scnc
/
phonopy
mirror of https://github.com/phonopy/phonopy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
phonopy/doc/qe.md

353 lines
11 KiB
Markdown
Raw Permalink Blame History

(qe_interface)=
# Quantum ESPRESSO (QE) & phonopy calculation
Quantum ESPRESSO package itself has a set of the phonon calculation
system. But the document here explains how to calculate phonons using
phonopy, i.e., using the finite displacement and supercell approach.
## Supported QE-PW tags
Currently QE-PW tags that phonopy can read are shown below. Only
`ibrav = 0` type representation of crystal structure is supported.
More tags may be supported on request.
```
nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS
```
Chemical symbols with natural number for `ATOMIC_SPECIES` like `Xn` (`n>0`),
e.g.. `Fe1`, can be used. The formats of `X_*` and `X-*` are not supported. When
this extended symbol is used, masses of all atoms including usual chemical
symbols are read from QE structure file. Otherwise, masses of respective
chemical symbols implemented in phonopy are used. Note that when using the
extended symbol, if the unit cell of QE structure file is not a primitive cell,
and the primitive cell is defined by the transformation matrix (`PRIMITIVE_AXES`
tag or `--pa` option), atoms with the extended symbols in the unit cell have to
be mapped properly to those in the primitive cell.
## How to run
The procedure of QE-phonopy calculation is shown below using the
NaCl example found in `example/NaCl-QE` directory.
1) Read a QE-PW input file and create supercells with
{ref}`qe_mode` option:
```bash
% phonopy --qe -d --dim="2 2 2" -c NaCl.in
```
In this example, 2x2x2 supercells are created. `supercell.in` and
`supercell-xxx.in` (`xxx` are numbers) give the perfect
supercell and supercells with displacements, respectively. In the
case of the NaCl example, two files `supercell-001.in` and
`supercell-002.in` are created. In these supercell files, lines
only relevant to crystal structures are
given. `phonopy_disp.yaml` is also generated, which contains
information about supercell and displacements.
2) To make QE-PW input files, necessary setting information is added to
`supercell-xxx.in` files, e.g., by:
```bash
% for i in {001,002};do cat header.in supercell-$i.in >| NaCl-$i.in; done
```
where `header.in` is specially made for this NaCl example and
this file is found in `example/NaCl-QE` directory. This
setting is of course dependent on systems and has to be written for
each interested system. Note that supercells with displacements
must not be relaxed in the force calculations, because atomic
forces induced by a small atomic displacement are what we need for
phonon calculation.
Then QE-PW supercell calculations are executed to obtain force on
atoms, e.g., as follows:
```bash
% mpirun pw.x -i NaCl-001.in |& tee NaCl-001.out
% mpirun pw.x -i NaCl-002.in |& tee NaCl-002.out
```
3) To create `FORCE_SETS`, that is used by phonopy,
the following phonopy command is executed:
```bash
% phonopy -f NaCl-001.out NaCl-002.out
```
Here `.out` files are the saved text files of standard outputs of the
QE-PW calculations. If more supercells with displacements were
created in the step 1, all `.out` files are given in the above
command. To run this command, `phonopy_disp.yaml` has to be located in
the current directory because the information on atomic
displacements stored in `phonopy_disp.yaml` are used to generate
`FORCE_SETS`. See some more detail at
{ref}`qe_force_sets_option`.
4) Now post-process of phonopy is ready to run. The unit cell file
used in the step 1 has to be specified but `FORCE_SETS` is
automatically read. Examples of post-process are shown below.
```
% phonopy --qe -c NaCl.in -p band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
1.13.0
Python version 2.7.14
Spglib version 1.10.3
Calculator interface: qe
Band structure mode
Settings:
Supercell: [2 2 2]
Primitive axis:
[ 0. 0.5 0.5]
[ 0.5 0. 0.5]
[ 0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Computing force constants...
max drift of force constants: -0.001194 (zz) -0.000000 (zz)
Reciprocal space paths in reduced coordinates:
[ 0.00 0.00 0.00] --> [ 0.50 0.00 0.00]
[ 0.50 0.00 0.00] --> [ 0.50 0.50 0.00]
[ 0.50 0.50 0.00] --> [-0.00 -0.00 0.00]
[ 0.00 0.00 0.00] --> [ 0.50 0.50 0.50]
...
