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Merge pull request #269 from phonopy/show-interface 

Display interface mode in CLI
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Atsushi Togo 2024-09-01 09:22:06 +09:00 committed by GitHub
parent dd4c43ab10 3eaa76fa2c
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76
doc/command-options.md
View File

@ -86,8 +86,7 @@ These options have no respective configuration file tags.
This is used to create `FORCES_FC3` from `phono3py_disp.yaml` and force
calculator outputs containing forces in supercells. `phono3py_disp.yaml` has to
be located at the current directory. Calculator interface has to be specified
except for VASP (default) case.
be located at the current directory.
```bash
% phono3py --cf3 disp-{00001..00755}/vasprun.xml
@ -97,14 +96,26 @@ except for VASP (default) case.
% phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
```
````{note}
The calculator interface should be stored in `phono3py_disp.yaml`, so it is not
needed to set it manually. Command-line-options like `--qe` will be ignored. If
the calculator interface is missing from `phono3py_disp.yaml` but needed, please
update the `phono3py` section in the file as follows:
```yaml
phono3py:
calculator: qe
```
````
(cf3_file_option)=
### `--cf3-file` (command option only)
This is used to create `FORCES_FC3` from a text file containing a list of
calculator output file names. `phono3py_disp.yaml` has to be located at the
current directory. Calculator interface has to be specified except for VASP
(default) case.
current directory. The calculator interface is unnecessary to specify, see the
note at {ref}`--cf3 <cf3_option>`.
```bash
% phono3py --cf3-file file_list.dat
@ -130,8 +141,9 @@ together with `--cutoff-pair` option.
This is used to create `FORCES_FC2` similarly to `--cf3` option.
`phono3py_disp.yaml` has to be located at the current directory. This is
optional. Calculator interface has to be specified except for VASP (default)
case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
optional. `FORCES_FC2` is necessary to run with `--dim-fc2` option. The
calculator interface is unnecessary to specify, see the note at {ref}`--cf3
<cf3_option>`.
```bash
% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
@ -142,8 +154,8 @@ case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
### `--cfz` (command option only)
This is used to create `FORCES_FC3` and `FORCES_FC2` subtracting residual forces
combined with `--cf3` and `--cf2`, respectively. Calculator interface has to be
specified except for VASP (default) case.
combined with `--cf3` and `--cf2`, respectively. The calculator interface is
unnecessary to specify, see the note at {ref}`--cf3 <cf3_option>`.
In the following example, it is supposed that `disp3-00000/vasprun.xml` and
`disp2-00000/vasprun.xml` contain the forces of the perfect supercells. In ideal
@ -204,7 +216,6 @@ When using with `--cf2`, `--cf3` has to be specified simultaneously as below,
% phono3py --cf3 disp-{00001..00755}/vasprun.xml --cf2 disp_fc2-{00001..00002}/vasprun.xml --sp
```
## Supercell, primitive cell, masses, magnetic moments
(dim_option)=
@ -299,6 +310,7 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
## Displacement creation
(create_displacements_option)=
### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)
**`phono3py-load` doesn't have this option.**
@ -317,6 +329,7 @@ information about primitive cell (`primitive_matrix` key) in
```
(random_displacements_option)=
### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
**`phono3py-load` doesn't have this option.**
@ -336,6 +349,7 @@ and/or `--rd-fc2`,
```
(amplitude_option)=
### `--amplitude` (`DISPLACEMENT_DISTANCE`)
**`phono3py-load` doesn't have this option.**
@ -348,6 +362,7 @@ The default value depends on calculator. See
