python-code to directly define ASE's calculator. Python script must return the variable `calc`. Example:
type: list # py_script:
# - "from sevenn.calculator import SevenNetCalculator"
# - "sevenn_args = {'file_type: 'checkpoint'}"
# - "calc = SevenNetCalculator('sevenn_model.pth', **sevenn_args)"
### !SECTION
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
md: ### ANCHOR: Parameters to run AIMD/MD simulation
## Supported: NVE, NVT, NPT
## NVT with thermostat: 'Langevin', 'Nose_Hoover', 'Nose_Hoover_chain'
## NPT with: - 'Parrinello_Rahman' barostat + 'Nose_Hoover' thermostat
# - 'Iso_Nose_Hoover_chain' barostat and thermostat
type: dict
schema:
ensemble: # ensemble name. Choices: NVE, NVT, NPT. Default is NVE
type: string
dt: # timestep in fs. Default is 1.0 fs
type: float
temperature: # temperature in K. Default is 300 K
type: float
stress: # external stress in GPa. Default is None if not set. Accept: float, 6-vector, or 3x3 matrix.
type: [float, list]
equil_steps: # number of equilibration steps before running production. Default is 0.
type: integer
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
thermostat: # thermostat parameters.
type: dict
schema:
name: # thermostat name. Default is 'Nose_Hoover_chain'. Choices: 'Langevin', 'Nose_Hoover', 'Nose_Hoover_chain'
type: string
allowed: ['Langevin', 'Nose_Hoover', 'Nose_Hoover_chain']
tdamp: # damping timesteps for Nose_Hoover thermostat. Default is 50.
type: integer
tchain: # number of Nose_Hoover chain for Nose_Hoover_chain thermostat. Default is 3.
type: integer
friction: # friction coefficient for Langevin thermostat. Default is 0.002 fs^-1
type: float
barostat: # barostat parameters.
type: dict
schema:
name: # barostat name. Default is 'Parrinello_Rahman'. Choices: 'Parrinello_Rahman', 'Iso_Nose_Hoover_chain'
type: string
allowed: ['Parrinello_Rahman', 'Iso_Nose_Hoover_chain', 'Aniso_Nose_Hoover_chain']
pfactor: # pressure factor for 'Parrinello_Rahman' barostat. Default is 2e6 GPa.
type: float
pdamp: # damping timesteps for 'Iso_Nose_Hoover_chain' barostat. Default is 1000.
type: integer
pchain: # number of Nose_Hoover chain for 'Iso_Nose_Hoover_chain' barostat. Default is 3.
type: integer
mask: # dimensions to relax computational box. Set to (1,1,1) to allow fully flexible box. Set to (1,1,0) to disallow elongations along the z-axis, etc. If not set, then only relax the periodic dimensions.
type: [list, boolean] # None or 3-tuple
Example configuration:¶
structure: # atomic structure information
from_extxyz: MoS2_triangular.extxyz # The EXTXYZ file for input structure
pbc: [1, 1, 1] # set this will overwrite the PBC in the EXTXYZ file. eg. [1, 1, 1]
calc:
gpaw: # accept GPAW parameters
mode:
name: 'pw' # use PlaneWave method energy cutoff in eV
ecut: 500
xc: "PBE" # exchange-correlation functional
kpts: {"density": 10, "gamma": False, 'even': True} # if not set `kpts`, then only Gamma-point is used
dftd3: # DFT-D3 method for Van der Waals correction
damping: "d3zero" # use DFT-D3 damping. Default is "d3zero" (zero-damping). Choices: "d3bj","d3zero","d3bjm","d3zerom","d3op".
ase: # define ASE's calculator by two ways: pyfile or pyscript. Script must define variable `calc`
pyfile: ase_calculator.py # python file that defines ASE's calculator
# pyscript: # list[str], directly define ASE's calculator in form of python code.
# - "from sevenn.calculator import SevenNetCalculator"
# - "sevenn_args = {'file_type': 'checkpoint'}"
# - "calc = SevenNetCalculator('sevenn_model.pth', **sevenn_args)"
optimize: # run DFT to optimize the structure
fmax: 0.05 # force convergence criteria. Default is 0.05 eV/Ang
relax_dim: [1,1,1,1,1,1] # 1x6 array, 1 for relax, 0 for fixed. Default is; pbc + [1,1,1]
max_steps: 10000 # maximum number of steps for optimization. Default is 10000
md: # run AIMD/MD simulation
### Supported: NVE, NVT, NPT
### NVT with thermostat: Langevin, Nose_Hoover, Nose_Hoover_chain
### NPT with:
# - Parrinello_Rahman barostat + Nose_Hoover thermostat
# - Iso_Nose_Hoover_chain barostat and thermostat
ensemble: 'NPT' # ensemble type. Choices: NVE, NVT, NPT. Default is NVE
dt: 1.0 # time step in fs. Default is 1.0 fs
temperature: 300 # temperature in K. Default is 300 K
stress: 0 # external stress in GPa. Default is None if not set. Accept float, 6-vector, or 3x3 matrix.
num_frames: 5 # number of frames to be collected. Then total MD nsteps = collect_frames * traj_freq
traj_freq: 3 # dump the frames every `traj_freq` steps
equil_steps: 0 # number of equilibration steps before production run. Default is 0 steps
thermostat: # thermostat type. Default is Nose_Hoover_chain. Choices: Langevin, Nose_Hoover, Nose_Hoover_chain
name: 'Nose_Hoover_chain'
tdamp: 100 # damping timesteps for Nose_Hoover thermostat. Default is 50.
# tchain: 3 # number of Nose_Hoover chain for Nose_Hoover_chain thermostat. Default is 3.
friction: 0.002 # friction coefficient for Langevin thermostat. Default is 0.002 fs^-1
barostat: # barostat type. Default is Parrinello_Rahman. Choices: Parrinello_Rahman, Iso_Nose_Hoover_chain
name: 'Iso_Nose_Hoover_chain'
pfactor: 2000000 # pressure for Parrinello_Rahman barostat. Default is 2e6 GPa.
pdamp: 1000 # damping timesteps for Parrinello_Rahman barostat. Default is 1000.
# pchain: 3 # number of Nose_Hoover chain for Iso_Nose_Hoover_chain barostat. Default is 3.