```
```{image} NaCl-pwscf-band.png
:width: 50%
```
`--qe -c NaCl.in` is specific for the QE-phonopy
calculation but the other settings are totally common among calculator
interfaces such as
```
% phonopy --qe -c NaCl.in --dim="2 2 2" [other-OPTIONS] [setting-file]
```
For settings and command options, see
{ref}`setting_tags` and {ref}`command_options`, respectively, and
for examples, see {ref}`examples_link`.
### Non-analytical term correction (Optional)
To activate non-analytical term correction, {ref}`born_file` is
required. This file contains the information of Born effective charge
and dielectric constant. These physical values are also obtained from
the PW (`pw.x`) & PH (`ph.x`) codes in Quantum ESPRESSO
package. There are two steps. The first step is usual self-consistent
field (SCF) calculation
by and the second step is running its response function calculations
under DFPT.
For the SCF calculation, the input file `NaCl.in` looks like:
```
&control
calculation = 'scf'
tprnfor = .true.
tstress = .true.
pseudo_dir = '/home/togo/espresso/pseudo/'
/
&system
ibrav = 0
nat = 8
ntyp = 2
ecutwfc = 70.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0d-9
/
ATOMIC_SPECIES
Na 22.98976928 Na.pbe-spn-kjpaw_psl.0.2.UPF
Cl 35.453 Cl.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
Na 0.0000000000000000 0.0000000000000000 0.0000000000000000
Na 0.0000000000000000 0.5000000000000000 0.5000000000000000
Na 0.5000000000000000 0.0000000000000000 0.5000000000000000
Na 0.5000000000000000 0.5000000000000000 0.0000000000000000
Cl 0.5000000000000000 0.5000000000000000 0.5000000000000000
Cl 0.5000000000000000 0.0000000000000000 0.0000000000000000
Cl 0.0000000000000000 0.5000000000000000 0.0000000000000000
Cl 0.0000000000000000 0.0000000000000000 0.5000000000000000
CELL_PARAMETERS angstrom
5.6903014761756712 0 0
0 5.6903014761756712 0
0 0 5.6903014761756712
K_POINTS automatic
8 8 8 1 1 1
```
where more the k-point mesh numbers are specified. This may be exectued as:
```bash
% mpirun ~/espresso/bin/pw.x -i NaCl.in |& tee NaCl.out
```
Many files whose names stating with `pwscf` should be created. These
are used for the next calculation. The input file for the response
function calculations, `NaCl.ph.in`, is
created as follows:
```
&inputph
tr2_ph = 1.0d-14,
epsil = .true.
/
0 0 0
```
Similary `ph.x` is executed:
```bash
% mpirun ~/espresso/bin/ph.x -i NaCl.ph.in |& tee NaCl.ph.out
```
Finally the Born effective charges and dielectric constant are obtained in the
output file `NaCl.ph.out`. The `BORN` file has to be created following the
`BORN` format ({ref}`born_file`). The `BORN` file for this NaCl calculation
would be something like below:
```
default value
2.472958201 0 0 0 2.472958201 0 0 0 2.472958201
1.105385 0 0 0 1.105385 0 0 0 1.105385
-1.105385 0 0 0 -1.105385 0 0 0 -1.105385
```
This `BORN` file can be made using `phonopy-qe-born` command.
