Changes in velph 0.15

Changes in velph 0.15#

velph 0.15 changes the format of velph.toml and of the velph init template, and some subcommands. This page lists the changes from velph 0.14.

Note

To write a velph.toml of velph 0.14 in the format of velph 0.15, run velph convert. See Converting velph.toml with velph convert.

Project folders made by velph 0.14#

A project folder made by velph init of velph 0.14 has velph.toml and the directories of the calculations. This section describes how velph 0.15 uses such a folder.

Converting velph.toml with velph convert#

velph convert writes a velph.toml of velph 0.14 in the format of velph 0.15. It does not change the original file, and it does not overwrite an existing file. It prints the settings that were removed and the k-point blocks whose kspacing was replaced by mesh:

% velph convert velph.toml velph-new.toml
fft_mesh of [phelel] was removed.
"velph-new.toml" was written from "velph.toml".

To use the new file, rename velph-new.toml to velph.toml.

The velph subcommands also read a velph.toml of velph 0.14 without velph convert. They convert the settings to those of velph 0.15 when they read the file, and they do not change the file. In both cases, kspacing in a k-point block is converted to mesh in the same way as velph 0.14 does.

[vasp.el_bands] of velph 0.10 and earlier#

velph convert and the subcommands also convert [vasp.el_bands] of velph 0.10 and earlier. In these versions, [vasp.el_bands] is one input set with both kpoints_opt and kpoints_dense. velph el_bands generate of these versions writes the band structure with kpoints_opt and the INCAR tags without lorbit and nedos, and the DOS with kpoints_dense and all the INCAR tags. In the same way, [vasp.el_bands] is converted to two input sets:

  • [vasp.el_bands] without kpoints_dense, and without lorbit and nedos in [vasp.el_bands.incar].

  • [vasp.el_dos] without kpoints_opt. It is written only when [vasp.el_bands] has kpoints_dense.

velph convert prints these changes:

% velph convert velph.toml velph-new.toml
fft_mesh of [phelel] was removed.
[vasp.el_bands] was split into [vasp.el_bands] with kpoints_opt and [vasp.el_dos] with kpoints_dense.
lorbit and nedos were removed from [vasp.el_bands.incar].
"velph-new.toml" was written from "velph.toml".

Settings that velph 0.15 does not use#

The following settings of velph 0.14 have no place in velph 0.15. velph convert removes them, and the subcommands do not use them:

  • fft_mesh of [phelel]. velph phelel differentiate computes the FFT mesh (see Subcommands).

  • phonon_supercell_dimension and phonon_supercell_matrix of [phelel] and [phono3py], and [vasp.phelel.phonon] and [vasp.phono3py.phonon]. velph phelel init writes phelel/phelel_disp.yaml without the phonon supercell and prints no message about it. To use a phonon supercell, see Phonon supercells.

  • [vasp.incar].

A key that velph 0.15 does not know is an error, also in a velph.toml of velph 0.14. velph 0.14 did not use such a key and printed no message.

scheduler_name in [scheduler] or in [vasp.<input set>.scheduler] of a velph.toml of velph 0.14 is replaced by scheduler_template, so that the job scripts are those that velph 0.14 writes (see Job scripts of scheduler_name). velph convert and the subcommands do this in the same way, and velph convert prints it:

% velph convert velph.toml velph-new.toml
fft_mesh of [phelel] was removed.
scheduler_name = "sge" of [scheduler] was removed.
scheduler_template was written to give the job scripts that velph 0.14 writes for scheduler_name.
"velph-new.toml" was written from "velph.toml".

scheduler_name in a velph.toml of velph 0.15 is an error.

Directories with new names#

The results of velph 0.14 in the following directories are not read by velph 0.15, because the directories have new names (see Subcommands):

  • el_bands/bands and el_bands/dos, which are now el_bands and el_dos.

  • ph_bands/bands, which is now ph_bands.

  • phelel/ph-disp-*, the calculations of the phonon supercell. When phelel/phelel_disp.yaml has the phonon supercell, velph phelel differentiate reads these calculations from phonopy/disp-*, and it stops when phonopy/phonopy_disp.yaml does not exist.

velph.toml#

See velph.toml file for the format of velph 0.15.

  • [velph] version replaces version of [phelel]. A velph.toml without [velph] version is read as a file of velph 0.14.

  • [vasp.el_bands.bands] and [vasp.el_bands.dos] are now [vasp.el_bands] and [vasp.el_dos].

  • fft_mesh of [phelel] is removed.

  • phonon_supercell_dimension and phonon_supercell_matrix of [phelel] and [phono3py], and [vasp.phelel.phonon] and [vasp.phono3py.phonon], are removed.

  • [vasp.incar] and incar_unset are settings of a template only. Each input set of velph.toml has all of its INCAR tags, and velph.toml with [vasp.incar] or incar_unset is an error.

  • kspacing in a k-point block is an error. velph init converts it to mesh.

  • velph init writes nosym in [phelel], [phonopy] and [phono3py].

  • velph phono3py init uses number_of_snapshots of [phono3py] when --rd is not given.

  • scheduler_name of [scheduler] and [vasp.<input set>.scheduler] is removed. The job script is written from scheduler_template only (see Job scripts of scheduler_name).

  • A key that velph does not know is an error.

velph init template#

See velph init template for the template of velph 0.15. velph init stops with an error for a template of velph 0.14, and the error lists the changes that concern the file.

