Input file
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
main
block consists of the major options that the user has to
provided. A sample block is shown below.
main:
temperature: [1000, 1400]
pressure: [0]
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 areBCC
,FCC
,HCP
,DIA
,SC
andLQD
.nsims
: The number of independent calculations to be carried out for finding the error in the estimated free energy.
md
block
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 simulationspair_style
: Pair style used in LAMMPS. Supported pair styles arepace
,eam
and its variants,sw
andsnap
.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.
queue
block
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 arelocal
,slurm
orsge
.cores
: Number of cores to be used for the md runs.jobname
: Name of the job. Ignored forlocal
.walltime
: Walltime for the job. Ignored forlocal
.queuename
: Name of the submission queue. Ignored forlocal
.memory
: Total memory requested per core. Ignored forlocal
.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.