```bash
% phonopy-qe-born NaCl.in | tee BORN
```
Once this is made, the non-analytical term correction is included
just adding the `--nac` option as follows:
```bash
% phonopy --qe --nac -c NaCl.in -p band.conf
```
```{image} NaCl-pwscf-band-NAC.png
:width: 50%
```
(qe_q2r)=
## Using `q2r.x` to create phonopy force constants file
**Experimental**
A parser of `q2r.x` output is implemented experimentally. Currently
command-line user interface is not prepared. Using the following
script, the force constants file readable by phonopy is
created. Probably thus obtained force constants are required to be
symmetrized by the translational invariance condition using
`FC_SYMMETRY = .TRUE.`.
```python
#!/usr/bin/env python
import sys
from phonopy.interface.qe import read_pwscf, PH_Q2R
primcell_filename = sys.argv[1]
q2r_filename = sys.argv[2]
cell, _ = read_pwscf(primcell_filename)
q2r = PH_Q2R(q2r_filename)
q2r.run(cell)
q2r.write_force_constants()
```
Saving this script as `make_fc_q2r.py`, this is used as, e.g.,
```bash
% python make_fc_q2r.py NaCl.in NaCl.fc
```
This gives `force_constants.hdf5` file in the compact format (see
{ref}`file_force_constants`). From version 1.13.2, full supercell
force constants can be written by `q2r.run(cell, is_full_fc=True)`
instead of `q2r.run(cell)` in the above
script. `FORCE_CONSTANTS` file instead of `force_constants.hdf5`
can be obtained by `q2r.write_force_constants(fc_format='text')`.
### Non-analytical term correction
Treatment of non-analytical term correction (NAC) is different between
phonopy and QE. For insulator, QE automatically calculate dielectric
constant and Born effective charges at PH calculation when q-point
mesh sampling mode (`ldisp = .true.`), and these data are written in
the Gamma point dynamical matrix file (probably in `.dyn1`
file). When running `q2r.x`, these files are read including the
dielectric constant and Born effective charges, and the real space
force constants where QE-NAC treatment is done are written to the q2r
output file. This is not that phonopy expects. Therefore the
dielectric constant and Born effective charges data have to be removed
manually from the Gamma point dynamical matrix file before running
`q2r.x`. Alternatively Gamma point only PH calculation with 'epsil =
.false.' can generate the dynamical matrix file without the dielectric
constant and Born effective charges data. So it is possible to replace
the Gamma point file by this Gamma point only file to run `q2r.x`
for phonopy.
#### Creating BORN file
If the `q2r.x` output contains dielectric constant and Born
effective charges, the following script can generate `BORN` format
text.
```python
#!/usr/bin/env python
import sys
import numpy as np
from phonopy.structure.symmetry import elaborate_borns_and_epsilon
from phonopy.interface.qe import read_pwscf, PH_Q2R
primcell_filename = sys.argv[1]
q2r_filename = sys.argv[2]
cell, _ = read_pwscf(primcell_filename)
q2r = PH_Q2R(q2r_filename)
q2r.run(cell, parse_fc=False)
if q2r.epsilon is not None:
borns, epsilon, _ = elaborate_borns_and_epsilon(
cell,
q2r.borns,
q2r.epsilon,
supercell_matrix=np.diag(q2r.dimension),
symmetrize_tensors=True)
print("default")
print(("%13.8f" * 9) % tuple(epsilon.ravel()))
for z in borns:
print(("%13.8f" * 9) % tuple(z.ravel()))
```
Saving this script as `make_born_q2r.py`,
```bash
% python make_born_q2r.py NaCl.in NaCl.fc > BORN
```
#### NaCl example
NaCl example is found at
<https://github.com/phonopy/phonopy/tree/master/example/NaCl-QE-q2r>.
```bash
% phonopy --qe -c NaCl.in --dim="8 8 8" --band="0 0 0 1/2 0 0 1/2 1/2 0 0 0 0 1/2 1/2 1/2" --readfc --readfc-format=hdf5 --fc-symmetry --nac -p
```
```{image} NaCl-q2r-band-NAC.png
:width: 50%
```
Reference in New Issue View Git Blame Copy Permalink