pytint uses a
yaml file for specifying the input options. In
this section, the various blocks of the input file is discussed. A
complete sample input file is also provided in the Examples section.
main block consists of the major options that the user has to
provided. A sample block is shown below.
main: temperature: [1000, 1400] pressure:  element: 'Cu' lattice: [FCC, LQD] nsims: 3
temperature: List of temperatures at which NEHI calculations have to be done. In case of regular use, one calculation will be started for each temperature. In case of
--mode rs, one NEHI calculation will be done for the first temperature. After that, reversible scaling calculation will be done to extend the free energy upto the last temperature specified.
pressure: Pressure for the calculation. Currently only zero pressure (Helmholtz free energy) is supported.
element: The chemical symbol of the element used.
lattice: The lattices for which the free energy calculations have to be done. Supported lattices are
nsims: The number of independent calculations to be carried out for finding the error in the estimated free energy.
md: timestep: 0.001 pair_style: pace pair_coeff: "* * Cu.ace Cu" mass: 63.546 tdamp: 0.1 pdamp: 0.1 nx: 5 ny: 5 nz: 5 te: 25000 ts: 50000
timestep: Timestep in ps for the md simulations
pair_style: Pair style used in LAMMPS. Supported pair styles are
eamand its variants,
pair_coeff: Pair coefficient command used in LAMMPS. The relative/full path of the input potential file is also specified here.
mass: Atomic mass of the element.
tdamp: Thermostat damping in units of time.
pdamp: Barostat damping in units of time.
nx: Number of units cells in the 001 direction.
ny: Number of units cells in the 010 direction.
nz: Number of units cells in the 100 direction.
te: Number of time steps for equilibration runs.
ts: Number of time steps for switching runs.
This block specifies the input parameters for submitting the job on a cluster
queue: scheduler: slurm cores: 40 jobname: cu walltime: "23:50:00" queuename: shorttime memory: 3GB modules: - anaconda/4 commands: - source .bashrc - conda activate py3 #any other extra options #options: # - "-j Y"
scheduler: The scheduler to be used for calculations. Supported options are
cores: Number of cores to be used for the md runs.
jobname: Name of the job. Ignored for
walltime: Walltime for the job. Ignored for
queuename: Name of the submission queue. Ignored for
memory: Total memory requested per core. Ignored for
modules: Name of module that need to be loaded.
commands: Extra commands that will be run in the beginning of the submission script. If a conda environment is used, the activate statements will be here.
options: Further special options for the submission script.