{ref}`default_displacement_distance_for_calculator`.
(fc_calculator_option)=
### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)
Choice of force constants calculator.
@ -357,14 +372,17 @@ Choice of force constants calculator.
```
To use different force constants calculators for fc2 and fc3
```bash
% phono3py-load --fc-calc "symfc|" ...
```
Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
employ the finite difference method for systematic displacements generated by
the option `-d`.
(fc_calculator_options_option)=
### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)
Special options for force constants calculators.
@ -608,9 +626,9 @@ $$
\bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2
\left\{(n_{\lambda'}+ n_{\lambda''}+1)
\delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right.
+ (n_{\lambda'}-n_{\lambda''})
* (n_{\lambda'}-n_{\lambda''})
\left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''})
+ \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
* \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
\right]\right\}.
$$
@ -840,7 +858,7 @@ $$
\bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
(n_{\lambda_1}-n_{\lambda_2})
\left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
+ \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
* \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
\right]
\end{align*}
$$
@ -854,7 +872,7 @@ $$
\bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
(n_{\lambda_1}+ n_{\lambda_2}+1)
\left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
+ \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
* \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
\end{align*},
$$
@ -922,11 +940,11 @@ $$
\bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2 &
\left\{(n_{\lambda_1}+ n_{\lambda_2}+1)
\left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
+ \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
* \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
\\
& + (n_{\lambda_1}-n_{\lambda_2})
\left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
+ \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
* \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
\right]\right\},
\end{align*}
$$
@ -941,14 +959,14 @@ $$
\left\{
\left[ \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})_\mathrm{p}}
+ \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
* \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
(\omega+\omega_{\lambda_1}+\omega_{\lambda_2})_\mathrm{p}}
\right]
\right. \\
& + \left[
\frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega +
\omega_{\lambda_1} - \omega_{\lambda_2})_\mathrm{p}}
+ \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
* \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
\omega_{\lambda_1} + \omega_{\lambda_2})_\mathrm{p}}
\right]\right\},
\end{align*}
@ -1012,7 +1030,7 @@ A_\lambda(\omega) = \frac{1}{\pi} \frac{4\Omega^2_\lambda
\Gamma_\lambda(\omega)}
{\left[\omega^2 - \Omega^2_\lambda -
2\Omega_\lambda \Delta_\lambda(\omega) \right]^2
+ \left[ 2\Omega_\lambda
* \left[ 2\Omega_\lambda
\Gamma_\lambda(\omega) \right]^2},
$$
@ -1348,12 +1366,12 @@ Using this option, output file names are slightly modified. For example, with
This rule is applied to
+ `fc3.hdf5`
+ `fc2.hdf5`
+ `kappa-xxx.hdf5`
+ `phonon-xxx.hdf5`
+ `pp-xxx.hdf5`
+ `gamma_detail-xxx.hdf5` (write only)
* `fc3.hdf5`
* `fc2.hdf5`
* `kappa-xxx.hdf5`
* `phonon-xxx.hdf5`
* `pp-xxx.hdf5`
* `gamma_detail-xxx.hdf5` (write only)
(input_filename_option)=
@ -1367,11 +1385,11 @@ specifying `-i iso --fc3`, a file name `fc3.iso.hdf5` is read instead of
This rule is applied to
+ `fc3.hdf5`
+ `fc2.hdf5`
+ `kappa-xxx.hdf5`
+ `phonon-xxx.hdf5`
+ `pp-xxx.hdf5`
* `fc3.hdf5`
* `fc2.hdf5`
* `kappa-xxx.hdf5`
* `phonon-xxx.hdf5`
* `pp-xxx.hdf5`
### `--io` (command option only)

