velph.toml file

velph.toml file#

The velph.toml file contains the settings required to perform electron-phonon interaction calculations using the phelel and VASP codes. Ideally, once created, it should remain unchanged throughout the duration of a calculation project for the reproducibility.

There are several ways to create a velph.toml file:

  • Using the default template (see velph init command)

  • Using a user-defined template (velph init --template-toml), as explained in velph init template

  • Copying and modifying an existing velph.toml file

Regardless of how it is created, the velph.toml file is used in conjunction with the velph command to generate VASP input files and operate other tools, based on the information it contains. This page provides guidance on how to interpret and effectively use the contents of velph.toml.

[phelel]#

This section contains information specific to the phelel code and must be included to execute the velph phelel subcommand.

[phelel]
version = "0.6.5"
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true
fft_mesh = [30, 30, 30]

[vasp]#

There are sub-sections for respective specific calculations:

  • [vasp.phelel]

  • [vasp.relax]

  • [vasp.nac]

  • [vasp.el_bands]

  • [vasp.ph_bands]

  • [vasp.phono3py]

  • [vasp.phonopy]

In each section, VASP calculation and job script settings can be written, e.g.,

[vasp.phelel.incar]
lwap = true
isym = 0
kpar = 2
ismear = 0
sigma = 0.01
ediff = 1e-08
encut = 400
prec = "accurate"
lreal = false
lwave = false
lcharg = false
ncore = 4
gga = "PS"
[vasp.phelel.kpoints]
mesh = [4, 4, 4]
shift = [0.500000, 0.500000, 0.500000]
[vasp.phelel.scheduler]
pe = "mpi* 48"

When velph.toml is generated from a template using the velph init --template-toml command, not all information needs to be explicitly specified. Default settings for each calculation can automatically populate the relevant sections, leveraging the VASP INCAR parameters defined in the [vasp.incar] section of the template.

[scheduler] : Job script setting#

The parameters used for generating the job submission script are specified as strings in [scheduler]. If [vasp.CALC_TYPE.scheduler] is specified, [scheduler] settings are overwritten by the settings for [vasp.CALC_TYPE]. The content in this section operates through Python string formatting, using replacement fields named after keyword arguments. Each parameter line in the [scheduler] section is treated as a keyword argument, which is then inserted into the string format.

In the [scheduler] section, the parameters scheduler_name and scheduler_template have special roles:

  • scheduler_name: Specifies the template type, with options slurm, sge, or custom. For slurm and sge, the template string (i.e., scheduler_template) is hard-coded. If custom is selected, the string provided by scheduler_template is used, into which the parameters are inserted.

  • scheduler_template: The string template where parameters defined in this section are inserted.

An example is shown below.

[scheduler]
scheduler_name = "sge"
job_name = "PbTe"
mpirun_command = "mpirun"
vasp_binary = "/usr/local/cluster-1/bin/vasp_std"
pe = "vienna 32"
prepend_text = '''
source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
'''

...
[vasp.phelel.scheduler]
scheduler_template = '''#!/bin/bash
#QSUB2 core 192
#QSUB2 mpi 192
#QSUB2 smp 1
#QSUB2 wtime 48:00:00
#PBS -N {job_name}
cd $PBS_O_WORKDIR

{prepend_text}
{mpirun_command} {vasp_binary} | tee vasp_output
{append_text}
'''
job_name = "PbTe"
mpirun_command = "mpijob"
vasp_binary = "/usr/local/cluster-2/bin/vasp_std"
prepend_text = '''
. /etc/profile.d/modules.sh
module load inteloneapi22u3
'''
append_text = ""

...
[vasp.phono3py.scheduler]
pe = "paris 24"

[phono3py]#

This section contains information specific to the phono3py code and must be included to execute the velph phono3py subcommand.

[phono3py]
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true

[phonopy]#

This section contains information specific to the phono3py code and must be included to execute the velph phonopy subcommand.

[phonopy]
supercell_dimension = [2, 2, 2]
amplitude = 0.03
diagonal = false
plusminus = true