  • [init.options] is now [init]. The keys of [init] are those of the command-line options of velph init (see [init]). amplitude, diagonal, plusminus, nosym and the supercell keys in [init] are used for all the codes in codes.

  • phelel_nosym of [init.options] is now nosym of [init].

  • An INCAR tag set to an empty table {} is not used. To exclude a tag of [vasp.incar] from an input set, list it in incar_unset of the input set (see [vasp.incar] and incar_unset).

  • kspacing can be given in every kpoints and kpoints_dense block, including [vasp.ph_bands.kpoints].

  • scheduler_name is removed, as in velph.toml.

Job scripts of scheduler_name#

With scheduler_name = "sge" or "slurm", velph 0.14 wrote a job script of SGE or Slurm that was written in velph, and it did not use scheduler_template. velph 0.15 writes the job script from scheduler_template only. For a velph.toml of velph 0.14, velph convert and the subcommands replace scheduler_name by the following scheduler_template, which gives the job script that velph 0.14 wrote (see Converting velph.toml with velph convert). In a template of velph init, remove scheduler_name and give this scheduler_template.

For scheduler_name = "sge",

scheduler_template = '''#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#$ -m n
#$ -N {job_name}
#$ -V
#$ -o _scheduler-stdout.txt
#$ -e _scheduler-stderr.txt
#$ -pe {pe}
#$ -l h_rt={walltime}

{prepend_text}

{mpirun_command} {vasp_binary}

{append_text}
'''

velph 0.14 wrote the line of -pe only when pe was given, and the line of -l h_rt only when walltime was given. Remove the line of a key that is not given. velph init of velph 0.14 wrote walltime = "96:00:00" by default. When pe is given only in some [vasp.<input set>.scheduler], give scheduler_template with the line of -pe in those sections.

For scheduler_name = "slurm",

scheduler_template = '''#!/bin/bash
#SBATCH --job-name={job_name}
#SBATCH --partition={partition}
#SBATCH --nodes={nodes}
#SBATCH --ntasks={ntasks}
#SBATCH --time=96:00:00      # Time limit hrs:min:sec
#SBATCH --output=ci_%j.log   # Standard output and error log

{prepend_text}

{mpirun_command} {vasp_binary}

{append_text}
'''

velph 0.14 wrote --time=96:00:00 and did not use walltime. To use walltime, write --time={walltime}.

Subcommands#

See velph init and velph subcommands for the subcommands of velph 0.15.

velph convert#

velph convert is a new subcommand, which writes a velph.toml of velph 0.14 in the format of velph 0.15 (see Converting velph.toml with velph convert).

velph init#

  • --code chooses the codes whose sections are written. Repeat it for more than one code.

  • --nosym replaces --phelel-nosym, and it is used for all the chosen codes.

  • When velph init stops with an error, the exit code is 1. velph 0.14 gave 0.

  • With --symmetrize-cell, the k-point meshes of the input sets on the unit cell are computed with the symmetry of the unit cell. velph 0.14 used the symmetry of the input cell. For example, for a rhombohedral input cell, the mesh on the hexagonal unit cell can differ along the c axis.

  • With --max-num-atoms, the supercell has at most that number of atoms, also with --no-find-primitive. With a primitive cell as input, velph 0.14 could give a larger supercell.

  • When a supercell has fewer rotations than the unit cell, velph init prints a warning.

  • velph init writes [scheduler] only when its template has [scheduler], and it writes the [scheduler] of the template as it is. velph 0.14 wrote a default [scheduler] with a job script of Slurm, which [scheduler] of a template updated key by key. See velph.toml-[scheduler] section.

velph el_bands, velph el_dos and velph ph_bands#

  • velph el_bands generate writes the input files in el_bands only, in place of el_bands/bands and el_bands/dos.

  • velph el_dos generate is a new subcommand, which writes the input files of the DOS calculation in el_dos.

  • velph el_dos plot is a new subcommand, which plots the DOS.

  • velph el_bands plot_eigenvalues is now velph el_dos plot_eigenvalues.

  • velph ph_bands generate writes the input files in ph_bands, in place of ph_bands/bands.

  • The band paths that seekpath gives are written in the basis of [primitive_cell]. velph 0.14 wrote the coordinates in the basis that seekpath chose, which put the points in wrong places when the two bases differ, for example for a body-centred tetragonal cell with --primitive-cell-choice reduced.

Phonon supercells#

The phonon supercells of phelel and phono3py are taken from phonopy:

  1. velph phonopy init and velph phonopy generate make the phonon supercells in phonopy.

  2. velph phelel init --phonon-from-phonopy and velph phono3py init --phonon-from-phonopy take the phonon supercells from phonopy/phonopy_disp.yaml.

  3. velph phelel differentiate reads the calculations of the phonon supercells from phonopy/disp-*.

velph phelel generate and velph phono3py generate no longer write ph-disp-*. See velph phelel init.

velph phelel differentiate#

The FFT mesh written in phelel/phelel_params.hdf5 is computed from encut and prec in the INCAR tags of the electron-phonon input sets, or from --encut (see velph phelel differentiate). velph 0.14 read fft_mesh of [phelel]. A missing prec is taken as Normal, the default of VASP.

Other subcommands#

  • velph generate takes the file name of velph.toml by --toml-filename, as the other subcommands do. -f of velph 0.14 is removed.

  • check-fft of velph selfenergy and velph transport is removed.

  • When CONTCAR of the previous step does not exist, velph relax generate stops with an error and does not make the next directory. velph 0.14 made the next directory empty.