7
phono3py/cui/create_force_constants.py
View File

@ -259,7 +259,6 @@ def parse_forces(
distance_to_A=physical_units["distance_to_A"],
force_to_eVperA=physical_units["force_to_eVperA"],
)
assert dataset is not None
if "natom" in dataset and dataset["natom"] != natom:
@ -273,6 +272,12 @@ def parse_forces(
f'Displacement dataset for {fc_type} was read from "{filename_read_from}".'
)
if calculator is not None and log_level:
print(
f"Displacements and forces were converted from {calculator} "
"unit to A and eV/A."
)
# Overwrite dataset['cutoff_distance'] when necessary.
if fc_type == "fc3" and cutoff_pair_distance:
if "cutoff_distance" not in dataset or (

27
phono3py/cui/create_force_sets.py
View File

@ -44,7 +44,7 @@ import numpy as np
from phonopy.cui.create_force_sets import check_number_of_force_files
from phonopy.cui.load_helper import get_nac_params
from phonopy.cui.phonopy_script import file_exists, files_exist, print_error
from phonopy.file_IO import parse_FORCE_SETS, write_FORCE_SETS
from phonopy.file_IO import is_file_phonopy_yaml, parse_FORCE_SETS, write_FORCE_SETS
from phonopy.interface.calculator import get_calc_dataset
from phono3py.file_IO import (
@ -72,10 +72,24 @@ def create_FORCES_FC3_and_FORCES_FC2(
"""
interface_mode = settings.calculator
disp_filename_candidates = [
"phono3py_disp.yaml",
]
if cell_filename is not None:
if log_level:
print("")
if (
log_level
and cell_filename is not None
and not is_file_phonopy_yaml(cell_filename, keyword="phono3py")
):
print(f'*Unnecessary to specify "{cell_filename}".')
if cell_filename is not None and is_file_phonopy_yaml(
cell_filename, keyword="phono3py"
):
disp_filename_candidates.insert(0, cell_filename)
disp_filenames = files_exist(
disp_filename_candidates, log_level=log_level, is_any=True
@ -86,6 +100,10 @@ def create_FORCES_FC3_and_FORCES_FC2(
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
if interface_mode is not None:
if log_level:
print(f"Calculator interface: {interface_mode}")
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
calc_dataset_fc3 = _get_force_sets_fc3(
settings, ph3py_yaml.dataset, disp_filename, interface_mode, log_level
@ -172,7 +190,9 @@ def create_FORCE_SETS_from_FORCES_FCx(
phonon_smat, input_filename: Optional[str], cell_filename: Optional[str], log_level
):
"""Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
if cell_filename is not None:
if cell_filename is not None and is_file_phonopy_yaml(
cell_filename, keyword="phono3py"
):
disp_filename = cell_filename
elif input_filename is None:
disp_filename = "phono3py_disp.yaml"
@ -286,7 +306,6 @@ def _get_force_sets_fc3(
settings, disp_dataset, disp_filename, interface_mode, log_level
) -> dict:
if log_level:
print("")
print(f'FC3 Displacement dataset was read from "{disp_filename}".')
if "first_atoms" in disp_dataset: # type-1

3
phono3py/cui/phono3py_script.py
View File

@ -281,7 +281,7 @@ def read_phono3py_settings(args, argparse_control, log_level):
args=args, default_settings=argparse_control
)
cell_filename = args.filename[0]
else:
else: # args.filename[0] is assumed to be phono3py-conf file.
phono3py_conf_parser = Phono3pyConfParser(
filename=args.filename[0],
args=args,
@ -1033,6 +1033,7 @@ def main(**argparse_control):
unitcell_filename,
input_filename,
output_filename,
interface_mode,
)
if phono3py.supercell.magnetic_moments is None:

32
phono3py/cui/show_log.py
View File

@ -46,7 +46,13 @@ from phono3py.cui.settings import Phono3pySettings
def show_general_settings(
settings, run_mode, phono3py, cell_filename, input_filename, output_filename
settings,
run_mode,
phono3py,
cell_filename,
input_filename,
output_filename,
interface_mode,
):
"""Show general setting information."""
is_primitive_axes_auto = (
@ -58,28 +64,32 @@ def show_general_settings(
phonon_supercell_matrix = phono3py.phonon_supercell_matrix
print("-" * 29 + " General settings " + "-" * 29)
print("Run mode: %s" % run_mode)
if run_mode:
print("Run mode: {run_mode}")
if output_filename:
print("Output filename is modified by %s." % output_filename)
print(f"Output filename is modified by {output_filename}.")
if input_filename:
print("Input filename is modified by %s." % input_filename)
print(f"Input filename is modified by {input_filename}.")
if settings.hdf5_compression:
print("HDF5 data compression filter: %s" % settings.hdf5_compression)
if phono3py.calculator:
print("Calculator interface: %s" % phono3py.calculator)
print('Crystal structure was read from "%s".' % cell_filename)
print(f"HDF5 data compression filter: {settings.hdf5_compression}")
if interface_mode:
print(
f'Crystal structure was read from "{cell_filename}" '
f"in {interface_mode} unit."
)
else:
print(f'Crystal structure was read from "{cell_filename}".')
print_supercell_matrix(supercell_matrix, phonon_supercell_matrix)
if is_primitive_axes_auto:
print("Primitive matrix (Auto):")
for v in primitive_matrix:
print(" %s" % v)
print(f" {v}")
elif primitive_matrix is not None:
print("Primitive matrix:")
for v in primitive_matrix:
print(" %s" % v)
print(f" {v}")
def print_supercell_matrix(