phelel command#
Command-line tools perform steps 1 and 3 in the el-ph calculation workflow. Their usage parallels that of the phonopy
command in phonopy for
phonon calculations.
The following example demonstrates operations using the phelel command:
% phelel -d --dim 2 2 2 -c POSCAR-unitcell --pa auto --pm
# After running VASP calculations in directories corresponding to displacements:
% phelel --cd disp-000 disp-001 disp-002 disp-003 disp-004
Generation of displacements in supercell#
Supercells with displacements can be generated by combining the following command options. For example:
% phelel -d --dim 2 2 2 -c POSCAR-unitcell --pa auto --pm
Here, POSCAR-unitcell is the unit cell structure in VASP POSCAR format. After
this operation, a file named phelel_disp.yaml, containing information about
the displacements, is created. Additionally, the supercell structures SPOSCAR,
POSCAR-001, and so on are generated.
-d#
This triggers an execution mode that generates supercells with systematically introduced displacements. The displacements are determined by crystal symmetry, with exactly one displacement applied in each supercell.
--dim#
Three or nine integer values specify the supercell shape with respect to the
unit cell structure indicated by the -c option. If nine values are provided,
they correspond to the supercell matrix as defined in the phonopy
documentation. If
three values are given, they represent the diagonal elements of the supercell
matrix, meaning each axis of the input unit cell is simply extended by the
corresponding integer factor.
% phelel --dim 2 2 2 [OPTIONS]
% phelel --dim 0 1 1 1 0 1 1 1 0 [OPTIONS]
-c, --cell#
Unit cell structure is specified.
% phelel -c POSCAR-unitcell [OPTIONS]
--pm#
Unless specified, only one directional displacement is selected among symmetrically equivalent displacements in the opposite direction. With this option specified, both directions are included in the generated supercells with dispacements. Use of this option is recommended.
% phelel --pm [OPTIONS]
Calculation of derivatives of potentials#
After running VASP calculations to calculate local potentials and PAW strenghts under the configurations of displacements in supercells, those data are stored in cetain files. Those are read and then the derivatives are computed by the following command option, e.g.,
% phelel --cd disp-000 disp-001 disp-002 disp-003 disp-004
Here disp-000, disp-001, …, indicate the directories in which VASP
calculations were performed for respective supercells with displacements, i.e.,
SPOSCAR, POSCAR-001, …, as generated in the first step. It is necessary to
have phelel_disp.yaml in the current directory to perform this operation.
--cd, --create-derivatives#
This triggers two sequential operations. First, VASP calculation results are
collected from the specified directories in the order given by the command
options. Displacement information is obtained from the phelel_disp.yaml file
in the current directory. Next, using these collected data, the derivatives of
local potentials and PAW strengths with respect to displacement are calculated
and stored in phelel_params.hdf5.